Merge branch 'feature-cs/update-watir' into 'dev'

Update watir

See merge request !398

.gitlab-ci.yml

@@ -222,7 +222,7 @@ test_browser-functional:
   script:
     - make -C browser
     - source /etc/profile.d/rvm.sh
-    - rvm use 2.1.1
+    - rvm use 2.6.1
     - HEADLESS=1 make -C browser/test functional
   artifacts:
     paths:
@@ -241,7 +241,7 @@ test_browser-functional-external:
   script:
     - make -C browser
     - source /etc/profile.d/rvm.sh
-    - rvm use 2.1.1
+    - rvm use 2.6.1
     - HEADLESS=1 make -C browser/test external
   artifacts:
     paths:
@@ -306,7 +306,7 @@ test_server_functional:
     - docker exec docker_uwsgi_1 sed -i "s/^\(FILE_SOURCE .*\)/FILE_SOURCE = '\/usr\/share\/vidjil\/demo'/" /usr/share/vidjil/server/web2py/applications/vidjil/modules/defs.py
     - docker exec docker_nginx_1 make -C /usr/share/vidjil browser
     - source /etc/profile.d/rvm.sh
-    - rvm use 2.1.1
+    - rvm use 2.6.1
     - HEADLESS=1 make functional_server || (cd docker && docker-compose stop; docker stop $(docker ps -aq); docker rm $(docker ps -aq); docker rmi "vidjil/server:test" "vidjil/client:test"; false)
     - cd docker && docker-compose stop
     - docker stop $(docker ps -aq)

browser/index.html

@@ -198,8 +198,6 @@
                             normalization
                             <form name="normalize_list" id="normalize_list">
                             </form>
-                            <form name="normalize_list" id="normalize_list"> <!--  class="devel-mode"> -->
-                            </form>
                         </div>
                         <div class="menu_box">
                             size display</br>

browser/test/functional/browser_test.rb

 require 'rubygems'
 gem "minitest"
-require 'watir-webdriver'
+require 'watir'
 require 'test/unit'
 require "minitest/autorun"
 require 'minitest/ci'
@@ -65,7 +65,7 @@ class BrowserTest < MiniTest::Test
       print "Welcome popup.\n"
 
       # wait for the welcoming popup
-      $b.div(:class => 'popup_msg').wait_until_present(2)
+      $b.div(:class => 'popup_msg').wait_until(timeout: 2){ |el| el.present? }
     
       # close the welcoming popup
       $b.div(:class => 'popup_msg').button(:text => 'ok').click
@@ -83,12 +83,12 @@ class BrowserTest < MiniTest::Test
     
     # select data file
     print "  data:     " + data_path + "\n"
-    $b.div(:id => 'file_menu').file_field(:name,"json").set(data_path)
+    $b.div(:id => 'file_menu').file_field(name: "json").set(data_path)
 
     # select analysis file
     if analysis_path != nil
       print "  analysis: " + analysis_path + "\n"
-      $b.div(:id => 'file_menu').file_field(:name, "pref").set(analysis_path)
+      $b.div(:id => 'file_menu').file_field(name: "pref").set(analysis_path)
     end
 
     $b.div(:id => 'file_menu').button(:text => 'start').click

browser/test/functional/external_test_imgt-igblast.rb

@@ -19,7 +19,7 @@ class ExternalTest < BrowserTest
 
   def test_10_imgt
     begin
-      $b.clone_in_scatterplot('25').wait_until_present
+      $b.clone_in_scatterplot('25').wait_until(&:present?)
       $b.clone_in_scatterplot('25').click
       
       $b.span(:id => "toIMGT" ).click
@@ -53,7 +53,7 @@ class ExternalTest < BrowserTest
     begin
       $b.clone_in_scatterplot('25').click
       $b.span(:id => "toIMGTSeg" ).click
-      $b.segmenter_checkbox_imgt_vdj.wait_until_present
+      $b.segmenter_checkbox_imgt_vdj.wait_until(&:present?)
 
       clone_info = $b.clone_info_segmenter('25')
       productive_title = clone_info[:axis].element(:class => 'productivity-IMGT').title
@@ -67,8 +67,8 @@ class ExternalTest < BrowserTest
         assert (h.style('width').to_i >= 100), "Highlights should have a reasonable width, found to be %s" % h.style('width')
       end
 
-      Watir::Wait.until(timeout=10) { clone_info[:identity].span.exists? }
-      clone_info[:identity].element(:text => "NaN%").wait_while_present
+      Watir::Wait.until(timeout: 10) { clone_info[:identity].span.exists? }
+      clone_info[:identity].element(:text => "NaN%").wait_while(&:present?)
       assert ((clone_info[:identity].text =~ /^[0-9\.]+%$/) == 0 ), "We should have identity rate (found: %s)" % clone_info[:identity].text
 
       $b.unselect
@@ -78,7 +78,7 @@ class ExternalTest < BrowserTest
   
   def test_11_igBlast
     begin
-      $b.clone_in_scatterplot('25').wait_until_present
+      $b.clone_in_scatterplot('25').wait_until(&:present?)
       $b.clone_in_scatterplot('25').click
       
       $b.span(:id => "toIgBlast" ).click

browser/test/functional/external_test_segmenter.rb

@@ -17,8 +17,8 @@ GGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACGACAT
 
     $b.button(:id => 'form_submit').click
 
-    $b.element(:class => 'imgAjaxLoading').wait_until_present
-    $b.clone_in_scatterplot('0').wait_until_present
+    $b.element(:class => 'imgAjaxLoading').wait_until(&:present?)
+    $b.clone_in_scatterplot('0').wait_until(&:present?)
     
     assert ($b.element(:class => 'segmenter').present?), "Segmenter should be present"
     assert ($b.element(:class => 'scatterplot').present?), "Segmenter should be present"
@@ -27,15 +27,15 @@ GGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACGACAT
   def test_05_imgt_post
     begin
       $b.span(:id => "toIMGTSeg" ).click
-      $b.segmenter_checkbox_imgt_vdj.wait_until_present
-      Watir::Wait.until(timeout=10) { $b.span(:class => "identityBad").exists? }
+      $b.segmenter_checkbox_imgt_vdj.wait_until(&:present?)
+      Watir::Wait.until(timeout: 10) { $b.span(:class => "identityBad").exists? }
       clone_info = $b.clone_info_segmenter('0')
-      clone_info[:identity].element(:text => "NaN%").wait_while_present
+      clone_info[:identity].element(:text => "NaN%").wait_while(&:present?)
       productive_title = clone_info[:axis].element(:class => 'productivity-IMGT').title
       assert (productive_title.include? 'productivity'), "IMGT should tell us the productivity of the sequence"
 
       clone_segmenter = $b.clone_in_segmenter('0')
-      Watir::Wait.until(timeout=10) { $b.execute_script("return typeof model.clone(0).seg.imgt['N-REGION end']") != "undefined" }
+      Watir::Wait.until(timeout: 10) { $b.execute_script("return typeof model.clone(0).seg.imgt['N-REGION end']") != "undefined" }
       $b.segmenter_checkbox_imgt_vdj.click
       highlights = clone_segmenter.spans(:class => 'highlight_border')
 

browser/test/functional/test_analysis-example1.rb

@@ -7,19 +7,21 @@ class TestSimple < BrowserTest
     super
     if not defined? $b
       set_browser("/doc/analysis-example1.vidjil")
-      $b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
+      if $b.div(id: 'tip-container').present?
+        $b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
+      end
     end
   end
   
   def test_00_graph_hidden
-#    assert (not $b.clone_in_graph('0').visible?), "Graph lines should not be visible"
+#    assert (not $b.clone_in_graph('0').present?), "Graph lines should not be visible"
     assert (not $b.graph.exists?), "Graph should not exist"
   end
 
   def test_00_double_scatterplot
     # analysis-example has only one sample, second scatterplot expected
-    assert ( $b.scatterplot.visible?), "First scatterplot should be found"
-    assert ( $b.scatterplot(2).visible?), "Second scatterplot should be found"
+    assert ( $b.scatterplot.present?), "First scatterplot should be found"
+    assert ( $b.scatterplot(2).present?), "Second scatterplot should be found"
   end
 
   def test_01_legend_scatterplot
@@ -35,12 +37,12 @@ class TestSimple < BrowserTest
   def test_02_deactivate_locus
     initial_read_nb = $b.info_selected_locus.text
     $b.locus_topleft('TRG').click
-    $b.clone_in_scatterplot('0').wait_while_present
+    $b.clone_in_scatterplot('0').wait_while(&:present?)
     assert ($b.info_selected_locus.text == "no read"), "When unselected we have no reads"
 
     # Reactivate
     $b.locus_topleft('TRG').click
-    $b.clone_in_scatterplot('0').wait_until_present
+    $b.clone_in_scatterplot('0').wait_until(&:present?)
     assert ($b.info_selected_locus.text == initial_read_nb), "Read number should be identical to what we had at first"
   end
 

browser/test/functional/test_loading_analysis.rb

@@ -7,8 +7,10 @@ class TestLoadingAnalysis < BrowserTest
     super
     if not defined? $b
       set_browser("/doc/analysis-example2.vidjil", "/doc/analysis-example2.analysis")
-      $b.clone_in_scatterplot('0').wait_until_present
-      $b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
+      $b.clone_in_scatterplot('0').wait_until(&:present?)
+      if $b.div(id: 'tip-container').present?
+        $b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
+      end
     end
   end
 
@@ -30,9 +32,9 @@ class TestLoadingAnalysis < BrowserTest
 
     $b.select_tag('0').click
 
-    assert (not $b.clone_in_list('0').visible?)
-    assert (not $b.clone_in_scatterplot('0').visible?)
-    assert (not $b.clone_in_graph('0').visible?)
+    assert (not $b.clone_in_list('0').present?)
+    assert (not $b.clone_in_scatterplot('0').present?)
+    assert (not $b.clone_in_graph('0').present?)
 
     $b.select_tag('0').click
   end
@@ -61,36 +63,36 @@ class TestLoadingAnalysis < BrowserTest
   end
 
   def test_04_hide_clone
-    assert ($b.clone_in_list('0').visible?)
-    assert ($b.clone_in_scatterplot('0').visible?)
-    assert ($b.clone_in_graph('0').visible?)
+    assert ($b.clone_in_list('0').present?)
+    assert ($b.clone_in_scatterplot('0').present?)
+    assert ($b.clone_in_graph('0').present?)
 
     # Hide the clone by affecting it to a hidden tag
     $b.clone_info('0')[:star].click
     $b.tag_item('4')[:name].click
 
-    assert (not $b.clone_in_list('0').visible?)
-    assert (not $b.clone_in_scatterplot('0').visible?)
-    assert (not $b.clone_in_graph('0').visible?)
+    assert (not $b.clone_in_list('0').present?)
+    assert (not $b.clone_in_scatterplot('0').present?)
+    assert (not $b.clone_in_graph('0').present?)
 
     # Unhide clone
     $b.element(:id => 'fastTag4', :class => 'inactiveTag').click
     assert (not $b.element(:id => 'fastTag4', :class => 'inactiveTag').exists?)
-    assert ($b.clone_in_list('0').visible?)
-    assert ($b.clone_in_scatterplot('0').visible?)
-    assert ($b.clone_in_graph('0').visible?)
+    assert ($b.clone_in_list('0').present?)
+    assert ($b.clone_in_scatterplot('0').present?)
+    assert ($b.clone_in_graph('0').present?)
   end
 
   def test_05_check_cluster
     clustered = $b.clone_info('1')
     assert (clustered[:name].text == 'clone2'), "First clone of cluster should be clone2"
-    assert ($b.clone_in_scatterplot('1').visible?)
-    assert (not $b.clone_in_scatterplot('2').visible?)
+    assert ($b.clone_in_scatterplot('1').present?)
+    assert (not $b.clone_in_scatterplot('2').present?)
 
     clustered[:cluster].click
 
-    assert ($b.clone_in_scatterplot('1').visible?)
-    assert ($b.clone_in_scatterplot('2').visible?)
+    assert ($b.clone_in_scatterplot('1').present?), "First clone should still be present"
+    $b.clone_in_scatterplot('2').wait_until(&:present?)
 
     first_in_cluster = $b.clone_in_cluster('1', '1')
     second_in_cluster = $b.clone_in_cluster('1', '2')
@@ -105,12 +107,13 @@ end
   def test_06_remove_cluster
     clustered = $b.clone_info('1')
     clustered[:cluster].click
+    $b.clone_in_cluster('1', '2')[:delete].wait_until(&:present?)
     $b.clone_in_cluster('1', '2')[:delete].click
 
-    assert (not $b.clone_cluster('1').visible?)
+    assert (not $b.clone_cluster('1').present?)
     
-    assert ($b.clone_in_scatterplot('1').visible?)
-    assert ($b.clone_in_scatterplot('2').visible?)
+    assert ($b.clone_in_scatterplot('1').present?)
+    assert ($b.clone_in_scatterplot('2').present?)
 
     clone3 = $b.clone_info('2')
     assert (clone3[:name].text == "clone3")
@@ -125,8 +128,8 @@ end
 
     clustered = $b.clone_info('1')
     assert (clustered[:name].text == 'clone2')
-    assert ($b.clone_in_scatterplot('1').visible?)
-    assert (not $b.clone_in_scatterplot('2').visible?)
+    assert ($b.clone_in_scatterplot('1').present?)
+    assert (not $b.clone_in_scatterplot('2').present?)
   end
 
   def test_08_select_cluster

browser/test/functional/test_multilocus.rb

@@ -9,7 +9,9 @@ class TestMultilocus < BrowserTest
     super
     if not defined? $b
       set_browser("/doc/analysis-example.vidjil")
-      $b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
+      if $b.div(id: 'tip-container').present?
+        $b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
+      end
     end
   end
 
@@ -44,7 +46,7 @@ class TestMultilocus < BrowserTest
   def test_00_info_point
     assert (not $b.div(:id => 'info_timepoint').present?), "Info timepoint should not be present"
     $b.info_point.i.click
-    assert ($b.div(:id => 'info_timepoint').visible?), "After clicking info timepoint should be visible"
+    assert ($b.div(:id => 'info_timepoint').present?), "After clicking info timepoint should be visible"
 
     table = $b.div(:id => 'info_timepoint').table
     assert (table[1][1].text == '786861'), "Incorrect  number of reads in infopoint"
@@ -107,7 +109,7 @@ class TestMultilocus < BrowserTest
     begin
       $b.unselect
       #test hover a clone in the list
-      $b.clone_in_scatterplot('25').wait_until_present
+      $b.clone_in_scatterplot('25').wait_until(&:present?)
       $b.clone_in_list('25').hover
 
       check_when_list_or_scatterplot_focused
@@ -117,7 +119,7 @@ class TestMultilocus < BrowserTest
   def test_05_focus_in_scatterplot
     begin
       $b.unselect
-      $b.clone_in_scatterplot('25').wait_until_present
+      $b.clone_in_scatterplot('25').wait_until(&:present?)
       $b.clone_in_scatterplot('25').hover
 
       check_when_list_or_scatterplot_focused
@@ -140,7 +142,7 @@ class TestMultilocus < BrowserTest
 
   def test_08_click_in_list
     #test select a clone in the list
-    $b.clone_in_scatterplot('25').wait_until_present
+    $b.clone_in_scatterplot('25').wait_until(&:present?)
     $b.clone_info('25')[:name].click()
 
     check_when_list_or_scatterplot_clicked
@@ -150,7 +152,7 @@ class TestMultilocus < BrowserTest
   end
 
   def test_08_click_in_scatterplot
-    $b.clone_in_scatterplot('25').wait_until_present
+    $b.clone_in_scatterplot('25').wait_until(&:present?)
     $b.clone_in_scatterplot('25').click
 
     check_when_list_or_scatterplot_clicked
@@ -159,9 +161,9 @@ class TestMultilocus < BrowserTest
     assert (not $b.clone_in_list('25').class_name.include? "list_select"), ">> Incorrect class name, clone is not unselected'"
   end
 
-  def TODO_test_09_normalize
+  def test_09_normalize
     $b.clone_info('25')[:star].click
-    $b.tag_selector_edit_normalisation.wait_until_present
+    $b.tag_selector_edit_normalisation.wait_until(&:present?)
     $b.tag_selector_edit_normalisation.set('0.01')
     $b.tag_selector_normalisation_validator.click 
     
@@ -175,7 +177,7 @@ class TestMultilocus < BrowserTest
   end
 
   def test_0a_shortcuts_numpad
-    $b.clone_in_scatterplot('25').wait_until_present
+    $b.clone_in_scatterplot('25').wait_until(&:present?)
     $b.clone_in_scatterplot('25').click
 
     assert ($b.preset_selector.selected? "[0] V/J (genes)"), ">> preset selector badly set"
@@ -187,9 +189,9 @@ class TestMultilocus < BrowserTest
     begin
       $b.clone_info('25')[:star].click
       name = $b.tag_item('0')[:name]
-      name.wait_until_present
+      name.wait_until(&:present?)
       name.click
-      name.wait_while_present
+      name.wait_while(&:present?)
 
       assert ($b.clone_info('25')[:name].style('color') ==  'rgba(220, 50, 47, 1)' ) , ">> fail tag : clone color hasn't changed"
     end
@@ -202,9 +204,9 @@ class TestMultilocus < BrowserTest
     $b.clone_in_scatterplot('90').click(:control)
 
     $b.menu_item_export_fasta.click
-    assert ( $b.window(:title => "").exists? ) , ">> fail opening fasta export "
-    $b.window(:title => "").use do
-      assert ($b.text.include? ">TRBV29*01 -1/0/-0 TRBD1*01 -2/0/-5 TRBJ2-5*01"), "header name"
+    assert ( $b.window(:url => /about:blank/ )) , ">> fail opening fasta export "
+    $b.window(:url => /about:blank/).use do
+      assert ($b.text.include? ">TRBV29*01 -1/0/-0 TRBD1*01 -2/0/-5 TRBJ2-5*01"), "header name: "+$b.text
       assert ($b.text.include? "YYGGGYYACGYAYAGCGGYGYTTYYCCTYTYTGYTYTGCYAAAYAACYYYYTGTGYCTYTGTGCYGYGTTYCCCGGYYYAAACYCYCYYCCTYGG\nCYAGGYCYGG"), "sequence"
       assert ($b.text.include? ">ERG-4F 0/TCT/0 ERG-Seq-R"), "header name locus ERG"
       assert (not $b.text.include? ">ERG-4F\n"), "header name of segment should not exist (segment is not present in germline)"
@@ -258,11 +260,11 @@ class TestMultilocus < BrowserTest
 
       assert (smaller.text.include?("smaller clones")), "We should have smaller clones at index %d of the list, instead we have %s " % [i, smaller.text]
 
-      assert (smaller.visible?), "Smaller clones #%d should be visible, it is not" % [i]
+      assert (smaller.present?), "Smaller clones #%d should be visible, it is not" % [i]
       smaller.hover
-      assert (smaller.visible?), "Smaller clones #%d should still be visible after hovering it" % [i]
+      assert (smaller.present?), "Smaller clones #%d should still be visible after hovering it" % [i]
 
-      assert (not $b.clone_in_scatterplot(smaller.id).visible?), "Smaller clone %d should not be visible in scatterplot" % [i]
+      assert (not $b.clone_in_scatterplot(smaller.id).present?), "Smaller clone %d should not be visible in scatterplot" % [i]
     end
   end
 
@@ -308,7 +310,7 @@ class TestMultilocus < BrowserTest
 
   def test_18_empty_clone_invisible
     assert ( $b.execute_script("return m.clones[66].reads[0]") == 0), "Clone should have no read"
-    assert (not $b.clone_in_scatterplot('66').visible?), "Clone should not be visible"
+    assert (not $b.clone_in_scatterplot('66').present?), "Clone should not be visible"
   end
 
   def TODO_test_14_edit_tag
@@ -317,7 +319,7 @@ class TestMultilocus < BrowserTest
       $b.clone_info('25')[:star].click
 
       edit = $b.tag_item('0')[:edit]
-      edit.wait_until_present
+      edit.wait_until(&:present?)
       edit.click
       $b.tag_selector_edit_name.set 'renamed_click'
       $b.tag_selector_name_validator.click
@@ -329,7 +331,7 @@ class TestMultilocus < BrowserTest
       $b.clone_info('24')[:star].click
 
       edit = $b.tag_item('1')[:edit]
-      edit.wait_until_present
+      edit.wait_until(&:present?)
       edit.click
       $b.tag_selector_edit_name.set 'renamed_return'
       $b.send_keys :return
@@ -340,7 +342,7 @@ class TestMultilocus < BrowserTest
       ## check renames (on again another clone)
       $b.clone_info('23')[:star].click
       edit = $b.tag_item('1')[:edit]
-      edit.wait_until_present
+      edit.wait_until(&:present?)
 
       assert ($b.tag_selector.text.include? 'renamed_click'),  "fail edit tag with mouse : tag name in tag selector hasn't changed"
       assert ($b.tag_selector.text.include? 'renamed_return'), "fail edit tag with keyboard : tag name in tag selector hasn't changed"

browser/test/functional/test_normalization.rb

@@ -8,8 +8,10 @@ class TestNormalization < BrowserTest
     def setup
         super
         if not defined? $b
-        set_browser("/doc/analysis-example.vidjil")
-        $b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
+          set_browser("/doc/analysis-example.vidjil")
+          if $b.div(id: 'tip-container').present?
+            $b.div(:id => 'tip-container').div(:class => 'tip_1').element(:class => 'icon-cancel').click
+          end
         end
     end
 
@@ -20,45 +22,43 @@ class TestNormalization < BrowserTest
 
     def test_00_normalization_none
         $b.element(:id => 'settings_menu').click
-        assert ($b.div(:id => 'normalize_list').visible?), "After clicking normalize_list form should be visible"
-        assert ($b.div(:id => 'reset_norm').present?), "Form have the input for reset normalization"
-        $b.execute_script(' showSelector("settingsSelector"); console.log( "hide settings")')
-        $b.send_keys :escape
-    end
+        assert ($b.form(:id => 'normalize_list').present?), "After clicking normalize_list form should be visible"
+        assert ($b.input(:id => 'reset_norm').present?), "Form have the input for reset normalization"
+        $b.clone_in_list('25').hover # Just put the mouse somewhere else to close the menu
+     end
 
 
     def test_01_normalization_expected
-        set_browser("/doc/analysis-example.vidjil")
-        
-        $b.div(:id => 'color25').click
-        $b.text_field(:id => 'norm_button').set '0.1'
+        assert ($b.clone_info('25')[:size].text == '0.129%'), "Span show correct size before normalization"
+
+        $b.clone_info('25')[:star].click
+        $b.tag_selector_edit_normalisation.set '0.1'
         $b.send_keys :enter
         
-        assert ($b.span(:text => '10.00%').present?), "Span show correct normalized size"
+        assert ($b.clone_info('25')[:size].text == '10.00%'), "Span show correct normalized size"
 
-        $b.element(:id => 'settings_menu').click
-        assert ($b.div(:id => 'normalize_list').visible?), "After clicking normalize_list form should be visible"
+        $b.menu_settings.click
+        assert ($b.form(:id => 'normalize_list').present?), "After clicking normalize_list form should be visible"
         assert ($b.div(:id => 'normalizetest25').present?), "Form have the input for expected normalization"
         
-        $b.div(:id => 'reset_norm').click
+        $b.input(:id => 'reset_norm').click
         $b.send_keys :escape
         
-        assert ($b.span(:text => '0.129%').present?), "Span show correct size after reset normalization"
+        assert ($b.clone_info('25')[:size].text == '0.129%'), "Span show correct size after reset normalization"
     end
 
 
     def test_02_normalization_external
-        set_browser("/doc/analysis-example.vidjil")
-        assert ($b.span(:text => '0.122%').present?), "Span show correct normalized size (external) by default"
+        assert ($b.clone_info('1')[:size].text == '0.081%'), "Span show correct size after reset normalization"
         
-        $b.element(:id => 'settings_menu').click
-        assert ($b.div(:id => 'normalize_list').visible?), "After clicking normalize_list form should be visible"
+        $b.menu_settings.click
+        assert ($b.form(:id => 'normalize_list').present?), "After clicking normalize_list form should be visible"
         assert ($b.div(:id => 'normalize_external').present?), "Form have the input for external normalization"
-        assert (not $b.div(:id => 'normalizetest25').present?), "Form have not the input for expected normalization"
+        assert ($b.div(:id => 'normalizetest25').present?), "Form still have the input for expected normalization"
         
-        $b.div(:id => 'reset_norm').click
+        $b.div(:id => 'normalize_external').click
         
-        assert ($b.span(:text => '0.081%').present?), "Span show correct size after reset normalization"
+        assert ($b.clone_info('1')[:size].text == '0.122%'), "Span should show correct normalized size (external) (" + $b.clone_info('1')[:size].text+")"
     end
 
 

browser/test/functional/test_segmenter-page.rb

@@ -17,23 +17,23 @@ GGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACGACAT
 
     $b.button(:id => 'form_submit').click
 
-    $b.element(:class => 'imgAjaxLoading').wait_until_present
-    $b.clone_in_scatterplot('0').wait_until_present
+    $b.element(:class => 'imgAjaxLoading').wait_until(&:present?)
+    $b.clone_in_scatterplot('0').wait_until(&:present?)
     
     assert ($b.element(:class => 'segmenter').present?), "Segmenter should be present"
     assert ($b.element(:class => 'scatterplot').present?), "Segmenter should be present"
   end
 
   def test_01_segmenter
-    assert ($b.clone_in_segmenter('0').visible?), "Clone 0 should be in segmenter"
-    assert ($b.clone_in_segmenter('1').visible?), "Clone 1 should be in segmenter"
+    assert ($b.clone_in_segmenter('0').present?), "Clone 0 should be in segmenter"
+    assert ($b.clone_in_segmenter('1').present?), "Clone 1 should be in segmenter"
     assert (not $b.clone_in_segmenter('2').exists?), "Clone 2 should not exist"
   end
 
   def test_02_scatterplot
-    assert ($b.clone_in_scatterplot('0').visible?), "Clone 0 should be in scatterplot"
-    assert ($b.clone_in_scatterplot('1').visible?), "Clone 1 should be in scatterplot"
-    assert (not $b.clone_in_scatterplot('2').visible?), "Clone 2 should not be visible"
+    assert ($b.clone_in_scatterplot('0').present?), "Clone 0 should be in scatterplot"
+    assert ($b.clone_in_scatterplot('1').present?), "Clone 1 should be in scatterplot"
+    assert (not $b.clone_in_scatterplot('2').present?), "Clone 2 should not be visible"
   end
 
   def test_03_change_color
@@ -44,6 +44,7 @@ GGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACGACAT
     $b.tag_item('3')[:name].click
     $b.clone_in_segmenter('1').hover # Change clone to hover: on hover color doesn't change
 
+    sleep(1)
     assert ($b.clone_info_segmenter('0')[:name].style('color') == tagColor), "Clone has not changed color in segmenter"
 
     # Must remove rgb from the start of the fill style, and the closing parentheses at the end,
@@ -58,7 +59,7 @@ GGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACGACAT
     for i in ['0', '1']
       for gene in ['V', 'J']
         span = $b.clone_in_segmenter(i).span(:class => gene)
-        assert (span.visible?), "#{gene} span should be visible"
+        assert (span.present?), "#{gene} span should be visible"
       end
     end
   end
@@ -74,8 +75,8 @@ GGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACGACAT
   def test_07_export_fasta
     $b.element(:id => 'btn_exportfasta').click
     
-    assert ( $b.window(:title => "").exists? ) , ">> fail opening fasta export "
-    $b.window(:title => "").use do
+    assert ( $b.window(:url => /about:blank/).exists? ) , ">> fail opening fasta export "
+    $b.window(:url => /about:blank/).use do
       assert ($b.text.index(/TRGV5.*200 nt/) > 0), "header name"
       assert ($b.text.index(/IGHV3-13.*374 nt/) > 0), "header name"
       assert ($b.text.include? "CCTGGG\nGGGCCAG\nATT"), "sequence"

browser/test/functional/test_segmenter_page_errors.rb

@@ -12,7 +12,7 @@ class TestSegmenterPageErrors < SegmenterTest
 
     $b.button(:id => 'form_submit').click
 
-    $b.element(:class => 'flash_2').wait_until_present
+    $b.element(:class => 'flash_2').wait_until(&:present?)
     assert ($b.element(:class => 'flash_2', :index => 1).text.include? "invalid sequences"), "We should have an error_message"
     
     assert (not $b.element(:class => 'segmenter').present?), "Segmenter should not be present"
@@ -30,8 +30,8 @@ CGTCTT"
 
     $b.button(:id => 'form_submit').click
 
-