add unit tests

3 files changed, 165 insertions, 0 deletions

diff --git a/Rakefile b/Rakefile
index ead64f1..9a49df7 100755
--- a/Rakefile
+++ b/Rakefile
@@ -37,6 +37,11 @@ task :install_gems do
   end
 end
 
+desc "Perform unit tests"
+task :test do
+  require 'test/unit_test.rb'
+end
+
 =begin
 
 desc "Installs gems and inits db migration"
diff --git a/data/hamster_carcinogenicity.mini.csv b/data/hamster_carcinogenicity.mini.csv
new file mode 100644
index 0000000..4267235
--- /dev/null
+++ b/data/hamster_carcinogenicity.mini.csv
@@ -0,0 +1,11 @@
+SMILES, Hamster Carcinogenicity

+CC=O,1

+C12C3=C(C=CC=C3)CC1=CC(=CC=2)NC(C)=O,1

+O=C(N)\C(C2=CC=CO2)=C/C1=CC=C([N+]([O-])=O)O1,1

+C1(N=CNN=1)N,0

+Br(=O)(=O)[O-].[K+],1

+[Cl-].[Cd+2].[Cl-],0

+O=S(=O)([O-])[O-].[Cd+2],0

+ClC1=CC(=NC(=N1)SCC(=O)O)NC2=CC=CC(=C2C)C,0

+ClCOC,1

+C=C(Cl)C=C,0

diff --git a/test/unit_test.rb b/test/unit_test.rb
new file mode 100644
index 0000000..d76e156
--- /dev/null
+++ b/test/unit_test.rb
@@ -0,0 +1,149 @@
+
+require "rubygems"
+require "sinatra"
+require "uri"
+require "yaml"
+ENV['RACK_ENV'] = 'test'
+require 'application.rb'
+require 'test/unit'
+require 'rack/test'
+require 'lib/test_util.rb'
+require 'test/test_examples.rb'
+
+TEST_USER = "guest"
+TEST_PW = "guest"
+  
+#LOGGER = OTLogger.new(STDOUT)
+#LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
+#LOGGER.formatter = Logger::Formatter.new
+
+module Sinatra
+  set :raise_errors, false
+  set :show_exceptions, false
+end
+
+class Exception
+  def message
+    errorCause ? errorCause.to_yaml : to_s
+  end
+end
+
+class ValidationTest < Test::Unit::TestCase
+  include Rack::Test::Methods
+  include Lib::TestUtil
+  
+  def global_setup
+    puts "login and upload datasets"
+    if AA_SERVER
+      @@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
+      raise "could not log in" unless @@subjectid
+      puts "logged in: "+@@subjectid.to_s
+    else
+      puts "AA disabled"
+      @@subjectid = nil
+    end
+    f = File.new("data/hamster_carcinogenicity.mini.csv")
+    @@data_class_mini = ValidationExamples::Util.upload_dataset(f, @@subjectid)
+    @@feat_class_mini = ValidationExamples::Util.prediction_feature_for_file(f)
+  end
+  
+  def global_teardown
+    puts "delete and logout"
+    OpenTox::Dataset.find(@@data_class_mini,@@subjectid).delete(@@subjectid)
+    @@cv.delete(@@subjectid) if defined?@@cv
+    @@report.delete(@@subjectid) if defined?@@report
+    OpenTox::Authorization.logout(@@subjectid) if AA_SERVER
+  end
+ 
+  def test_crossvalidation
+    puts "test_crossvalidation"
+    assert_rest_call_error OpenTox::NotFoundError do 
+      OpenTox::Crossvalidation.find(File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/noexistingid"))
+    end
+    p = { 
+      :dataset_uri => @@data_class_mini,
+      :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
+      :algorithm_params => "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"),
+      :prediction_feature => @@feat_class_mini,
+      :num_folds => 2 }
+    cv = OpenTox::Crossvalidation.create(p, @@subjectid)
+    assert cv.uri.uri?
+    if @@subjectid
+      assert_rest_call_error OpenTox::NotAuthorizedError do
+        OpenTox::Crossvalidation.find(cv.uri)
+      end
+    end
+    cv = OpenTox::Crossvalidation.find(cv.uri, @@subjectid)
+    assert cv.uri.uri?
+    if @@subjectid
+      assert_rest_call_error OpenTox::NotAuthorizedError do
+        cv.summary(cv)
+      end
+    end
+    summary = cv.summary(@@subjectid)
+    assert_kind_of Hash,summary
+    @@cv = cv
+  end
+    
+  def test_crossvalidation_report
+    puts "test_crossvalidation_report"
+    assert defined?@@cv,"no crossvalidation defined"
+    assert_kind_of OpenTox::Crossvalidation,@@cv
+    assert_rest_call_error OpenTox::NotFoundError do 
+      OpenTox::CrossvalidationReport.find_for_crossvalidation(@@cv)
+    end
+    if @@subjectid
+      assert_rest_call_error OpenTox::NotAuthorizedError do
+        OpenTox::CrossvalidationReport.create(@@cv)
+      end
+    end
+    report = OpenTox::CrossvalidationReport.create(@@cv,@@subjectid)
+    assert report.uri.uri?
+    if @@subjectid
+      assert_rest_call_error OpenTox::NotAuthorizedError do
+        OpenTox::CrossvalidationReport.find(report.uri)
+      end
+    end
+    report = OpenTox::CrossvalidationReport.find(report.uri,@@subjectid)
+    assert report.uri.uri?
+    report2 = OpenTox::CrossvalidationReport.find_for_crossvalidation(@@cv,@@subjectid)
+    assert_equal report.uri,report2.uri
+    report3 = @@cv.find_or_create_report(@@subjectid)
+    assert_equal report.uri,report3.uri
+    @report = report
+  end
+
+  def app
+    Sinatra::Application
+  end
+  
+  def assert_rest_call_error( ex )
+    if ex==OpenTox::NotAuthorizedError and @@subjectid==nil
+      puts "AA disabled: skipping test for not authorized"
+      return
+    end
+    begin
+      yield
+    rescue OpenTox::RestCallError => e
+      report = e.errorCause
+      while report.errorCause
+        report = report.errorCause
+      end
+      assert_equal report.errorType,ex.to_s
+    end
+  end
+  
+  def teardown
+    if((@@expected_test_count-=1) == 0)
+      global_teardown
+    end
+  end
+
+  def setup
+    unless defined?@@expected_test_count
+      @@expected_test_count = (self.class.instance_methods.reject{|method| method[0..3] != 'test'}).length
+      global_setup
+    end
+  end
+
+end