remove unit tests from validation repository (move to test)

1 files changed, 0 insertions, 321 deletions

diff --git a/test/unit_test.rb b/test/unit_test.rb
deleted file mode 100644
index 5984f42..0000000
--- a/test/unit_test.rb
+++ /dev/null
@@ -1,321 +0,0 @@
-#TEST_USER = "mgtest"
-#TEST_PW = "mgpasswd"
-ENV['RACK_ENV'] = 'production'
-
-require "rubygems"
-require "sinatra"
-require "uri"
-require "yaml"
-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
-
-    @@data = []
-    files = { File.new("data/hamster_carcinogenicity.mini.csv") => :crossvalidation,  
-              File.new("data/EPAFHM.mini.csv") => :crossvalidation,
-              File.new("data/hamster_carcinogenicity.csv") => :validation,
-              File.new("data/EPAFHM.csv") => :validation,
-#              File.new("data/StJudes-HepG2-testset_Class.csv") => :crossvalidation
-               }
-    files.each do |file,type|
-      @@data << { :type => type,
-        :data => ValidationExamples::Util.upload_dataset(file, @@subjectid),
-        :feat => ValidationExamples::Util.prediction_feature_for_file(file),
-        :info => file.path, :delete => true} 
-    end
-#    @@data << { :type => :crossvalidation,
-#      :data => "http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=50",
-#      :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/21573",
-#      :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=50" }
-#    @@data << { :type => :validation,
-#      :data => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=50",
-#      :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/26221",
-#      :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=50" } 
-  end
-  
-  def global_teardown
-    puts "delete and logout"
-    @@data.each{|data| OpenTox::Dataset.find(data[:data],@@subjectid).delete(@@subjectid) if data[:delete]}
-    @@vs.each{|v| v.delete(@@subjectid)} if defined?@@vs
-    @@cvs.each{|cv| cv.delete(@@subjectid)} if defined?@@cvs
-    @@reports.each{|report| report.delete(@@subjectid)} if defined?@@reports
-    @@qmrfReports.each{|qmrfReport| qmrfReport.delete(@@subjectid)} if defined?@@qmrfReports
-    OpenTox::Authorization.logout(@@subjectid) if AA_SERVER
-  end
-  
-  def test_validation_list
-    puts "test_validation_list"
-    list = OpenTox::Validation.list
-    assert list.is_a?(Array)
-    list.each do |l|
-      assert l.uri?
-    end
-  end
- 
-  def test_training_test_split
-    
-    @@vs = []
-    @@data.each do |data|
-      if data[:type]==:validation
-        puts "test_training_test_split "+data[:info].to_s
-        p = { 
-          :dataset_uri => data[:data],
-          :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
-          :algorithm_params => "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"),
-          :prediction_feature => data[:feat],
-          :split_ratio => 0.95,
-          :random_seed => 2}
-        t = OpenTox::SubTask.new(nil,0,1)
-        def t.progress(pct)
-          if !defined?@last_msg or @last_msg+3<Time.new
-            puts "waiting for training-test-split validation: "+pct.to_s
-            @last_msg=Time.new
-          end
-        end
-        def t.waiting_for(task_uri); end
-        v = OpenTox::Validation.create_training_test_split(p, @@subjectid, t)
-        assert v.uri.uri?
-        if @@subjectid
-          assert_rest_call_error OpenTox::NotAuthorizedError do
-            OpenTox::Crossvalidation.find(v.uri)
-          end
-        end
-        v = OpenTox::Validation.find(v.uri, @@subjectid)
-        assert v.uri.uri?
-        
-        model = v.metadata[OT.model]
-        assert model.uri?
-        v_list = OpenTox::Validation.list( {:model => model} )
-        assert v_list.size==1 and v_list.include?(v.uri)
-        @@vs << v
-      end
-    end
-  end
-  
-  def test_validation_report
-    #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/48", @@subjectid)
-    
-    @@reports = [] unless defined?@@reports
-    @@vs.each do |v|
-      puts "test_validation_report"
-      assert defined?v,"no validation defined"
-      assert_kind_of OpenTox::Validation,v
-      if @@subjectid
-        assert_rest_call_error OpenTox::NotAuthorizedError do
-          OpenTox::CrossvalidationReport.create(v.uri)
-        end
-      end
-      report = OpenTox::ValidationReport.find_for_validation(v.uri,@@subjectid)
-      assert report==nil,"report already exists for validation\nreport: "+(report ? report.uri.to_s : "")+"\nvalidation: "+v.uri.to_s
-      report = OpenTox::ValidationReport.create(v.uri,@@subjectid)
-      assert report.uri.uri?
-      if @@subjectid
-        assert_rest_call_error OpenTox::NotAuthorizedError do
-          OpenTox::CrossvalidationReport.find(report.uri)
-        end
-      end
-      report = OpenTox::ValidationReport.find(report.uri,@@subjectid)
-      assert report.uri.uri?
-      report2 = OpenTox::ValidationReport.find_for_validation(v.uri,@@subjectid)
-      assert_equal report.uri,report2.uri
-      report3_uri = v.find_or_create_report(@@subjectid)
-      assert_equal report.uri,report3_uri
-      @@reports << report2
-    end  
-  end
-
-  def test_crossvalidation_list
-    puts "test_crossvalidation_list"
-    list = OpenTox::Crossvalidation.list
-    assert list.is_a?(Array)
-    list.each do |l|
-      assert l.uri?
-    end
-  end
-
-  def test_crossvalidation
-    
-    #assert_rest_call_error OpenTox::NotFoundError do 
-    #  OpenTox::Crossvalidation.find(File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/noexistingid"))
-    #end
-    @@cvs = []
-    @@data.each do |data|
-      if data[:type]==:crossvalidation
-        puts "test_crossvalidation "+data[:info].to_s
-        p = { 
-          :dataset_uri => data[:data],
-          :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
-          :algorithm_params => "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"),
-          :prediction_feature => data[:feat],
-          :num_folds => 2 }
-        t = OpenTox::SubTask.new(nil,0,1)
-        def t.progress(pct)
-          if !defined?@last_msg or @last_msg+3<Time.new
-            puts "waiting for crossvalidation: "+pct.to_s
-            @last_msg=Time.new
-          end
-        end
-        def t.waiting_for(task_uri); end
-        cv = OpenTox::Crossvalidation.create(p, @@subjectid, t)
-        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
-        
-        algorithm = cv.metadata[OT.algorithm]
-        assert algorithm.uri?
-        cv_list = OpenTox::Crossvalidation.list( {:algorithm => algorithm} )
-        assert cv_list.include?(cv.uri)
-        cv_list.each do |cv_uri|
-          alg = OpenTox::Crossvalidation.find(cv_uri).metadata[OT.algorithm]
-          assert alg==algorithm,"wrong algorithm for filtered crossvalidation, should be: '"+algorithm.to_s+"', is: '"+alg.to_s+"'"
-        end
-        
-        @@cvs << cv
-      end
-    end
-  end
-    
-  def test_crossvalidation_report
-    #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/48", @@subjectid)
-    
-    @@reports = [] unless defined?@@reports
-    @@cvs.each do |cv|
-      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.uri)
-      #end
-      if @@subjectid
-        assert_rest_call_error OpenTox::NotAuthorizedError do
-          OpenTox::CrossvalidationReport.create(cv.uri)
-        end
-      end
-      assert OpenTox::ValidationReport.find_for_validation(cv.uri,@@subjectid)==nil
-      report = OpenTox::CrossvalidationReport.create(cv.uri,@@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.uri,@@subjectid)
-      assert_equal report.uri,report2.uri
-      report3_uri = cv.find_or_create_report(@@subjectid)
-      assert_equal report.uri,report3_uri
-      @@reports << report2
-    end  
-  end
-  
-  def test_qmrf_report
-    #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/13", @@subjectid)
-    
-    @@qmrfReports = []
-    @@cvs.each do |cv|
-      puts "test_qmrf_report"
-      assert defined?cv,"no crossvalidation defined"
-      validations = cv.metadata[OT.validation]
-      assert_kind_of Array,validations
-      assert validations.size==cv.metadata[OT.numFolds].to_i,validations.size.to_s+"!="+cv.metadata[OT.numFolds].to_s
-      val = OpenTox::Validation.find(validations[0], @@subjectid)
-      model_uri = val.metadata[OT.model]
-      
-      model = OpenTox::Model::Generic.find(model_uri, @@subjectid)
-      assert model!=nil
-      
-      #assert_rest_call_error OpenTox::NotFoundError do 
-      #  OpenTox::QMRFReport.find_for_model(model_uri, @@subjectid)
-      #end
-      
-      @@qmrfReports << OpenTox::QMRFReport.create(model_uri, @@subjectid)
-    end
-  end
-  
-  ################### utils and overrides ##########################
-  
-  def app
-    Sinatra::Application
-  end
-  
-  # checks RestCallError type
-  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
-  
-  # hack to have a global_setup and global_teardown 
-  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
-
-