A&A added

8 files changed, 90 insertions, 88 deletions

diff --git a/Rakefile b/Rakefile
index d8026a6..01050c8 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,22 +1,27 @@
 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|
+[:all, :feature, :dataset, :fminer, :lazar, :authorization].each do |t|
   task :teardown => t
   task t => :setup 
 end
diff --git a/algorithm.rb b/algorithm.rb
index a5f35d1..db6fdec 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 b12ae49..3772638 100644
--- a/authorization.rb
+++ b/authorization.rb
@@ -1,9 +1,7 @@
 require "rubygems"
-require "opentox-ruby-api-wrapper"
+require "opentox-ruby"
 require "test/unit"
 
-TEST_USER = "guest"
-TEST_PW   = "guest"
 TEST_URI  = "http://only_a_test/test/" + rand(1000000).to_s
 
 class TestOpenToxAuthorizationBasic < Test::Unit::TestCase
@@ -14,9 +12,7 @@ class TestOpenToxAuthorizationBasic < Test::Unit::TestCase
   end
  
   def test_02_get_token
-    tok = login
-    assert_not_nil tok
-    logout(tok)
+    assert_not_nil @@subjectid
   end
   
   def test_03_is_valid_token
@@ -32,9 +28,7 @@ class TestOpenToxAuthorizationBasic < Test::Unit::TestCase
   end
   
   def test_05_list_policies
-    tok = login
-    assert_kind_of Array, OpenTox::Authorization.list_policies(tok)
-    logout(tok)
+    assert_kind_of Array, OpenTox::Authorization.list_policies(@@subjectid)
   end
   
 end
@@ -42,21 +36,15 @@ end
 class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
 
   def test_01_list_groups
-    tok = login
-    assert_kind_of Array, OpenTox::Authorization.list_groups(tok)
-    logout(tok)
+    assert_kind_of Array, OpenTox::Authorization.list_groups(@@subjectid)
   end  
 
   def test_02_list_user_groups
-    tok = login
-    assert_kind_of Array, OpenTox::Authorization.list_groups(tok)
-    logout(tok)
+    assert_kind_of Array, OpenTox::Authorization.list_groups(@@subjectid)
   end
   
   def test_03_get_user
-    tok = login
-    assert_equal TEST_USER, OpenTox::Authorization.get_user(tok)
-    logout(tok)
+    assert_equal TEST_USER, OpenTox::Authorization.get_user(@@subjectid)
   end
 
 end
@@ -64,43 +52,49 @@ end
 class TestOpenToxAuthorizationLDAP < Test::Unit::TestCase
 
   def test_01_create_check_delete_default_policies
-    tok = login
-    res = OpenTox::Authorization.send_policy(TEST_URI, tok)
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
     assert res
-    assert OpenTox::Authorization.uri_has_policy(TEST_URI, tok)
-    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, tok)
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
     assert_kind_of Array, policies
     policies.each do |policy|
-      assert OpenTox::Authorization.delete_policy(policy, tok)
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
     end
-    logout(tok)
   end
 
   def test_02_check_policy_rules
-    tok = login
     tok_anonymous = OpenTox::Authorization.authenticate("anonymous","anonymous")
     assert_not_nil tok_anonymous
-    res = OpenTox::Authorization.send_policy(TEST_URI, tok)
+    res = OpenTox::Authorization.send_policy(TEST_URI, @@subjectid)
     assert res
-    assert OpenTox::Authorization.uri_has_policy(TEST_URI, tok)
+    assert OpenTox::Authorization.uri_has_policy(TEST_URI, @@subjectid)
     owner_rights = {"GET" => true, "POST" => true, "PUT" => true, "DELETE" => true}
     groupmember_rights = {"GET" => true, "POST" => nil, "PUT" => nil, "DELETE" => nil}
     owner_rights.each do |request, right|
-      assert_equal right, OpenTox::Authorization.authorize(TEST_URI, request, tok), "#{TEST_USER} requests #{request} to #{TEST_URI}"
+      assert_equal right, OpenTox::Authorization.authorize(TEST_URI, request, @@subjectid), "#{TEST_USER} requests #{request} to #{TEST_URI}"
     end
     groupmember_rights.each do |request, r|
       assert_equal r, OpenTox::Authorization.authorize(TEST_URI, request, tok_anonymous), "anonymous requests #{request} to #{TEST_URI}"
     end
     
-    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, tok)
+    policies = OpenTox::Authorization.list_uri_policies(TEST_URI, @@subjectid)
     assert_kind_of Array, policies
     policies.each do |policy|
-      assert OpenTox::Authorization.delete_policy(policy, tok)
+      assert OpenTox::Authorization.delete_policy(policy, @@subjectid)
     end
-    logout(tok)
+    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 9cf8e63..cc8f50e 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
@@ -40,14 +40,14 @@ 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
-    datasets = OpenTox::Dataset.all
+    datasets = OpenTox::Dataset.all(CONFIG[:services]["opentox-dataset"], @@subjectid)
     assert_kind_of Array, datasets
   end
 
@@ -65,37 +65,38 @@ 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
+    @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")}).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
+    @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.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
     @datasets.each do |uri,data|
-      @dataset = OpenTox::Dataset.find(uri)
+      @dataset = OpenTox::Dataset.find(uri, @@subjectid)
       assert @dataset.metadata.size != 0
     end
   end
@@ -103,7 +104,7 @@ class DatasetTest < Test::Unit::TestCase
   def test_load_compounds
     @datasets.each do |uri,data|
       @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_compounds
+      @dataset.load_compounds(@@subjectid)
       assert_equal @dataset.compounds.size,data[:nr_compounds]
     end
   end
@@ -119,7 +120,7 @@ class DatasetTest < Test::Unit::TestCase
   def test_load_all
     @datasets.each do |uri,data|
       @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset.load_all(@@subjectid)
       validate data
     end
   end
@@ -127,7 +128,7 @@ class DatasetTest < Test::Unit::TestCase
   def test_yaml
     @datasets.each do |uri,data|
       @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset.load_all(@@subjectid)
       #@dataset = YAML.load @dataset.to_yaml
       validate data
     end
@@ -136,7 +137,7 @@ class DatasetTest < Test::Unit::TestCase
   def test_csv
     @datasets.each do |uri,data|
       @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @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
@@ -146,7 +147,7 @@ class DatasetTest < Test::Unit::TestCase
   def test_excel
     @datasets.each do |uri,data|
       @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @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}
@@ -156,7 +157,7 @@ class DatasetTest < Test::Unit::TestCase
   def test_ntriples
     @datasets.each do |uri,data|
       @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @dataset.load_all(@@subjectid)
       assert_kind_of String, @dataset.to_ntriples
     end
   end
@@ -164,7 +165,7 @@ class DatasetTest < Test::Unit::TestCase
   def test_owl
     @datasets.each do |uri,data|
       @dataset = OpenTox::Dataset.new(uri)
-      @dataset.load_all
+      @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 3b22c64..c52f78c 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -9,40 +9,40 @@ class FminerTest < Test::Unit::TestCase
 =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}).to_s
+    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
     assert_equal 41, d.features.size
     #validate_owl
-    d.delete
+    d.delete(@@subjectid)
   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}).to_s
+    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
     assert_equal 35, d.features.size
     #validate_owl
-    d.delete
+    d.delete(@@subjectid)
   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}).to_s
+    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
     assert_equal 222, d.features.size
-    d.delete
+    d.delete(@@subjectid)
   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}).to_s
+    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
     assert_equal 16, d.features.size
-    d.delete
+    d.delete(@@subjectid)
   end
 =begin
 =end
diff --git a/lazar.rb b/lazar.rb
index e3c6908..440d50c 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
-    lazar = OpenTox::Model::Lazar.find model_uri
+    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
     compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
-    prediction_uri = lazar.run(:compound_uri => compound.uri)
-    prediction = OpenTox::LazarPrediction.find(prediction_uri)
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
     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
-    lazar = OpenTox::Model::Lazar.find model_uri
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => @@classification_training_dataset.uri, :subjectid => @@subjectid}).to_s
+    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)
-    prediction = OpenTox::LazarPrediction.find(prediction_uri)
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => @@subjectid)
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, @@subjectid)
     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, @@subjectid
     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), @@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
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"