Merge branch 'seek-1.14' into main

app/helpers/bootstrap_helper.rb

@@ -140,7 +140,7 @@ def objects_input(element_name, existing_objects = [], options = {}, value_metho
 
     tag = select_tag(element_name, select_options, options)
     if options[:multiple]
-      hidden_field_tag(element_name, '', name: options[:name]) + tag
+      hidden_field_tag(element_name, '', name: options[:name], id: nil) + tag
     else
       tag
     end

app/models/sample_attribute.rb

@@ -8,6 +8,7 @@ class SampleAttribute < ApplicationRecord
 
   belongs_to :isa_tag
 
+  auto_strip_attributes :pid
   validates :sample_type, presence: true
   validates :pid, format: { with: URI::regexp, allow_blank: true, allow_nil: true, message: 'not a valid URI' }
   validate :validate_against_editing_constraints, if: -> { sample_type.present? }

app/views/projects/guided_join.html.erb

@@ -6,8 +6,7 @@
         <% if @project %>
           You are requesting to join <%= link_to(@project.title, @project) %>
 
-          <%= hidden_field_tag 'projects',@project.id %>
-
+          <%= hidden_field_tag 'project_ids[]', @project.id, id: 'project_ids' %>
         <% else %>
 
           <div class="help-block">
@@ -63,9 +62,8 @@
 <script type='application/javascript'>
 
   function checkSubmitButtonEnabled() {
-    var enabled = $j('select#institution_id').val()
-      && $j('select#project_ids').val()
-    $j('#submit-button').prop('disabled',!enabled);    
+    var enabled = $j('select#institution_id').val() && $j('#project_ids').val();
+    $j('#submit-button').prop('disabled', !enabled);
   }
 
   $j(document).ready(function () {

lib/tasks/seek_upgrades.rake

@@ -11,6 +11,7 @@ namespace :seek do
     decouple_extracted_samples_policies
     decouple_extracted_samples_projects
     link_sample_datafile_attributes
+    strip_sample_attribute_pids
   ]
 
   # these are the tasks that are executes for each upgrade as standard, and rarely change
@@ -47,6 +48,19 @@ namespace :seek do
     end
   end
 
+  task(strip_sample_attribute_pids: [:environment]) do
+    puts '... Stripping Sample Attribute PIds ...'
+    n = 0
+    SampleAttribute.where('pid is NOT NULL AND pid !=?','').each do |attribute|
+      new_pid = attribute.pid.strip
+      if attribute.pid != new_pid
+        attribute.update_column(:pid, new_pid)
+        n += 1
+      end
+    end
+    puts "... Finished stripping #{n} Sample Attribute PIds."
+  end
+
   task(decouple_extracted_samples_policies: [:environment]) do
     puts '... creating independent policies for extracted samples...'
     decoupled = 0

test/functional/assays_controller_test.rb

@@ -1061,14 +1061,14 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links
     assert_response :success
 
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'new should include tags element' do
     get :new, params: { class: :experimental }
     assert_response :success
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'edit should include not include tags element when tags disabled' do
@@ -1078,7 +1078,7 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links
       assert_response :success
 
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 
@@ -1087,7 +1087,7 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links
       get :new, params: { class: :experimental }
       assert_response :success
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 

test/functional/data_files_controller_test.rb

@@ -1711,14 +1711,14 @@ def test_show_item_attributed_to_jerm_file
     assert_response :success
 
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'register form should include tags element' do
     register_content_blob
     assert_response :success
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'edit should include not include tags element when tags disabled' do
@@ -1728,7 +1728,7 @@ def test_show_item_attributed_to_jerm_file
       assert_response :success
 
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 
@@ -1737,7 +1737,7 @@ def test_show_item_attributed_to_jerm_file
       register_content_blob
       assert_response :success
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 

test/functional/investigations_controller_test.rb

@@ -766,15 +766,15 @@ def test_title
     get :new
     assert_response :success
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'new should not include tags element when tags disabled' do
     with_config_value :tagging_enabled, false do
       get :new
       assert_response :success
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 
@@ -784,7 +784,7 @@ def test_title
     assert_response :success
 
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'edit should not include tags element when tags disabled' do
@@ -794,7 +794,7 @@ def test_title
       assert_response :success
 
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 
@@ -804,7 +804,7 @@ def test_title
     assert_response :success
 
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'show should not include tags box when tags disabled' do
@@ -814,7 +814,7 @@ def test_title
       assert_response :success
 
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 

test/functional/projects_controller_test.rb

@@ -1730,7 +1730,7 @@ def test_admin_can_edit
 
     get :guided_join, params: { id: project.id }
     assert_response :success
-    assert_select 'input#projects', value: project.id
+    assert_select '#project_ids', value: project.id
   end
 
   test 'invalid guided join' do

test/functional/sops_annotation_test.rb

@@ -256,11 +256,11 @@ class SopsAnnotationTest < ActionController::TestCase
     login_as p.user
     get :new
     assert_response :success
-    assert_select 'input#tag_list'
+    assert_select 'select#tag_list'
 
     sop = FactoryBot.create :sop, contributor: p
     get :edit, params: { id: sop }
     assert_response :success
-    assert_select 'input#tag_list'
+    assert_select 'select#tag_list'
   end
 end

test/functional/studies_controller_test.rb

@@ -1902,15 +1902,15 @@ def test_should_show_investigation_tab
     get :new
     assert_response :success
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'new should not include tags element when tags disabled' do
     with_config_value :tagging_enabled, false do
       get :new
       assert_response :success
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 
@@ -1920,7 +1920,7 @@ def test_should_show_investigation_tab
     assert_response :success
 
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'edit should not include tags element when tags disabled' do
@@ -1930,7 +1930,7 @@ def test_should_show_investigation_tab
       assert_response :success
 
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 
@@ -1940,7 +1940,7 @@ def test_should_show_investigation_tab
     assert_response :success
 
     assert_select 'div.panel-heading', text: /Tags/, count: 1
-    assert_select 'input#tag_list', count: 1
+    assert_select 'select#tag_list', count: 1
   end
 
   test 'show should not include tags box when tags disabled' do
@@ -1950,7 +1950,7 @@ def test_should_show_investigation_tab
       assert_response :success
 
       assert_select 'div.panel-heading', text: /Tags/, count: 0
-      assert_select 'input#tag_list', count: 0
+      assert_select 'select#tag_list', count: 0
     end
   end
 

test/unit/sample_attribute_test.rb

@@ -66,6 +66,7 @@ class SampleAttributeTest < ActiveSupport::TestCase
                                     sample_attribute_type: FactoryBot.create(:integer_sample_attribute_type),
                                     sample_type: FactoryBot.create(:simple_sample_type)
     refute attribute.valid?
+
     attribute.pid = 'http://somewhere.org#fish'
     assert attribute.valid?
     attribute.pid = 'dc:fish'
@@ -76,6 +77,17 @@ class SampleAttributeTest < ActiveSupport::TestCase
     refute attribute.valid?
   end
 
+  test 'auto strip pid' do
+    attribute = SampleAttribute.new title: 'fish', pid:"   wibble:12\t  ",
+                                    sample_attribute_type: FactoryBot.create(:integer_sample_attribute_type),
+                                    sample_type: FactoryBot.create(:simple_sample_type)
+    assert attribute.valid?
+    assert_equal 'wibble:12', attribute.pid
+    attribute.pid = "  wibble:12\n "
+    assert attribute.valid?
+    assert_equal 'wibble:12', attribute.pid
+  end
+
   test 'validate value - without required' do
     attribute = SampleAttribute.new title: 'fish', sample_attribute_type: FactoryBot.create(:integer_sample_attribute_type),
                                     sample_type: FactoryBot.create(:simple_sample_type)