change fixed variables to globals in test.rb configuration file

6 files changed, 53 insertions, 54 deletions

diff --git a/test/authorization.rb b/test/authorization.rb
index 1556187..f23fe02 100644
--- a/test/authorization.rb
+++ b/test/authorization.rb
@@ -1,12 +1,6 @@
 require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb")
 
 TEST_URI  = "http://only_a_test/test/" + rand(1000000).to_s
-unless defined? $aa[:uri] #overwrite turned off A&A server for testing
-  $aa[:uri] = "https://opensso.in-silico.ch"
-  @@subjectid = OpenTox::Authorization.authenticate($aa[:user],$aa[:password])
-end
-
-@@subjectid ||= OpenTox::Authorization.authenticate($aa[:user],$aa[:password]) 
 
 class TestOpenToxAuthorizationBasic < Test::Unit::TestCase
  
diff --git a/test/compound.rb b/test/compound.rb
index 7573f58..8480892 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -1,38 +1,41 @@
 require 'test/unit'
 require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb")
 
-class CompoundTest < Test::Unit::TestCase
+begin
+  @@service_uri = $compound[:uri]
+rescue
+  puts "Configuration Error: $compound[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
+  exit
+end
 
-  def setup
-    @service_uri = "http://ot-dev.in-silico.ch/compound"
-  end
+class CompoundTest < Test::Unit::TestCase
 
   def test_compound_from_smiles_0
-    c = OpenTox::Compound.from_smiles @service_uri, "F[B-](F)(F)F.[Na+]"
+    c = OpenTox::Compound.from_smiles @@service_uri, "F[B-](F)(F)F.[Na+]"
     assert_equal "InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1", c.to_inchi
     assert_equal "[Na+].F[B-](F)(F)F", c.to_smiles # still does not work on 64bit machines
   end
 
   def test_compound_from_smiles_1
-    c = OpenTox::Compound.from_smiles @service_uri, "CC(=O)CC(C)C#N"
+    c = OpenTox::Compound.from_smiles @@service_uri, "CC(=O)CC(C)C#N"
     assert_equal "InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3", c.to_inchi
     assert_equal "CC(CC(=O)C)C#N", c.to_smiles
   end
 
   def test_compound_from_name
-    c = OpenTox::Compound.from_name @service_uri, "Benzene"
+    c = OpenTox::Compound.from_name @@service_uri, "Benzene"
     assert_equal "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H", c.to_inchi
     assert_equal "c1ccccc1", c.to_smiles
   end
 
   def test_compound_from_smiles_2  
-    c = OpenTox::Compound.from_smiles @service_uri, "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
+    c = OpenTox::Compound.from_smiles @@service_uri, "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
     assert_equal "InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1", c.to_inchi
     assert_equal "N#[N+]c1ccccc1.F[B-](F)(F)F", c.to_smiles
   end
 
   def test_compound_from_inchi
-    c = OpenTox::Compound.from_inchi @service_uri, "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+    c = OpenTox::Compound.from_inchi @@service_uri, "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
     assert_equal "c1ccccc1", c.to_smiles
   end
 
@@ -44,7 +47,7 @@ class CompoundTest < Test::Unit::TestCase
 
 =begin
   def test_match_hits
-    c = OpenTox::Compound.from_smiles @service_uri, "N=C=C1CCC(=F=FO)C1"
+    c = OpenTox::Compound.from_smiles @@service_uri, "N=C=C1CCC(=F=FO)C1"
     assert_equal ({"FF"=>2, "CC"=>10, "C"=>6, "C1CCCC1"=>10, "C=C"=>2}), c.match_hits(['CC','F=F','C','C=C','FF','C1CCCC1','OO'])
   end
 =end
diff --git a/test/dataset.rb b/test/dataset.rb
index 8730154..71629c6 100644
--- a/test/dataset.rb
+++ b/test/dataset.rb
@@ -4,23 +4,29 @@ DATASET = "http://ot-dev.in-silico.ch/dataset"
 DATA_DIR = File.join(File.dirname(__FILE__),"data")
 # TODO: add subjectids
 
+begin
+  @@service_uri = $dataset[:uri]
+rescue
+  puts "Configuration Error: $dataset[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
+  exit
+end
 
 class DatasetTest < Test::Unit::TestCase
 
   def test_all
-    datasets = OpenTox::Dataset.all DATASET, @@subjectid
+    datasets = OpenTox::Dataset.all @@service_uri, @@subjectid
     assert_equal OpenTox::Dataset, datasets.first.class
   end
 
   def test_create_empty
-    d = OpenTox::Dataset.create DATASET, @@subjectid
+    d = OpenTox::Dataset.create @@service_uri, @@subjectid
     assert_equal OpenTox::Dataset, d.class
-    assert_match /#{DATASET}/, d.uri.to_s
+    assert_match /#{@@service_uri}/, d.uri.to_s
     d.delete :subjectid => @@subjectid
   end
 
   def test_create_from_file
-    d = OpenTox::Dataset.from_file DATASET, File.join(DATA_DIR,"EPAFHM.mini.csv"), @@subjectid
+    d = OpenTox::Dataset.from_file @@service_uri, File.join(DATA_DIR,"EPAFHM.mini.csv"), @@subjectid
     assert_equal OpenTox::Dataset, d.class
     assert_equal d.uri, d[RDF::XSD.anyURI]
     assert_equal "EPAFHM.mini",  d.metadata[RDF::URI("http://purl.org/dc/elements/1.1/title")].first.to_s # DC.title is http://purl.org/dc/terms/title
@@ -32,7 +38,7 @@ class DatasetTest < Test::Unit::TestCase
   end
 
   def test_from_yaml
-    @dataset = OpenTox::Dataset.from_file DATASET, File.join(DATA_DIR,"hamster_carcinogenicity.yaml"), @@subjectid
+    @dataset = OpenTox::Dataset.from_file @@service_uri, File.join(DATA_DIR,"hamster_carcinogenicity.yaml"), @@subjectid
     assert_equal OpenTox::Dataset, @dataset.class
     assert_equal "hamster_carcinogenicity", @dataset[RDF::URI("http://purl.org/dc/elements/1.1/title")]
     hamster_carc?
@@ -42,7 +48,7 @@ class DatasetTest < Test::Unit::TestCase
 =begin
 # TODO: fix (mime type??0 and add Egons example
   def test_sdf_with_multiple_features
-    @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/CPDBAS_v5c_1547_29Apr2008part.sdf"
+    @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/CPDBAS_v5c_1547_29Apr2008part.sdf"
     assert_equal OpenTox::Dataset, @dataset.class
     puts @dataset.features.size
     puts @dataset.compounds.size
@@ -51,14 +57,14 @@ class DatasetTest < Test::Unit::TestCase
 =end
 
   def test_multicolumn_csv
-    @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/multicolumn.csv", @@subjectid
+    @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/multicolumn.csv", @@subjectid
     assert_equal 5, @dataset.features.size
     assert_equal 4, @dataset.compounds.size
     @dataset.delete :subjectid => @@subjectid
   end
 
   def test_from_csv
-    @dataset = OpenTox::Dataset.from_file DATASET, "#{DATA_DIR}/hamster_carcinogenicity.csv", @@subjectid
+    @dataset = OpenTox::Dataset.from_file @@service_uri, "#{DATA_DIR}/hamster_carcinogenicity.csv", @@subjectid
     assert_equal OpenTox::Dataset, @dataset.class
     hamster_carc?
     @dataset.delete :subjectid => @@subjectid
@@ -66,7 +72,7 @@ class DatasetTest < Test::Unit::TestCase
 
 =begin
   def test_save
-    d = OpenTox::Dataset.create DATASET
+    d = OpenTox::Dataset.create @@service_uri
     d.metadata
     d.metadata[RDF::DC.title] = "test"
     d.save
diff --git a/test/policy.rb b/test/policy.rb
index 11014be..6babcc6 100644
--- a/test/policy.rb
+++ b/test/policy.rb
@@ -11,12 +11,6 @@ POLICY_NAME = "test_policy_#{rand(100000)}"
 RULE_NAME = "test_rule_#{rand(100000)}"
 SUBJECT_NAME = "test_subject_#{rand(100000)}"
 
-AA ||= "https://opensso.in-silico.ch"
-AA_USER = "guest"
-AA_PASS = "guest"
-
-@@subjectid = OpenTox::Authorization.authenticate(AA_USER,AA_PASS)
-
 class PolicyTest < Test::Unit::TestCase
 
   def test_01_class
@@ -67,16 +61,16 @@ class PolicyTest < Test::Unit::TestCase
 
   def test_04_group_user
     policies = OpenTox::Policies.new()
-    policies.load_default_policy(AA_USER, TEST_URI, "member")
+    policies.load_default_policy($aa[:user], TEST_URI, "member")
     assert_equal "member", policies.policies["policy_group"].group
-    assert_equal AA_USER, policies.policies["policy_user"].user
+    assert_equal $aa[:user], policies.policies["policy_user"].user
   end
 
   def test_05_DN
     policies = OpenTox::Policies.new()
     policies.new_policy(POLICY_NAME)
     policy = policies.policies[policies.names[0]]
-    policy.set_ot_user(AA_USER)
+    policy.set_ot_user($aa[:user])
     assert_equal USER_VALUE, policy.value
     assert_equal USER_TYPE, policy.type
     policy.set_ot_group(USER_GROUP)
diff --git a/test/setup.rb b/test/setup.rb
index c63a17c..b035a80 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -4,8 +4,11 @@ Bundler.require
 require 'opentox-client'
 require File.join(ENV["HOME"],".opentox","config","test.rb")
 
-if defined? $aa
-  @@subjectid = OpenTox::Authorization.authenticate($aa[:user], $aa[:password])
-else
-  @@subjectid = ""
+begin
+  AA = $aa[:uri]
+  @@subjectid = OpenTox::Authorization.authenticate($aa[:user],$aa[:password])
+  raise if !OpenTox::Authorization.is_token_valid(@@subjectid)
+rescue
+  puts "Configuration Error: $aa[:uri], $aa[:user] or $aa[:password] are not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
+  exit
 end
diff --git a/test/task.rb b/test/task.rb
index c45704b..f368663 100644
--- a/test/task.rb
+++ b/test/task.rb
@@ -2,17 +2,17 @@ require 'test/unit'
 require File.join(File.expand_path(File.dirname(__FILE__)),"setup.rb")
 #require "./validate-owl.rb"
 
-TASK_SERVICE_URI = "http://ot-dev.in-silico.ch/task" 
-#TASK_SERVICE_URI = "http://ot-test.in-silico.ch/task" 
-#TASK_SERVICE_URI = "https://ambit.uni-plovdiv.bg:8443/ambit2/task" #not compatible
+begin
+  @@service_uri = $task[:uri]
+rescue
+  puts "Configuration Error: $task[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
+  exit
+end
 
 class TaskTest < Test::Unit::TestCase
 
-
-=begin
-=end
   def test_all
-    all = OpenTox::Task.all(TASK_SERVICE_URI)
+    all = OpenTox::Task.all(@@service_uri)
     assert_equal Array, all.class
     t = all.last
     assert_equal OpenTox::Task, t.class
@@ -20,23 +20,22 @@ class TaskTest < Test::Unit::TestCase
   end
 
   def test_create_and_complete
-    task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test" do
+    task = OpenTox::Task.create @@service_uri, :description => "test" do
       sleep 1
-      TASK_SERVICE_URI
+      @@service_uri
     end
     assert task.running?
     assert_equal "Running", task.hasStatus
     task.wait
     assert task.completed?
     assert_equal "Completed", task.hasStatus
-    assert_equal TASK_SERVICE_URI, task.resultURI
+    assert_equal @@service_uri, task.resultURI
   end
 
-
   def test_create_and_cancel
-    task = OpenTox::Task.create TASK_SERVICE_URI do
+    task = OpenTox::Task.create @@service_uri do
       sleep 2
-      TASK_SERVICE_URI
+      @@service_uri
     end
     assert task.running?
     task.cancel
@@ -44,7 +43,7 @@ class TaskTest < Test::Unit::TestCase
   end
 
   def test_create_and_fail
-    task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do
+    task = OpenTox::Task.create @@service_uri, :description => "test failure", :creator => "http://test.org/fake_creator" do
       sleep 1
       raise "A runtime error occured"
     end
@@ -56,7 +55,7 @@ class TaskTest < Test::Unit::TestCase
   end
 
   def test_create_and_fail_with_opentox_error
-    task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test failure", :creator => "http://test.org/fake_creator" do
+    task = OpenTox::Task.create @@service_uri, :description => "test failure", :creator => "http://test.org/fake_creator" do
       sleep 1
       raise OpenTox::Error.new 500, "An OpenTox::Error occured"
     end
@@ -70,7 +69,7 @@ class TaskTest < Test::Unit::TestCase
 =begin
   # temporarily removed until uri checking from virtual machines has been fixed
   def test_wrong_result_uri
-    task = OpenTox::Task.create TASK_SERVICE_URI, :description => "test wrong result uri", :creator => "http://test.org/fake_creator" do
+    task = OpenTox::Task.create @@service_uri, :description => "test wrong result uri", :creator => "http://test.org/fake_creator" do
       sleep 1
       "Asasadasd"
     end