From e5387e5f902f896b29dcfe80d0711100ac29473b Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Wed, 30 Oct 2024 10:38:39 +0100
Subject: [PATCH 01/22] Fix: project page ontologies not selected (#790)

* fix the issue in the projects page when the ontologies are private

* fix ontologies selector name in projects from

* pass the correct project ontologies value in project ontologies selector

* pass an empty array if used ontologies of a group is nil
---
 app/controllers/projects_controller.rb | 14 +++++++-------
 app/views/projects/_form.html.haml     |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb
index 490072b4bd..5816730466 100644
--- a/app/controllers/projects_controller.rb
+++ b/app/controllers/projects_controller.rb
@@ -26,13 +26,13 @@ def show
       redirect_to projects_path
       return
     end
-    
+
     @project = projects.first
     @ontologies_used = []
     onts_used = @project.ontologyUsed
     onts_used.each do |ont_used|
       ont = LinkedData::Client::Models::Ontology.find(ont_used)
-      unless ont.nil?
+      unless ont.nil? || ont.errors
         @ontologies_used << Hash["name", ont.name, "acronym", ont.acronym]
       end
     end
@@ -62,7 +62,7 @@ def edit
     @project = projects.first
     @user_select_list = LinkedData::Client::Models::User.all.map {|u| [u.username, u.id]}
     @user_select_list.sort! {|a,b| a[1].downcase <=> b[1].downcase}
-    @usedOntologies = @project.ontologyUsed || []
+    @usedOntologies = @project.ontologyUsed&.map{|o| o.split('/').last}
     @ontologies = LinkedData::Client::Models::Ontology.all
   end
 
@@ -76,7 +76,7 @@ def create
 
     @project = LinkedData::Client::Models::Project.new(values: project_params)
     @project_saved = @project.save
-    
+
     # Project successfully created.
     if response_success?(@project_saved)
       flash[:notice] = t('projects.project_successfully_created')
@@ -160,10 +160,10 @@ def destroy
   def project_params
     p = params.require(:project).permit(:name, :acronym, :institution, :contacts, { creator:[] }, :homePage,
                                         :description, { ontologyUsed:[] })
-
+                                        
     p[:creator]&.reject!(&:blank?)
-    p[:ontologyUsed]&.reject!(&:blank?)
-    p.to_h
+    p[:ontologyUsed] ||= []
+    p = p.to_h
   end
 
   def flash_error(msg)
diff --git a/app/views/projects/_form.html.haml b/app/views/projects/_form.html.haml
index cd3eea4235..55bdb61edc 100644
--- a/app/views/projects/_form.html.haml
+++ b/app/views/projects/_form.html.haml
@@ -53,5 +53,5 @@
   %div#ontology_picker_project{style: "padding-top: 2em;"}
     - selected_ontologies = @project.ontologyUsed && @project.ontologyUsed.map {|id| id.split('/').last } || []
     - locals = { sel_text: t('projects.form.select_ontologies'), selected_ontologies: selected_ontologies, form_object: :project, form_attribute: "ontologyUsed" }
-    = ontologies_selector(id:'projects_page_ontologies_selector' ,name: 'ontologies')              
+    = ontologies_selector(id:'projects_page_ontologies_selector' ,name: 'project[ontologyUsed][]', selected: @usedOntologies)              
 

From 1aa8d3850eb5f87b39d84b13f78edaa14f8abfa2 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Wed, 30 Oct 2024 10:40:04 +0100
Subject: [PATCH 02/22] fix collection tree issue by including
 MultiLanguagesHelper to make sure main_language_label is defined in
 collections helper (#793)

---
 app/helpers/collections_helper.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/helpers/collections_helper.rb b/app/helpers/collections_helper.rb
index b366a1401c..9a80d24111 100644
--- a/app/helpers/collections_helper.rb
+++ b/app/helpers/collections_helper.rb
@@ -1,4 +1,5 @@
 module CollectionsHelper
+  include MultiLanguagesHelper
 
 
   def get_collections(ontology, add_colors: false)

From 70f0e4daa445de6006baa15f420c5874b40d1bd7 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Wed, 30 Oct 2024 10:45:32 +0100
Subject: [PATCH 03/22] Fix: ontologies selector localization text and add
 "[view]" of the views in the list (#791)

* fix ontologies selector weird results sentence

* show [view] beside ontology views in ontologies selector
---
 app/helpers/application_helper.rb                             | 4 ++--
 .../ontologies_selector/ontologies_selector_results.html.haml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 3f69732afd..acf5335c1c 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -107,14 +107,14 @@ def error_message_alert
   end
 
   def onts_for_select(include_views: false)
-    ontologies ||= LinkedData::Client::Models::Ontology.all({include: "acronym,name", include_views: include_views})
+    ontologies ||= LinkedData::Client::Models::Ontology.all({include: "acronym,name,viewOf", include_views: include_views})
     onts_for_select = [['', '']]
     ontologies.each do |ont|
       next if ( ont.acronym.nil? or ont.acronym.empty? )
       acronym = ont.acronym
       name = ont.name
       abbreviation = acronym.empty? ? "" : "(#{acronym})"
-      ont_label = "#{name.strip} #{abbreviation}"
+      ont_label = "#{name.strip} #{abbreviation}#{ont.viewOf ? ' [view]' : ''}"
       onts_for_select << [ont_label, acronym]
     end
     onts_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase }
diff --git a/app/views/ontologies/ontologies_selector/ontologies_selector_results.html.haml b/app/views/ontologies/ontologies_selector/ontologies_selector_results.html.haml
index 2aeafa23df..9bd25a770a 100644
--- a/app/views/ontologies/ontologies_selector/ontologies_selector_results.html.haml
+++ b/app/views/ontologies/ontologies_selector/ontologies_selector_results.html.haml
@@ -2,7 +2,7 @@
     .ontologies-selector-results
         .horizontal-line                  
         .results-number
-            = t("ontologies.showing_ontologies_size", ontologies_size: @ontologies.length, analytics_size: @total_ontologies_number)
+            = t("ontologies.showing_ontologies_size", ontologies_size: @ontologies.length, analytics_size: @total_ontologies_number, portals: portal_name)
             %span.select-all{'data-action': 'click->ontologies-selector#selectall'}
                 = t('ontologies_selector.select_all')
         .ontologies

From 1e4b80996ec39f9f70191d9f45043ac7c6596887 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Wed, 30 Oct 2024 15:57:12 +0100
Subject: [PATCH 04/22] Fix: update select_language_label  helper to select f
 no english found any language remaining over the not tagged (#795)

* update select_language_label  helper to select f no english found any language remaining over the not tagged

* fix tests by fixing a dependency change

* fix login system tests after securing the user delete action in the API
---
 Gemfile.lock                             |  2 +-
 app/components/tree_link_component.rb    | 46 ++++++++++++++--------
 app/helpers/multi_languages_helper.rb    |  2 +-
 test/helpers/application_test_helpers.rb | 50 +++++++++++++++---------
 test/system/login_flows_test.rb          |  2 -
 test/system/submission_flows_test.rb     | 16 +++-----
 6 files changed, 69 insertions(+), 49 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 3bb8c68812..73328d8412 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -160,7 +160,7 @@ GEM
     ed25519 (1.3.0)
     erubi (1.13.0)
     erubis (2.7.0)
-    excon (1.0.0)
+    excon (0.112.0)
     execjs (2.10.0)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
diff --git a/app/components/tree_link_component.rb b/app/components/tree_link_component.rb
index 73da902f20..fd23706d96 100644
--- a/app/components/tree_link_component.rb
+++ b/app/components/tree_link_component.rb
@@ -2,26 +2,19 @@
 
 class TreeLinkComponent < ViewComponent::Base
   include MultiLanguagesHelper, ModalHelper, ApplicationHelper
-  def initialize(child:, href:, children_href: , selected: false , data: {}, muted: false, target_frame: nil, open_in_modal: false, is_reused: nil)
+
+  def initialize(child:, href:, children_href:, selected: false, data: {}, muted: false, target_frame: nil, open_in_modal: false, is_reused: nil)
+    super
+
     @child = child
     @active_style = selected ? 'active' : ''
-    #@icons = child.relation_icon(node)
     @muted_style = muted ? 'text-muted' : ''
     @href = href
     @children_link = children_href
-    label = (@child.prefLabel || @child.label) rescue @child.id
-    if label.nil?
-      @pref_label_html = link_last_part(child.id)
-    else
-      pref_label_lang, @pref_label_html = select_language_label(label)
-      pref_label_lang = pref_label_lang.to_s.upcase
-      @tooltip = pref_label_lang.eql?("@NONE") ? "" : pref_label_lang
 
-      if child.obsolete?
-        @pref_label_html = "<span class='obsolete_class'>#{@pref_label_html}</span>".html_safe
-      end
-    end
-    @data ||= { controller: 'tooltip', 'tooltip-position-value': 'right', turbo: true, 'turbo-frame': target_frame, action: 'click->simple-tree#select'}
+    @pref_label_html, @tooltip = node_label(child)
+
+    @data ||= { controller: 'tooltip', 'tooltip-position-value': 'right', turbo: true, 'turbo-frame': target_frame, action: 'click->simple-tree#select' }
 
     @data.merge!(data) do |_, old, new|
       "#{old} #{new}"
@@ -32,7 +25,6 @@ def initialize(child:, href:, children_href: , selected: false , data: {}, muted
     @is_reused = is_reused
   end
 
-
   # This gives a very hacky short code to use to uniquely represent a class
   # based on its parent in a tree. Used for unique ids in HTML for the tree view
   def short_uuid
@@ -49,7 +41,7 @@ def open?
   end
 
   def border_left
-    !@child.hasChildren  ?  'pl-3 tree-border-left' :  ''
+    !@child.hasChildren ? 'pl-3 tree-border-left' : ''
   end
 
   def li_id
@@ -75,4 +67,26 @@ def open_children_link
 
   end
 
+  private
+
+  def node_label(child)
+    label = begin
+              child.prefLabel || child.label
+            rescue
+              child.id
+            end
+
+    if label.nil?
+      pref_label_html = link_last_part(child.id)
+    else
+      pref_label_lang, pref_label_html = select_language_label(label)
+      pref_label_lang = pref_label_lang.to_s.upcase
+      tooltip = pref_label_lang.eql?("@NONE") ? "" : pref_label_lang
+
+      pref_label_html = "<span class='obsolete_class'>#{pref_label_html}</span>".html_safe if child.obsolete?
+    end
+
+    [pref_label_html, tooltip]
+  end
+
 end
diff --git a/app/helpers/multi_languages_helper.rb b/app/helpers/multi_languages_helper.rb
index 9e21f2e0ed..6e127b94e0 100644
--- a/app/helpers/multi_languages_helper.rb
+++ b/app/helpers/multi_languages_helper.rb
@@ -153,7 +153,7 @@ def select_language_label(concept_label, platform_languages = %i[en fr])
       end
     end
 
-    concept_value || concept.to_a.first
+    concept_value || concept.reject { |k| k.to_s.eql?('@none') }.first || concept.first
   end
 
   def main_language_label(label)
diff --git a/test/helpers/application_test_helpers.rb b/test/helpers/application_test_helpers.rb
index 975c220eac..28530711f7 100644
--- a/test/helpers/application_test_helpers.rb
+++ b/test/helpers/application_test_helpers.rb
@@ -16,17 +16,27 @@ module Users
     def sign_in_as(username)
       user = fixtures(:users)[username]
       logged_in_user = LinkedData::Client::Models::User.authenticate(user.username, user.password)
-      if logged_in_user && !logged_in_user.errors
-        logged_in_user = create_user(user)
-      end
+      logged_in_user = create_user(user) if logged_in_user && !logged_in_user.errors
       logged_in_user
     end
 
     def create_user(user, admin: false)
-      admin_user = LinkedData::Client::Models::User.authenticate('admin', 'password') if admin
+      admin_user = LinkedData::Client::Models::User.authenticate('admin', 'password')
       existent_user = LinkedData::Client::Models::User.find_by_username(user.username).first
 
-      existent_user.delete if existent_user
+      conn = Faraday.new(url: LinkedData::Client.settings.rest_url) do |faraday|
+        faraday.request :url_encoded
+        faraday.response :logger
+        faraday.adapter Faraday.default_adapter
+        faraday.headers = {
+          "Accept" => "application/json",
+          "Authorization" => "apikey token=#{admin_user.apikey}",
+          "User-Agent" => "NCBO API Ruby Client v0.1.0"
+        }
+
+      end
+
+      conn.delete("/users/#{user.username}") if existent_user
 
       values = user.to_h
       values[:role] = ["ADMINISTRATOR"] if admin
@@ -34,17 +44,6 @@ def create_user(user, admin: false)
 
       if admin
         # Overwrite the normal ".save" to accept creating admin user
-        conn = Faraday.new(url: LinkedData::Client.settings.rest_url) do |faraday|
-          faraday.request :url_encoded
-          faraday.response :logger
-          faraday.adapter Faraday.default_adapter
-          faraday.headers = {
-            "Accept" => "application/json",
-            "Authorization" => "apikey token=#{admin_user.apikey}",
-            "User-Agent" => "NCBO API Ruby Client v0.1.0"
-          }
-
-        end
         conn.post(existent_user.class.collection_path, existent_user.to_hash.to_json, 'Content-Type' => 'application/json')
       else
         existent_user.save
@@ -61,7 +60,22 @@ def delete_users(users = LinkedData::Client::Models::User.all)
     end
 
     def delete_user(user)
-      LinkedData::Client::Models::User.find_by_username(user.username).first&.delete
+      admin_user = LinkedData::Client::Models::User.authenticate('admin', 'password')
+      existent_user = LinkedData::Client::Models::User.find_by_username(user.username).first
+
+      conn = Faraday.new(url: LinkedData::Client.settings.rest_url) do |faraday|
+        faraday.request :url_encoded
+        faraday.response :logger
+        faraday.adapter Faraday.default_adapter
+        faraday.headers = {
+          "Accept" => "application/json",
+          "Authorization" => "apikey token=#{admin_user.apikey}",
+          "User-Agent" => "NCBO API Ruby Client v0.1.0"
+        }
+
+      end
+
+      conn.delete("/users/#{user.username}") if existent_user
     end
   end
 
@@ -133,4 +147,4 @@ def delete_agents(agents = LinkedData::Client::Models::Agent.all)
       Array(agents).each { |g| g.delete }
     end
   end
-end
\ No newline at end of file
+end
diff --git a/test/system/login_flows_test.rb b/test/system/login_flows_test.rb
index d6ff0deb49..8bed283d20 100644
--- a/test/system/login_flows_test.rb
+++ b/test/system/login_flows_test.rb
@@ -22,8 +22,6 @@ class LoginFlowsTest < ApplicationSystemTestCase
     new_user = @user_john
     delete_user(new_user)
 
-    LinkedData::Client::Models::User.find_by_username(new_user.username).first&.delete
-
     fill_in 'user_firstName', with: new_user.firstName
     fill_in 'user_lastName', with: new_user.lastName
     fill_in 'user_username', with: new_user.username
diff --git a/test/system/submission_flows_test.rb b/test/system/submission_flows_test.rb
index 6045308d04..a0c06a4f47 100644
--- a/test/system/submission_flows_test.rb
+++ b/test/system/submission_flows_test.rb
@@ -46,7 +46,6 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
       assert_text cat.acronym.titleize
     end
 
-
     assert_text @new_submission.URI
     assert_text @new_submission.description
     assert_text @new_submission.pullLocation
@@ -103,7 +102,6 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
       click_on "Licensing"
       submission_licensing_edit_fill(ontology_2, submission_2)
 
-
       # Persons and organizations tab
       click_on "Persons and organizations"
       submission_agent_edit_fill(submission_2)
@@ -148,7 +146,10 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
 
     assert_text submission_2.URI
     assert_text submission_2.versionIRI
+
+    wait_for '.submission-status'
     assert_selector '.submission-status', text: submission_2.version
+
     assert_selector ".flag-icon-fr" # todo fix this
     submission_2.identifier.each do |id|
       assert_text id
@@ -258,7 +259,6 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
     assert_text "rdfs"
     assert_text "dct"
 
-
     open_dropdown "#configuration"
 
     submission_2.keyClasses.each do |key|
@@ -341,10 +341,8 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
     sleep 0.5
     click_button 'Back'
 
-
     fill_ontology(ontology_2, submission_2, add_submission: true)
 
-
     assert_selector 'h2', text: 'Ontology submitted successfully!'
     click_on current_url.gsub("/ontologies/success/#{existent_ontology.acronym}", '') + ontology_path(existent_ontology.acronym)
 
@@ -362,7 +360,6 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
     assert_text submission_2.description
     assert_text submission_2.pullLocation
 
-
     # check
     assert_selector '.fas.fa-key' if submission_2.status.eql?('private')
 
@@ -380,7 +377,6 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
       assert_text group.name
     end
 
-
     open_dropdown "#dates"
     assert_date submission_2.modificationDate
     assert_date existent_submission.released
@@ -483,7 +479,6 @@ def submission_agent_edit_fill(submission)
 
     list_inputs "#submissioncontact_from_group_input", "submission[contact]", submission.contact
 
-
     agent1 = fixtures(:agents)[:agent1]
     agent2 = fixtures(:agents)[:agent2]
 
@@ -624,7 +619,6 @@ def fill_ontology(new_ontology, new_submission, add_submission: false)
       list_checks new_ontology.hasDomain.map(&:acronym), @categories.map(&:acronym)
       list_checks new_ontology.group.map(&:acronym), @groups.map(&:acronym)
 
-
       click_button 'Next'
 
       # Page 2
@@ -644,9 +638,9 @@ def fill_ontology(new_ontology, new_submission, add_submission: false)
 
       # Page 3
       if add_submission
-       date_picker_fill_in 'submission[modificationDate]', new_submission.modificationDate
+        date_picker_fill_in 'submission[modificationDate]', new_submission.modificationDate
       else
-       date_picker_fill_in 'submission[released]', new_submission.released
+        date_picker_fill_in 'submission[released]', new_submission.released
       end
 
       list_inputs "#submissioncontact_from_group_input", "submission[contact]", new_submission.contact

From d67ba52615725d5768353877ca29a535090c2dbb Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Wed, 30 Oct 2024 16:00:49 +0100
Subject: [PATCH 05/22] Fix: clean concepts controller code to improve tree
 view performance (#794)

---
 app/controllers/concepts_controller.rb | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/app/controllers/concepts_controller.rb b/app/controllers/concepts_controller.rb
index 196a61f97d..1063c953b4 100644
--- a/app/controllers/concepts_controller.rb
+++ b/app/controllers/concepts_controller.rb
@@ -45,14 +45,15 @@ def index
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
     @ob_instructions = helpers.ontolobridge_instructions_template(@ontology)
 
-    @submission = @ontology.explore.latest_submission(include: 'all')
+    @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri')
+
+    @concept = @ontology.explore.single_class({dispay: 'prefLabel'}, params[:id])
 
-    @concept = @ontology.explore.single_class({full: true}, params[:id])
     concept_not_found(params[:id]) if @concept.nil?
     @schemes = params[:concept_schemes].split(',')
 
     @concept.children = @concept.explore.children(pagesize: 750, concept_schemes: Array(@schemes).join(','), language: request_lang, display: 'prefLabel,obsolete,hasChildren').collection || []
-    @concept.children.sort! { |x, y| (x.prefLabel || "").downcase <=> (y.prefLabel || "").downcase } unless @concept.children.empty?
+
     render turbo_stream: [
       replace(helpers.child_id(@concept) + '_open_link') { TreeLinkComponent.tree_close_icon },
       replace(helpers.child_id(@concept) + '_childs') do

From e616842389ae436b47d09f95fe7cc5bfbf2911e2 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Wed, 30 Oct 2024 17:38:56 +0100
Subject: [PATCH 06/22] Fix: Disable slices not hiding the slices section in
 the home page  (#797)

* update select_language_label  helper to select f no english found any language remaining over the not tagged

* hide the slices section in the home page if slices disabled
---
 app/helpers/application_helper.rb | 3 +++
 app/views/home/index.html.haml    | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index acf5335c1c..6d565bdb22 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -121,6 +121,9 @@ def onts_for_select(include_views: false)
     onts_for_select
   end
 
+  def slices_enabled?
+    $ENABLE_SLICES.eql?(true)
+  end
 
   def at_slice?
     !@subdomain_filter.nil? && !@subdomain_filter[:active].nil? && @subdomain_filter[:active] == true
diff --git a/app/views/home/index.html.haml b/app/views/home/index.html.haml
index 253e0546ad..8bc39eba97 100644
--- a/app/views/home/index.html.haml
+++ b/app/views/home/index.html.haml
@@ -176,7 +176,7 @@
       .home-statistics-link.justify-content-end{style: @analytics.empty? && "visibility: hidden"}
         = link_to t("home.see_details"),'/statistics', target: "_blank"
 
-  - if @slices
+  - if slices_enabled?
     .home-section
       .home-section-title
         .text

From f1773c1c09e3014d488906c047215c75bdd3c961 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Thu, 31 Oct 2024 12:54:09 +0100
Subject: [PATCH 07/22] Feature: update concept mappings table UI (#798)

* fix mappings table style

* hide relations column when it's completely empty

* use icons and Abbreviations types and sources

* hide actions column if no mapping is of type REST

* update create new mapping button style

* remove concept mapping table padding

* remove relation column and remove Action title

* make the column width for the mapping to and ontology larger

* move some mappings helper to the mapping controller as used only there

* move the logic from the mapping table view to helpers

* fix link text component icon size

* change mappings action icons colors to primary color

* pass button component in create new mapping instead of using only the css of it

* internationalize create new mapping button text

* internationalize mapping types description

* fix interportal mapping issue when the interportal_hash is empty

* limit mapping type tooltip by 300px width

---------

Co-authored-by: Syphax <gs_bouazzouni@esi.dz>
---
 app/assets/stylesheets/mappings.scss          |  25 +++
 app/components/link_text_component.rb         |   2 +-
 app/controllers/mappings_controller.rb        |  54 +++++-
 app/helpers/mappings_helper.rb                | 174 +++++++++---------
 .../mappings/_concept_mappings.html.haml      |  17 +-
 app/views/mappings/_mapping_table.html.haml   |  12 +-
 app/views/mappings/_show_line.html.haml       |  57 ++----
 config/locales/en.yml                         |   7 +
 config/locales/fr.yml                         |   8 +
 9 files changed, 202 insertions(+), 154 deletions(-)

diff --git a/app/assets/stylesheets/mappings.scss b/app/assets/stylesheets/mappings.scss
index 89a7ebffbe..20ddbb6940 100644
--- a/app/assets/stylesheets/mappings.scss
+++ b/app/assets/stylesheets/mappings.scss
@@ -320,6 +320,28 @@ div#map_from_concept_details_table, div#map_to_concept_details_table {
 
 #concept_mappings_table {
   width: 100%;
+  word-break: break-word;
+  font-size: 13px;
+}
+.mappings-table-mapping-to{
+  width: 45%;
+}
+.mappings-table-mapping-to .chip-button-component-container{
+  text-wrap: wrap !important;
+}
+.mappings-table-mapping-to a{
+  background-color: unset;
+  line-height: unset;
+  padding: unset;
+  font-weight: unset;
+  font-size: unset;
+}
+.mappings-table-icon{
+  width: 18px;
+  height: 18px;
+}
+.mappings-table-icon path{
+  fill: var(--gray-color);
 }
 
 .summary-mappings-tab-table {
@@ -341,4 +363,7 @@ div#map_from_concept_details_table, div#map_to_concept_details_table {
   padding: 10px;
   outline: none;
   margin-left: 0 !important;
+}
+.mappings-table-actions svg path{
+  fill: var(--primary-color);
 }
\ No newline at end of file
diff --git a/app/components/link_text_component.rb b/app/components/link_text_component.rb
index 47ea0f6dfc..36dc79ba33 100644
--- a/app/components/link_text_component.rb
+++ b/app/components/link_text_component.rb
@@ -10,7 +10,7 @@ def initialize(text:, icon: nil, target: nil)
   end
 
   def call
-    svg_icon = !@icon&.empty? ? inline_svg(@icon) : ''
+    svg_icon = !@icon&.empty? ? inline_svg(@icon, width: '14px', height: '14px') : ''
     extra_span = @text == t('mappings.upload_mappings') ? '' : "<span class='mx-1'>#{svg_icon}</span>"
     "#{@text}#{extra_span}".html_safe
   end
diff --git a/app/controllers/mappings_controller.rb b/app/controllers/mappings_controller.rb
index b1bcfc8c32..df582acb4e 100644
--- a/app/controllers/mappings_controller.rb
+++ b/app/controllers/mappings_controller.rb
@@ -342,4 +342,56 @@ def valid_values?(values)
     end
     errors
   end
-end
\ No newline at end of file
+
+  def set_mapping_target(concept_to_id:, ontology_to:, mapping_type: )
+    case mapping_type
+    when 'interportal'
+      @map_to_interportal, @map_to_interportal_ontology = ontology_to.match(%r{(.*)/ontologies/(.*)}).to_a[1..]
+      @map_to_interportal_class = concept_to_id
+    when 'external'
+      @map_to_external_ontology = ontology_to
+      @map_to_external_class = concept_to_id
+    else
+      @map_to_bioportal_ontology_id = ontology_to
+      @map_to_bioportal_full_id = concept_to_id
+    end
+  end
+
+  def get_mappings_target_params
+    mapping_type = Array(params[:mapping_type]).first
+    external = true
+    case mapping_type
+    when 'interportal'
+      ontology_to = "#{params[:map_to_interportal]}/ontologies/#{params[:map_to_interportal_ontology]}"
+      concept_to_id = params[:map_to_interportal_class]
+    when 'external'
+      ontology_to = params[:map_to_external_ontology]
+      concept_to_id = params[:map_to_external_class]
+    else
+      ontology_to = params[:map_to_bioportal_ontology_id]
+      concept_to_id = params[:map_to_bioportal_full_id]
+      external = false
+    end
+    [ontology_to, concept_to_id, external]
+  end
+
+  def get_mappings_target
+    ontology_to, concept_to_id, external_mapping = get_mappings_target_params
+    target = ''
+    if external_mapping
+      target_ontology = ontology_to
+      target = concept_to_id
+    else
+      if helpers.link?(ontology_to)
+        target_ontology = LinkedData::Client::Models::Ontology.find(ontology_to)
+      else
+        target_ontology = LinkedData::Client::Models::Ontology.find_by_acronym(ontology_to).first
+      end
+      if target_ontology
+        target = target_ontology.explore.single_class(concept_to_id).id
+        target_ontology = target_ontology.id
+      end
+    end
+    [target_ontology, target, external_mapping]
+  end
+end
diff --git a/app/helpers/mappings_helper.rb b/app/helpers/mappings_helper.rb
index bfe583a41b..c1e503b547 100644
--- a/app/helpers/mappings_helper.rb
+++ b/app/helpers/mappings_helper.rb
@@ -2,43 +2,85 @@ module MappingsHelper
 
   # Used to replace the full URI by the prefixed URI
   RELATIONSHIP_PREFIX = {
-    "http://www.w3.org/2004/02/skos/core#" => "skos:",
-    "http://www.w3.org/2000/01/rdf-schema#" => "rdfs:",
-    "http://www.w3.org/2002/07/owl#" => "owl:",
-    "http://www.w3.org/1999/02/22-rdf-syntax-ns#" => "rdf:",
-    "http://purl.org/linguistics/gold/" => "gold:",
-    "http://lemon-model.net/lemon#" => "lemon:"
+    'http://www.w3.org/2004/02/skos/core#' => 'skos:',
+    'http://www.w3.org/2000/01/rdf-schema#' => 'rdfs:',
+    'http://www.w3.org/2002/07/owl#' => 'owl:',
+    'http://www.w3.org/1999/02/22-rdf-syntax-ns#' => 'rdf:',
+    'http://purl.org/linguistics/gold/' => 'gold:',
+    'http://lemon-model.net/lemon#' => 'lemon:'
   }
 
   INTERPORTAL_HASH = $INTERPORTAL_HASH
 
-
-  # a little method that returns true if the URIs array contain a gold:translation or gold:freeTranslation
-  def translation?(relation_array)
-    if relation_array.kind_of?(Array)
-      relation_array.map!(&:downcase)
-      if relation_array.include? "http://purl.org/linguistics/gold/translation"
-        true
-      elsif relation_array.include? "http://purl.org/linguistics/gold/freetranslation"
-        true
-      else
-        false
+  def mapping_links(mapping, concept)
+    target_concept = mapping.classes.select do |c|
+      c.id != concept.id && c.links['ontology'] != concept.links['ontology']
+    end.first
+    target_concept ||= mapping.classes.last
+    process = mapping.process || {}
+
+    if inter_portal_mapping?(target_concept)
+      cls_link = ajax_to_inter_portal_cls(target_concept)
+      ont_name = target_concept.links['ontology']
+      ont_link = link_to ont_name, get_inter_portal_ui_link(ont_name, process['name']), target: '_blank'
+      source_tooltip = 'Internal-portal'
+    elsif internal_mapping?(target_concept)
+      begin
+        ont = target_concept.explore.ontology
+        ont_name = ont.acronym
+        ont_link = link_to ont_name, ontology_path(ont_name), 'data-turbo-frame': '_top'
+      rescue
+        ont_name = target_concept.links['ontology'] || target_concept.id
+        ont_link = ont_name
       end
+      cls_link = raw(get_link_for_cls_ajax(target_concept.id, ont_name, '_top'))
+      source_tooltip = 'Internal'
     else
-      false
+      cls_label = ExternalLinkTextComponent.new(text: target_concept.links['self']).call
+      cls_link = raw("<a href='#{target_concept.links["self"]}' target='_blank'>#{cls_label}</a>")
+      ont_name = target_concept.links['ontology']
+      ont_link = link_to ExternalLinkTextComponent.new(text: ont_name).call, target_concept.links['ontology'],
+                         target: '_blank'
+      source_tooltip = 'External'
     end
+
+    [cls_link, ont_link, source_tooltip]
+  end
+
+  def mapping_prefixed_relations(mapping)
+    process = mapping.process || {}
+    Array(process[:relation]).each { |relation| get_prefixed_uri(relation) }
+  end
+
+  def mapping_type_tooltip(map)
+    relations = mapping_prefixed_relations(map)
+    process = map.process || {}
+    type = if map.source.to_s.include? 'SKOS'
+             'SKOS'
+           else
+             map.source
+           end
+    types_description = {
+      'CUI' => t('mappings.types_description.cui'),
+      'LOOM' => t('mappings.types_description.loom'),
+      'REST' => t('mappings.types_description.rest'),
+      'SAME_URI' => t('mappings.types_description.same_uri'),
+      'SKOS' => t('mappings.types_description.skos')
+    }
+    type_tooltip = content_tag(:div, "#{map.source} #{relations.join(', ')} : #{types_description[type]} #{process[:source_name]}".strip, style: 'width: 300px')
+    [type, type_tooltip]
   end
 
   # a little method that returns the uri with a prefix : http://purl.org/linguistics/gold/translation become gold:translation
   def get_prefixed_uri(uri)
     RELATIONSHIP_PREFIX.each { |k, v| uri.sub!(k, v) }
-    return uri
+    uri
   end
 
   # method to get (using http) prefLabel for interportal classes
   # Using bp_ajax_controller.ajax_process_interportal_cls will try to resolve class labels.
   def ajax_to_inter_portal_cls(cls)
-    inter_portal_acronym = get_inter_portal_acronym(cls.links["ui"])
+    inter_portal_acronym = get_inter_portal_acronym(cls.links['ui'])
     href_cls = " href='#{cls.links["ui"]}' "
     if inter_portal_acronym
       data_cls = " data-cls='#{cls.links["self"]}?apikey=' "
@@ -52,7 +94,7 @@ def ajax_to_inter_portal_cls(cls)
 
   def ajax_to_internal_cls(cls)
     link_to("#{cls.id}<span href='/ajax/classes/label?ontology=#{cls.links["ontology"]}&concept=#{escape(cls.id)}' class='get_via_ajax'></span>".html_safe,
-            ontology_path(cls.explore.ontology.acronym, p: 'classes', conceptid: cls.id), target: "_blank")
+            ontology_path(cls.explore.ontology.acronym, p: 'classes', conceptid: cls.id), target: '_blank')
   end
 
   # to get the apikey from the interportal instance of the interportal class.
@@ -60,7 +102,7 @@ def ajax_to_internal_cls(cls)
   def get_inter_portal_acronym(class_ui_url)
     if !INTERPORTAL_HASH.nil?
       INTERPORTAL_HASH.each do |key, value|
-        if class_ui_url.start_with?(value["ui"])
+        if class_ui_url.start_with?(value['ui'])
           return key
         else
           return nil
@@ -71,11 +113,11 @@ def get_inter_portal_acronym(class_ui_url)
 
   # method to extract the prefLabel from the external class URI
   def get_label_for_external_cls(class_uri)
-    if class_uri.include? "#"
-      prefLabel = class_uri.split("#")[-1]
-    else
-      prefLabel = class_uri.split("/")[-1]
-    end
+    prefLabel = if class_uri.include? '#'
+                  class_uri.split('#')[-1]
+                else
+                  class_uri.split('/')[-1]
+                end
     return prefLabel
   end
 
@@ -86,11 +128,11 @@ def ajax_to_external_cls(cls)
   # Replace the inter_portal mapping ontology URI (that link to the API) by the link to the ontology in the UI
   def get_inter_portal_ui_link(uri, process_name)
     process_name = '' if process_name.nil?
-    interportal_acronym = process_name.split(" ")[2]
-    if interportal_acronym.nil? || interportal_acronym.empty?
+    interportal_acronym = process_name.split(' ')[2]
+    if interportal_acronym.nil? || interportal_acronym.empty? || INTERPORTAL_HASH[interportal_acronym].nil?
       uri
     else
-      uri.sub!(INTERPORTAL_HASH[interportal_acronym]["api"], INTERPORTAL_HASH[interportal_acronym]["ui"])
+      uri.sub!(INTERPORTAL_HASH[interportal_acronym]['api'], INTERPORTAL_HASH[interportal_acronym]['ui'])
     end
   end
 
@@ -99,66 +141,14 @@ def internal_mapping?(cls)
   end
 
   def inter_portal_mapping?(cls)
-    !internal_mapping?(cls) && cls.links.has_key?("ui")
-  end
-
-  def get_mappings_target_params
-    mapping_type = Array(params[:mapping_type]).first
-    external = true
-    case mapping_type
-    when 'interportal'
-      ontology_to = "#{params[:map_to_interportal]}/ontologies/#{params[:map_to_interportal_ontology]}"
-      concept_to_id = params[:map_to_interportal_class]
-    when 'external'
-      ontology_to = params[:map_to_external_ontology]
-      concept_to_id = params[:map_to_external_class]
-    else
-      ontology_to = params[:map_to_bioportal_ontology_id]
-      concept_to_id = params[:map_to_bioportal_full_id]
-      external = false
-    end
-    [ontology_to, concept_to_id, external]
-  end
-
-  def set_mapping_target(concept_to_id:, ontology_to:, mapping_type: )
-    case mapping_type
-    when 'interportal'
-      @map_to_interportal, @map_to_interportal_ontology = ontology_to.match(%r{(.*)/ontologies/(.*)}).to_a[1..]
-      @map_to_interportal_class = concept_to_id
-    when 'external'
-      @map_to_external_ontology = ontology_to
-      @map_to_external_class = concept_to_id
-    else
-      @map_to_bioportal_ontology_id = ontology_to
-      @map_to_bioportal_full_id = concept_to_id
-    end
-  end
-
-  def get_mappings_target
-    ontology_to, concept_to_id, external_mapping = get_mappings_target_params
-    target = ''
-    if external_mapping
-      target_ontology = ontology_to
-      target = concept_to_id
-    else
-      if helpers.link?(ontology_to)
-        target_ontology = LinkedData::Client::Models::Ontology.find(ontology_to)
-      else
-        target_ontology = LinkedData::Client::Models::Ontology.find_by_acronym(ontology_to).first
-      end
-      if target_ontology
-        target = target_ontology.explore.single_class(concept_to_id).id
-        target_ontology = target_ontology.id
-      end
-    end
-    [target_ontology, target, external_mapping]
+    !internal_mapping?(cls) && cls.links.has_key?('ui')
   end
 
   def type?(type)
     @mapping_type.nil? && type.eql?('internal') || @mapping_type.eql?(type)
   end
 
-  def concept_mappings_loader(ontology_acronym: ,concept_id: )
+  def concept_mappings_loader(ontology_acronym:, concept_id:)
     content_tag(:span, id: 'mapping_count') do
       concat(content_tag(:div, class: 'concepts-mapping-count ml-1 mr-1') do
         render(TurboFrameComponent.new(
@@ -173,21 +163,23 @@ def concept_mappings_loader(ontology_acronym: ,concept_id: )
   end
 
   def client_filled_modal
-    link_to_modal "", ""
+    link_to_modal '', ''
   end
 
   def mappings_bubble_view_legend
     content_tag(:div, class: 'mappings-bubble-view-legend') do
-      mappings_legend_section(t('mappings.bubble_view_legend.bubble_size'), t('mappings.bubble_view_legend.bubble_size_desc'), 'mappings-bubble-size-legend') +
+      mappings_legend_section(t('mappings.bubble_view_legend.bubble_size'),
+                              t('mappings.bubble_view_legend.bubble_size_desc'), 'mappings-bubble-size-legend') +
         mappings_legend_section(
-          t('mappings.bubble_view_legend.color_degree'),t('mappings.bubble_view_legend.color_degree_desc'),'mappings-bubble-color-legend') +
+          t('mappings.bubble_view_legend.color_degree'), t('mappings.bubble_view_legend.color_degree_desc'), 'mappings-bubble-color-legend') +
         content_tag(:div, class: 'content-container') do
           content_tag(:div, class: 'bubble-view-legend-item') do
             content_tag(:div, class: 'title') do
-              content_tag(:div, t('mappings.bubble_view_legend.yellow_bubble'), class: 'd-inline') + content_tag(:span, t('mappings.bubble_view_legend.selected_bubble'))
+              content_tag(:div, t('mappings.bubble_view_legend.yellow_bubble'),
+                          class: 'd-inline') + content_tag(:span, t('mappings.bubble_view_legend.selected_bubble'))
             end +
-              content_tag(:div, class: "mappings-bubble-size-legend d-flex justify-content-center") do
-                content_tag(:div, '', class: "bubble yellow")
+              content_tag(:div, class: 'mappings-bubble-size-legend d-flex justify-content-center') do
+                content_tag(:div, '', class: 'bubble yellow')
               end
           end
         end
@@ -209,7 +201,7 @@ def mappings_legend_section(title_text, description_text, css_class)
   def mappings_legend(css_class)
     content_tag(:div, class: css_class) do
       content_tag(:div, t('mappings.bubble_view_legend.less_mappings'), class: 'mappings-legend-text') +
-        (1..6).map { |i| content_tag(:div, "", class: "bubble bubble#{i}") }.join.html_safe +
+        (1..6).map { |i| content_tag(:div, '', class: "bubble bubble#{i}") }.join.html_safe +
         content_tag(:div, t('mappings.bubble_view_legend.more_mappings'), class: 'mappings-legend-text')
     end
   end
diff --git a/app/views/mappings/_concept_mappings.html.haml b/app/views/mappings/_concept_mappings.html.haml
index c71fe9066b..2a6b56b29e 100644
--- a/app/views/mappings/_concept_mappings.html.haml
+++ b/app/views/mappings/_concept_mappings.html.haml
@@ -2,17 +2,16 @@
   = "#{@mappings.size}"
 
 = turbo_frame_tag @type.eql?('modal') ? 'application_modal_content' : 'concept_mappings' do
-  %div{:style => "padding: 1%; width: 98%"}
+  %div.p-1
     - if session[:user].nil?
       = link_to "Create New Mapping", "/login?redirect=/ontologies/#{@ontology.acronym}/?p=classes&t=mappings&conceptid=#{escape(@concept.id)}", :method => :get, :class => "btn btn-default mb-3"
     - else
-      = link_to_modal("Create New Mapping",
-                new_mapping_path(ontology_from: "#{@ontology.id}", conceptid_from: "#{@concept.id}"),
-                id: "new_mapping_btn",
-                role: "button",
-                class: "btn btn-default mb-3",
-                data: { show_modal_title_value: "Create a new mapping for #{@concept.prefLabel}" },
-                )
+      %div{style: 'width: 250px; margin: 0 0 10px 0;'}
+        = link_to_modal(nil,
+                  new_mapping_path(ontology_from: "#{@ontology.id}", conceptid_from: "#{@concept.id}"),
+                  data: { show_modal_title_value: "Create a new mapping for #{@concept.prefLabel}" },
+                  ) do
+          = render Buttons::RegularButtonComponent.new(id:'new_mapping_btn' , value:t('mappings.create_new_mapping'), variant: 'secondary', size: 'slim', state: 'no-anim')
 
     #mapping_details
-      = render :partial => '/mappings/mapping_table'
\ No newline at end of file
+      = render :partial => '/mappings/mapping_table'
diff --git a/app/views/mappings/_mapping_table.html.haml b/app/views/mappings/_mapping_table.html.haml
index 1d91b3b5bb..20efcd92d5 100644
--- a/app/views/mappings/_mapping_table.html.haml
+++ b/app/views/mappings/_mapping_table.html.haml
@@ -1,16 +1,14 @@
 = check_box_tag "delete_mappings_permission", @delete_mapping_permission, @delete_mapping_permission, style: "display: none;"
 %div#concept_mappings_tables_div
   = render_alerts_container(MappingsController)
-  %table#concept_mappings_table.table-content-stripped.table-content{width: "100%", style:'word-break: break-word'}
+  %table#concept_mappings_table.table-content-stripped.table-content.table-mini
     %thead
       %tr
         %th= t("mappings.mapping_table.mapping_to")
-        %th{width: "30%"}= t("mappings.count.ontology")
-        %th= t("mappings.mapping_table.relations")
-        %th= t("mappings.mapping_table.source")
+        %th= t("mappings.count.ontology")
         %th= t("mappings.mapping_table.type")
-        - if current_user_admin?
-          %th{:class => 'delete_mappings_column'}= t("mappings.mapping_table.actions")
+        - if current_user_admin? && !@mappings.all? { |obj| !obj.source.eql?('REST') }
+          %th{:class => 'delete_mappings_column'}
     %tbody#concept_mappings_table_content
       - @mappings.each do |map|
         = render partial: 'mappings/show_line' , locals: {map: map, concept: @concept}
@@ -19,4 +17,4 @@
 :javascript
   jQuery(document).ready(function(){
     ajax_process_init();
-  })
\ No newline at end of file
+  })
diff --git a/app/views/mappings/_show_line.html.haml b/app/views/mappings/_show_line.html.haml
index bbfab2b78e..4c94555c4d 100644
--- a/app/views/mappings/_show_line.html.haml
+++ b/app/views/mappings/_show_line.html.haml
@@ -1,56 +1,23 @@
-- process = map.process || {}
-- source = "#{map.source} #{process[:source_name]}"
-- relations = process[:relation]&.each { |relation| get_prefixed_uri(relation)}
+- type, type_tooltip = mapping_type_tooltip(map)
+- cls_link, ont_link, source_tooltip = mapping_links(map, concept)
 - map_id = map.id.to_s.split("/").last
-- target_concept = map.classes.select {|target_concept| target_concept.id != concept.id && target_concept.links['ontology'] != concept.links['ontology']}.first || map.classes.last
 
-- if inter_portal_mapping?(target_concept)
-  - cls_link = ajax_to_inter_portal_cls(target_concept)
-  - ont_name = target_concept.links['ontology']
-  - ont_acronym = ont_name
-  - ont_link = link_to ont_acronym , get_inter_portal_ui_link(target_concept.links['ontology'], process["name"]), target: '_blank'
-  - type = 'Inter-portal'
-- elsif internal_mapping?(target_concept)
-  - begin
-    - ont = target_concept.explore.ontology
-    - ont_name = ont.acronym
-    - ont_link =  link_to ont_name, ontology_path(ont_name), 'data-turbo-frame':'_top'
-  - rescue
-    - ont_name =   target_concept.links['ontology'] || target_concept.id
-    - ont_link =   ont_name
-  - cls_link = raw(get_link_for_cls_ajax(target_concept.id, ont_name, '_top'))
-  - type = 'Internal'
-- else
-  - cls_label = get_label_for_external_cls(target_concept.links["self"])
-  - cls_link = raw("<a href='#{target_concept.links["self"]}' target='_blank'>#{cls_label}</a>")
-  - ont_name = target_concept.links['ontology']
-  - ont_link = link_to ont_name, target_concept.links['ontology'], target: "_blank"
-  - type = 'External'
-  
 %tr.human{:id => map_id}
-  %td
+  %td.mappings-table-mapping-to
     = cls_link
-  %td
+  %td.mappings-table-mapping-to
     = ont_link
   %td
-    - relations&.each do  |r|
-      = r
-      %br/
-  %td
-    #{source}
-    - if !process.nil?
-      - if translation?(process["relation"])
-        %img{:src => asset_path('sifr/english_language_flag.png'), :style => "padding: 5px", :align => "right", :title => "Traduction"}
-  %td
-    = type
+    = render ChipButtonComponent.new(class: 'chip_button_small mr-1', text: type, tooltip:"#{source_tooltip} mapping of type #{type_tooltip}")
+
   - if current_user_admin?
     %td{:class => 'delete_mappings_column'}
       - if map.id && !map.id.empty? && session[:user] && (session[:user].id.to_i == map.creator || session[:user].admin?) && map.source.eql?('REST')
-        %div.d-flex
-          = link_to_modal(t("mappings.show_line.edit_modal"),
+        %div.d-flex.mappings-table-actions
+          = link_to_modal(nil,
                   mapping_path(map_id, {conceptid_from: @concept.id}),
-                  role: "button",
-                  class: "btn btn-link",
+                  class: 'btn btn-link p-0 mr-1',
                   data: { show_modal_title_value: t("mappings.show_line.edit_mapping", preflabel: @concept.prefLabel)},
-                  )
-          = button_to t("mappings.show_line.delete_button"), CGI.unescape(mapping_path(map.id)), method: :delete, class:'btn btn-link',  form: {data: { turbo: true, turbo_confirm: t("mappings.show_line.turbo_confirm"), turbo_frame: '_top'}}
\ No newline at end of file
+                  ) do
+            = inline_svg_tag "edit.svg", width: '15px', height: '15px'
+          = button_to inline_svg_tag('icons/delete.svg', width: '16px', heigth: '16px'), CGI.unescape(mapping_path(map.id)), class: 'btn btn-link p-0', method: :delete,  form: {data: { turbo: true, turbo_confirm: t("mappings.show_line.turbo_confirm"), turbo_frame: '_top'}}
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 4f9ee4c48b..a63e3500eb 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -572,12 +572,19 @@ en:
     date: Date
     ontology_visits: Ontology visits
   mappings:
+    create_new_mapping: Create new mapping
     all: All
     description: Dive into an overview of the mappings in the bubble view, efficiently locate a specific ontology in the table view or upload your own mappings.
     tabs:
       bubble_view: Bubbles view
       table_view: Table view
       upload_mappings: Upload mappings
+    types_description:
+      cui: Created between 2 concepts that have the same CUI (Concept Unique Identifiers)
+      loom: Lexical mappings created between 2 concepts with very similar labels (preferred name)
+      rest: A mapping added by a user using the REST API (or the UI, which is calling the API to create it)
+      same_uri: Created between 2 concepts with the same URI.
+      skos: Mappings based on SKOS relationships, (e.g. skos:exactMatch or skos:closeMatch)
     filter_ontologies: Filter ontologies in the bubble view
     filter_bubbles: Filter bubbles
     external_mappings: "External Mappings (%{number_with_delimiter})"
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index 0b319d391e..d0969e5795 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -580,12 +580,20 @@ fr:
     ontology_visits: Visites d'ontologies
 
   mappings:
+    create_new_mapping: Créer un nouveau mapping
     all: Tous
     description: Plongez dans une vue d'ensemble des mappings dans la vue en bulles, localisez efficacement une ontologie spécifique dans la vue en tableau ou téléchargez vos propres mappings.
     tabs:
       bubble_view: Vue en bulles
       table_view: Vue en tableau
       upload_mappings: Télécharger des mappings
+    types_description:
+      cui: Créé entre 2 concepts ayant le même CUI (Identifiants Uniques de Concepts)
+      loom: Mappings lexicaux créés entre 2 concepts avec des libellés très similaires (nom préféré)
+      rest: Un mapping ajouté par un utilisateur via l'API REST (ou l'interface utilisateur, qui appelle l'API pour le créer)
+      same_uri: Créé entre 2 concepts ayant la même URI.
+      skos: Mapping basés sur des relations SKOS (par exemple, skos:exactMatch ou skos:closeMatch)
+
     filter_ontologies: Filtrer les ontologies dans la vue en bulles
     filter_bubbles: Filtrer les bulles
     external_mappings: "Mappings externes (%{number_with_delimiter})"

From b7318e03ccce5777ed05695e90852970ceaf4c43 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Tue, 5 Nov 2024 15:41:33 +0100
Subject: [PATCH 08/22] Fix: Browse page switch style, and don't display
 current portal name button in browse results (#828)

* fix broken switch style when using a long text with it

* don't show current portal name button in browse page results

* adjest switch text max-width only for browse filter

* don't show portal name only if it's unique in browse page federated results
---
 app/assets/stylesheets/browse.scss            | 3 +++
 app/controllers/concerns/submission_filter.rb | 1 +
 2 files changed, 4 insertions(+)

diff --git a/app/assets/stylesheets/browse.scss b/app/assets/stylesheets/browse.scss
index a55292bde0..57e857442c 100644
--- a/app/assets/stylesheets/browse.scss
+++ b/app/assets/stylesheets/browse.scss
@@ -266,6 +266,9 @@
   z-index: 1;
 
 }
+.browse-filter .switch-filter > p, .switch-filter > div{
+  max-width: 207px;
+}
 
 .browse-search-bar input:focus {
   box-shadow: rgba(100, 100, 111, 0.2) 0px 7px 29px 0px;
diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index c039147280..5bb9937e1a 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -72,6 +72,7 @@ def merge_by_acronym(submissions)
     submissions.group_by { |x| x[:ontology]&.acronym }.each do |acronym, ontologies|
       ontology = canonical_ontology(ontologies)
       ontology[:sources] = ontologies.map { |x| x[:id] }
+      ontology[:sources].reject! { |id| id.include?(portal_name.downcase) } if ontology[:sources].size.eql?(1)
       merged_submissions << ontology
     end
     merged_submissions

From a9dd3b7148f426434cdce965a118f5d271a9434e Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Thu, 7 Nov 2024 05:32:42 +0100
Subject: [PATCH 09/22] Fix: Search federation duplicated results merging issue
 (#830)

* replace unexisting key :ontology_acronym and get the ontology acronym from the ontology_id when checking ontology duplication in federation

* clean code of merge federated results method
---
 app/controllers/concerns/search_aggregator.rb | 28 ++++++++++++-------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 078c89c5c9..f1f074272f 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -251,17 +251,15 @@ def blacklist_cls_id_components(cls_id, blacklist_words)
   def merge_federated_results(search_results)
     search_results.each do |element|
       element[:root][:other_portals] = []
+
       element[:reuses].reject! do |reuse|
-        if (element[:root][:ontology_acronym] == reuse[:root][:ontology_acronym]) && (element[:root][:uri] == reuse[:root][:uri])
-          portal_name = reuse[:root][:portal_name]
-          link = reuse[:root][:link]
-          element[:root][:other_portals] << {
-            name: portal_name,
-            color: federated_portal_color(portal_name),
-            light_color: federated_portal_light_color(portal_name),
-            link: link,
-            ontology_id: reuse[:root][:ontology_id]
-          }
+        element_ontology_id = element[:root][:ontology_id].split('/').last
+        element_uri = element[:root][:uri]
+        reuse_ontology_id = reuse[:root][:ontology_id].split('/').last
+        reuse_uri = reuse[:root][:uri]
+
+        if element_ontology_id == reuse_ontology_id && element_uri == reuse_uri
+          element[:root][:other_portals] << build_other_portal_entry(reuse)
           true
         else
           false
@@ -270,6 +268,16 @@ def merge_federated_results(search_results)
     end
   end
 
+  def build_other_portal_entry(reuse)
+    {
+      name: reuse[:root][:portal_name],
+      color: federated_portal_color(reuse[:root][:portal_name]),
+      light_color: federated_portal_light_color(reuse[:root][:portal_name]),
+      link: reuse[:root][:link],
+      ontology_id: reuse[:root][:ontology_id]
+    }
+  end
+
   def swap_canonical_portal_results_first(search_results)
     all_submissions = LinkedData::Client::Models::OntologySubmission.all(include: 'pullLocation', include_views: true, display_links: false, display_context: false)
 

From a3b1d97e034a6500d703d1c94487e8ef5057b0f3 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 7 Nov 2024 10:15:19 +0100
Subject: [PATCH 10/22] Feature: Migrate Label Ajax stimulus and Jquery code to
 Turbo  (#821)

* update select_language_label  helper to select f no english found any language remaining over the not tagged

* disable label ajax container

* create label fetch component that for a id/uri fetch its label if found

* add the possibility for the turbo frame to have custom error messages

* remove and replace ontology entities link helpers

* replace the label-ajax stimulus with turbo frame using  ajax_link_chip

* fix an uncatched error in concept label helper

* remove label-ajax stimulus code

* remove bp_ajax_controller old js code and update mappings to use the label fetcher component

* fix bug of not opening eternal mapping details popup

* remove label_link component

* add a helper for the label fetcher component for clarity

* add extern_link argument to ajax_link_chip to enforce external or not
---
 app/assets/javascripts/application.js         |   3 -
 app/assets/javascripts/bp_ajax_controller.js  | 187 ------------------
 .../chip_button_component.html.haml           |   2 +-
 app/components/label_fetcher_component.rb     |  56 ++++++
 .../label_fetcher_component.html.haml         |  10 +
 app/components/label_link_component.rb        |  22 ---
 app/components/turbo_frame_component.rb       |   1 +
 .../turbo_frame_component.html.haml           |   8 +-
 app/controllers/collections_controller.rb     |  11 +-
 app/controllers/concepts_controller.rb        |  16 +-
 app/controllers/label_xl_controller.rb        |   7 +-
 app/controllers/mappings_controller.rb        |   3 +-
 app/controllers/schemes_controller.rb         |  13 +-
 app/helpers/application_helper.rb             |  96 ++-------
 app/helpers/collections_helper.rb             |  10 +-
 app/helpers/components_helper.rb              |   4 +
 app/helpers/concepts_helper.rb                |  16 +-
 app/helpers/mappings_helper.rb                |  39 ++--
 app/helpers/schemes_helper.rb                 |  11 +-
 app/javascript/controllers/index.js           |   6 -
 .../controllers/label_ajax_controller.js      |  83 --------
 .../labels_ajax_container_controller.js       |  10 -
 .../turbo_frame_error_controller.js           |   5 +-
 app/views/collections/_list_view.html.haml    |   2 +-
 app/views/concepts/_show.html.haml            |   2 +-
 app/views/mappings/_mapping_table.html.haml   |   4 -
 app/views/mappings/_show.html.haml            |   9 +-
 27 files changed, 162 insertions(+), 474 deletions(-)
 delete mode 100644 app/assets/javascripts/bp_ajax_controller.js
 create mode 100644 app/components/label_fetcher_component.rb
 create mode 100644 app/components/label_fetcher_component/label_fetcher_component.html.haml
 delete mode 100644 app/components/label_link_component.rb
 delete mode 100644 app/javascript/controllers/label_ajax_controller.js
 delete mode 100644 app/javascript/controllers/labels_ajax_container_controller.js

diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js
index 1a42c65807..617e38d373 100644
--- a/app/assets/javascripts/application.js
+++ b/app/assets/javascripts/application.js
@@ -12,7 +12,6 @@
 //
 //= require bioportal
 //= require admin/licenses
-//= require bp_ajax_controller
 //= require bp_notes
 //= require bp_form_complete
 //= require bp_admin
@@ -20,5 +19,3 @@
 //= require projects
 //= require Chart.min
 //= require application_esbuild
-
-
diff --git a/app/assets/javascripts/bp_ajax_controller.js b/app/assets/javascripts/bp_ajax_controller.js
deleted file mode 100644
index a67e66550a..0000000000
--- a/app/assets/javascripts/bp_ajax_controller.js
+++ /dev/null
@@ -1,187 +0,0 @@
-
-"use strict";
-
-// Note similar code in concepts_helper.rb mirrors the following code:
-function bp_ont_link(ont_acronym){
-  return "/ontologies/" + ont_acronym;
-}
-function bp_cls_link(cls_id, ont_acronym){
-  return bp_ont_link(ont_acronym) + "?p=classes&conceptid=" + encodeURIComponent(cls_id);
-}
-function get_link_for_cls_ajax(cls_id, ont_acronym) {
-  // ajax call will replace the class label using data attributes (triggered by class='cls4ajax')
-    let ajax_uri = '/ajax/classes/label'
-    let data_cls = `data-label-ajax-cls-id-value='${cls_id}' `
-    let data_ont = `data-label-ajax-ontology-acronym-value='${ont_acronym}'`
-    let data_ajax_uri = `data-label-ajax-ajax-uri-value='${ajax_uri}' `
-
-    let data = `data-controller='label-ajax' ${data_ont} ${data_cls} ${data_ajax_uri}`
-
-    return `<a  ${data} href="${bp_cls_link(cls_id, ont_acronym)}">${cls_id}</a>`
-}
-
-function get_link_for_ont_ajax(ont_acronym) {
-  var data_ont = " data-ont='" + ont_acronym + "' ";
-  return "<a class='ont4ajax'" + data_ont + "href='" + bp_ont_link(ont_acronym) + "'>" + ont_acronym + "</a>";
-}
-
-var
-  ajax_process_interportal_cls_interval = null,
-  ajax_process_ont_interval = null,
-  ajax_process_timeout = 20, // Timeout after 20 sec.
-  ajax_process_timing = 250; // It takes about 250 msec to resolve a class ID to a prefLabel
-
-var ajax_process_init = function () {
-  ajax_process_ont_init();
-  ajax_process_interportal_cls_init();
-};
-
-var ajax_process_halt = function () {
-  ajax_process_ont_halt();
-  ajax_process_interportal_cls_halt();
-};
-
-
-// **************************************************************************************
-// ONTOLOGY NAMES
-
-// Note: If we don't query every time, using the array should be faster; it
-//       means the ajax_ont_init must be called after all the elements
-//       are created because they will not be detected in a dynamic iteration.
-var ajax_ont_array = [];
-var ajax_process_ont_init = function() {
-  ajax_ont_array = jQuery("a.ont4ajax").toArray();
-  ajax_process_ont_interval = window.setInterval(ajax_process_ont, ajax_process_timing);
-};
-var ajax_process_ont_halt = function () {
-  ajax_ont_array = [];
-  window.clearInterval(ajax_process_ont_interval); // stop the ajax process
-  // Note: might leave faulty href links, but it usually means moving on to entirely different content
-  //       so it's not likely those links will be available for interaction.
-  // clear all the classes and ontologies to be resolved by ajax
-  //jQuery("a.ont4ajax").removeClass('ont4ajax');
-  //jQuery("a.ajax-modified-ont").removeClass('ajax-modified-ont');
-};
-var ajax_process_ont = function() {
-  if( ajax_ont_array.length === 0 ){
-    ajax_process_ont_halt();
-    return true;
-  }
-  // Note: If we don't query every time, using the array should be faster; it
-  //       means the ajax_ont_init must be called after all the elements
-  //       are created because they will not be detected in a dynamic iteration.
-  //var linkA = jQuery("a.ont4ajax").first();
-  var linkA = ajax_ont_array.shift();
-  if(linkA === undefined){
-    return true;
-  }
-  linkA = jQuery(linkA);
-  if(linkA.hasClass('ajax-modified-ont') ){
-    // How did we get here? It should not have the ont4ajax class!
-    linkA.removeClass('ont4ajax');
-    return true; // processed this one already.
-  }
-  linkA.removeClass('ont4ajax'); // processing this one.
-  var ont_acronym = linkA.attr('data-ont');
-  var ajax_uri = "/ajax/json_ontology/?ontology=" + encodeURIComponent(ont_acronym);
-  jQuery.ajax({
-    url: ajax_uri,
-    timeout: ajax_process_timeout * 1000,
-    success: function(data){
-      if(typeof data !== "undefined" && data.hasOwnProperty('name')){
-        var ont_name = data.name;
-        linkA.text(ont_name);
-        linkA.addClass('ajax-modified-ont'); // processed this one.
-        // find and process any identical ontologies
-        jQuery('a[href="/ontologies/' + data.acronym + '"]').each(function(i,e){
-          var link = jQuery(this);
-          if(! link.hasClass('ajax-modified-ont') ){
-            link.removeClass('ont4ajax');   // processing this one.
-            link.text(ont_name);
-            link.addClass('ajax-modified-ont'); // processed this one.
-          }
-        });
-      }
-    },
-    error: function(data){
-      linkA.addClass('ajax-error'); // processed this one.
-    }
-  });
-};
-
-
-// **************************************************************************************
-// INTERPORTAL CLASS LABELS
-
-// Note: If we don't query every time, using the array should be faster; it
-//       means the ajax_process_init must be called after all the elements
-//       are created because they will not be detected in a dynamic iteration.
-var ajax_interportal_cls_array = [];
-
-var ajax_process_interportal_cls_init = function() {
-    ajax_interportal_cls_array = jQuery("a.interportalcls4ajax").toArray();
-    ajax_process_interportal_cls_interval = window.setInterval(ajax_process_interportal_cls, ajax_process_timing);
-};
-
-var ajax_process_interportal_cls_halt = function () {
-    ajax_interportal_cls_array = [];
-    window.clearInterval(ajax_process_interportal_cls_interval); // stop the ajax process
-    // Note: might leave faulty href links, but it usually means moving on to entirely different content
-    //       so it's not likely those links will be available for interaction.
-    // clear all the classes and ontologies to be resolved by ajax
-    //jQuery("a.cls4ajax").removeClass('cls4ajax');
-    //jQuery("a.ajax-modified-cls").removeClass('ajax-modified-cls');
-};
-
-var ajax_process_interportal_cls = function() {
-    // Check on whether to stop the ajax process
-    if( ajax_interportal_cls_array.length === 0 ){
-        ajax_process_interportal_cls_halt();
-        return true;
-    }
-    // Note: If we don't query every time, using the array should be faster; it
-    //       means the ajax_process_init must be called after all the elements
-    //       are created because they will not be detected in a dynamic iteration.
-    //var linkA = jQuery("a.cls4ajax").first();
-    var linkA = ajax_interportal_cls_array.shift(); // put first item in linkA and delete it from array
-    if(linkA === undefined){
-        return true;
-    }
-    linkA = jQuery(linkA);
-    if(linkA.hasClass('ajax-modified-cls') ){
-        // How did we get here? It should not have the interportalcls4ajax class!
-        linkA.removeClass('interportalcls4ajax');
-        return true; // processing or processed this one already.
-    }
-    linkA.removeClass('interportalcls4ajax'); // processing this one.
-    var unique_id = linkA.attr('href');
-
-    var portal_acronym = linkA.attr('portal-cls');
-    var ajax_uri = linkA.attr('data-cls') + jQuery(document).data().bp.config.interportal_hash[portal_acronym].apikey;
-    jQuery.ajax({
-        url: ajax_uri,
-        timeout: ajax_process_timeout * 1000,
-        success: function(data){
-            var label = data.prefLabel
-            if (typeof label !== "undefined" && label.length > 0) {
-                linkA.html(label);
-                linkA.addClass('ajax-modified-cls');
-                // find and process any identical classes (low probability)
-                jQuery( 'a[href="' + unique_id + '"]').each(function(i,e){
-                    var link = jQuery(this);
-                    if(! link.hasClass('ajax-modified-cls') ){
-                        link.removeClass('interportalcls4ajax');   // processing this one.
-                        link.html(label);
-                        link.addClass('ajax-modified-cls'); // processed this one.
-                    }
-                });
-            } else {
-                // remove the unique_id separator and the ontology acronym from the href
-                linkA.addClass('ajax-modified-cls');
-            }
-        },
-        error: function(data){
-            linkA.addClass('ajax-error'); // processed this one.
-        }
-    });
-};
diff --git a/app/components/chip_button_component/chip_button_component.html.haml b/app/components/chip_button_component/chip_button_component.html.haml
index 26172a5487..f2dd0d3dd0 100644
--- a/app/components/chip_button_component/chip_button_component.html.haml
+++ b/app/components/chip_button_component/chip_button_component.html.haml
@@ -4,7 +4,7 @@
       = @text || content
   - elsif !content
     %a.chip_button_container_clickable{@html_options}
-      = @text
+      = @text.html_safe
   - else
     %span.chip_button_container_clickable{@html_options}
       = content
diff --git a/app/components/label_fetcher_component.rb b/app/components/label_fetcher_component.rb
new file mode 100644
index 0000000000..f89f39d16e
--- /dev/null
+++ b/app/components/label_fetcher_component.rb
@@ -0,0 +1,56 @@
+# frozen_string_literal: true
+
+class LabelFetcherComponent < ViewComponent::Base
+  include UrlsHelper, Turbo::FramesHelper, ModalHelper
+
+  def initialize(id:, label: nil, link: nil, ajax_src: nil, open_in_modal: false, target: nil, external: false)
+    super
+    @id = id
+    @link = link
+    @ajax_src = ajax_src
+    @open_in_modal = open_in_modal
+    @target = target
+    @external = external
+    @label = label
+
+    if external_link?
+      @link = id
+      @target ||= '_blank'
+    else
+      @target ||= '_top'
+    end
+
+  end
+
+  def external_link?
+    (@label.nil? || @label.eql?(@id)) && @external
+  end
+
+  def label_fetcher_container(&block)
+    id = "#{escape(@id)}_label"
+    if @ajax_src
+      render(TurboFrameComponent.new(id: id, src: "#{@ajax_src}&target=#{@target}", loading: 'lazy')) do |t|
+        t.loader do
+          render ChipButtonComponent.new(url: @id, text: "#{@id} #{render(LoaderComponent.new(small: true))}", type: 'clickable', target: '_blank')
+        end
+
+        t.error do
+          capture(&block)
+        end
+      end
+    else
+      turbo_frame_tag(id) do
+        capture(&block)
+      end
+    end
+
+  end
+
+  def link_with_icon
+    if external_link?
+      ExternalLinkTextComponent.new(text: @label).call
+    else
+      InternalLinkTextComponent.new(text: @label).call
+    end
+  end
+end
diff --git a/app/components/label_fetcher_component/label_fetcher_component.html.haml b/app/components/label_fetcher_component/label_fetcher_component.html.haml
new file mode 100644
index 0000000000..80587133d1
--- /dev/null
+++ b/app/components/label_fetcher_component/label_fetcher_component.html.haml
@@ -0,0 +1,10 @@
+= label_fetcher_container do
+  - if @open_in_modal
+    = render ChipButtonComponent.new(type: 'clickable') do
+      = link_to_modal(@label, @link)
+  - else
+    %span
+      = render ChipButtonComponent.new(url: @link,
+                                         type: 'clickable',
+                                         text: link_with_icon,
+                                         target: @target)
diff --git a/app/components/label_link_component.rb b/app/components/label_link_component.rb
deleted file mode 100644
index 3d8ecee988..0000000000
--- a/app/components/label_link_component.rb
+++ /dev/null
@@ -1,22 +0,0 @@
-# frozen_string_literal: true
-
-class LabelLinkComponent < ViewComponent::Base
-
-  def initialize(id:, text:, icon: 'popup-link')
-    @id = id
-    @text = text
-    @icon = icon
-  end
-
-  def call
-    if @id.eql?(@text)
-      ExternalLinkTextComponent.new(text: @text).call
-    else
-      InternalLinkTextComponent.new(text: @text).call
-    end
-  end
-
-  def self.inline(id, text)
-    { plain: LabelLinkComponent.new(id: id, text: text).call }
-  end
-end
diff --git a/app/components/turbo_frame_component.rb b/app/components/turbo_frame_component.rb
index d25322e154..1e54e24ce8 100644
--- a/app/components/turbo_frame_component.rb
+++ b/app/components/turbo_frame_component.rb
@@ -4,6 +4,7 @@ class TurboFrameComponent < ViewComponent::Base
   include Turbo::FramesHelper
 
   renders_one :loader
+  renders_one :error
 
   def initialize(id:, src: '', **html_options)
     @id = id
diff --git a/app/components/turbo_frame_component/turbo_frame_component.html.haml b/app/components/turbo_frame_component/turbo_frame_component.html.haml
index 1c5d0d9f59..a288d8eaca 100644
--- a/app/components/turbo_frame_component/turbo_frame_component.html.haml
+++ b/app/components/turbo_frame_component/turbo_frame_component.html.haml
@@ -8,5 +8,9 @@
     - else
       %div.p-3
         = render LoaderComponent.new(type: 'pulsing')
-  %div{'data-turbo-frame-error-target': 'errorMessage', style:'display: none; width: 100%'}
-    = render Display::AlertComponent.new(type:'danger')
\ No newline at end of file
+  %span{'data-turbo-frame-error-target': 'errorMessage', style:'display: none; width: 100%'}
+    - if error?
+      = error
+    - else
+      %div
+        = render Display::AlertComponent.new(type:'danger')
diff --git a/app/controllers/collections_controller.rb b/app/controllers/collections_controller.rb
index c01c0cf879..fcfda0256d 100644
--- a/app/controllers/collections_controller.rb
+++ b/app/controllers/collections_controller.rb
@@ -1,7 +1,6 @@
 class CollectionsController < ApplicationController
   include CollectionsHelper,SearchContent
 
-
   def index
     acronym = params[:ontology]
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first
@@ -47,11 +46,13 @@ def show
 
   def show_label
     collection_label = ''
-    collection  = get_request_collection
-    collection_label =  collection['prefLabel'] if collection
-    collection_label = params[:id]  if collection_label.nil? || collection_label.empty?
+    collection = get_request_collection
+    collection_label = collection['prefLabel'] if collection
+    collection_label = params[:id] if collection_label.nil? || collection_label.empty?
 
-    render LabelLinkComponent.inline(params[:id], helpers.main_language_label(collection_label))
+    label = helpers.main_language_label(collection_label)
+    link = collection_path(collection_id: params[:id], ontology_id: params[:ontology_id], language: request_lang)
+    render(inline: helpers.ajax_link_chip(params[:id], label, link, external: collection.blank?), layout: false)
   end
 
   def show_members
diff --git a/app/controllers/concepts_controller.rb b/app/controllers/concepts_controller.rb
index 1063c953b4..97e316c6af 100644
--- a/app/controllers/concepts_controller.rb
+++ b/app/controllers/concepts_controller.rb
@@ -63,10 +63,14 @@ def index
   end
 
   def show_label
-    cls_id = params[:concept] || params[:id]  # cls_id should be a full URI
-    ont_id = params[:ontology]  # ont_id could be a full URI or an acronym
-
-    render LabelLinkComponent.inline(cls_id, helpers.main_language_label(concept_label(ont_id, cls_id)))
+    cls_id = params[:concept] || params[:id]
+    ont_id = params[:ontology]
+    pref_label = concept_label(ont_id, cls_id)
+    cls = @ontology.explore.single_class({ language: request_lang, include: 'prefLabel' }, cls_id)
+    label = helpers.main_language_label(pref_label)
+    link = concept_path(cls_id, ont_id, request_lang)
+
+    render(inline: helpers.ajax_link_chip(cls_id, label, link, external: cls.nil? || cls.errors), layout: nil)
   end
 
   def show_definition
@@ -87,8 +91,8 @@ def show_tree
       not_found(t('concepts.missing_roots')) if @root.nil?
 
       render inline: helpers.concepts_tree_component(@root, @concept,
-                                      @ontology.acronym, Array(params[:concept_schemes]&.split(',')), request_lang,
-                                      id: 'concepts_tree_view', auto_click: params[:auto_click] || true)
+                                                     @ontology.acronym, Array(params[:concept_schemes]&.split(',')), request_lang,
+                                                     id: 'concepts_tree_view', auto_click: params[:auto_click] || true)
     end
   end
 
diff --git a/app/controllers/label_xl_controller.rb b/app/controllers/label_xl_controller.rb
index 521d35fb7a..e62a749084 100644
--- a/app/controllers/label_xl_controller.rb
+++ b/app/controllers/label_xl_controller.rb
@@ -1,5 +1,5 @@
 class LabelXlController < ApplicationController
-  include LabelXlHelper
+  include LabelXlHelper, UrlsHelper
 
   def show
     @label_xl = get_request_label_xl
@@ -9,8 +9,9 @@ def show_label
     label_xl = get_request_label_xl
     label_xl_label = label_xl ? label_xl['literalForm'] : nil
     label_xl_label = params[:id] if label_xl_label.nil? || label_xl_label.empty?
-
-    render LabelLinkComponent.inline(params[:id], helpers.main_language_label(label_xl_label))
+    label = helpers.main_language_label(label_xl_label)
+    link = "/ajax/label_xl/?id=#{escape(params[:id])}&ontology=#{params[:ontology_id]}&cls_id=#{escape(params[:cls_id])}"
+    render(inline: helpers.ajax_link_chip(params[:id], label, link, open_in_modal: true, external: label_xl.blank?), layout: false)
   end
 
   private
diff --git a/app/controllers/mappings_controller.rb b/app/controllers/mappings_controller.rb
index df582acb4e..0ca5fd8b77 100644
--- a/app/controllers/mappings_controller.rb
+++ b/app/controllers/mappings_controller.rb
@@ -118,7 +118,7 @@ def show_mappings
       ontology_acronym = @ontology.acronym
       @ontology_name = ontology_acronym
     end
-    if @target_ontology.nil?
+    if @target_ontology.nil? || @target_ontology.errors
       if params[:target] == EXTERNAL_MAPPINGS_GRAPH
         target_acronym = EXTERNAL_URL_PARAM_STR
         @target_ontology_name = t('mappings.external_mappings')
@@ -132,7 +132,6 @@ def show_mappings
     end
 
     ontologies = [ontology_acronym, target_acronym]
-
     @mapping_pages = LinkedData::Client::HTTP.get("#{MAPPINGS_URL}", { page: page, ontologies: ontologies.join(',') })
     not_found(@mapping_pages.errors) if @mapping_pages.respond_to?(:errors)
     @mappings = @mapping_pages.collection
diff --git a/app/controllers/schemes_controller.rb b/app/controllers/schemes_controller.rb
index 8c5c97f1f0..1116e6a740 100644
--- a/app/controllers/schemes_controller.rb
+++ b/app/controllers/schemes_controller.rb
@@ -23,9 +23,9 @@ def index
 
 
       render inline: helpers.render_search_paginated_list(container_id: 'schemes_sorted_list',
-                         next_page_url: "/ontologies/#{@ontology.acronym}/schemes",
-                         child_url: "/ontologies/#{@ontology.acronym}/schemes/show", child_turbo_frame: 'scheme',
-                         child_param: :schemeid,
+                                                          next_page_url: "/ontologies/#{@ontology.acronym}/schemes",
+                                                          child_url: "/ontologies/#{@ontology.acronym}/schemes/show", child_turbo_frame: 'scheme',
+                                                          child_param: :schemeid,
                          results:  results, next_page:  next_page, total_count: total_count)
 
     end
@@ -35,7 +35,7 @@ def show
     redirect_to(ontology_path(id: params[:ontology], p: 'schemes', schemeid: params[:id],lang: request_lang)) and return unless turbo_frame_request?
 
     @scheme = get_request_scheme
-    
+
     render partial: "schemes/show"
   end
 
@@ -43,8 +43,9 @@ def show_label
     scheme = get_request_scheme
     scheme_label = scheme ? scheme['prefLabel'] : params[:id]
     scheme_label = scheme_label.nil? || scheme_label.empty? ? params[:id] : scheme_label
-
-    render LabelLinkComponent.inline(params[:id], helpers.main_language_label(scheme_label))
+    label = helpers.main_language_label(scheme_label)
+    link = scheme_path(scheme_id: params[:id], ontology_id: params[:ontology_id])
+    render(inline: helpers.ajax_link_chip(params[:id], label, link, external: scheme.blank?), layout: false)
   end
 
   private
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 6d565bdb22..2a319d6874 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -9,7 +9,7 @@ module ApplicationHelper
   REST_URI = $REST_URL
   API_KEY = $API_KEY
 
-  include ModalHelper, MultiLanguagesHelper, UrlsHelper
+  include ModalHelper, MultiLanguagesHelper, UrlsHelper, ComponentsHelper
 
 
   RESOLVE_NAMESPACE = {:omv => "http://omv.ontoware.org/2005/05/ontology#", :skos => "http://www.w3.org/2004/02/skos/core#", :owl => "http://www.w3.org/2002/07/owl#",
@@ -19,7 +19,7 @@ module ApplicationHelper
                         :umls => "http://bioportal.bioontology.org/ontologies/umls/", :door => "http://kannel.open.ac.uk/ontology#", :dct => "http://purl.org/dc/terms/",
                         :void => "http://rdfs.org/ns/void#", :foaf => "http://xmlns.com/foaf/0.1/", :vann => "http://purl.org/vocab/vann/", :adms => "http://www.w3.org/ns/adms#",
                         :voaf => "http://purl.org/vocommons/voaf#", :dcat => "http://www.w3.org/ns/dcat#", :mod => "http://www.isibang.ac.in/ns/mod#", :prov => "http://www.w3.org/ns/prov#",
-                       :cc => "http://creativecommons.org/ns#", :schema => "http://schema.org/", :doap => "http://usefulinc.com/ns/doap#", :bibo => "http://purl.org/ontology/bibo/",
+                        :cc => "http://creativecommons.org/ns#", :schema => "http://schema.org/", :doap => "http://usefulinc.com/ns/doap#", :bibo => "http://purl.org/ontology/bibo/",
                        :wdrs => "http://www.w3.org/2007/05/powder-s#", :cito => "http://purl.org/spar/cito/", :pav => "http://purl.org/pav/", :nkos => "http://w3id.org/nkos/nkostype#",
                        :oboInOwl => "http://www.geneontology.org/formats/oboInOwl#", :idot => "http://identifiers.org/idot/", :sd => "http://www.w3.org/ns/sparql-service-description#",
                        :cclicense => "http://creativecommons.org/licenses/",
@@ -55,7 +55,6 @@ def get_apikey
     end
   end
 
-
   def omniauth_providers_info
     $OMNIAUTH_PROVIDERS
   end
@@ -76,7 +75,6 @@ def current_user_admin?
     session[:user] && session[:user].admin?
   end
 
-
   def child_id(child)
     child.id.to_s.split('/').last
   end
@@ -155,7 +153,6 @@ def add_proposal_button(parent_id, parent_type)
     end
   end
 
-
   def subscribe_button(ontology_id)
     return if ontology_id.nil?
     render TurboFrameComponent.new(id: 'subscribe_button', src: ontology_subscriptions_path(ontology_id: ontology_id.split('/').last), class: 'ml-1') do |t|
@@ -226,95 +223,40 @@ def notification_type(flash_key)
     bootstrap_alert_class[flash_key]
   end
 
-  def bp_ont_link(ont_acronym)
-    return "/ontologies/#{ont_acronym}"
-  end
-
-  def bp_class_link(cls_id, ont_acronym)
-    return "#{bp_ont_link(ont_acronym)}?p=classes&conceptid=#{escape(cls_id)}&language=#{request_lang}"
-  end
-
-  def bp_scheme_link(scheme_id, ont_acronym)
-    return "#{bp_ont_link(ont_acronym)}?p=schemes&schemeid=#{escape(scheme_id)}"
-  end
-
-  def bp_label_xl_link(label_xl_id, ont_acronym)
-    return "#{bp_ont_link(ont_acronym)}/?label_xl_id=#{escape(label_xl_id)}"
-  end
-
-  def bp_collection_link(collection_id, ont_acronym)
-    "#{bp_ont_link(ont_acronym)}?p=collection&collectionid=#{escape(collection_id)}"
-  end
+  def label_ajax_link(id, ont_acronym, ajax_uri, target)
+    ajax_uri = if ajax_uri.include?('?')
+                 "#{ajax_uri}&ontology=#{ont_acronym}&id=#{escape(id)}"
+               else
+                 "#{ajax_uri}?ontology=#{ont_acronym}&id=#{escape(id)}"
+               end
 
-  def label_ajax_data_h(cls_id, ont_acronym, ajax_uri, cls_url)
-    { data:
-        {
-          'label-ajax-cls-id-value': cls_id,
-          'label-ajax-ontology-acronym-value': ont_acronym,
-          'label-ajax-ajax-url-value': ajax_uri,
-          'label-ajax-cls-id-url-value': cls_url
-        }
-    }
-  end
-
-  def label_ajax_data(cls_id, ont_acronym, ajax_uri, cls_url)
-    label_ajax_data_h(cls_id, ont_acronym, ajax_uri, cls_url)
-  end
-
-  def label_ajax_link(link, cls_id, ont_acronym, ajax_uri, cls_url, target = nil)
-    data = label_ajax_data(cls_id, ont_acronym, ajax_uri, cls_url)
-    options = {  'data-controller': 'label-ajax' }.merge(data)
-    options = options.merge({ target: target }) if target
-    content_tag(:span, class: 'mx-1') do
-      render ChipButtonComponent.new(url: link, text: cls_id, type: 'clickable', **options)
+    content_tag(:span, class: 'concepts-mapping-count') do
+      ajax_link_chip(id, ajax_src: ajax_uri, target: target)
     end
   end
 
   def get_link_for_cls_ajax(cls_id, ont_acronym, target = nil)
     if cls_id.start_with?('http://') || cls_id.start_with?('https://')
-      link = bp_class_link(cls_id, ont_acronym)
       ajax_url = '/ajax/classes/label'
-      cls_url = "/ontologies/#{ont_acronym}?p=classes&conceptid=#{CGI.escape(cls_id)}"
-      label_ajax_link(link, cls_id, ont_acronym, ajax_url , cls_url ,target)
+      label_ajax_link(cls_id, ont_acronym, ajax_url, target)
     else
       content_tag(:div, cls_id)
     end
   end
 
-  def get_link_for_ont_ajax(ont_acronym)
-    # ajax call will replace the acronym with an ontology name (triggered by class='ont4ajax')
-    href_ont = " href='#{bp_ont_link(ont_acronym)}' "
-    data_ont = " data-ont='#{ont_acronym}' "
-    return "<a class='ont4ajax' #{data_ont} #{href_ont}>#{ont_acronym}</a>"
-  end
-
   def get_link_for_scheme_ajax(scheme, ont_acronym, target = '_blank')
-    link = bp_scheme_link(scheme, ont_acronym)
     ajax_url = "/ajax/schemes/label?language=#{request_lang}"
-    scheme_url = "?p=schemes&schemeid=#{CGI.escape(scheme)}"
-    label_ajax_link(link, scheme, ont_acronym, ajax_url, scheme_url, target)
+    label_ajax_link(scheme, ont_acronym, ajax_url, target)
   end
 
   def get_link_for_collection_ajax(collection, ont_acronym, target = '_blank')
-    link = bp_collection_link(collection, ont_acronym)
     ajax_url = "/ajax/collections/label?language=#{request_lang}"
-    collection_url = "?p=collections&collectionid=#{CGI.escape(collection)}"
-    label_ajax_link(link, collection, ont_acronym, ajax_url, collection_url, target)
-  end
-
-  def get_link_for_label_xl_ajax(label_xl, ont_acronym, cls_id, modal: true)
-    link = label_xl
-    ajax_uri = "/ajax/label_xl/label?cls_id=#{CGI.escape(cls_id)}"
-    label_xl_url = "/ajax/label_xl/?id=#{CGI.escape(label_xl)}&ontology=#{ont_acronym}&cls_id=#{CGI.escape(cls_id)}"
-    data = label_ajax_data_h(label_xl, ont_acronym, ajax_uri, label_xl_url)
-    data[:data][:controller] = 'label-ajax'
-    if modal
-      link_to_modal(cls_id, link, {data: data[:data] , class: 'btn btn-sm btn-light m-1'})
-    else
-      link_to(link,'', {data: data[:data], class: 'btn btn-sm btn-light m-1', target: '_blank'})
-    end
-
+    label_ajax_link(collection, ont_acronym, ajax_url, target)
+  end
 
+  def get_link_for_label_xl_ajax(label_xl, ont_acronym, cls_id, target = nil)
+    ajax_url = "/ajax/label_xl/label?cls_id=#{CGI.escape(cls_id)}"
+    label_ajax_link(label_xl, ont_acronym, ajax_url, target)
   end
 
   def ontology_viewer_page_name(ontology_name, concept_label, page)
@@ -449,14 +391,14 @@ def prefixed_url(url)
   def show_advanced_options_button(text: nil, init: nil)
     content_tag(:div, class: "#{init ? 'd-none' : ''} advanced-options-button", 'data-action': 'click->reveal-component#show', 'data-reveal-component-target': 'showButton') do
       inline_svg_tag('icons/settings.svg') +
-      content_tag(:div, text, class: 'text')
+        content_tag(:div, text, class: 'text')
     end
   end
 
   def hide_advanced_options_button(text: nil, init: nil)
     content_tag(:div, class: "#{init ? '' : 'd-none'} advanced-options-button", 'data-action': 'click->reveal-component#hide', 'data-reveal-component-target': 'hideButton') do
       inline_svg_tag('icons/hide.svg') +
-      content_tag(:div, text, class: 'text')
+        content_tag(:div, text, class: 'text')
     end
   end
 
diff --git a/app/helpers/collections_helper.rb b/app/helpers/collections_helper.rb
index 9a80d24111..f8593cba2e 100644
--- a/app/helpers/collections_helper.rb
+++ b/app/helpers/collections_helper.rb
@@ -1,5 +1,5 @@
 module CollectionsHelper
-  include MultiLanguagesHelper
+  include MultiLanguagesHelper, UrlsHelper
 
 
   def get_collections(ontology, add_colors: false)
@@ -49,8 +49,8 @@ def no_collections_alert
     end
   end
 
-  def collection_path(collection_id = '', language = '')
-    "/ontologies/#{@ontology.acronym}/collections/show?id=#{escape(collection_id)}&language=#{language}"
+  def collection_path(collection_id: '', ontology_id: @ontology.acronym, language: request_lang)
+    "/ontologies/#{ontology_id}/collections/show?id=#{escape(collection_id)}&language=#{language}"
   end
 
   def request_collection_id
@@ -65,8 +65,8 @@ def link_to_collection(collection, selected_collection_id)
     pref_label_lang, pref_label_html = get_collection_label(collection)
     tooltip  = pref_label_lang.to_s.eql?('@none') ? '' :  "data-controller='tooltip' data-tooltip-position-value='right' title='#{pref_label_lang.upcase}'"
     <<-EOS
-          <a id="#{collection['@id']}" href="#{collection_path(collection['@id'], request_lang)}"
-            data-turbo="true" data-turbo-frame="collection" data-collectionid="#{collection['@id']}"
+          <a id="#{collection['@id']}" href="#{collection_path(collection_id: collection['@id'], ontology_id: @ontology.acronym, language: request_lang)}"
+            data-turbo="true" data-turbo-frame="collection" data-collectionid="#{collection['@id']}" 
            #{tooltip}
             class="#{selected_collection_id.eql?(collection['@id']) ? 'active' : nil}">
               #{pref_label_html}
diff --git a/app/helpers/components_helper.rb b/app/helpers/components_helper.rb
index a63ba8edb5..180ea336e9 100644
--- a/app/helpers/components_helper.rb
+++ b/app/helpers/components_helper.rb
@@ -172,6 +172,10 @@ def tree_component(root, selected, target_frame:, sub_tree: false, id: nil, auto
     end
   end
 
+  def ajax_link_chip(id, label = nil, link = nil, external: false, open_in_modal: false, ajax_src: nil, target: '_blank')
+    render LabelFetcherComponent.new(id: id, label: label, link: link, open_in_modal: open_in_modal, ajax_src: ajax_src, target: target, external: external)
+  end
+
   def chart_component(title: '', type:, labels:, datasets:, index_axis: 'x', show_legend: false)
     data = {
       controller: 'load-chart',
diff --git a/app/helpers/concepts_helper.rb b/app/helpers/concepts_helper.rb
index 3cec8ade6b..1b62c06d76 100644
--- a/app/helpers/concepts_helper.rb
+++ b/app/helpers/concepts_helper.rb
@@ -1,6 +1,11 @@
 # frozen_string_literal: true
 module ConceptsHelper
-  include TermsReuses
+  include TermsReuses, UrlsHelper
+
+  def concept_path(id, ontology_id, language)
+    "/ontologies/#{ontology_id}?p=classes&conceptid=#{escape(id)}&language=#{language}"
+  end
+
   def concept_link(acronym, child, language)
     child.id.eql?('bp_fake_root') ? '#' : "/ontologies/#{acronym}/concepts/show?id=#{CGI.escape(child.id)}&language=#{language}"
   end
@@ -76,14 +81,9 @@ def default_sub_menu_class
   def concept_label(ont_id, cls_id)
     @ontology = LinkedData::Client::Models::Ontology.find(ont_id)
     @ontology ||= LinkedData::Client::Models::Ontology.find_by_acronym(ont_id).first
-    ontology_not_found(ont_id) unless @ontology
-    # Retrieve a class prefLabel or return the class ID (URI)
-    # - mappings may contain class URIs that are not in bioportal (e.g. obo-xrefs)
+    ontology_not_found(ont_id) if @ontology.nil? || @ontology.errors
     cls = @ontology.explore.single_class({language: request_lang, include: 'prefLabel'}, cls_id)
-    # TODO: log any cls.errors
-    # TODO: NCBO-402 might be implemented here, but it throws off a lot of ajax result rendering.
-    #cls_label = cls.prefLabel({:use_html => true}) || cls_id
-    cls.prefLabel || cls_id
+    cls&.prefLabel || cls_id
   end
 
   def concept_id_param_exist?(params)
diff --git a/app/helpers/mappings_helper.rb b/app/helpers/mappings_helper.rb
index c1e503b547..09b2c4d67e 100644
--- a/app/helpers/mappings_helper.rb
+++ b/app/helpers/mappings_helper.rb
@@ -77,24 +77,10 @@ def get_prefixed_uri(uri)
     uri
   end
 
-  # method to get (using http) prefLabel for interportal classes
-  # Using bp_ajax_controller.ajax_process_interportal_cls will try to resolve class labels.
-  def ajax_to_inter_portal_cls(cls)
-    inter_portal_acronym = get_inter_portal_acronym(cls.links['ui'])
-    href_cls = " href='#{cls.links["ui"]}' "
-    if inter_portal_acronym
-      data_cls = " data-cls='#{cls.links["self"]}?apikey=' "
-      portal_cls = " portal-cls='#{inter_portal_acronym}' "
-      raw("<a class='interportalcls4ajax' #{data_cls} #{portal_cls} #{href_cls} target='_blank'>#{cls.id}</a>")
-    else
-      raw("<a #{href_cls} target='_blank'>#{cls.id}</a>")
-    end
-
-  end
-
   def ajax_to_internal_cls(cls)
-    link_to("#{cls.id}<span href='/ajax/classes/label?ontology=#{cls.links["ontology"]}&concept=#{escape(cls.id)}' class='get_via_ajax'></span>".html_safe,
-            ontology_path(cls.explore.ontology.acronym, p: 'classes', conceptid: cls.id), target: '_blank')
+    cls_id = cls.id
+    ont_acronym = cls.links['ontology'].split('/').last
+    get_link_for_cls_ajax(cls_id, ont_acronym, '_blank')
   end
 
   # to get the apikey from the interportal instance of the interportal class.
@@ -111,18 +97,15 @@ def get_inter_portal_acronym(class_ui_url)
     end
   end
 
-  # method to extract the prefLabel from the external class URI
-  def get_label_for_external_cls(class_uri)
-    prefLabel = if class_uri.include? '#'
-                  class_uri.split('#')[-1]
-                else
-                  class_uri.split('/')[-1]
-                end
-    return prefLabel
-  end
-
   def ajax_to_external_cls(cls)
-    raw("<a href='#{cls.links['self']}' target='_blank'>#{get_label_for_external_cls(cls.id)}</a>")
+    class_uri = cls.id
+    text = if class_uri.include? '#'
+             class_uri.split('#')[-1]
+           else
+             class_uri.split('/')[-1]
+           end
+    text = render(ExternalLinkTextComponent.new(text: text))
+    link_to text, cls.links['self'], target: '_blank'
   end
 
   # Replace the inter_portal mapping ontology URI (that link to the API) by the link to the ontology in the UI
diff --git a/app/helpers/schemes_helper.rb b/app/helpers/schemes_helper.rb
index 9d3019cd36..7eec737c73 100644
--- a/app/helpers/schemes_helper.rb
+++ b/app/helpers/schemes_helper.rb
@@ -1,4 +1,5 @@
 module SchemesHelper
+  include UrlsHelper
 
   def get_schemes(ontology)
     ontology.explore.schemes(language: request_lang)
@@ -47,8 +48,8 @@ def section_name(section)
     t("ontology_details.sections.#{section}")
   end
 
-  def scheme_path(scheme_id = '', language = '')
-    "/ontologies/#{@ontology.acronym}/schemes/show?id=#{escape(scheme_id)}&lang=#{language}"
+  def scheme_path(ontology_id: @ontology.acronym, scheme_id: '', language: request_lang)
+    "/ontologies/#{ontology_id}/schemes/show?id=#{escape(scheme_id)}&lang=#{language}"
   end
 
   def no_main_scheme?
@@ -64,6 +65,7 @@ def no_main_scheme_alert
       t('schemes.no_main_scheme_alert')
     end
   end
+
   def no_schemes_alert
     render Display::AlertComponent.new do
       t('schemes.no_schemes_alert', acronym: @ontology.acronym)
@@ -88,7 +90,6 @@ def schemes_tree(schemes_labels, main_scheme_label, selected_scheme_id, submissi
       scheme
     end.compact
 
-
     main_scheme = nil
     if main_scheme_label.nil?
       children = schemes
@@ -105,8 +106,8 @@ def schemes_tree(schemes_labels, main_scheme_label, selected_scheme_id, submissi
     root.children = children
     selected_scheme = selected_scheme || main_scheme || root.children.first
     tree_component(root, selected_scheme, target_frame: 'scheme', auto_click: false, submission: submission) do |child|
-      href = scheme_path(child['@id'], request_lang) rescue  ''
-      data = { schemeid: (child['@id'] rescue '')}
+      href = scheme_path(scheme_id: child['@id'], ontology_id: @ontology.acronym, language: request_lang)
+      data = { schemeid: child['@id']}
       ["#", data, href]
     end
   end
diff --git a/app/javascript/controllers/index.js b/app/javascript/controllers/index.js
index fa09b85416..7b99fc21d4 100644
--- a/app/javascript/controllers/index.js
+++ b/app/javascript/controllers/index.js
@@ -34,12 +34,6 @@ application.register("form-options-display", FormDisplayController)
 import HistoryController from "./history_controller"
 application.register("history", HistoryController)
 
-import LabelAjaxController from "./label_ajax_controller"
-application.register("label-ajax", LabelAjaxController)
-
-import LabelsAjaxContainerController from "./labels_ajax_container_controller"
-application.register("labels-ajax-container", LabelsAjaxContainerController)
-
 import LanguageChangeController from "./language_change_controller"
 application.register("language-change", LanguageChangeController)
 
diff --git a/app/javascript/controllers/label_ajax_controller.js b/app/javascript/controllers/label_ajax_controller.js
deleted file mode 100644
index d3cbcfff46..0000000000
--- a/app/javascript/controllers/label_ajax_controller.js
+++ /dev/null
@@ -1,83 +0,0 @@
-import {Controller} from "@hotwired/stimulus"
-import useAjax from "../mixins/useAjax";
-
-// Connects to data-controller="label-ajax"
-export default class extends Controller {
-    static values = {
-        clsId: String,
-        ontologyAcronym: String,
-        ajaxUrl: String,
-        clsIdUrl: String,
-    }
-
-    connect() {
-        setTimeout(() => {
-            this.linkA = jQuery(this.element);
-
-            if (this.linkA.hasClass('ajax-modified-cls')) {
-                return true
-            }
-
-            this.cls_id = this.clsIdValue;
-            this.ont_acronym = this.ontologyAcronymValue;
-    
-            let ajax_uri = new URL(this.ajaxUrlValue, document.location.origin)
-    
-            ajax_uri.searchParams.set('ontology', this.ont_acronym)
-            ajax_uri.searchParams.set('id', this.cls_id)
-    
-    
-            this.request = useAjax({
-                url: ajax_uri.pathname + ajax_uri.search,
-                timeout: ajax_process_timeout * 1000,
-                success: this.#ajaxSuccess.bind(this),
-                error: this.#ajaxError.bind(this)
-            });
-          },1)
-    }
-
-    abort() {
-        if (this.request) {
-            this.request.abort()
-            this.request = null
-        }
-    }
-
-    disconnect() {
-        this.abort()
-    }
-
-    #ajaxSuccess(data) {
-        data = data.trim();
-        if (typeof data !== "undefined" && data.length > 0 && data.indexOf("http") !== 0) {
-            let cls_name = data
-            let cls_uri = this.clsIdUrlValue
-            this.linkA.html(cls_name);
-            this.linkA.attr('href', cls_uri);
-            this.linkA.addClass('ajax-modified-cls');
-            //find and process any identical classes (low probability)
-            this.#fillIdenticalIds(cls_name, cls_uri)
-        } else {
-            // remove the unique_id separator and the ontology acronym from the href
-            this.linkA.attr('href', this.cls_id);  // it may not be an ontology class, don't use the cls_uri
-            this.linkA.addClass('ajax-modified-cls');
-        }
-    }
-
-    #ajaxError() {
-        this.linkA.addClass('ajax-error')
-    }
-
-    #fillIdenticalIds(cls_name, cls_uri) {
-
-        let unique_id = this.linkA.attr('href');
-        jQuery('a[href="' + unique_id + '"]').each(function () {
-            let link = jQuery(this);
-            if (!link.hasClass('ajax-modified-cls')) {
-                link.html(cls_name);
-                link.attr('href', cls_uri);
-                link.addClass('ajax-modified-cls')
-            }
-        });
-    }
-}
diff --git a/app/javascript/controllers/labels_ajax_container_controller.js b/app/javascript/controllers/labels_ajax_container_controller.js
deleted file mode 100644
index a8f606114c..0000000000
--- a/app/javascript/controllers/labels_ajax_container_controller.js
+++ /dev/null
@@ -1,10 +0,0 @@
-import {Controller} from "@hotwired/stimulus"
-
-// Connects to data-controller="labels-ajax-container"
-export default class extends Controller {
-    static outlets = ['label-ajax']
-
-    abortAll() {
-        this.labelAjaxOutlets.forEach((link) => {link.abort()})
-    }
-}
diff --git a/app/javascript/controllers/turbo_frame_error_controller.js b/app/javascript/controllers/turbo_frame_error_controller.js
index 782166bc54..16d2cbbd28 100644
--- a/app/javascript/controllers/turbo_frame_error_controller.js
+++ b/app/javascript/controllers/turbo_frame_error_controller.js
@@ -34,7 +34,10 @@ export default class extends Turbo_frame_controller {
     Array.from(styles).forEach(e => el.removeChild(e))
 
     let body = el.querySelector('h1')
-    this.errorMessageTarget.firstElementChild.querySelector('.alert-message').innerHTML =  (body ? body.innerText : el.innerHTML)
+    let alertContainer = this.errorMessageTarget.firstElementChild?.querySelector('.alert-message')
+    if(alertContainer){
+      alertContainer.innerHTML =  (body ? body.innerText : el.innerHTML)
+    }
     $(this.errorMessageTarget).show()
   }
 
diff --git a/app/views/collections/_list_view.html.haml b/app/views/collections/_list_view.html.haml
index a50abe0ce2..d0594f157f 100644
--- a/app/views/collections/_list_view.html.haml
+++ b/app/views/collections/_list_view.html.haml
@@ -11,6 +11,6 @@
           - scheme = OpenStruct.new(collection)
           - scheme.prefLabel = Array(get_collection_label(collection)).last
           - scheme.id = scheme['@id']
-          - tree_child.child(child: scheme, href: collection_path(collection['@id'], request_lang),
+          - tree_child.child(child: scheme, href: collection_path(collection_id: collection['@id'], ontology_id: @ontology.acronym, language: request_lang),
                            children_href: '#', selected: scheme.id.eql?(selected_collection_id),
                            target_frame: 'collection', data: {collectionid: collection['@id']}, is_reused: concept_reused?(submission: @submission, concept_id: scheme.id))
diff --git a/app/views/concepts/_show.html.haml b/app/views/concepts/_show.html.haml
index 8d690b65fd..bbbb95614b 100644
--- a/app/views/concepts/_show.html.haml
+++ b/app/views/concepts/_show.html.haml
@@ -1,4 +1,4 @@
-= render TurboFrameComponent.new(id: 'concept_show', data: {controller:'labels-ajax-container', 'action': 'turbo:before-fetch-request->labels-ajax-container#abortAll', 'labels-ajax-container-label-ajax-outlet': '#concept_show a[data-controller="label-ajax"]'}) do
+= render TurboFrameComponent.new(id: 'concept_show') do
   - if @concept.id.eql?("bp_fake_root")
     = render Display::AlertComponent.new do
       = t('concepts.use_jump_to')
diff --git a/app/views/mappings/_mapping_table.html.haml b/app/views/mappings/_mapping_table.html.haml
index 20efcd92d5..1492ce2eca 100644
--- a/app/views/mappings/_mapping_table.html.haml
+++ b/app/views/mappings/_mapping_table.html.haml
@@ -14,7 +14,3 @@
         = render partial: 'mappings/show_line' , locals: {map: map, concept: @concept}
       %tr.empty-state
         %td.text-center{:colspan => "6"}= t("mappings.mapping_table.no_mappings")
-:javascript
-  jQuery(document).ready(function(){
-    ajax_process_init();
-  })
diff --git a/app/views/mappings/_show.html.haml b/app/views/mappings/_show.html.haml
index 6ca1cffe1f..60bebf6d9e 100644
--- a/app/views/mappings/_show.html.haml
+++ b/app/views/mappings/_show.html.haml
@@ -15,9 +15,7 @@
             %tr
               - map.classes.each do |cls|
                 %td
-                  - if inter_portal_mapping?(cls)
-                    = ajax_to_inter_portal_cls(cls)
-                  - elsif internal_mapping?(cls)
+                  - if internal_mapping?(cls)
                     = ajax_to_internal_cls(cls)
                   - else
                     = ajax_to_external_cls(cls)
@@ -25,8 +23,3 @@
                 #{map.source} #{(map.process || {})[:source_name]}
       .mappings-table-pagination
         = will_paginate @page_results, :update => 'mappings', :params => { :target => params[:target] }
-
-  :javascript
-    jQuery(document).ready(function(){
-      ajax_process_init();  // see bp_ajax_controller.js
-    })
\ No newline at end of file

From aa7e2475d5f2de6bcc2a8725ad28db8cbd392346 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 7 Nov 2024 10:16:37 +0100
Subject: [PATCH 11/22] Fix: Remove ontolobrigde code and some Jquery code 
 (#822)

* update select_language_label  helper to select f no english found any language remaining over the not tagged

* remove ontology bridge code

* remove ont_viewer data jquery code

* remove no existent fetch_results action code
---
 .env.sample                                   |   2 -
 app/assets/javascripts/bp_ontolobridge.js     | 359 ------------------
 .../stylesheets/application.css.scss.erb      |   1 -
 app/assets/stylesheets/ontolobridge.scss      |  35 --
 app/controllers/concepts_controller.rb        |   2 -
 app/controllers/ontolobridge_controller.rb    |  64 ----
 app/controllers/ontologies_controller.rb      |   1 -
 app/helpers/application_helper.rb             |   5 -
 .../class_search_auto_complete_controller.js  |  11 +-
 app/views/concepts/_request_term.html.haml    |  47 ---
 app/views/layouts/_header.html.erb            |   6 +-
 app/views/layouts/_ontology_viewer.html.haml  |  20 -
 app/views/layouts/appliance.html.haml         |   2 -
 app/views/layouts/component_preview.html.erb  |   6 +-
 .../component_preview_not_centred.html.erb    |   6 +-
 app/views/layouts/popup.html.erb              |   2 -
 app/views/layouts/tool.html.haml              |   3 +-
 .../ontologies/sections/visualize.html.haml   |   8 -
 config/application.rb                         |   1 -
 config/bioportal_config_env.rb.sample         |   9 -
 config/locales/en.yml                         |  31 +-
 config/locales/fr.yml                         |  32 --
 config/routes.rb                              |  25 +-
 db/schema.rb                                  |   2 +-
 24 files changed, 21 insertions(+), 659 deletions(-)
 delete mode 100644 app/assets/javascripts/bp_ontolobridge.js
 delete mode 100644 app/assets/stylesheets/ontolobridge.scss
 delete mode 100644 app/controllers/ontolobridge_controller.rb
 delete mode 100644 app/views/concepts/_request_term.html.haml

diff --git a/.env.sample b/.env.sample
index 94f4a336b4..6a8e41d243 100644
--- a/.env.sample
+++ b/.env.sample
@@ -39,5 +39,3 @@ OP_API_URL="https://data.bioontology.org"
 API_IMAGE_REPOSITORY=agroportal
 ## Image tag/version from which the ontoportal api will be built
 API_IMAGE_TAG=master
-
-
diff --git a/app/assets/javascripts/bp_ontolobridge.js b/app/assets/javascripts/bp_ontolobridge.js
deleted file mode 100644
index d4acc3e977..0000000000
--- a/app/assets/javascripts/bp_ontolobridge.js
+++ /dev/null
@@ -1,359 +0,0 @@
-function bindAddRequestTermClick() {
-  jQuery("a.add_request_term").live('click', function(){
-    var id = jQuery(this).attr("data-parent-id");
-    addRequestTermBox(id);
-  });
-}
-
-function bindCancelRequestTermClick() {
-  jQuery(".request_term_form_div .cancel").live('click', function() {
-    removeRequestTermBox();
-  });
-}
-
-function bindNewTermInstructionsClick() {
-  jQuery("#new_term_instructions").live("click", function() {
-    jQuery(this).trumbowyg({
-      btns: [
-        ['viewHTML'],
-        ['undo', 'redo'], // Only supported in Blink browsers
-        ['formatting'],
-        ['strong', 'em', 'del'],
-        ['superscript', 'subscript'],
-        ['link'],
-        ['insertImage'],
-        ['justifyLeft', 'justifyCenter', 'justifyRight', 'justifyFull'],
-        ['unorderedList', 'orderedList'],
-        ['horizontalRule'],
-        ['removeformat'],
-        ['fullscreen']
-      ]
-    });
-    jQuery("#new_term_instructions_submit").show();
-    jQuery("#new_term_instructions_cancel").show();
-  });
-}
-
-function bindNewTermInstructionsSubmit() {
-  jQuery("#new_term_instructions_submit").live("click", function() {
-    saveNewTermInstructions();
-  });
-}
-
-function bindNewTermInstructionsCancel() {
-  jQuery("#new_term_instructions_cancel").live("click", function() {
-    var oldVal = jQuery("#new_term_instructions_old").val().trim();
-    var curVal = jQuery('#new_term_instructions').html().trim();
-
-    if (oldVal != curVal) {
-      if (confirm('Are you sure you want to discard your changes?')) {
-        jQuery('#new_term_instructions').trumbowyg('destroy');
-        jQuery('#new_term_instructions').html(oldVal);
-        hideButtons();
-      }
-    } else {
-      jQuery('#new_term_instructions').trumbowyg('destroy');
-      hideButtons();
-    }
-  });
-}
-
-function preventNewTermInstructionsFormSubmit() {
-  jQuery("#new_term_instructions_form").submit(function(e) {
-    e.preventDefault(e);
-  });
-}
-
-function clearProgressMessage(parentContainerID) {
-  var progMsgElem = jQuery("#" + parentContainerID + " #progress_message");
-  progMsgElem.hide();
-  progMsgElem.html("");
-}
-
-function showProgressMessage(parentContainerID) {
-  clearProgressMessage(parentContainerID);
-  var msg = "Saving...";
-  var progMsgElem = jQuery("#" + parentContainerID + " #progress_message");
-  progMsgElem.text(msg).html();
-  progMsgElem.show();
-}
-
-function saveNewTermInstructions() {
-  var params = jQuery('#new_term_instructions_form').serialize();
-  var newInstructions = jQuery('#new_term_instructions').html().trim();
-  params += '&new_term_instructions=' + newInstructions;
-  var parentContainerID = 'new_term_instructions_container';
-  showProgressMessage(parentContainerID);
-
-  jQuery.ajax({
-    type: "POST",
-    url: "/ontolobridge/save_new_term_instructions",
-    dataType: "json",
-    data: params,
-    success: function(data) {
-      var status = data[1];
-
-      if (status && status >= 400 || data[0]['error'].length) {
-        showStatusMessages('', data[0]['error']);
-      } else {
-        jQuery('#new_term_instructions').trumbowyg('destroy');
-        jQuery("#new_term_instructions_old").val(newInstructions);
-        showStatusMessages(data[0]["success"], '');
-        setTimeout(function() { clearStatusMessages(); }, 5000);
-      }
-    },
-    error: function(request, textStatus, errorThrown) {
-      showStatusMessages('', errorThrown);
-    },
-    complete: function(request, textStatus) {
-      clearProgressMessage(parentContainerID);
-      hideButtons();
-    }
-  });
-}
-
-function hideButtons() {
-  jQuery("#new_term_instructions_submit").hide();
-  jQuery("#new_term_instructions_cancel").hide();
-}
-
-function bindRequestTermSaveClick() {
-  var success = "";
-  var error = "";
-  var user = jQuery(document).data().bp.user;
-  var ontology_id = jQuery(document).data().bp.ont_viewer.ontology_id;
-  var params = jQuery("#request_term_form").serialize();
-  params += "&ontology=" + ontology_id + "&email=" + user["email"]
-
-  if (user["firstName"] && user["lastName"]) {
-    params += "&submitter=" + user["firstName"] + " " + user["lastName"];
-  }
-
-  var parentContainerID = 'proposal_buttons';
-  showProgressMessage(parentContainerID);
-
-  jQuery.ajax({
-    type: "POST",
-    url: "/ontolobridge",
-    data: params,
-    dataType: "json",
-    success: function(data) {
-      var status = data[1];
-
-      if (status && status >= 400) {
-        showStatusMessages('', data[0]["error"]);
-      } else {
-        var msg = "<strong>A new term request has been submitted successfully:</strong><br/><br/>";
-        removeRequestTermBox();
-
-        for (var i in data[0]) {
-          msg += i + ": " + data[0][i] + "<br/>";
-        }
-        showStatusMessages(msg, error);
-      }
-    },
-    error: function(request, textStatus, errorThrown) {
-      error = "The following error has occurred: " + errorThrown + ". Please try again.";
-      showStatusMessages(success, error);
-    },
-    complete: function(request, textStatus) {
-      clearProgressMessage(parentContainerID);
-    }
-  });
-}
-
-function removeRequestTermBox() {
-  jQuery(".request_term_form_div").html("");
-}
-
-function addRequestTermBox(id) {
-  clearStatusMessages();
-  var formContainer = jQuery(".request_term_form_div");
-  var requestTermForm = requestTermFields(id, formContainer);
-  var formID = requestTermForm.attr('id');
-  var isPopulated = window.localStorage.getItem(formID + '_populated');
-
-  if (isPopulated) {
-    for (var key in window.localStorage) {
-      if (key.startsWith(formID)) {
-        var elemID = key.replace(formID + '_', '');
-        var elem = jQuery('#' + formID + ' #' + elemID);
-
-        if (elem.attr('type') === "checkbox") {
-          elem.prop("checked", true);
-        } else if (elem.length > 0) {
-          var val = window.localStorage.getItem(key);
-          elem.val(val);
-        }
-        window.localStorage.removeItem(key);
-      }
-    }
-  }
-  formContainer.show();
-  jQuery("#label").focus();
-}
-
-function clearStatusMessages() {
-  jQuery("#ob_success_message").hide();
-  jQuery("#ob_error_message").hide();
-  jQuery("#ob_success_message").html("");
-  jQuery("#ob_error_message").html("");
-}
-
-function showStatusMessages(success, error) {
-  if (success.length > 0) {
-      let ob = jQuery("#ob_success_message")
-      console.log('show ob message')
-      console.log(ob)
-      ob.html(success);
-      ob.show();
-  }
-
-  if (error.length > 0) {
-    jQuery("#ob_error_message").text(error).html();
-    jQuery("#ob_error_message").show();
-  }
-}
-
-function requestTermButtons() {
-  var buttonSubmit = jQuery("<button>")
-    .attr("class", "btn")
-    .attr("type", "submit")
-    .attr("onclick", "")
-    .addClass("save")
-    .css("margin-right", "5px")
-    .html("Submit");
-  var buttonCancel = jQuery("<button>")
-    .attr("class", "btn")
-    .attr("type", "button")
-    .attr("onclick", "")
-    .addClass("cancel")
-    .html("Cancel");
-  var progressMessage = jQuery("<span>")
-    .attr("id", "progress_message")
-    .css("display", "none")
-    .css("margin-left", "20px");
-  return buttonSubmit.add(buttonCancel).add(progressMessage);
-}
-
-function appendTextArea(id, placeholder, div, isRequired, invalidMessage) {
-  if (jQuery.browser.msie && parseInt(jQuery.browser.version) < 10) {
-    div.append(jQuery("<span>").css("font-weight", "bold").html(text));
-    div.append("<br/>");
-  }
-
-  var txtArea = jQuery("<textarea>", {
-    rows: 1,
-    cols: 1,
-    id: id,
-    name: id,
-    placeholder: placeholder,
-    css: {"width": "500px", "height": "100px", "margin": "5px 0 5px 0"}
-  });
-
-  jQuery(txtArea).on("invalid", function(e) {
-    this.setCustomValidity(invalidMessage);
-  });
-
-  jQuery(txtArea).on("input", function(e) {
-    this.setCustomValidity('');
-  });
-
-  if (isRequired) {
-    txtArea.prop('required', true);
-    txtArea.attr("class", "req");
-  }
-  div.append(txtArea);
-  div.append("<br/>");
-}
-
-function appendField(id, text, div, isRequired, invalidMessage) {
-  if (jQuery.browser.msie && parseInt(jQuery.browser.version) < 10) {
-    div.append(jQuery("<span>").css("font-weight", "bold").html(text));
-    div.append("<br/>");
-  }
-
-  var ipt = jQuery("<input>", {
-    type: 'text',
-    id: id,
-    name: id,
-    placeholder: text,
-    css: {"width": "500px", "margin": "5px 0 5px 0"}
-  });
-
-  jQuery(ipt).on("invalid", function(e) {
-    this.setCustomValidity(invalidMessage);
-  });
-
-  jQuery(ipt).on("input", function(e) {
-    this.setCustomValidity('');
-  });
-
-  if (isRequired) {
-    ipt.prop('required', true);
-    ipt.attr("class", "req");
-  }
-  div.append(ipt);
-  div.append("<br/>");
-}
-
-function requestTermFields(id, container) {
-  container.html("");
-  var requestTermForm = jQuery("<form/>", {id: 'request_term_form', name: 'request_term_form'});
-
-  appendField("label", "Enter term label (required)", requestTermForm, true, 'Please enter a label for a new term');
-  appendTextArea("description", "Enter term description (required)", requestTermForm, true, 'Please enter a description for a new term');
-
-  requestTermForm.append(jQuery("<span>").css("font-weight", "bold").css("margin", "5px 0 5px 0").html("Superclass: "));
-  requestTermForm.append(g_prefLabel + "<br/>");
-
-  appendField("references", "Enter references - links that provide more info on the term", requestTermForm, false, 'Please enter references for a new term. References are any links (either URIs or URLs) that provide more information about the term.');
-  appendTextArea("justification", "Enter justification for the term - the reason it should be added", requestTermForm, false, 'Please enter a justification. Justifications are notes provided by the submitter to justify the term; often this will not be necessary, since for most routine cases the label/description/position will be sufficient, but sometimes it may be necessary to justify why a new term is necessary.');
-
-  requestTermForm.append(jQuery("<input>").attr("type", "checkbox").attr("name", "notification_request").attr("id", "notification_request").css("height", "15px")).append("&nbsp;&nbsp;");
-  requestTermForm.append(jQuery("<input>").attr("type", "hidden").attr("name", "superclass").attr("id", "superclass").attr("value", id));
-  requestTermForm.append(jQuery("<label>").attr("for", "notification_request").attr("id", "notification_request").css("margin", "0 0 10px 0").append("Email submitter when there is a status change"));
-  requestTermForm.append(jQuery("<div>").attr("id", "proposal_buttons").append(requestTermButtons()));
-  container.append(requestTermForm);
-
-  requestTermForm.submit(function(e) {
-    e.preventDefault(e);
-    bindRequestTermSaveClick();
-    return false;
-  });
-
-  return requestTermForm;
-}
-
-function obTriggerNewTermRequestFormSave() {
-  var ont = jQuery(document).data().bp.ontology;
-  var ob_onts = jQuery(document).data().bp.ontolobridge_ontologies;
-
-  // Execute only if ontology is Ontolobridge-enabled
-  if (Object.entries(ont).length > 0 && ob_onts && ob_onts.length > 0 && ob_onts.includes(ont["acronym"])) {
-    var formName = 'request_term_form';
-
-    jQuery("#" + formName + " input, #" + formName + " textarea").each(function() {
-      var input = jQuery(this);
-      var val = input.val().trim();
-
-      if (input.attr('type') === "checkbox" && input.prop('checked') === true) {
-        window.localStorage.setItem(formName + '_' + input.attr('name'), 'checkbox_checked');
-        window.localStorage.setItem(formName + '_populated', true);
-      } else if (input.attr('type') !== "hidden" && input.attr('type') !== "checkbox" && val) {
-        window.localStorage.setItem(formName + '_' + input.attr('name'), val);
-        window.localStorage.setItem(formName + '_populated', true);
-      }
-    });
-  }
-}
-
-jQuery(document).ready(function() {
-  clearStatusMessages();
-  bindAddRequestTermClick();
-  bindCancelRequestTermClick();
-  preventNewTermInstructionsFormSubmit();
-  bindNewTermInstructionsSubmit();
-  bindNewTermInstructionsCancel();
-  bindNewTermInstructionsClick();
-});
diff --git a/app/assets/stylesheets/application.css.scss.erb b/app/assets/stylesheets/application.css.scss.erb
index 52b88a0a6d..5f86b22144 100755
--- a/app/assets/stylesheets/application.css.scss.erb
+++ b/app/assets/stylesheets/application.css.scss.erb
@@ -32,7 +32,6 @@
 @import "recommender";
 @import "search";
 @import "submissions";
-@import "ontolobridge";
 @import "fair_assement";
 @import "instances_table";
 @import "register";
diff --git a/app/assets/stylesheets/ontolobridge.scss b/app/assets/stylesheets/ontolobridge.scss
deleted file mode 100644
index ebcc8e9426..0000000000
--- a/app/assets/stylesheets/ontolobridge.scss
+++ /dev/null
@@ -1,35 +0,0 @@
-/* message boxes */
-.message-box {
-  color: #555;
-  border-radius: 3px;
-  font-family: Tahoma, Geneva, Arial, sans-serif;
-  font-size: 11px;
-  padding: 10px;
-  margin: 10px 0 0 0;
-}
-
-.message-box span {
-  font-weight: bold;
-  text-transform: uppercase;
-}
-
-.error-msg {
-  //background-color: #eee;
-  border: 1px solid #f5aca6;
-}
-
-.success-msg {
-  //background-color: #eee;
-  border: 1px solid #a6ca8a;
-}
-
-input.req,
-textarea.req {
-  border-color: darksalmon !important;
-}
-
-blockquote {
-  padding: 0 1em;
-  color: #6a737d;
-  border-left: .25em solid #dfe2e5;
-}
diff --git a/app/controllers/concepts_controller.rb b/app/controllers/concepts_controller.rb
index 97e316c6af..c52bbcf884 100644
--- a/app/controllers/concepts_controller.rb
+++ b/app/controllers/concepts_controller.rb
@@ -23,7 +23,6 @@ def show
     redirect_to(ontology_path(id: params[:ontology], p: 'classes', conceptid: params[:id], lang: request_lang)) and return unless turbo_frame_request?
 
     @submission = get_ontology_submission_ready(@ontology)
-    @ob_instructions = helpers.ontolobridge_instructions_template(@ontology)
     @concept = @ontology.explore.single_class({full: true, language: request_lang}, params[:id])
     @instances_concept_id = @concept.id
 
@@ -43,7 +42,6 @@ def index
 
     # Note that find_by_acronym includes views by default
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
-    @ob_instructions = helpers.ontolobridge_instructions_template(@ontology)
 
     @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri')
 
diff --git a/app/controllers/ontolobridge_controller.rb b/app/controllers/ontolobridge_controller.rb
deleted file mode 100644
index 89d3d62b6d..0000000000
--- a/app/controllers/ontolobridge_controller.rb
+++ /dev/null
@@ -1,64 +0,0 @@
-require 'rest-client'
-require 'multi_json'
-
-class OntolobridgeController < ApplicationController
-
-  # POST /ontolobridge
-  # POST /ontolobridge.xml
-  def create
-    request_term
-  end
-
-  def request_term
-    response = {}
-    endpoint = "/RequestTerm"
-    h_params = {}
-    response_raw = nil
-    code = 200
-
-    begin
-      params.delete("controller")
-      params.delete("action")
-      params.each { |k, v|
-        if v === "on"
-          h_params[k] = true
-        else
-          h_params[k] = v
-        end
-      }
-
-      headers = {'Authorization' => $ONTOLOBRIDGE_AUTHENTICATION_TOKEN}
-      response_raw = RestClient.post("#{$ONTOLOBRIDGE_BASE_URL}#{endpoint}", h_params, headers)
-      code = response_raw.code
-      response.merge!(MultiJson.load(response_raw))
-    rescue RestClient::BadRequest => e
-      code = 400
-      response["error"] = e.message
-    rescue Exception => e
-      code = 500
-      response["error"] = t('ontolobridge.problem_of_creating_new_term', endpoint: endpoint, class: e.class, message: e.message)
-    end
-
-    render json: [response, code], status: code
-  end
-
-  def save_new_term_instructions
-    code = 200
-    response = {error: '', success: ''}
-    response[:success] = t('ontolobridge.new_term_instructions_saved', acronym: params['acronym'])
-    ont_data = Ontology.find_by(acronym: params['acronym'])
-    ont_data ||= Ontology.new
-    ont_data.acronym = params['acronym']
-    ont_data.new_term_instructions = params['new_term_instructions']
-
-    begin
-      ont_data.save
-    rescue Exception => e
-      code = 500
-      response[:error] = t('ontolobridge.error_saving_new_term_instructions', acronym: params['acronym'])
-    end
-    sleep(1)
-    render json: [response, code], status: code
-  end
-
-end
diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb
index 041c1e6361..9d5f267777 100644
--- a/app/controllers/ontologies_controller.rb
+++ b/app/controllers/ontologies_controller.rb
@@ -276,7 +276,6 @@ def show
       params[:p] = "summary"
     end
 
-    #@ob_instructions = helpers.ontolobridge_instructions_template(@ontology)
 
     # Get the latest submission (not necessarily the latest 'ready' submission)
 
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 2a319d6874..0da7946e0d 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -185,11 +185,6 @@ def subscribed_to_ontology?(ontology_acronym, user)
     return false
   end
 
-  def ontolobridge_instructions_template(ontology)
-    ont_data = Ontology.find_by(acronym: ontology.acronym)
-    ont_data.nil? || ont_data.new_term_instructions.empty? ? t('concepts.request_term.new_term_instructions') : ont_data.new_term_instructions
-  end
-
   # http://stackoverflow.com/questions/1293573/rails-smart-text-truncation
   def smart_truncate(s, opts = {})
     opts = {:words => 20}.merge(opts)
diff --git a/app/javascript/controllers/class_search_auto_complete_controller.js b/app/javascript/controllers/class_search_auto_complete_controller.js
index 831cfee410..0a42a8d343 100644
--- a/app/javascript/controllers/class_search_auto_complete_controller.js
+++ b/app/javascript/controllers/class_search_auto_complete_controller.js
@@ -11,14 +11,9 @@ export default class extends OntoportalAutocompleteController {
 
     onFindValue(li) {
         if (li == null) {
-            // User performs a search
-            let search = confirm("Class could not be found.\n\nPress OK to go to the Search page or Cancel to continue browsing");
-
-            if (search) {
-                jQuery("#search_keyword").val(jQuery("#search_box").val());
-                jQuery("#search_form").submit();
-                return
-            }
+            // No result found
+            // TODO in this case show a message to redirect to the global search page
+            return
         }
 
         // Appropriate value selected
diff --git a/app/views/concepts/_request_term.html.haml b/app/views/concepts/_request_term.html.haml
deleted file mode 100644
index 85c364f60e..0000000000
--- a/app/views/concepts/_request_term.html.haml
+++ /dev/null
@@ -1,47 +0,0 @@
-:plain
-  <div id="trumbowyg-icons">
-    <svg xmlns="http://www.w3.org/2000/svg"><symbol id="trumbowyg-blockquote" viewBox="0 0 72 72"><path d="M21.3 31.9h-.6c.8-1.2 1.9-2.2 3.4-3.2 2.1-1.4 5-2.7 9.2-3.3l-1.4-8.9c-4.7.7-8.5 2.1-11.7 4-2.4 1.4-4.3 3.1-5.8 4.9-2.3 2.7-3.7 5.7-4.5 8.5-.8 2.8-1 5.4-1 7.5 0 2.3.3 4 .4 4.8 0 .1.1.3.1.4 1.2 5.4 6.1 9.5 11.9 9.5 6.7 0 12.2-5.4 12.2-12.2s-5.5-12-12.2-12zM49.5 31.9h-.6c.8-1.2 1.9-2.2 3.4-3.2 2.1-1.4 5-2.7 9.2-3.3l-1.4-8.9c-4.7.7-8.5 2.1-11.7 4-2.4 1.4-4.3 3.1-5.8 4.9-2.3 2.7-3.7 5.7-4.5 8.5-.8 2.8-1 5.4-1 7.5 0 2.3.3 4 .4 4.8 0 .1.1.3.1.4 1.2 5.4 6.1 9.5 11.9 9.5 6.7 0 12.2-5.4 12.2-12.2s-5.5-12-12.2-12z"/></symbol><symbol id="trumbowyg-bold" viewBox="0 0 72 72"><path d="M51.1 37.8c-1.1-1.4-2.5-2.5-4.2-3.3 1.2-.8 2.1-1.8 2.8-3 1-1.6 1.5-3.5 1.5-5.3 0-2-.6-4-1.7-5.8-1.1-1.8-2.8-3.2-4.8-4.1-2-.9-4.6-1.3-7.8-1.3h-16v42h16.3c2.6 0 4.8-.2 6.7-.7 1.9-.5 3.4-1.2 4.7-2.1 1.3-1 2.4-2.4 3.2-4.1.9-1.7 1.3-3.6 1.3-5.7.2-2.5-.5-4.7-2-6.6zM40.8 50.2c-.6.1-1.8.2-3.4.2h-9V38.5h8.3c2.5 0 4.4.2 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-  </div>
-.notes_list_container
-  .add_request_term{style: "float: left; margin-right: 1em;"}
-    %div#ob_success_message{class: "message-box success-msg", style: "display: none; margin: 10px 0;"}
-    %div#ob_error_message{class: "message-box error-msg", style: "display: none; margin: 10px 0;"}
-    - if !session[:user].nil? && @ontology.admin?(session[:user])
-      %p
-        %em
-          = t('concepts.request_terms_instructions', acronym: @ontology.acronym)
-      %div#new_term_instructions_container{style: 'clear: both;'}
-        %form#new_term_instructions_form
-          = hidden_field nil, :acronym, value: @ontology.acronym
-          = hidden_field nil, :new_term_instructions_old, value: @ob_instructions.html_safe
-          %div#new_term_instructions
-            = @ob_instructions.html_safe
-          %button#new_term_instructions_submit{class: "btn", type: "button", title: t('concepts.submit_changes'), alt: "Submit Changes", style: 'display: none;'}
-            = t('concepts.submit_changes')
-          %button#new_term_instructions_cancel{class: "btn", type: "button", title: t('concepts.cancel'), alt: "Cancel", style: 'display: none;'}
-            = t('concepts.cancel')
-          %span#progress_message{style: 'display: none; margin-left: 20px;'}
-    - else
-      %div
-        = @ob_instructions.html_safe
-    - if session[:user].nil?
-      = link_to t('concepts.request_new_term'), login_index_path, style: "font-size: .9em;"
-    - else
-      = link_to t('concepts.request_new_term'), "javascript:void(0);", class: "add_request_term", style: "font-size: .9em;", data: { parent_id: "#{@concept.id}" }
-  %div.request_term_form_div{style: "display: none; clear: both; padding-top: 1em;"}
-
-:javascript
-  var g_prefLabel;
-
-  jQuery(document).ready(function() {
-    g_prefLabel = '#{@concept.prefLabel({:use_html => false}).html_safe}';
-
-    if (!g_prefLabel) {
-      g_prefLabel = '#{@concept.id}';
-    }
-    var isPopulated = window.localStorage.getItem('request_term_form_populated');
-
-    if (isPopulated) {
-      addRequestTermBox("#{@concept.id}");
-    }
-  });
diff --git a/app/views/layouts/_header.html.erb b/app/views/layouts/_header.html.erb
index 1340bdbb26..9e765dbe00 100644
--- a/app/views/layouts/_header.html.erb
+++ b/app/views/layouts/_header.html.erb
@@ -46,10 +46,6 @@
       {
       }
       ;
-      jQuery(document).data().bp.ontolobridge_ontologies =
-      <%=$NEW_TERM_REQUEST_ONTOLOGIES.to_json.html_safe%> ||
-      [];
-      jQuery(document).data().bp.ont_viewer = {};
       jQuery(document).data().bp.ont_chart = {};
   </script>
 
@@ -60,4 +56,4 @@
 <%= turbo_frame_tag :cookies_modal, src: cookies_path if cookies[:cookies_accepted].nil? && !(Rails.env.development? || Rails.env.test?) %>
 
 <div class="flex-grow-1">
-<%= render partial: 'layouts/notices' %>
\ No newline at end of file
+<%= render partial: 'layouts/notices' %>
diff --git a/app/views/layouts/_ontology_viewer.html.haml b/app/views/layouts/_ontology_viewer.html.haml
index e7f3010e16..95fe55300d 100644
--- a/app/views/layouts/_ontology_viewer.html.haml
+++ b/app/views/layouts/_ontology_viewer.html.haml
@@ -4,26 +4,6 @@
 
 = render :partial =>'layouts/header'
 %div#bd.bg-white.ontology-viewer
-  :javascript
-    // Ontology viewer vars
-    jQuery(document).data().bp.ont_viewer = {};
-    jQuery(document).data().bp.ont_viewer.ontology_id = jQuery(document).data().bp.ontology.acronym;
-    jQuery(document).data().bp.ont_viewer.ontology_version_id = jQuery(document).data().bp.submission_latest.submissionId;
-    jQuery(document).data().bp.ont_viewer.ontology_name = "#{@ontology.name}";
-    jQuery(document).data().bp.ont_viewer.org_site = "#{$ORG_SITE}";
-    jQuery(document).data().bp.ont_viewer.concept_id = "#{params[:conceptid] || (@concept ? @concept.id : 'root')}";
-    jQuery(document).data().bp.ont_viewer.content_section = "#{sanitize(h(content_section))}";
-    jQuery(document).data().bp.ont_viewer.concept_param = "#{"conceptid=\#{params[:conceptid]}" unless params[:conceptid].nil? || params[:conceptid].empty?}";
-    jQuery(document).data().bp.ont_viewer.concept_name = "#{@concept.prefLabel unless @concept.nil?}";
-    jQuery(document).data().bp.ont_viewer.metadata_only = "#{@ontology.summaryOnly}";
-    jQuery(document).data().bp.ont_viewer.current_purl = "#{@current_purl}";
-    jQuery(document).data().bp.ont_viewer.purl_prefix = "#{($PURL_ENABLED ? $PURL_PREFIX+"/"+@ontology.acronym : '')}";
-    jQuery(document).data().bp.ont_viewer.concept_name_title = (jQuery(document).data().bp.ont_viewer.concept_name == "") ?
-        "" : " - " + jQuery(document).data().bp.ont_viewer.concept_name;
-
-
-
-
   = modal_frame_container
 
   = render partial: 'concepts/perma_link_modal'
diff --git a/app/views/layouts/appliance.html.haml b/app/views/layouts/appliance.html.haml
index 3e306068c0..801d72caba 100644
--- a/app/views/layouts/appliance.html.haml
+++ b/app/views/layouts/appliance.html.haml
@@ -21,7 +21,6 @@
       jQuery(document).data({bp: {config: #{bp_config_json.html_safe}, user: #{(session[:user] || {}).to_hash.to_json.html_safe}}});
       jQuery(document).data().bp.ontology = #{@ontology.to_json.html_safe} || {};
       jQuery(document).data().bp.submission_latest = #{@submission_latest.to_json.html_safe} || {};
-      jQuery(document).data().bp.ont_viewer = {};
       jQuery(document).data().bp.ont_chart = {};
 
   %body{:class => "#{controller_name} #{action_name}"}
@@ -35,4 +34,3 @@
       = yield
 
     = render partial: "layouts/footer"
-
diff --git a/app/views/layouts/component_preview.html.erb b/app/views/layouts/component_preview.html.erb
index 429f630109..04686f6ce4 100644
--- a/app/views/layouts/component_preview.html.erb
+++ b/app/views/layouts/component_preview.html.erb
@@ -41,10 +41,6 @@
       {
       }
       ;
-      jQuery(document).data().bp.ontolobridge_ontologies =
-      <%=$NEW_TERM_REQUEST_ONTOLOGIES.to_json.html_safe%> ||
-      [];
-      jQuery(document).data().bp.ont_viewer = {};
       jQuery(document).data().bp.ont_chart = {};
   </script>
 </head>
@@ -57,4 +53,4 @@
 
 
 </body>
-</html>
\ No newline at end of file
+</html>
diff --git a/app/views/layouts/component_preview_not_centred.html.erb b/app/views/layouts/component_preview_not_centred.html.erb
index 81b1c29645..f44418358d 100644
--- a/app/views/layouts/component_preview_not_centred.html.erb
+++ b/app/views/layouts/component_preview_not_centred.html.erb
@@ -41,10 +41,6 @@
       {
       }
       ;
-      jQuery(document).data().bp.ontolobridge_ontologies =
-      <%=$NEW_TERM_REQUEST_ONTOLOGIES.to_json.html_safe%> ||
-      [];
-      jQuery(document).data().bp.ont_viewer = {};
       jQuery(document).data().bp.ont_chart = {};
   </script>
 </head>
@@ -53,4 +49,4 @@
   <%= yield %> <!-- rendered preview will be injected here -->
   <%= javascript_include_tag "application" %>
 </body>
-</html>
\ No newline at end of file
+</html>
diff --git a/app/views/layouts/popup.html.erb b/app/views/layouts/popup.html.erb
index 7262ec44fc..8050bf57a7 100644
--- a/app/views/layouts/popup.html.erb
+++ b/app/views/layouts/popup.html.erb
@@ -17,7 +17,6 @@
     jQuery(document).data({bp: {config: <%=bp_config_json.html_safe%>, user: <%=(session[:user] || {}).to_hash.to_json.html_safe%>}});
     jQuery(document).data().bp.ontology = <%=@ontology.to_json.html_safe%> || {};
     jQuery(document).data().bp.submission_latest = <%=@submission_latest.to_json.html_safe%> || {};
-    jQuery(document).data().bp.ont_viewer = {};
     jQuery(document).data().bp.ont_chart = {};
   </script>
   <%= csrf_meta_tag %>
@@ -63,4 +62,3 @@
 
 </body>
 </html>
-
diff --git a/app/views/layouts/tool.html.haml b/app/views/layouts/tool.html.haml
index 26350b57b1..94b8efef7d 100644
--- a/app/views/layouts/tool.html.haml
+++ b/app/views/layouts/tool.html.haml
@@ -22,7 +22,6 @@
   = javascript_include_tag "vendor"
   :javascript
     jQuery(document).data({bp: {config: {ui_url: ''}, user: {}}});
-    jQuery(document).data().bp.ont_viewer = {};
     jQuery(document).data().bp.ont_chart = {};
 
 %body{class: " #{controller_name} #{action_name}", style: 'background-color: var(--light-color);'}
@@ -39,4 +38,4 @@
     = yield
 
 
-= javascript_include_tag "application"
\ No newline at end of file
+= javascript_include_tag "application"
diff --git a/app/views/ontologies/sections/visualize.html.haml b/app/views/ontologies/sections/visualize.html.haml
index 121b57daa1..2bed4ee9c3 100644
--- a/app/views/ontologies/sections/visualize.html.haml
+++ b/app/views/ontologies/sections/visualize.html.haml
@@ -1,8 +1,6 @@
 =  render TurboFrameComponent.new(id: "classes", data: {"turbo-frame-target": "frame"} ) do
   - unless @error || @concept.nil?
     - @title = "#{@ontology.acronym} - #{@concept.prefLabel}"
-    - @new_term_request_ontologies
-    - @enable_ontolobridge = !$NEW_TERM_REQUEST_ONTOLOGIES.nil? && $NEW_TERM_REQUEST_ONTOLOGIES.include?(@ontology.acronym)
     %div.tooltip
     %div#bd_content.bd_content.explore{data:{controller: 'container-splitter'}}
       %div.sidebar{data:{'container-splitter-target': 'container'}}
@@ -10,12 +8,6 @@
       %div#concept_content.d-flex.flex-column{data:{'container-splitter-target': 'container'}}
         = render partial: 'concepts/show'
 
-    - form_for(:search, :url => {:controller =>'search',:action=>'fetch_results'},:html=>{:id=>'search_form'}) do |f|
-      %input{:name => "search[ontologies][]", :type => "hidden", :value => @ontology.acronym}/
-      = hidden_field :search, :search_type, :value=>"contains"
-      = hidden_field :search, :keyword, :value=>"",:id=>"search_keyword"
   - else
     = render Display::AlertComponent.new(type: 'danger') do
       =  @concept.nil? ? t("ontologies.sections.no_class_concept_found") : @error
-
-
diff --git a/config/application.rb b/config/application.rb
index d6796fca19..0b91b1434e 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -26,7 +26,6 @@ class Application < Rails::Application
 
     config.autoload_paths += %W[#{config.root}/app/lib/kgcl]
 
-
     config.settings = config_for :settings
     # Initialize configuration for KGCL change request functionality.
     config.change_request = config_for :change_request
diff --git a/config/bioportal_config_env.rb.sample b/config/bioportal_config_env.rb.sample
index 90dad17f3c..8d6c4b52e7 100644
--- a/config/bioportal_config_env.rb.sample
+++ b/config/bioportal_config_env.rb.sample
@@ -93,14 +93,6 @@ $MULTIPLE_RECOGNIZERS = false
 # ["CPT","ICD10","ICNP","ICPC2P","MDDB","MEDDRA","MSHFRE","MSHSPA_1","NDDF","NDFRT","NIC","RCD","SCTSPA","SNOMEDCT","WHO-ART"]
 $RESTRICTED_DOWNLOADS = []
 
-# Ontolobridge endpoint url
-$ONTOLOBRIDGE_BASE_URL = 'https://ontolobridge.ccs.miami.edu/api-test/requests'
-# Ontolobridge authentication token
-$ONTOLOBRIDGE_AUTHENTICATION_TOKEN = 'Token Uq2pae73ktMtmgjUgtnhEOuHxr9sZeuK'
-
-# Ontologies for which to enable the new term request (Ontolobridge) tab
-$NEW_TERM_REQUEST_ONTOLOGIES = []
-
 # Legacy REST core service address (BioPortal v3.x and lower)
 $LEGACY_REST_URL = 'http://example.org:8080/bioportal'
 
@@ -341,4 +333,3 @@ if $HOSTNAME
     require_relative "bioportal_config_development_#{$HOSTNAME}"
   end
 end
-
diff --git a/config/locales/en.yml b/config/locales/en.yml
index a63e3500eb..c7785c7416 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -310,40 +310,15 @@ en:
     date_sorted_list_error: The Classes/Concepts didn't define <strong>creation</strong> or <strong>modifications</strong> dates with dcterms
     list_error: The Collection didn't define any member
     close: Close
-    request_terms_instructions: |
-      The text below is displayed to the user as the instructions on how to request new terms for your ontology.
-      You can change this text for %{acronym} ontology by clicking anywhere on the existing text to 
-      bring up the editing dialog.
-      Click 'Submit Changes' to save or 'Cancel' to discard your changes.
     submit_changes: Submit Changes
-    cancel: Cancel
-    request_new_term: Request New Term
     use_jump_to: Use the "Jump To" to find a class and display details, visualization, notes, and mappings
     instances: Instances
     notes: Notes
     details: Details
     visualization: Visualization
     mappings: Mappings
-    new_term_requests: New Term Requests
     permanent_link_class: Get a permanent link to this class
-    request_term:
-      new_term_instructions: |
-        <p>This ontology integrates with OntoloBridge, allowing community users to suggest additions to the public ontology. Complete the template below to submit a term request directly to the Ontology Manager.</p>
-          <blockquote>
-            <p>Term label (required)<br>Suggested term name. If a term can be described with more than one synonym, enter only the preferred name here.</p>
-          </blockquote>
-          <blockquote>
-            <p>Term Description (required)<br>A brief definition, description, or usage of the suggested term. Synonyms of additional terms may be listed in this section.</p>
-          </blockquote>
-          <blockquote>
-            <p>Superclass (required)<br>The parent term of the suggested term. The parent term must be an existing entry in the current ontology. The superclass can be selected directly from the class tree.</p>
-          </blockquote>
-          <blockquote>
-            <p>References (optional)<br>Provide evidence that the requested term exists, such as IDs of articles or links to other resources describing the term.</p>
-          </blockquote>
-          <blockquote>
-            <p>Justification (optional)<br>Provide here any additional information about the requested term.</p>
-          </blockquote>
+
   home:
     bug: Bug
     proposition: Proposition
@@ -974,10 +949,6 @@ en:
       comment: Comment
       save: Save
       cancel: Cancel
-  ontolobridge:
-    problem_of_creating_new_term: "Problem creating a new term %{endpoint}: %{class} - %{message}"
-    new_term_instructions_saved: New term request instructions for %{acronym} saved
-    error_saving_new_term_instructions: Unable to save new term instructions for %{acronym} due to a server error
   submissions:
     filter:
       all_formats: All formats
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index d0969e5795..901311dee8 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -312,40 +312,13 @@ fr:
     date_sorted_list_error: Les Classes/Concepts n'ont pas défini de dates de <strong>création</strong> ou de <strong>modifications</strong> avec dcterms
     list_error: La Collection n'a défini aucun membre
     close: Fermer
-    request_terms_instructions: |
-      Le texte ci-dessous est affiché à l'utilisateur comme les instructions sur la manière de demander de nouveaux termes pour votre ontologie.
-      Vous pouvez changer ce texte pour l'ontologie %{acronym} en cliquant n'importe où sur le texte existant pour
-      ouvrir la boîte de dialogue d'édition.
-      Cliquez sur 'Soumettre les changements' pour sauvegarder ou sur 'Annuler' pour abandonner vos changements.
-    submit_changes: Soumettre les changements
-    cancel: Annuler
-    request_new_term: Demander un nouveau terme
     use_jump_to: Utilisez le "Jump To" pour trouver une classe et afficher les détails, la visualisation, les notes et les mappages
     instances: Instances
     notes: Notes
     details: Détails
     visualization: Visualisation
     mappings: Alignements
-    new_term_requests: Nouvelles demandes de termes
     permanent_link_class: Obtenir un lien permanent vers cette classe
-    request_term:
-      new_term_instructions: |
-        <p>Cette ontologie s'intègre avec OntoloBridge, permettant aux utilisateurs de la communauté de suggérer des ajouts à l'ontologie publique. Complétez le modèle ci-dessous pour soumettre directement une demande de terme au Gestionnaire de l'Ontologie.</p>
-          <blockquote>
-            <p>Libellé du terme (obligatoire)<br>Nom suggéré pour le terme. Si un terme peut être décrit avec plus d'un synonyme, entrez uniquement le nom préféré ici.</p>
-          </blockquote>
-          <blockquote>
-            <p>Description du terme (obligatoire)<br>Une brève définition, description ou utilisation du terme suggéré. Les synonymes d'autres termes peuvent être listés dans cette section.</p>
-          </blockquote>
-          <blockquote>
-            <p>Superclasse (obligatoire)<br>Le terme parent du terme suggéré. Le terme parent doit être une entrée existante dans l'ontologie actuelle. La superclasse peut être sélectionnée directement à partir de l'arbre des classes.</p>
-          </blockquote>
-          <blockquote>
-            <p>Références (optionnel)<br>Fournissez des preuves que le terme demandé existe, telles que des IDs d'articles ou des liens vers d'autres ressources décrivant le terme.</p>
-          </blockquote>
-          <blockquote>
-            <p>Justification (optionnel)<br>Fournissez ici toute information supplémentaire concernant le terme demandé.</p>
-          </blockquote>
 
   home:
     ontoportal_instances: "Autres installations d’OntoPortal"
@@ -993,11 +966,6 @@ fr:
       save: Sauvegarder
       cancel: Annuler
 
-  ontolobridge:
-    problem_of_creating_new_term: "Problème de création d'un nouveau terme %{endpoint} : %{class} - %{message}"
-    new_term_instructions_saved: Instructions de demande de nouveau terme pour %{acronym} enregistrées
-    error_saving_new_term_instructions: Impossible d'enregistrer les nouvelles instructions de terme pour %{acronym} en raison d'une erreur serveur
-
   submissions:
     filter:
       all_formats: Tous les formats
diff --git a/config/routes.rb b/config/routes.rb
index b3760280fb..0a06e89136 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -2,7 +2,7 @@
   match 'cookies', to: 'home#set_cookies', via: [:post, :get]
 
   root to: 'home#index'
-  mount LetterOpenerWeb::Engine, at: "/letter_opener" if Rails.env.development?
+  mount LetterOpenerWeb::Engine, at: '/letter_opener' if Rails.env.development?
 
   get'/tools', to: 'home#tools'
   get 'auth/:provider/callback', to: 'login#create_omniauth'
@@ -21,9 +21,7 @@
   resources :agents, constraints: { id: /.+/ }
   post 'agents/:id', to: 'agents#update', constraints: { id: /.+/ }
 
-  resources :ontolobridge do
-    post :save_new_term_instructions, on: :collection
-  end
+
 
   resources :projects, constraints: { id: /[^\/]+/ }
 
@@ -144,8 +142,8 @@
   get 'statistics/index'
 
   # Error pages
-  match "/404", to: "errors#not_found", via: :all
-  match "/500", to: "errors#internal_server_error", via: :all
+  match '/404', to: 'errors#not_found', via: :all
+  match '/500', to: 'errors#internal_server_error', via: :all
 
   # Robots.txt
   get '/robots.txt' => 'robots#index'
@@ -188,16 +186,16 @@
   get '/ajax/classes/date_sorted_list' => 'concepts#show_date_sorted_list'
   get '/ajax/properties/children' => 'properties#show_children'
   get '/ajax/properties/tree' => 'concepts#property_tree'
-  get 'ajax/schemes/label', to: "schemes#show_label"
-  get 'ajax/collections/label', to: "collections#show_label"
-  get 'ajax/label_xl/label', to: "label_xl#show_label"
-  get 'ajax/label_xl', to: "label_xl#show"
+  get 'ajax/schemes/label', to: 'schemes#show_label'
+  get 'ajax/collections/label', to: 'collections#show_label'
+  get 'ajax/label_xl/label', to: 'label_xl#show_label'
+  get 'ajax/label_xl', to: 'label_xl#show'
   get '/ajax/biomixer' => 'concepts#biomixer'
   get '/ajax/fair_score/html' => 'fair_score#details_html'
   get '/ajax/submission/show_licenses/:id' => 'ontologies#show_licenses'
   get '/ajax/fair_score/json' => 'fair_score#details_json'
-  get '/ajax/ontologies', to: "ontologies#ajax_ontologies"
-  get '/ajax/agents', to: "agents#ajax_agents"
+  get '/ajax/ontologies', to: 'ontologies#ajax_ontologies'
+  get '/ajax/agents', to: 'agents#ajax_agents'
   get '/ajax/images/show' => 'application#show_image_modal'
 
   # User
@@ -214,6 +212,7 @@
 
   # Search
   get 'search', to: 'search#index'
+  get 'search/json_search/:id', to: 'search#json_search'
   get 'ajax/search/ontologies/content', to: 'search#json_ontology_content_search'
 
   get 'check_resolvability' => 'check_resolvability#index'
@@ -222,5 +221,5 @@
   # Install the default route as the lowest priority.
   get '/:controller(/:action(/:id))'
 
-  mount Lookbook::Engine, at: "/lookbook"
+  mount Lookbook::Engine, at: '/lookbook'
 end
diff --git a/db/schema.rb b/db/schema.rb
index 22dc2b318a..ec76487f77 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2020_09_21_120918) do
+ActiveRecord::Schema[7.0].define(version: 2023_11_30_210229) do
   create_table "analytics", id: :integer, charset: "utf8mb4", collation: "utf8mb4_0900_ai_ci", force: :cascade do |t|
     t.string "segment"
     t.string "action"

From ef83f9594a36117a93d6c27ba0b938347cf26c0a Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 7 Nov 2024 23:30:52 +0100
Subject: [PATCH 12/22] Feature: Move metrics section up in homepage and
 Summary page  (#747)

* in home page move metrics up and have news if not enabled

* move metrics section up in the summary page

* Update home statistics layout to improve balance and alignment

---------

Co-authored-by: Bilel KIHAL <kb_kihal@esi.dz>
---
 app/assets/stylesheets/home.scss              |   2 +-
 app/views/home/index.html.haml                | 103 +++++++++---------
 .../ontologies/sections/_metadata.html.haml   |   2 +-
 db/schema.rb                                  |   2 +-
 4 files changed, 54 insertions(+), 55 deletions(-)

diff --git a/app/assets/stylesheets/home.scss b/app/assets/stylesheets/home.scss
index 9965d2bfd5..875138bdd7 100644
--- a/app/assets/stylesheets/home.scss
+++ b/app/assets/stylesheets/home.scss
@@ -222,7 +222,7 @@ i.fa.fa-caret-square-o-down {
 .home-statistics-container > div {
   display: flex;
   align-items: start;
-  justify-content: center;
+  justify-content: flex-start;
   flex-wrap: wrap;
 }
 .home-agroportal-figures{
diff --git a/app/views/home/index.html.haml b/app/views/home/index.html.haml
index 8bc39eba97..b89c46a470 100644
--- a/app/views/home/index.html.haml
+++ b/app/views/home/index.html.haml
@@ -62,6 +62,56 @@
         = upload_ontology_button
       .discover-ontologies
         = discover_ontologies_button
+  .home-section
+    %h4
+      = t('home.agroportal_figures', site: current_slice_name || portal_name)
+    %hr.home-section-line/
+    .home-statistics-container
+      .home-statistics
+        .home-statistics-item
+          %hr/
+          %div
+            %h4
+              = format_number_abbreviated(@metrics[:ontologies_count])
+            %p= t("home.ontologies")
+        .home-statistics-item
+          %hr/
+          %div
+            %h4
+              = format_number_abbreviated(@metrics[:class_count])
+            %p= t("home.classes")
+        .home-statistics-item
+          %hr/
+          %div
+            %h4
+              = format_number_abbreviated(@metrics[:individuals_count])
+            %p= t("home.individuals")
+        .home-statistics-item
+          %hr/
+          %div
+            %h4
+              = format_number_abbreviated(@metrics[:properties_count])
+            %p= t("home.properties")
+        .home-statistics-item
+          %hr/
+          %div
+            %h4
+              = format_number_abbreviated(@metrics[:projects_count])
+            %p= t("home.projects")
+        .home-statistics-item
+          %hr/
+          %div
+            %h4
+              = format_number_abbreviated(@metrics[:mappings_count])
+            %p= t("home.mappings")
+        .home-statistics-item
+          %hr/
+          %div
+            %h4
+              = format_number_abbreviated(@metrics[:users_count])
+            %p= t("home.users")
+      .home-statistics-link.justify-content-end{style: @analytics.empty? && "visibility: hidden"}
+        = link_to t("home.see_details"),'/statistics', target: "_blank"
 
   .home-section
     %h4
@@ -125,57 +175,6 @@
               = render LoaderComponent.new(type: 'pulsing')
           %script{:async => "", :charset => "utf-8", :src => "https://platform.twitter.com/widgets.js"}
 
-  .home-section
-    %h4
-      = t('home.agroportal_figures', site: current_slice_name || portal_name)
-    %hr.home-section-line/
-    .home-statistics-container
-      .home-statistics
-        .home-statistics-item
-          %hr/
-          %div
-            %h4
-              = format_number_abbreviated(@metrics[:ontologies_count])
-            %p= t("home.ontologies")
-        .home-statistics-item
-          %hr/
-          %div
-            %h4
-              = format_number_abbreviated(@metrics[:class_count])
-            %p= t("home.classes")
-        .home-statistics-item
-          %hr/
-          %div
-            %h4
-              = format_number_abbreviated(@metrics[:individuals_count])
-            %p= t("home.individuals")
-        .home-statistics-item
-          %hr/
-          %div
-            %h4
-              = format_number_abbreviated(@metrics[:properties_count])
-            %p= t("home.properties")
-        .home-statistics-item
-          %hr/
-          %div
-            %h4
-              = format_number_abbreviated(@metrics[:projects_count])
-            %p= t("home.projects")
-        .home-statistics-item
-          %hr/
-          %div
-            %h4
-              = format_number_abbreviated(@metrics[:mappings_count])
-            %p= t("home.mappings")
-        .home-statistics-item
-          %hr/
-          %div
-            %h4
-              = format_number_abbreviated(@metrics[:users_count])
-            %p= t("home.users")
-      .home-statistics-link.justify-content-end{style: @analytics.empty? && "visibility: hidden"}
-        = link_to t("home.see_details"),'/statistics', target: "_blank"
-
   - if slices_enabled?
     .home-section
       .home-section-title
@@ -238,4 +237,4 @@
   }
   function submitRecommender(){
   document.getElementById("recommender_submit").click()
-  }
+  }
\ No newline at end of file
diff --git a/app/views/ontologies/sections/_metadata.html.haml b/app/views/ontologies/sections/_metadata.html.haml
index be2083e5cb..2c92a092d4 100755
--- a/app/views/ontologies/sections/_metadata.html.haml
+++ b/app/views/ontologies/sections/_metadata.html.haml
@@ -3,10 +3,10 @@
   .summary-page-center
     .summary-page-first-row
       = render partial: 'ontologies/sections/metadata/ontology_description_section'
+      = render partial: 'ontologies/sections/metadata/ontology_metrics_section'
       = render partial: 'ontologies/sections/metadata/ontology_fairness_section'
       = render partial: 'ontologies/sections/metadata/ontology_relations_network'
       = render partial: 'ontologies/sections/metadata/ontology_submissions_section'
-      = render partial: 'ontologies/sections/metadata/ontology_metrics_section'
     .summary-page-second-row
       = ontology_depiction_card
       = properties_card(t('ontologies.sections.identifiers'),t("ontologies.sections.identifiers"), @identifiers) do |values|
diff --git a/db/schema.rb b/db/schema.rb
index ec76487f77..22dc2b318a 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2023_11_30_210229) do
+ActiveRecord::Schema[7.0].define(version: 2020_09_21_120918) do
   create_table "analytics", id: :integer, charset: "utf8mb4", collation: "utf8mb4_0900_ai_ci", force: :cascade do |t|
     t.string "segment"
     t.string "action"

From 43e4d445d9f1fe04c0a107ce6f1c55569c976c90 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 7 Nov 2024 23:41:16 +0100
Subject: [PATCH 13/22] if analytics not enabled use the metrics to display
 home page visits (#746)

Co-authored-by: Bilel KIHAL <kb_kihal@esi.dz>
---
 app/controllers/home_controller.rb | 14 +++++++++++---
 app/views/home/index.html.haml     | 14 +++++++-------
 config/locales/en.yml              |  1 +
 config/locales/fr.yml              |  1 +
 4 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb
index 2d20328b74..0607d5b059 100644
--- a/app/controllers/home_controller.rb
+++ b/app/controllers/home_controller.rb
@@ -23,11 +23,19 @@ def index
 
     @anal_ont_names = []
     @anal_ont_numbers = []
-    @analytics.sort_by{|ont, count| -count}[0..4].each do |ont, count|
-      @anal_ont_names << ont
-      @anal_ont_numbers << count
+    if @analytics.empty?
+      all_metrics.sort_by{|x| -(x.classes + x.individuals)}[0..4].each do |x|
+        @anal_ont_names << x.links["ontology"].split('/').last
+        @anal_ont_numbers << x.classes + x.individuals
+      end
+    else
+      @analytics.sort_by{|ont, count| -count}[0..4].each do |ont, count|
+        @anal_ont_names << ont
+        @anal_ont_numbers << count
+      end
     end
 
+
   end
 
   def set_cookies
diff --git a/app/views/home/index.html.haml b/app/views/home/index.html.haml
index b89c46a470..43fc5ff02b 100644
--- a/app/views/home/index.html.haml
+++ b/app/views/home/index.html.haml
@@ -22,18 +22,18 @@
     .home-bubble.home-bubble-one
       %a.h5{href:"/ontologies/#{@anal_ont_names[0]}", style: "color: white !important"}
         = @anal_ont_names[0]
-      %p
-        = @anal_ont_numbers[0].to_s + " " + t('visits.visits')
+      %p 
+        = format_number_abbreviated(@anal_ont_numbers[0]) + " " + (@analytics.empty? ?  t('visits.count') :  t('visits.visits'))
     .home-bubble.home-bubble-two
       %a.h5{href:"/ontologies/#{@anal_ont_names[1]}", style: "color: white !important"}
         = @anal_ont_names[1]
-      %p
-        = @anal_ont_numbers[1].to_s + " " + t('visits.visits')
+      %p 
+        = format_number_abbreviated(@anal_ont_numbers[1]) + " " + (@analytics.empty? ?  t('visits.count') :  t('visits.visits'))
     .home-bubble.home-bubble-three
       %a.h5{href:"/ontologies/#{@anal_ont_names[2]}", style: "color: white !important"}
         = @anal_ont_names[2]
-      %p
-        = @anal_ont_numbers[2].to_s + " " + t('visits.visits')
+      %p 
+        = format_number_abbreviated(@anal_ont_numbers[2]) + " " + (@analytics.empty? ?  t('visits.count') :  t('visits.visits'))
     %a.home-bubble.home-bubble-four{:href => "/visits"}
       .h5 ...
 
@@ -47,7 +47,7 @@
 
 .home-body-container
   .home-section
-    %h4= t('home.ontology_upload')
+    %h4= t('home.ontology_upload', site: portal_name)
     %hr.home-section-line/
     %p= t('home.ontology_upload_desc')
     %p= t('home.ontology_upload_benefits', site: $SITE)
diff --git a/config/locales/en.yml b/config/locales/en.yml
index c7785c7416..214e4a403e 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1426,6 +1426,7 @@ en:
     ontology_visits: Ontology visits
     name: name
     visits: visits
+    count: concepts
   ontologies_selector:
     clear_selection: Clear selection
     ontologies_advanced_selection: Ontologies advanced selection
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index 901311dee8..b4bc55eda5 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1456,6 +1456,7 @@ fr:
     ontology_visits: Visites de l'ontologie
     name: nom
     visits: visites
+    count: concepts
 
   ontologies_selector:
     clear_selection: Effacer la sélection

From 10237aa03f57f857f236aec443e371bca809d3c8 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Fri, 8 Nov 2024 12:52:23 +0100
Subject: [PATCH 14/22] Fix: Watch button count and state (#838)

* include all when loading the user, to make sure we get ontologies acronyms in usrer.subscription list

* fix watch button count
---
 app/helpers/application_helper.rb | 3 +--
 app/helpers/ontologies_helper.rb  | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 0da7946e0d..1b57009861 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -175,10 +175,9 @@ def admin_block(ontology: @ontology, user: session[:user], class_css: "admin-bor
   end
 
   def subscribed_to_ontology?(ontology_acronym, user)
-    user = LinkedData::Client::Models::User.find(user.username, {include: 'subscription'}) if user.subscription.nil?
+    user = LinkedData::Client::Models::User.find(user.username, {include: 'all'}) if user.subscription.nil?
     return false if user.subscription.nil? or user.subscription.empty?
     user.subscription.each do |sub|
-      #sub = {ontology: ontology_acronym, notification_type: "NOTES"}
       sub_ont_acronym = sub[:ontology] ?  sub[:ontology].split('/').last : nil #  make sure we get the acronym, even if it's a full URI
       return true if sub_ont_acronym == ontology_acronym
     end
diff --git a/app/helpers/ontologies_helper.rb b/app/helpers/ontologies_helper.rb
index f3a7ae05f7..7f651afc97 100644
--- a/app/helpers/ontologies_helper.rb
+++ b/app/helpers/ontologies_helper.rb
@@ -627,7 +627,7 @@ def ontology_depiction_card
 
   def count_subscriptions(ontology_id)
     ontology_id = ontology_id.split('/').last
-    users = LinkedData::Client::Models::User.all(include: 'subscription', display_context: false, display_links: false)
+    users = LinkedData::Client::Models::User.all(include: 'all', display_context: false, display_links: false)
     users.select { |u| u.subscription.find { |s| s.ontology && s.ontology.split('/').last.eql?(ontology_id) } }.count
   end
 

From ff7e46d75a8f0c9e0d0eb34b435c1d2cb17781d8 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Fri, 8 Nov 2024 12:52:51 +0100
Subject: [PATCH 15/22] Fix: add"*" in agents search query (#837)

---
 app/controllers/agents_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/agents_controller.rb b/app/controllers/agents_controller.rb
index c058eb130f..5c06c79a39 100644
--- a/app/controllers/agents_controller.rb
+++ b/app/controllers/agents_controller.rb
@@ -18,7 +18,7 @@ def show
   end
 
   def ajax_agents
-    filters = { query: params[:query], qf: "identifiers_texts^20 acronym_text^15 name_text^10 email_text^10"}
+    filters = { query: "#{params[:query]}*", qf: "identifiers_texts^20 acronym_text^15 name_text^10 email_text^10"}
     @agents = LinkedData::Client::HTTP.get('/search/agents', filters)
     agents_json = @agents.collection.map do |x|
       {

From f5a6f375766b5988e178e356e1641cbb0ed6f278 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Fri, 8 Nov 2024 14:20:51 +0100
Subject: [PATCH 16/22] Fix: selecting a disabled language (e.g germany) as a
 local language  (#748)

* don't auto select as local language a disabled language (e.g DE)

* enforce resolvability-checks icons to always use portal primary color

* remove enforcing resolvability color
---
 app/assets/stylesheets/ontologies.scss    | 3 ++-
 app/controllers/application_controller.rb | 5 ++++-
 app/controllers/language_controller.rb    | 5 +++--
 app/helpers/components_helper.rb          | 2 +-
 app/helpers/multi_languages_helper.rb     | 4 ++++
 5 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/app/assets/stylesheets/ontologies.scss b/app/assets/stylesheets/ontologies.scss
index ccaf70d314..3b71432d37 100644
--- a/app/assets/stylesheets/ontologies.scss
+++ b/app/assets/stylesheets/ontologies.scss
@@ -2,6 +2,7 @@ $ont-metadata-bg-color: #e2ebf0;
 $widget-table-border-color: #EFEFEF;
 
 
+
 .admin-background{
   a.chip_button_container_clickable{
     color: var(--admin-color) !important;
@@ -314,4 +315,4 @@ $widget-table-border-color: #EFEFEF;
   color: white;
   border-radius: 10px;
   position: relative;
-}
\ No newline at end of file
+}
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 7af57ee341..1a8a3c8278 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -13,7 +13,7 @@
 # Likewise, all the methods added will be available for all controllers.
 
 class ApplicationController < ActionController::Base
-  include InternationalisationHelper
+  include InternationalisationHelper, MultiLanguagesHelper
 
   before_action :set_locale
 
@@ -26,6 +26,9 @@ def set_locale
     I18n.locale = cookies[:locale] || detect_locale
     cookies.permanent[:locale] = I18n.locale if cookies[:locale].nil?
     logger.debug "* Locale set to '#{I18n.locale}'"
+
+    I18n.locale = portal_lang if portal_language_enabled?(I18n.locale)
+
     session[:locale] = I18n.locale
   end
 
diff --git a/app/controllers/language_controller.rb b/app/controllers/language_controller.rb
index 0ccf6b59c5..56c647489a 100644
--- a/app/controllers/language_controller.rb
+++ b/app/controllers/language_controller.rb
@@ -1,11 +1,12 @@
 class LanguageController < ApplicationController
 
+    include MultiLanguagesHelper
     # set locale to the language selected by the user
     def set_locale_language
         language = params[:language].strip.downcase.to_sym
         supported_languages = I18n.available_locales
-
-        if language
+        
+        if language && portal_language_enabled?(language)
             if supported_languages.include?(language)
                  cookies.permanent[:locale] = language
             else
diff --git a/app/helpers/components_helper.rb b/app/helpers/components_helper.rb
index 180ea336e9..b773bce95f 100644
--- a/app/helpers/components_helper.rb
+++ b/app/helpers/components_helper.rb
@@ -107,7 +107,7 @@ def paginated_list_component(id:, results:, next_page_url:, child_url:, child_tu
   end
 
   def resolvability_check_tag(url)
-    content_tag(:span, check_resolvability_container(url), style: 'display: inline-block;', onClick: "window.open('#{check_resolvability_url(url: url)}', '_blank');")
+    content_tag(:span, check_resolvability_container(url),  class: 'resolvability-check',style: 'display: inline-block;', onClick: "window.open('#{check_resolvability_url(url: url)}', '_blank');")
   end
 
   def rounded_button_component(link)
diff --git a/app/helpers/multi_languages_helper.rb b/app/helpers/multi_languages_helper.rb
index 6e127b94e0..ada13053b1 100644
--- a/app/helpers/multi_languages_helper.rb
+++ b/app/helpers/multi_languages_helper.rb
@@ -22,6 +22,10 @@ def portal_languages
     }
   end
 
+  def portal_language_enabled?(lang)
+    portal_languages.reject { |_k, x| x[:disabled] }.keys.include?(lang)
+  end
+
   def portal_language_selector
     languages = portal_languages
     selected_language = portal_lang

From d18de9aa26a8fac8414a01824734df6562f74aed Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Sat, 9 Nov 2024 04:52:54 +0100
Subject: [PATCH 17/22] fix home page bubbles if no analytics enabled tests
 (#844)

---
 app/controllers/home_controller.rb | 5 +++--
 app/helpers/home_helper.rb         | 2 ++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb
index 0607d5b059..068d217b85 100644
--- a/app/controllers/home_controller.rb
+++ b/app/controllers/home_controller.rb
@@ -24,9 +24,10 @@ def index
     @anal_ont_names = []
     @anal_ont_numbers = []
     if @analytics.empty?
+      all_metrics = LinkedData::Client::Models::Metrics.all
       all_metrics.sort_by{|x| -(x.classes + x.individuals)}[0..4].each do |x|
-        @anal_ont_names << x.links["ontology"].split('/').last
-        @anal_ont_numbers << x.classes + x.individuals
+        @anal_ont_names << x.id.split('/')[-4]
+        @anal_ont_numbers << (x.classes + x.individuals) || 0
       end
     else
       @analytics.sort_by{|ont, count| -count}[0..4].each do |ont, count|
diff --git a/app/helpers/home_helper.rb b/app/helpers/home_helper.rb
index 2ddcdc5275..d521b517e1 100644
--- a/app/helpers/home_helper.rb
+++ b/app/helpers/home_helper.rb
@@ -13,6 +13,8 @@ def render_footer_link(options = {})
 
 
   def format_number_abbreviated(number)
+    number = 0 if number.nil?
+
     if number >= 1_000_000
       (number / 1_000_000).to_s + 'M'
     elsif number >= 1_000

From fe4c800fca86c5cc3fe5c0831feb6944ce2f79b3 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Sat, 9 Nov 2024 07:25:26 +0100
Subject: [PATCH 18/22] migrate notes table to use DataTable component fully
 and remove archived filter (#843)

---
 app/assets/javascripts/application.js |  1 -
 app/assets/javascripts/bp_notes.js    | 42 ---------------------------
 app/views/notes/_notes.html.haml      | 15 +---------
 3 files changed, 1 insertion(+), 57 deletions(-)
 delete mode 100644 app/assets/javascripts/bp_notes.js

diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js
index 617e38d373..52e60fbadd 100644
--- a/app/assets/javascripts/application.js
+++ b/app/assets/javascripts/application.js
@@ -12,7 +12,6 @@
 //
 //= require bioportal
 //= require admin/licenses
-//= require bp_notes
 //= require bp_form_complete
 //= require bp_admin
 //= require concepts
diff --git a/app/assets/javascripts/bp_notes.js b/app/assets/javascripts/bp_notes.js
deleted file mode 100644
index 61f9e8f447..0000000000
--- a/app/assets/javascripts/bp_notes.js
+++ /dev/null
@@ -1,42 +0,0 @@
-function hideOrUnhideArchivedOntNotes() {
-  if (jQuery("#hide_archived_ont:checked").val() !== undefined) {
-    // Checked
-    ontNotesTable.fnFilter('false', ont_columns.archived);
-  } else {
-    // Unchecked
-    ontNotesTable.fnFilter('', ont_columns.archived, true, false);
-  }
-}
-
-function wireOntTable(ontNotesTableNew, showTarget= true, enableDelete = false) {
-  jQuery.data(document.body, "ontology_id", "#{@ontology.acronym}");
-
-
-  let ont_columns = { archived: 3, date: 7, subjectSort: 2 };
-  var ontNotesTable = ontNotesTableNew;
-  let columns =  [
-    { "bVisible": enableDelete }, // Delete
-    { "iDataSort": ont_columns.subjectSort }, // Subject link
-    { "bVisible": false }, // Subject for sort
-    { "bVisible": false }, // Archived for filter
-    null, // Author
-    null, // Type
-    null // Created
-  ]
-
-  if(showTarget){
-    columns.push(null) // Target
-  }else {
-    ont_columns.date--
-  }
-
-  ontNotesTable.dataTable({
-    "iDisplayLength": 50,
-    "sPaginationType": "full_numbers",
-    "aaSorting": [[ont_columns.date, 'desc']],
-    "aoColumns": columns,
-  });
-  // Important! Table is somehow getting set to zero width. Reset here.
-  jQuery(ontNotesTable).css("width", "100%");
-  ontNotesTable.fnFilter('false', ont_columns.archived);
-}
diff --git a/app/views/notes/_notes.html.haml b/app/views/notes/_notes.html.haml
index f293e06a2a..84d654e51b 100644
--- a/app/views/notes/_notes.html.haml
+++ b/app/views/notes/_notes.html.haml
@@ -6,16 +6,12 @@
       = add_comment_button(parent_id, parent_type)
     .add_proposal.mx-1
       = add_proposal_button(parent_id, parent_type)
-  %div.ont_notes_filter.my-1.d-flex.justify-content-end.align-items-baseline
-    Filter:
-    %input#hide_archived_ont.mx-1{:checked => "true", :name => "hide_archived_ont", :type => "checkbox"}
-    %label{:for => "hide_archived_ont"}= t('notes.filter_hide_archived')
 
   = render_alerts_container("notes_#{parent_type}_list_table_alerts")
 
   .ont_notes_table_container
     - cols = [ (current_user_admin? ? 'Action' : nil), 'Subject', 'Author', 'Type', (parent_type.eql?('ontology') ? 'Class' : nil),'Created'].compact
-    = render TableComponent.new(id:"#{parent_type}_notes") do |t|
+    = render TableComponent.new(id:"#{parent_type}_notes", searching: true, paging: true, sort_column: @notes.empty? ? nil : (cols.size - 1).to_s, custom_class: 'border rounded p-1') do |t|
       - t.header do |row|
         - row.create(*cols.map{|col| {th: col}})
 
@@ -28,12 +24,3 @@
       - else
         - @notes.each do |note|
           = render partial: 'notes/note_line', locals: {note: note, ontology_acronym: @ontology.acronym, parent_type: parent_type}
-
-:javascript
-  jQuery(".ontologies.show").ready(function(){
-    jQuery("#hide_archived_ont").click(function(){
-      hideOrUnhideArchivedOntNotes();
-    });
-
-    wireOntTable(jQuery("##{notes_table_id}"), #{parent_type.eql?('ontology')}, #{current_user_admin?})
-  });
\ No newline at end of file

From 17ed0b679350fd45b3730d26fb45c69140dc78b8 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Wed, 13 Nov 2024 17:30:31 +0100
Subject: [PATCH 19/22] Fix: Notes buttons showing, some properties details,
 and no collection selection  showing content missing or an error alert (#846)

* enforce add comment and proposal buttons to use turbo top frame

to prevent content missing

* make the notes form use the correct button component

* fix property content missing message

* fix not selecting a collection message error
---
 app/controllers/collections_controller.rb | 25 ++++++++++++++---------
 app/helpers/application_helper.rb         |  4 ++--
 app/helpers/components_helper.rb          |  4 ++--
 app/helpers/ontologies_helper.rb          | 13 +++++++-----
 app/views/concepts/_list.html.haml        |  7 +++++--
 app/views/notes/_new_comment.html.haml    |  2 +-
 app/views/notes/_new_proposal.html.haml   |  2 +-
 7 files changed, 34 insertions(+), 23 deletions(-)

diff --git a/app/controllers/collections_controller.rb b/app/controllers/collections_controller.rb
index fcfda0256d..699eda2698 100644
--- a/app/controllers/collections_controller.rb
+++ b/app/controllers/collections_controller.rb
@@ -57,12 +57,19 @@ def show_label
 
   def show_members
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id] || params[:ontology]).first
-    @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri')
-    @collection = get_request_collection
+    @submission = @ontology.explore.latest_submission(include: 'uriRegexPattern,preferredNamespaceUri')
     page = params[:page] || '1'
     @auto_click = page.to_s.eql?('1')
-    @page = @collection.explore.members({page: page, language: request_lang})
-    @concepts = @page.collection
+    @collection = get_request_collection(@ontology)
+
+    if @collection
+      @page = @collection.explore.members({ page: page, language: request_lang })
+      @concepts = @page.collection
+    else
+      @page = OpenStruct.new({ nextPage: 1, page: 1 })
+      @concepts = []
+    end
+
     if @ontology.nil?
       ontology_not_found params[:ontology]
     else
@@ -72,14 +79,12 @@ def show_members
 
   private
 
-  def get_request_collection
+  def get_request_collection(ontology = nil)
     params[:id] = request_collection_id
 
-    if params[:id].nil? || params[:id].empty?
-      render plain: t('collections.error_valid_collection')
-      return
-    end
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id] || params[:ontology]).first
+    return nil if params[:id].nil? || params[:id].empty?
+
+    @ontology = ontology || LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id] || params[:ontology]).first
     ontology_not_found(params[:ontology_id]) if @ontology.nil?
     get_collection(@ontology, params[:id])
   end
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 1b57009861..c41d1734f3 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -129,7 +129,7 @@ def at_slice?
 
   def add_comment_button(parent_id, parent_type)
     if session[:user].nil?
-      link_to t('application.add_comment'),  login_index_path(redirect: request.url), class: "secondary-button regular-button slim"
+      link_to t('application.add_comment'),  login_index_path(redirect: request.url), class: "secondary-button regular-button slim", data: {'turbo-frame': '_top'}
     else
       link_to_modal t('application.add_comment'), notes_new_comment_path(parent_id: parent_id, parent_type: parent_type, ontology_id: @ontology.acronym),
                     class: "secondary-button regular-button slim", data: { show_modal_title_value: t('application.add_new_comment')}
@@ -146,7 +146,7 @@ def add_reply_button(parent_id)
 
   def add_proposal_button(parent_id, parent_type)
     if session[:user].nil?
-      link_to t('application.add_proposal'),  login_index_path(redirect: request.url), class: "secondary-button regular-button slim"
+      link_to t('application.add_proposal'),  login_index_path(redirect: request.url), class: "secondary-button regular-button slim",  data: {'turbo-frame': '_top'}
     else
       link_to_modal t('application.add_proposal'), notes_new_proposal_path(parent_id: parent_id, parent_type: parent_type, ontology_id: @ontology.acronym),
                     class: "secondary-button regular-button slim", data: { show_modal_title_value: t('application.add_new_proposal')}
diff --git a/app/helpers/components_helper.rb b/app/helpers/components_helper.rb
index b773bce95f..8c04a869df 100644
--- a/app/helpers/components_helper.rb
+++ b/app/helpers/components_helper.rb
@@ -280,8 +280,8 @@ def regular_button(id, value, variant: "secondary", state: "regular", size: "sli
     end
   end
 
-  def form_save_button
-    render Buttons::RegularButtonComponent.new(id: 'save-button', value: t('components.save_button'), variant: "primary", size: "slim", type: "submit") do |btn|
+  def form_save_button(enable_loading: true)
+    render Buttons::RegularButtonComponent.new(id: 'save-button', value: t('components.save_button'), variant: "primary", size: "slim", type: "submit", state: enable_loading ? 'animate' : '') do |btn|
       btn.icon_left do
         inline_svg_tag "check.svg"
       end
diff --git a/app/helpers/ontologies_helper.rb b/app/helpers/ontologies_helper.rb
index 7f651afc97..bc840b6c35 100644
--- a/app/helpers/ontologies_helper.rb
+++ b/app/helpers/ontologies_helper.rb
@@ -529,12 +529,15 @@ def render_concepts_json_button(link)
 
   def ontology_object_details_component(frame_id: , ontology_id:, objects_title:, object:, &block)
     render TurboFrameComponent.new(id: frame_id, data: {"turbo-frame-target": "frame"}) do
-      return if !object.present?
-      return alert_component(object.errors.join) if object.errors
+      return unless object.present?
 
-      ontology_object_tabs_component(ontology_id: ontology_id, objects_title: objects_title, object_id: object["@id"]) do |tabs|
-        tab_item_component(container_tabs: tabs, title: t('concepts.details'), path: '#details', selected: true) do
-          capture(&block)
+      if object.errors
+        alert_component(object.errors.join)
+      else
+        ontology_object_tabs_component(ontology_id: ontology_id, objects_title: objects_title, object_id: object["@id"]) do |tabs|
+          tab_item_component(container_tabs: tabs, title: t('concepts.details'), path: '#details', selected: true) do
+            capture(&block)
+          end
         end
       end
     end
diff --git a/app/views/concepts/_list.html.haml b/app/views/concepts/_list.html.haml
index 9c9a28a848..45d56b6f41 100644
--- a/app/views/concepts/_list.html.haml
+++ b/app/views/concepts/_list.html.haml
@@ -10,6 +10,9 @@
       = render TreeLinkComponent.new(child: concept, href: href,
           children_href: '#', selected: concept.id.eql?(concepts.first.id) && c.auto_click?,
           target_frame: 'concept_show', data: data, is_reused: concept_reused?(submission: @submission, concept_id: concept.id))
-  - c.error do
-    = t('concepts.list_error')
 
+  - c.error do
+    - if @collection.nil?
+      = t("ontologies.concepts_browsers.select_collection")
+    - else
+      = t('concepts.list_error')
diff --git a/app/views/notes/_new_comment.html.haml b/app/views/notes/_new_comment.html.haml
index 6cd8474203..94ce3fcd92 100644
--- a/app/views/notes/_new_comment.html.haml
+++ b/app/views/notes/_new_comment.html.haml
@@ -11,4 +11,4 @@
       %div.form-group
         %textarea.form-control.reply_body{cols: "1", name: "body", required: true, placeholder: t('notes.new_comment.comment'), rows: "1", style: "height: 100px;", tabindex: "0"}
 
-      = submit_tag t('notes.new_comment.save') , class:'btn btn-success btn-block'
+      = form_save_button(enable_loading: false)
diff --git a/app/views/notes/_new_proposal.html.haml b/app/views/notes/_new_proposal.html.haml
index 649d83407c..77666a4442 100644
--- a/app/views/notes/_new_proposal.html.haml
+++ b/app/views/notes/_new_proposal.html.haml
@@ -50,4 +50,4 @@
       .form-group
         = text_field_tag 'proposal[parent]','', placeholder: t('notes.new_proposal.parent'), class: "form-control", required: true
 
-    = submit_tag t('notes.new_proposal.save') , class:'btn btn-success btn-block'
\ No newline at end of file
+    = form_save_button(enable_loading: false)

From dc2bb130f453f98abf06c3bd9b51864a0036f6fe Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 14 Nov 2024 11:35:58 +0100
Subject: [PATCH 20/22] Fix: notes and zombie mappings class label fetching and
 optimize concept mapping table API calls (#842)

* fix label ajax for no more existent ontologies

* use label fetched for classes in the notes table

* optimize the calls done for the concept mapping table

* fix home page bubbles if no analytics enabled
---
 app/controllers/concepts_controller.rb |  8 ++++++--
 app/helpers/mappings_helper.rb         | 14 ++++----------
 app/views/notes/_note_line.html.haml   |  2 +-
 3 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/app/controllers/concepts_controller.rb b/app/controllers/concepts_controller.rb
index c52bbcf884..3d4923296f 100644
--- a/app/controllers/concepts_controller.rb
+++ b/app/controllers/concepts_controller.rb
@@ -63,8 +63,12 @@ def index
   def show_label
     cls_id = params[:concept] || params[:id]
     ont_id = params[:ontology]
-    pref_label = concept_label(ont_id, cls_id)
-    cls = @ontology.explore.single_class({ language: request_lang, include: 'prefLabel' }, cls_id)
+    pref_label = begin
+                   concept_label(ont_id, cls_id)
+                 rescue
+                   cls_id
+                 end
+    cls = @ontology.explore&.single_class({ language: request_lang, include: 'prefLabel' }, cls_id)
     label = helpers.main_language_label(pref_label)
     link = concept_path(cls_id, ont_id, request_lang)
 
diff --git a/app/helpers/mappings_helper.rb b/app/helpers/mappings_helper.rb
index 09b2c4d67e..129b1e4bf8 100644
--- a/app/helpers/mappings_helper.rb
+++ b/app/helpers/mappings_helper.rb
@@ -20,24 +20,18 @@ def mapping_links(mapping, concept)
     process = mapping.process || {}
 
     if inter_portal_mapping?(target_concept)
-      cls_link = ajax_to_inter_portal_cls(target_concept)
+      cls_link = target_concept.id
       ont_name = target_concept.links['ontology']
       ont_link = link_to ont_name, get_inter_portal_ui_link(ont_name, process['name']), target: '_blank'
       source_tooltip = 'Internal-portal'
     elsif internal_mapping?(target_concept)
-      begin
-        ont = target_concept.explore.ontology
-        ont_name = ont.acronym
-        ont_link = link_to ont_name, ontology_path(ont_name), 'data-turbo-frame': '_top'
-      rescue
-        ont_name = target_concept.links['ontology'] || target_concept.id
-        ont_link = ont_name
-      end
+      ont_name = target_concept.links['ontology'].split('/').last
+      ont_link = link_to ont_name, ontology_path(ont_name), 'data-turbo-frame': '_top'
       cls_link = raw(get_link_for_cls_ajax(target_concept.id, ont_name, '_top'))
       source_tooltip = 'Internal'
     else
       cls_label = ExternalLinkTextComponent.new(text: target_concept.links['self']).call
-      cls_link = raw("<a href='#{target_concept.links["self"]}' target='_blank'>#{cls_label}</a>")
+      cls_link = raw("<a href='#{target_concept.links['self']}' target='_blank'>#{cls_label}</a>")
       ont_name = target_concept.links['ontology']
       ont_link = link_to ExternalLinkTextComponent.new(text: ont_name).call, target_concept.links['ontology'],
                          target: '_blank'
diff --git a/app/views/notes/_note_line.html.haml b/app/views/notes/_note_line.html.haml
index ac29099511..6a12aff5f4 100644
--- a/app/views/notes/_note_line.html.haml
+++ b/app/views/notes/_note_line.html.haml
@@ -21,6 +21,6 @@
   - if parent_type.eql?('ontology')
     - row.td do
       - if note.relatedClass && note.relatedClass.length > 0
-        %a{href: "/ontologies/#{ontology_acronym}?p=classes&conceptid=#{CGI.escape(note.relatedClass.first)}", 'data-turbo': 'false'}= note.relatedClass.first
+        = get_link_for_cls_ajax(note.relatedClass.first, ontology_acronym, '_top')
   - row.td do
     = DateTime.parse(note.created).strftime("%Y-%m-%d")
\ No newline at end of file

From a0211c5f22e78117e44f79c4752e8759f2f471e1 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Mon, 18 Nov 2024 10:18:19 +0100
Subject: [PATCH 21/22] add a star for the required fields in the upload form
 (#852)

---
 app/helpers/submission_inputs_helper.rb       | 21 ++++++++++++-------
 .../_submission_location_form.html.haml       |  2 +-
 app/views/ontologies/new.html.haml            |  2 +-
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/app/helpers/submission_inputs_helper.rb b/app/helpers/submission_inputs_helper.rb
index 06ecee5b39..2636fdc68e 100644
--- a/app/helpers/submission_inputs_helper.rb
+++ b/app/helpers/submission_inputs_helper.rb
@@ -108,12 +108,12 @@ def attribute_input(attr_key, long_text: false, label: nil, show_tooltip: true,
 
   end
 
-  def ontology_name_input(ontology = @ontology)
-    text_input(name: 'ontology[name]', value: ontology.name)
+  def ontology_name_input(ontology = @ontology, label: 'Name')
+    text_input(name: 'ontology[name]', value: ontology.name, label: label_required(label))
   end
 
-  def ontology_acronym_input(ontology = @ontology, update: @is_update_ontology)
-    out = text_input(name: 'ontology[acronym]', value: ontology.acronym, disabled: update)
+  def ontology_acronym_input(ontology = @ontology, update: @is_update_ontology, label: 'Acronym')
+    out = text_input(name: 'ontology[acronym]', value: ontology.acronym, disabled: update, label: label_required(label))
     out += hidden_field_tag('ontology[acronym]', ontology.acronym) if update
     out
   end
@@ -123,7 +123,7 @@ def ontology_administered_by_input(ontology = @ontology, users_list = @user_sele
       users_list = LinkedData::Client::Models::User.all(include: "username").map { |u| [u.username, u.id] }
       users_list.sort! { |a, b| a[1].downcase <=> b[1].downcase }
     end
-    select_input(label: t('submission_inputs.administrators'), name: "ontology[administeredBy]", values: users_list, selected: ontology.administeredBy || session[:user].id, multiple: true)
+    select_input(label: label_required(t('submission_inputs.administrators')), name: "ontology[administeredBy]", values: users_list, selected: ontology.administeredBy || session[:user].id, multiple: true)
   end
 
   def ontology_categories_input(ontology = @ontology, categories = @categories)
@@ -213,7 +213,7 @@ def ontology_visibility_input(ontology = @ontology)
 
     render(Layout::RevealComponent.new(possible_values: %w[private public], selected: ontology.viewingRestriction)) do |c|
       c.button do
-        select_input(label: t('submission_inputs.visibility'), name: "ontology[viewingRestriction]", required: true,
+        select_input(label: label_required(t('submission_inputs.visibility')), name: "ontology[viewingRestriction]", required: true,
                      values: %w[public private],
                      selected: ontology.viewingRestriction)
       end
@@ -248,7 +248,7 @@ def contact_input(label: '', name: t('submission_inputs.contact'), show_help: tr
 
       render NestedFormInputsComponent.new(object_name: 'contact', default_empty_row: true) do |c|
         c.header do
-          content_tag(:div, name.blank? ? '' : t('submission_inputs.contact_name', name: name), class: 'w-50') + content_tag(:div, name.blank? ? '' : t('submission_inputs.contact_email', name: name), class: 'w-50')
+          content_tag(:div, name.blank? ? '' : label_required(t('submission_inputs.contact_name', name: name)), class: 'w-50') + content_tag(:div, name.blank? ? '' : label_required(t('submission_inputs.contact_email', name: name)), class: 'w-50')
         end
 
         c.template do
@@ -531,4 +531,11 @@ def attribute_help_text(attr)
       help_text
     end
   end
+
+  def label_required(label)
+    content_tag(:div) do
+      label.html_safe +
+      content_tag(:span, '*', style: 'color: var(--error-color);')
+    end
+  end
 end
diff --git a/app/views/ontologies/_submission_location_form.html.haml b/app/views/ontologies/_submission_location_form.html.haml
index f26f07009d..201c2eae8d 100644
--- a/app/views/ontologies/_submission_location_form.html.haml
+++ b/app/views/ontologies/_submission_location_form.html.haml
@@ -1,4 +1,4 @@
-= render Input::InputFieldComponent.new(label: t("ontologies.location"), name: '') do
+= render Input::InputFieldComponent.new(label: label_required(t("ontologies.location")), name: '') do
   .location-choice
     %input{type: "radio", name: "submission[isRemote]", value: "3", checked: summary_only?, id: "metadata_only", onchange: "displayMetadataOnlyForm()"}
     %label.title{for: "metadata_only"}
diff --git a/app/views/ontologies/new.html.haml b/app/views/ontologies/new.html.haml
index 67a9163866..281ae26167 100644
--- a/app/views/ontologies/new.html.haml
+++ b/app/views/ontologies/new.html.haml
@@ -39,7 +39,7 @@
                         .upload-ontology-field-container
                           - @submission.valid = nil unless @submission.status&.eql?('retired')
                           = attribute_input("valid")
-                  .upload-ontology-field-container
+                  .upload-ontology-field-container.mt-3
                     = render partial: 'ontologies/submission_location_form'
 
                 - c.page do

From f5dbf31c2f712f6fd2f26ee152e16606d8a13293 Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Mon, 18 Nov 2024 16:53:29 +0100
Subject: [PATCH 22/22] Fix: Improve taxonomy page, fix static portal name,
 detect description link (#850)

* detect if the taxonomy description is a link and handle that

* make portal name dynamic in taxonomy page description

* retouch taxonomy page description

* use link? helper in taxonomy card component instead of creating another one
---
 app/assets/stylesheets/taxonomy.scss               | 13 ++++++++++++-
 app/components/display/taxonomy_card_component.rb  |  1 +
 .../taxonomy_card_component.html.haml              | 14 ++++++++++++--
 app/views/taxonomy/index.html.haml                 |  2 +-
 config/locales/en.yml                              |  2 +-
 config/locales/fr.yml                              |  2 +-
 6 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/app/assets/stylesheets/taxonomy.scss b/app/assets/stylesheets/taxonomy.scss
index 6043973aa8..bf5c679ff5 100644
--- a/app/assets/stylesheets/taxonomy.scss
+++ b/app/assets/stylesheets/taxonomy.scss
@@ -63,7 +63,18 @@
 }
 .taxonomy-card .description{
     color: #666666;
-    padding-bottom: 5px;
+}
+
+.taxonomy-card .descriptionlink svg{
+    margin: 0px 2px;
+    height: 19px;
+}
+
+.taxonomy-card .descriptionlink svg path{
+    fill: #666666;
+}
+.category-link{
+    color: #666666 !important;
 }
 .taxonomy-slice-svg{
     width: 35px;
diff --git a/app/components/display/taxonomy_card_component.rb b/app/components/display/taxonomy_card_component.rb
index df896191b6..89b05bcb69 100644
--- a/app/components/display/taxonomy_card_component.rb
+++ b/app/components/display/taxonomy_card_component.rb
@@ -1,4 +1,5 @@
 class Display::TaxonomyCardComponent < ViewComponent::Base
+  include UrlsHelper
   def initialize(taxonomy: , ontologies_names: )
     @taxonomy = taxonomy
     @ontologies_names = ontologies_names
diff --git a/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml b/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml
index ab55aa41de..218eaca749 100644
--- a/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml
+++ b/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml
@@ -4,12 +4,22 @@
       = "#{@taxonomy.name} (#{@taxonomy.acronym})"
     %a{href: "https://#{@taxonomy.acronym}.#{$UI_URL.sub("https://", "")}"}
       = inline_svg_tag('icons/slices.svg', class: "taxonomy-slice-svg #{@taxonomy.is_slice ? '' : 'd-none'}")
+  
+  - if link?(@taxonomy.description)
+    .descriptionlink
+      %a.category-link{href: @taxonomy.description, target: '_blank'}
+        = @taxonomy.description
+        = inline_svg_tag 'icons/external-link.svg'
+  
   %a.ontologies{href: "/ontologies?#{@taxonomy.id.split('/')[-2]}=#{@taxonomy.acronym}"}
     = inline_svg_tag('icons/ontology.svg')
     .number-of-ontologies
       = "#{@taxonomy.ontologies.length} ontologies"
-  .description
-    = render TextAreaFieldComponent.new(value: @taxonomy.description)
+
+  - unless link?(@taxonomy.description)
+    .description.mb-1
+      = render TextAreaFieldComponent.new(value: @taxonomy.description)
+
   .ontologies-cards
     - @taxonomy.ontologies.each_with_index do |ontology, index|
       - if index>10
diff --git a/app/views/taxonomy/index.html.haml b/app/views/taxonomy/index.html.haml
index 967f63d330..b9b2b3a105 100644
--- a/app/views/taxonomy/index.html.haml
+++ b/app/views/taxonomy/index.html.haml
@@ -5,7 +5,7 @@
                 = t('taxonomy.groups_and_categories')
             .line
         .taxonomy-page-decription
-            = t('taxonomy.description')
+            = t('taxonomy.description', portal: portal_name)
 
         = render TabsContainerComponent.new do |c|
             - c.item(title: 'Groups', selected: !@category_section_active)
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 214e4a403e..5269b506bf 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1478,7 +1478,7 @@ en:
     privacy_policy_anchor: "#h-privacy-policy"
   taxonomy:
     groups_and_categories: Groups and Categories
-    description: In AgroPortal, ontologies are organized in groups and tagged with categories. Typically, groups associate ontologies from the same project or organization for better identification of the provenance. Whereas categories are about subjects/topics and enable to classify ontologies. As of 2016, AgroPortal's categories were established in cooperation with FAO AIMS. In 2024, we moved to UNESCO nomenclature for fields of science and technology. Groups and categories, along with other metadata, can be used on the “Browse” page of AgroPortal to filter out the list of ontologies.
+    description: "In %{portal}, ontologies are organized in groups and tagged with categories. Typically, groups associate ontologies from the same project or organization for better identification of the provenance. Whereas categories are about subjects/topics and enable to classify ontologies. As of 2016, %{portal}'s categories were established in cooperation with FAO AIMS. In 2024, we moved to UNESCO Thesaurus (https://vocabularies.unesco.org). Groups and categories, along with other metadata, can be used on the “Browse” page of %{portal} to filter out the list of ontologies."
     show_sub_categories: Show sub categories
 
   federation:
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index b4bc55eda5..dc47247020 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1514,7 +1514,7 @@ fr:
     privacy_policy_anchor: "#h-vie-privee"
   taxonomy:
     groups_and_categories: Groupes et Catégories
-    description: Dans AgroPortal, les ontologies sont organisées en groupes et étiquetées avec des catégories. Typiquement, les groupes associent des ontologies provenant du même projet ou de la même organisation pour une meilleure identification de la provenance. Tandis que les catégories concernent des sujets/thématiques et permettent de classifier les ontologies. En 2016, les catégories d'AgroPortal ont été établies en coopération avec FAO AIMS. En 2024, nous sommes passés à la nomenclature de l'UNESCO pour les domaines des sciences et des technologies. Les groupes et les catégories, ainsi que d'autres métadonnées, peuvent être utilisés sur la page “Parcourir” d'AgroPortal pour filtrer la liste des ontologies.
+    description: "Dans %{portal}, les ontologies sont organisées en groupes et étiquetées avec des catégories. Typiquement, les groupes associent des ontologies provenant du même projet ou de la même organisation pour une meilleure identification de la provenance. Tandis que les catégories concernent des sujets/thématiques et permettent de classifier les ontologies. En 2016, les catégories d'%{portal} ont été établies en coopération avec FAO AIMS. En 2024, nous sommes passés au Thésaurus de l'UNESCO (https://vocabularies.unesco.org). Les groupes et les catégories, ainsi que d'autres métadonnées, peuvent être utilisés sur la page “Parcourir” d'%{portal} pour filtrer la liste des ontologies."
     show_sub_categories: Afficher les sous-catégories
   federation:
     results_from_external_portals: Résultats provenant de portails externes