From 6e87b96f34c66e106c77d5adb86d7692372a2b32 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 01:09:08 +0200
Subject: [PATCH 01/72] simplify the header component to use content instead of
 a new section

---
 app/components/display/header_component.rb       |  4 ++--
 app/views/home/tools.html.haml                   | 11 +++++++++++
 .../ontologies/sections/_metadata.html.haml      | 16 +++++++---------
 3 files changed, 20 insertions(+), 11 deletions(-)
 create mode 100644 app/views/home/tools.html.haml

diff --git a/app/components/display/header_component.rb b/app/components/display/header_component.rb
index b814f55fc1..4542410196 100644
--- a/app/components/display/header_component.rb
+++ b/app/components/display/header_component.rb
@@ -2,7 +2,7 @@
 
 class Display::HeaderComponent < ViewComponent::Base
 
-  renders_one :text
+
 
   def initialize(text: nil, tooltip: nil)
     super
@@ -12,7 +12,7 @@ def initialize(text: nil, tooltip: nil)
 
   def call
     content_tag(:div, class: 'header-component') do
-      out = content_tag(:p, text || @text)
+      out = content_tag(:p, content&.html_safe || @text)
       if @info && !@info.empty?
         out = out + render(Display::InfoTooltipComponent.new(text: @info))
       end
diff --git a/app/views/home/tools.html.haml b/app/views/home/tools.html.haml
new file mode 100644
index 0000000000..d4f0455b69
--- /dev/null
+++ b/app/views/home/tools.html.haml
@@ -0,0 +1,11 @@
+%div.d-flex.px-5.py-3.rounded.tools-container
+  - @tools.each_value do |tool|
+    = link_to tool[:link], class: "mx-2 d-block", style: "width: 35%" do
+      = render Layout::CardComponent.new do |c|
+        - c.header do |h|
+          %div.d-flex.flex-column.align-items-center.text-primary.pt-4
+            =  inline_svg_tag(tool[:icon], height: "50px", width: "50px")
+            %h3.text-primary.mt-2
+              = tool[:title]
+        %p.px-4.tool-description
+          = tool[:description]
diff --git a/app/views/ontologies/sections/_metadata.html.haml b/app/views/ontologies/sections/_metadata.html.haml
index 3f84c40cf3..c037d11151 100755
--- a/app/views/ontologies/sections/_metadata.html.haml
+++ b/app/views/ontologies/sections/_metadata.html.haml
@@ -21,7 +21,7 @@
       = properties_dropdown('person_and_organization',t("ontologies.sections.person_and_organization"),'', @agents_properties) do |values|
         = horizontal_list_container(values) do |v|
           = agent_chip_component(v)
-            
+
       = properties_dropdown('link',t("ontologies.sections.other_links"), t("ontologies.sections.info_tooltip_links") , @links_properties) do |values|
         = horizontal_list_container(values) do |v|
           = render LinkFieldComponent.new(value: v, raw: true)
@@ -50,11 +50,10 @@
             = Array(@content_properties['metadataVoc']).map{|x| metadata_vocabulary_display(x)}.join.html_safe
       = render Layout::CardComponent.new do |c|
         - c.header do  |h|
-          - h.text do
-            = t("ontologies.sections.visits")
-            - if visits_data(@ontology)
-              = link_to(@ontology.links["analytics"] + "?apikey=#{get_apikey}&format=csv", title: t("ontologies.sections.download_as_csv")) do
-                = inline_svg("summary/download.svg", width: '30px', height: '20px')
+          = t("ontologies.sections.visits")
+          - if visits_data(@ontology)
+            = link_to(@ontology.links["analytics"] + "?apikey=#{get_apikey}&format=csv", title: t("ontologies.sections.download_as_csv")) do
+              = inline_svg("summary/download.svg", width: '30px', height: '20px')
 
         = render Layout::ListComponent.new do |l|
           - l.row do
@@ -63,9 +62,8 @@
       - unless @ontology.view?
         = render Layout::CardComponent.new do |d|
           - d.header do |h|
-            - h.text do
-              = t("ontologies.sections.views", acronym: @ontology.acronym)
-              = new_element_link(t("ontologies.sections.create_new_view"), new_view_path(@ontology.id))
+            = t("ontologies.sections.views", acronym: @ontology.acronym)
+            = new_element_link(t("ontologies.sections.create_new_view"), new_view_path(@ontology.id))
           = render Layout::ListComponent.new do |l|
             - l.row do
               = render partial: 'ontology_views'

From f3870cda9c0f07230eafcb5ec5126ded37419c0b Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 01:11:20 +0200
Subject: [PATCH 02/72] update dropdown  component to a custom title section
 instead of  text

---
 app/components/dropdown_container_component.rb               | 5 ++++-
 .../dropdown_container_component.html.haml                   | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/app/components/dropdown_container_component.rb b/app/components/dropdown_container_component.rb
index e06b3fa7ac..f9d8ce38d2 100644
--- a/app/components/dropdown_container_component.rb
+++ b/app/components/dropdown_container_component.rb
@@ -2,13 +2,16 @@
 
 class DropdownContainerComponent < ViewComponent::Base
   renders_one :empty_state
-  def initialize(title:, id:, tooltip:nil, is_open: false)
+  renders_one :title
+
+  def initialize(title: nil, id:, tooltip:nil, is_open: false)
     super
     @title = title
     @id = id
     @tooltip = tooltip
     @is_open = is_open
   end
+  
   def open_class
     @is_open ? "show" : ""
   end
diff --git a/app/components/dropdown_container_component/dropdown_container_component.html.haml b/app/components/dropdown_container_component/dropdown_container_component.html.haml
index 7b9d4965e8..398f3199a0 100644
--- a/app/components/dropdown_container_component/dropdown_container_component.html.haml
+++ b/app/components/dropdown_container_component/dropdown_container_component.html.haml
@@ -1,6 +1,9 @@
 .dropdown-container
   .dropdown-title-bar{"data-toggle" => "collapse", "data-target" => "##{@id}"}
-    = render Display::HeaderComponent.new(text: @title, tooltip: @tooltip)
+    - if title?
+      = title
+    - else
+      = render Display::HeaderComponent.new(text: @title, tooltip: @tooltip)
     = image_tag("summary/arrow-down.svg", class: 'ml-2')
 
   .collapse{id: @id, class: open_class}

From b21d74bed3544dee898b9809a0474062f6ff55f8 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 01:20:41 +0200
Subject: [PATCH 03/72] update browse page to use Dropdown component not
 bootsrap one

---
 app/views/ontologies/browser/browse.html.haml | 23 ++++++++++---------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
index cc2f9c982b..63c23ec429 100644
--- a/app/views/ontologies/browser/browse.html.haml
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -50,21 +50,22 @@
 
             - @filters.each do |key, values|
               - if session[:user]&.admin? ||  key != :missingStatus
-                .browse-filter{data:{controller: "show-filter-count browse-filters", action: "change->show-filter-count#updateCount change->browse-filters#dispatchFilterEvent"}, id: "#{key}_filter_container", style: "#{"border-color: var(--admin-color);" if key == :missingStatus}"}
-                  .browse-filter-title-bar{"data-target" => "#browse-#{key}-filter", "data-toggle" => "collapse"}
-                    %p
-                      = browse_filter_section_label(key)
-                      %span.badge.badge-primary{"data-show-filter-count-target":"countSpan", style: "#{values[2] && values[2].positive? ? '' : 'display: none;'}"}
-                        = values[2]
-                    = inline_svg_tag 'arrow-down.svg'
-                  .collapse{id: "browse-#{key}-filter", class: "#{values[2].positive? ? 'show': ''}"}
-                    .browse-filter-checks-container
+                %div{data:{controller: "show-filter-count browse-filters", action: "change->show-filter-count#updateCount change->browse-filters#dispatchFilterEvent"}, id: "#{key}_filter_container"}
+                  = render DropdownContainerComponent.new(id: "browse-#{key}-filter", is_open: values[2].positive?) do |d|
+                    - d.title do
+                      = render Display::HeaderComponent.new do
+                        %span
+                          = browse_filter_section_label(key)
+                        %span.badge.badge-primary{"data-show-filter-count-target":"countSpan", style: "#{values[2] && values[2].positive? ? '' : 'display: none;'}"}
+                          = values[2]
+
+                    .browse-filter-checks-container.px-1
                       - values.first.each do |object|
                         - title = (key.eql?(:categories) || key.eql?(:groups)) ? nil : ''
-                        = group_chip_component(name: key, object: object, checked: values[1]&.include?(object["id"]), title: title) do |c|
+                        = group_chip_component(name: key, object: object, checked: [link_last_part(object["id"]),link_last_part(object["value"])].include?(values[1]) , title: title) do |c|
                           - c.count do
                             %span.badge.badge-light.ml-1
-                              = turbo_frame_tag "count_#{key}_#{object["id"]}", busy: true
+                              = turbo_frame_tag "count_#{key}_#{link_last_part(object["id"])}", busy: true
                               %span.show-if-loading
                                 = render LoaderComponent.new(small:true)
 

From a4759c89676b19a903d532e920afb415728036fc Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 01:21:01 +0200
Subject: [PATCH 04/72] add color option to square badge component

---
 app/components/square_badge_component.rb | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/components/square_badge_component.rb b/app/components/square_badge_component.rb
index 9d85a8c34f..bfbc95c6db 100644
--- a/app/components/square_badge_component.rb
+++ b/app/components/square_badge_component.rb
@@ -2,15 +2,17 @@
 
 class SquareBadgeComponent < ViewComponent::Base
 
-  def initialize(label: , count: ,link: nil)
+  def initialize(label: , count: ,link: nil, color: nil)
     @label = label
     @count = count
     @link = link
+    @color = color
   end
+
   def call
     return  if @count.to_i.zero?
 
-    link_to(@link, class: 'browse-onology-card', 'data-turbo' => 'false') do
+    link_to(@link, class: 'browse-onology-card', 'data-turbo' => 'false', style: @color ? "color: #{@color} !important; border-color: #{@color}" : "") do
       concat(content_tag(:p, @count, class: 'browse-card-number'))
       concat(content_tag(:p, @label, class: 'browse-card-text'))
     end

From 273331232d61c999923427ef2df239669b31d854 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 03:29:09 +0200
Subject: [PATCH 05/72] add text and bg  colors options to ontology browse card
 component

---
 .../ontology_browse_card_component.rb         | 32 +++++++++++++-
 .../ontology_browse_card_component.html.haml  | 42 +++++++++++++------
 2 files changed, 60 insertions(+), 14 deletions(-)

diff --git a/app/components/ontology_browse_card_component.rb b/app/components/ontology_browse_card_component.rb
index 84251d7f0d..78fd781195 100644
--- a/app/components/ontology_browse_card_component.rb
+++ b/app/components/ontology_browse_card_component.rb
@@ -3,12 +3,42 @@
 class OntologyBrowseCardComponent < ViewComponent::Base
   include OntologiesHelper
 
-  def initialize(ontology: nil)
+  def initialize(ontology: nil, onto_link: nil, text_color: nil, bg_light_color: nil, portal_name: nil)
     super
     @ontology = ontology
+    @text_color = text_color
+    @bg_light_color =  bg_light_color
+    @onto_link = onto_link || "/ontologies/#{@ontology[:acronym]}" if @ontology
+    @portal_name = portal_name
   end
 
   def ontology
     @ontology
   end
+
+  def external_ontology?
+    !@portal_name.blank?
+  end
+
+  def external_portal_name
+    @portal_name
+  end
+
+  def onto_link
+    @onto_link
+  end
+
+  def style_text
+    external_ontology? ? "color: #{@text_color} !important" : ''
+  end
+
+  def portal_color
+    @text_color
+  end
+  alias :color :portal_color
+
+  def style_bg
+    external_ontology? ?  "#{style_text} ; background-color: #{@bg_light_color}" : ''
+  end
+
 end
diff --git a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
index 61daf0e9cb..e82e177c84 100644
--- a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
+++ b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
@@ -3,9 +3,11 @@
     .d-flex
       .browse-ontology-description
         .browse-ontology-title-bar
-          %a.browse-ontology-title{:href => "/ontologies/#{ontology[:acronym]}", data: {'turbo': 'false'}}
+          %a.browse-ontology-title{:href => onto_link, data: {'turbo': 'false'} , style: style_text}
             = ontology[:name]+" ("+ontology[:acronym]+")"
             = private_ontology_icon(ontology[:private])
+            - if external_ontology?
+              = render Display::InfoTooltipComponent.new(text: "Federated ontology from #{onto_link}", icon: 'external-link.svg')
             - if session[:user]&.admin?
               - ontology_status = status_string(ontology)
               = render Display::InfoTooltipComponent.new(text: ontology_status, icon: submission_status_icons(ontology_status))
@@ -21,27 +23,32 @@
               %p.browse-fair-title
                 = t('components.fair_score')
               .browse-progress-bar
-                .browse-faire-progress{:style => "width: #{ontology[:normalizedFairScore].to_s+"%"}"}
+                .browse-faire-progress{:style => "width: #{ontology[:normalizedFairScore].to_s+"%"}; #{color ? 'background-color:' + color : ''}"}
               %p.browse-fair-score
                 = ontology[:fairScore]
-              %a.browse-fair-details{:href => "/ontologies/#{ontology[:acronym]}#fair-details", 'data-turbo': 'false'}= t('components.details_details')
+              %a.browse-fair-details{:href => "#{onto_link}#fair-details", 'data-turbo': 'false', style: style_text}= t('components.details_details')
 
-      .browse-ontology-cards
-        = render SquareBadgeComponent.new(label: t('components.classes'),  count: ontology[:class_count_formatted], link:  "/ontologies/#{ontology[:acronym]}?p=classes" )
+      .browse-ontology-cards{style: color ? "color: #{color} !important" : ''}
+        = render SquareBadgeComponent.new(label: t('components.classes'),
+                                          count: ontology[:class_count_formatted],
+                                          link:  "#{onto_link}?p=classes",
+                                          color: color)
 
         = render SquareBadgeComponent.new(label: ontology[:format] == 'SKOS' ? t('components.concepts') : t('components.instances'),
-                                                   count: ontology[:individual_count_formatted],
-                                                  link:  "/ontologies/#{ontology[:acronym]}?p=#{ontology[:format] == 'SKOS' ? "classes" : "instances"}")
+                                                   count: ontology[:individual_count_formatted], color: color,
+                                                  link:  "#{onto_link}?p=#{ontology[:format] == 'SKOS' ? "classes" : "instances"}")
 
-        = render SquareBadgeComponent.new(label: t('components.projects'),  count: ontology[:project_count], link:  "/ontologies/#{ontology[:acronym]}#projects_section" )
+        = render SquareBadgeComponent.new(label: t('components.projects'),  count: ontology[:project_count], color: color,
+                                          link:  "#{onto_link}#projects_section" )
 
-        = render SquareBadgeComponent.new(label: t('components.notes'),  count: ontology[:note_count], link: "/ontologies/#{ontology[:acronym]}?p=notes" )
+        = render SquareBadgeComponent.new(label: t('components.notes'),  count: ontology[:note_count], color: color,
+                                          link: "#{onto_link}?p=notes" )
 
 
     .d-flex.align-items-baseline.mt-1
       - if ontology[:creationDate]
         %span.mr-1
-          = render ChipButtonComponent.new(type: "clickable") do
+          = render ChipButtonComponent.new(type: "clickable", style: style_bg) do
             %span.mr-1= t('components.submitted')
             %span.browse-uploaded-date{data:{controller: 'timeago', 'timeago-datetime-value': ontology[:creationDate], 'timeago-add-suffix-value': 'true'}}
             - if ontology[:contact]
@@ -52,19 +59,28 @@
       - if ontology[:released]
         - date = render DateTimeFieldComponent.new(value: ontology[:released])
         %span{data:{controller:'tooltip'}, title: t('components.creation_date', date: date)}
-          = render ChipButtonComponent.new(type: "clickable") do
+          = render ChipButtonComponent.new(type: "clickable", style: style_bg) do
             = DateTime.parse(date).year rescue date
 
       - if ontology[:format]
         %span.mx-1
-          = render ChipButtonComponent.new(type: "clickable") do
+          = render ChipButtonComponent.new(type: "clickable", style: style_bg) do
             = ontology[:format]
       - if ontology_retired?(ontology)
         %span.mx-1
           = ontology_retired_badge(ontology)
       - if ontology[:viewOfOnt]
         %span.mx-1{data:{controller:'tooltip'}, title: t('components.view_of_the_ontology', ontology: ontology[:viewOfOnt].split('/').last )}
-          = render ChipButtonComponent.new(type: "clickable", text: t('components.view'))
+          = render ChipButtonComponent.new(type: "clickable", text: t('components.view'), style: style_bg)
+
+      - if external_ontology?
+        %div.mx-1{title: content_tag(:div, "Source #{external_portal_name}"), data:{controller: 'tooltip', 'tooltip-interactive-value': 'true'}}
+          = render ChipButtonComponent.new(type: "clickable" , style: style_bg) do
+            %span.d-inline
+              %span.mr-1
+                = inline_svg 'logo-white.svg', width: "20", height: "20"
+              %span
+                = external_portal_name
 
       - if session[:user]&.admin?
         %div.mx-1{title: content_tag(:div, debug(ontology), style: 'height: 300px; overflow: scroll'), data:{controller: 'tooltip', 'tooltip-interactive-value': 'true'}}

From cc6c288e49b9be17bbbe8035fb35d4fad3e776d9 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 03:30:16 +0200
Subject: [PATCH 06/72] add federation helper code and config sample

---
 Gemfile                                      |   2 +-
 Gemfile.lock                                 | 145 +++++++++----------
 app/controllers/application_controller.rb    |   5 +-
 app/controllers/ontologies_controller.rb     |   5 +
 app/helpers/federation_helper.rb             |  84 +++++++++++
 config/bioportal_config_env.rb.sample        |  51 ++++++-
 config/initializers/ontologies_api_client.rb |   1 +
 7 files changed, 213 insertions(+), 80 deletions(-)
 create mode 100644 app/helpers/federation_helper.rb

diff --git a/Gemfile b/Gemfile
index 00fb43225b..67125fd61e 100644
--- a/Gemfile
+++ b/Gemfile
@@ -73,7 +73,7 @@ gem 'turnout'
 gem 'will_paginate', '~> 3.0'
 gem 'inline_svg'
 gem "lookbook", '~> 1.5.5'
-gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'development'
+gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'feature/federate-multiple-apis'
 gem "flag-icons-rails", "~> 3.4"
 gem "iso-639", "~> 0.3.6"
 
diff --git a/Gemfile.lock b/Gemfile.lock
index c66c92aa87..5b3b140032 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,10 +1,10 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 674193220f93d99587e6d3a969adcb384caf0a61
-  branch: development
+  revision: 7664229920b93ca163f1ee96b21e49d1323f843c
+  branch: feature/federate-multiple-apis
   specs:
     ontologies_api_client (2.2.0)
-      activesupport
+      activesupport (~> 7.0.4)
       excon
       faraday
       faraday-excon (~> 2.0.0)
@@ -12,6 +12,8 @@ GIT
       lz4-ruby
       multi_json
       oj
+      parallel
+      request_store
       spawnling (= 2.1.5)
 
 GEM
@@ -85,21 +87,14 @@ GEM
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     aes_key_wrap (1.1.0)
-    airbrussh (1.5.1)
+    airbrussh (1.5.2)
       sshkit (>= 1.6.1, != 1.7.0)
     ast (2.4.2)
     autoprefixer-rails (10.4.16.0)
       execjs (~> 2)
     base64 (0.2.0)
     bcrypt_pbkdf (1.1.0)
-    better_html (2.0.2)
-      actionview (>= 6.0)
-      activesupport (>= 6.0)
-      ast (~> 2.0)
-      erubi (~> 1.4)
-      parser (>= 2.4)
-      smart_properties
-    bigdecimal (3.1.6)
+    bigdecimal (3.1.8)
     bindata (2.5.0)
     bindex (0.8.1)
     bootsnap (1.18.3)
@@ -109,10 +104,10 @@ GEM
       popper_js (>= 1.14.3, < 2)
       sassc-rails (>= 2.0.0)
     brakeman (5.4.1)
-    bugsnag (6.26.3)
+    bugsnag (6.26.4)
       concurrent-ruby (~> 1.0)
     builder (3.2.4)
-    capistrano (3.18.0)
+    capistrano (3.18.1)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -139,16 +134,17 @@ GEM
       xpath (~> 3.2)
     chart-js-rails (0.1.7)
       railties (> 3.1)
+    childprocess (5.0.0)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
     crass (1.0.6)
-    css_parser (1.16.0)
+    css_parser (1.17.1)
       addressable
     cube-ruby (0.0.3)
     daemons (1.4.1)
     dalli (3.2.8)
     date (3.3.4)
-    debug (1.9.1)
+    debug (1.9.2)
       irb (~> 1.10)
       reline (>= 0.3.8)
     deepl-rb (2.5.3)
@@ -159,7 +155,7 @@ GEM
     erubi (1.12.0)
     erubis (2.7.0)
     eventmachine (1.2.7)
-    excon (0.109.0)
+    excon (0.110.0)
     execjs (2.9.1)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
@@ -178,9 +174,9 @@ GEM
     flamegraph (0.9.5)
     globalid (1.2.1)
       activesupport (>= 6.1)
-    graphql (2.2.10)
+    graphql (2.3.2)
       base64
-    graphql-client (0.20.0)
+    graphql-client (0.22.0)
       activesupport (>= 3.0)
       graphql (>= 1.13.0)
     haml (5.2.2)
@@ -203,7 +199,7 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
-    i18n (1.14.1)
+    i18n (1.14.5)
       concurrent-ruby (~> 1.0)
     i18n-tasks (1.0.13)
       activesupport (>= 4.0.2)
@@ -225,39 +221,40 @@ GEM
       activesupport (>= 3.0)
       nokogiri (>= 1.6)
     io-console (0.7.2)
-    irb (1.11.2)
-      rdoc
+    irb (1.13.1)
+      rdoc (>= 4.0.0)
       reline (>= 0.4.2)
     iso-639 (0.3.6)
     jquery-rails (4.6.0)
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
-    jquery-ui-rails (6.0.1)
+    jquery-ui-rails (7.0.0)
       railties (>= 3.2.16)
     jsbundling-rails (1.3.0)
       railties (>= 6.0.0)
-    json (2.7.1)
-    json-jwt (1.16.5)
+    json (2.7.2)
+    json-jwt (1.16.6)
       activesupport (>= 4.2)
       aes_key_wrap
       base64
       bindata
       faraday (~> 2.0)
       faraday-follow_redirects
-    jwt (2.8.0)
+    jwt (2.8.1)
       base64
     language_server-protocol (3.17.0.3)
-    launchy (2.5.2)
+    launchy (3.0.1)
       addressable (~> 2.8)
-    letter_opener (1.9.0)
-      launchy (>= 2.2, < 3)
+      childprocess (~> 5.0)
+    letter_opener (1.10.0)
+      launchy (>= 2.2, < 4)
     letter_opener_web (2.0.0)
       actionmailer (>= 5.2)
       letter_opener (~> 1.7)
       railties (>= 5.2)
       rexml
-    listen (3.8.0)
+    listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     loofah (2.22.0)
@@ -282,18 +279,18 @@ GEM
       net-imap
       net-pop
       net-smtp
-    marcel (1.0.2)
+    marcel (1.0.4)
     matrix (0.4.2)
-    method_source (1.0.0)
+    method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0206)
+    mime-types-data (3.2024.0507)
     mini_mime (1.1.5)
-    minitest (5.22.2)
+    minitest (5.22.3)
     msgpack (1.7.2)
     multi_json (1.15.0)
     multi_xml (0.6.0)
-    multipart-post (2.4.0)
+    multipart-post (2.4.1)
     mutex_m (0.2.0)
     mysql2 (0.5.6)
     net-ftp (0.2.1)
@@ -301,7 +298,7 @@ GEM
       time
     net-http (0.3.2)
       uri
-    net-imap (0.4.10)
+    net-imap (0.4.11)
       date
       net-protocol
     net-pop (0.1.2)
@@ -312,15 +309,13 @@ GEM
       net-ssh (>= 2.6.5, < 8.0.0)
     net-sftp (4.0.0)
       net-ssh (>= 5.0.0, < 8.0.0)
-    net-smtp (0.4.0.1)
+    net-smtp (0.5.0)
       net-protocol
-    net-ssh (7.2.1)
+    net-ssh (7.2.3)
     netrc (0.11.0)
-    newrelic_rpm (9.7.1)
-    nio4r (2.7.0)
-    nokogiri (1.15.5-x86_64-darwin)
-      racc (~> 1.4)
-    nokogiri (1.15.5-x86_64-linux)
+    newrelic_rpm (9.9.0)
+    nio4r (2.7.3)
+    nokogiri (1.15.6-x86_64-linux)
       racc (~> 1.4)
     oauth2 (2.0.9)
       faraday (>= 0.17.3, < 3.0)
@@ -338,11 +333,11 @@ GEM
     omniauth-github (2.0.1)
       omniauth (~> 2.0)
       omniauth-oauth2 (~> 1.8)
-    omniauth-google-oauth2 (1.1.1)
+    omniauth-google-oauth2 (1.1.2)
       jwt (>= 2.0)
-      oauth2 (~> 2.0.6)
+      oauth2 (~> 2.0)
       omniauth (~> 2.0)
-      omniauth-oauth2 (~> 1.8.0)
+      omniauth-oauth2 (~> 1.8)
     omniauth-keycloak (1.5.2)
       faraday
       json-jwt (> 1.13.0)
@@ -359,7 +354,7 @@ GEM
       omniauth (~> 2.0)
     open_uri_redirections (0.2.1)
     parallel (1.24.0)
-    parser (3.3.0.5)
+    parser (3.3.1.0)
       ast (~> 2.4.1)
       racc
     popper_js (1.16.1)
@@ -367,11 +362,11 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     psych (3.3.4)
-    public_suffix (5.0.4)
+    public_suffix (5.0.5)
     puma (5.6.8)
       nio4r (~> 2.0)
     racc (1.7.3)
-    rack (2.2.8.1)
+    rack (2.2.9)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-mini-profiler (3.3.1)
@@ -402,7 +397,7 @@ GEM
     rails-html-sanitizer (1.6.0)
       loofah (~> 2.21)
       nokogiri (~> 1.14)
-    rails-i18n (7.0.8)
+    rails-i18n (7.0.9)
       i18n (>= 0.7, < 2)
       railties (>= 6.0.0, < 8)
     rails_autolink (1.1.8)
@@ -417,42 +412,44 @@ GEM
       thor (~> 1.0)
       zeitwerk (~> 2.5)
     rainbow (3.1.1)
-    rake (13.1.0)
+    rake (13.2.1)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rdoc (6.3.3)
+    rdoc (6.3.4.1)
     recaptcha (5.9.0)
       json
     redcarpet (3.6.0)
     regexp_parser (2.9.0)
-    reline (0.4.2)
+    reline (0.5.5)
       io-console (~> 0.5)
+    request_store (1.7.0)
+      rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     rexml (3.2.6)
-    rouge (4.2.0)
+    rouge (4.2.1)
     rspec-core (3.13.0)
       rspec-support (~> 3.13.0)
     rspec-expectations (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-mocks (3.13.0)
+    rspec-mocks (3.13.1)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-rails (6.1.1)
+    rspec-rails (6.1.2)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       railties (>= 6.1)
-      rspec-core (~> 3.12)
-      rspec-expectations (~> 3.12)
-      rspec-mocks (~> 3.12)
-      rspec-support (~> 3.12)
-    rspec-support (3.13.0)
-    rubocop (1.60.2)
+      rspec-core (~> 3.13)
+      rspec-expectations (~> 3.13)
+      rspec-mocks (~> 3.13)
+      rspec-support (~> 3.13)
+    rspec-support (3.13.1)
+    rubocop (1.63.4)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -460,11 +457,11 @@ GEM
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.30.0, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.30.0)
-      parser (>= 3.2.1.0)
+    rubocop-ast (1.31.3)
+      parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
     ruby_dig (0.0.2)
@@ -508,7 +505,8 @@ GEM
       actionpack (>= 5.2)
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
-    sshkit (1.22.0)
+    sshkit (1.22.2)
+      base64
       mutex_m
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
@@ -519,18 +517,18 @@ GEM
     temple (0.10.3)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
-    terser (1.2.0)
+    terser (1.2.2)
       execjs (>= 0.3.0, < 3)
     thin (1.8.2)
       daemons (~> 1.0, >= 1.0.9)
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
-    thor (1.3.0)
+    thor (1.3.1)
     tilt (2.3.0)
     time (0.3.0)
       date
     timeout (0.4.1)
-    turbo-rails (2.0.4)
+    turbo-rails (2.0.5)
       actionpack (>= 6.0.0)
       activejob (>= 6.0.0)
       railties (>= 6.0.0)
@@ -543,7 +541,7 @@ GEM
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.5.0)
     uri (0.13.0)
-    version_gem (1.1.3)
+    version_gem (1.1.4)
     view_component (2.83.0)
       activesupport (>= 5.2.0, < 8.0)
       concurrent-ruby (~> 1.0)
@@ -560,12 +558,11 @@ GEM
     will_paginate (3.3.1)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    yard (0.9.34)
+    yard (0.9.36)
     zeitwerk (2.6.13)
 
 PLATFORMS
-  x86_64-darwin-23
-  x86_64-linux
+  x86_64-linux-musl
 
 DEPENDENCIES
   bcrypt_pbkdf (>= 1.0, < 2.0)
@@ -647,4 +644,4 @@ DEPENDENCIES
   will_paginate (~> 3.0)
 
 BUNDLED WITH
-   2.3.23
+   2.4.22
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 964be01714..4aa6d0e7b9 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -124,7 +124,7 @@ def domain_ontology_set
       subdomain = host_parts[0].downcase
 
       slices = LinkedData::Client::Models::Slice.all
-      slices_acronyms = slices.map {|s| s.acronym}
+      slices_acronyms = slices.map {|s| s.acronym} rescue binding.pry
 
       # Set custom ontologies if we're on a subdomain that has them
       # Else, make sure user ontologies are set appropriately
@@ -205,6 +205,9 @@ def rest_url
     "#{protocol}://#{cleaned_path}"
   end
 
+  def request_portals
+    helpers.request_portals
+  end
 
   def check_http_file(url)
     session = Net::HTTP.new(url.host, url.port)
diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb
index 07f1ad9a32..e8f27b3a78 100644
--- a/app/controllers/ontologies_controller.rb
+++ b/app/controllers/ontologies_controller.rb
@@ -23,6 +23,8 @@ class OntologiesController < ApplicationController
 
   before_action :authorize_and_redirect, :only => [:edit, :update, :create, :new]
   before_action :submission_metadata, only: [:show]
+  before_action :set_federated_portals, only: [:index, :ontologies_filter]
+
   KNOWN_PAGES = Set.new(["terms", "classes", "mappings", "notes", "widgets", "summary", "properties", "instances", "schemes", "collections", "sparql"])
   EXTERNAL_MAPPINGS_GRAPH = "http://data.bioontology.org/metadata/ExternalMappings"
   INTERPORTAL_MAPPINGS_GRAPH = "http://data.bioontology.org/metadata/InterportalMappings"
@@ -561,4 +563,7 @@ def determine_layout
     end
   end
 
+  def set_federated_portals
+    RequestStore.store[:federated_portals] =  params[:portals]&.split(',')
+  end
 end
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
new file mode 100644
index 0000000000..0539a40028
--- /dev/null
+++ b/app/helpers/federation_helper.rb
@@ -0,0 +1,84 @@
+module FederationHelper
+
+  def federated_portals
+    $FEDERATED_PORTALS
+  end
+
+  def federated_portal_config(name_key)
+    $FEDERATED_PORTALS[name_key.to_sym]
+  end
+
+  def federated_portal_name(key)
+    config = federated_portal_config(key)
+    config ? config[:name] : key
+  end
+
+  def federated_portal_color(key)
+    config = federated_portal_config(key)
+    config[:color] if config
+  end
+
+  def federated_portal_light_color(key)
+    config = federated_portal_config(key)
+    config[:'light-color'] if config
+  end
+
+
+  def ontology_portal_config(id)
+    rest_url = id.split('/')[0..-3].join('/')
+    $FEDERATED_PORTALS.select{|_, config| config[:api].start_with?(rest_url)}.first
+  end
+
+  def ontology_portal_name(id)
+    portal_key, _ =  ontology_portal_config(id)
+    portal_key ? federated_portal_name(portal_key) : 'not found'
+  end
+
+
+  def ontology_portal_color(id)
+    portal_key, _ =  ontology_portal_config(id)
+    federated_portal_color(portal_key) if portal_key
+  end
+
+
+  def ontoportal_ui_link(id)
+    portal_key, config =  ontology_portal_config(id)
+    return id  unless portal_key
+
+    ui_link = config[:ui]
+    api_link = config[:api]
+
+    id.gsub(api_link, "#{ui_link}/") rescue id
+  end
+
+  def internal_ontology?(id)
+    id.start_with?(helpers.rest_url)
+  end
+
+  def federated_ontology?(id)
+    !internal_ontology?(id)
+  end
+
+  def request_portals
+    portals = RequestStore.store[:federated_portals] || []
+    [portal_name] + portals
+  end
+
+  def request_portals_names
+    request_portals.map do |x|
+      config = federated_portal_config(x)
+
+      if config
+        name = config[:name]
+        color = config[:color]
+      elsif portal_name.downcase.eql?(x.downcase)
+        name = portal_name
+        color = nil
+      else
+        next nil
+      end
+
+      content_tag(:span, federated_portal_name(name), style: color ? "color: #{color}" :  "", class: color ? "" : "text-primary")
+    end.compact
+  end
+end
diff --git a/config/bioportal_config_env.rb.sample b/config/bioportal_config_env.rb.sample
index cb1ae1ccf2..c95bbd6f84 100644
--- a/config/bioportal_config_env.rb.sample
+++ b/config/bioportal_config_env.rb.sample
@@ -28,10 +28,53 @@ $NCBO_API_KEY = ENV['NCBO_API_KEY']
 # Fairness Assessment.
 $FAIRNESS_DISABLED = ENV['FAIRNESS_DISABLED']
 $FAIRNESS_URL = ENV['FAIRNESS_URL']
-# Announcements sympa mailing list REQUEST address, EX: list-request@lists.example.org
-$ANNOUNCE_LIST_SERVICE ||= 'SERVICE_EXAMPLE'
-$ANNOUNCE_SERVICE_HOST ||= 'service@test.com'
-$ANNOUNCE_LIST ||= 'users-list@test'
+
+
+# Federation configuration
+$FEDERATED_PORTALS = {
+  bioportal: {
+    name: "BioPortal",
+    api: 'https://data.bioontology.org/',
+    ui: 'https://bioportal.bioontology.org/',
+    apikey: '8b5b7825-538d-40e0-9e9e-5ab9274a9aeb',
+    color: '#234979',
+    'light-color': '#E9F2FA',
+  },
+  agroportal: {
+    name: "AgroPortal",
+    api: 'https://data.agroportal.lirmm.fr',
+    ui: 'https://agroportal.lirmm.fr',
+    apikey: '1de0a270-29c5-4dda-b043-7c3580628cd5',
+    color: '#349696',
+    'light-color': '#F1F6FA',
+  },
+  ecoportal: {
+    name: "EcoPortal",
+    api: 'https://data.ecoportal.lifewatch.eu/',
+    ui: 'https://ecoportal.lifewatch.eu',
+    apikey: "43a437ba-a437-4bf0-affd-ab520e584719",
+    color: '#2076C9',
+    'light-color': '#E9F2FA',
+  },
+  # earthportal: {
+  #   name: 'EarthPortal',
+  #   api: 'https://earthportal.eu:8443/',
+  #   ui: 'https://earthportal.eu',
+  #   apikey: "c9147279-954f-41bd-b068-da9b0c441288",
+  #   color: '#404696',
+  #   'light-color': '#404696'
+  # },
+  biodivportal: {
+    name: "BioDivPortal",
+    api: 'https://data.biodivportal.gfbio.org/',
+    ui: 'https://biodivportal.gfbio.org/',
+    apikey: "47a57aa3-7b54-4f34-b695-dbb5f5b7363e",
+    color: '#349696',
+    'light-color': '#EBF5F5',
+  }
+}
+
+
 # Used to define other bioportal that can be mapped to
 # Example to map to ncbo bioportal : {"ncbo" => {"api" => "http://data.bioontology.org", "ui" => "http://bioportal.bioontology.org", "apikey" => ""}
 # Then create the mapping using the following class in JSON : "http://purl.bioontology.org/ontology/MESH/C585345": "ncbo:MESH"
diff --git a/config/initializers/ontologies_api_client.rb b/config/initializers/ontologies_api_client.rb
index ca8f07e9eb..fb2d6f94f2 100644
--- a/config/initializers/ontologies_api_client.rb
+++ b/config/initializers/ontologies_api_client.rb
@@ -7,4 +7,5 @@
   config.debug_client = $DEBUG_RUBY_CLIENT || false
   config.debug_client_keys = $DEBUG_RUBY_CLIENT_KEYS || []
   config.apikey = $API_KEY
+  config.federated_portals = $FEDERATED_PORTALS
 end

From 8a8bb8e16c173571f794a0fe01626e0c0e73123e Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 03:31:13 +0200
Subject: [PATCH 07/72] add portals filters in the browse page

---
 app/views/ontologies/browser/browse.html.haml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
index 63c23ec429..e02125f724 100644
--- a/app/views/ontologies/browser/browse.html.haml
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -68,6 +68,11 @@
                               = turbo_frame_tag "count_#{key}_#{link_last_part(object["id"])}", busy: true
                               %span.show-if-loading
                                 = render LoaderComponent.new(small:true)
+          %div{data:{controller: "show-filter-count browse-filters", action: "change->show-filter-count#updateCount change->browse-filters#dispatchFilterEvent"}, id: "portals_filter_container"}
+            = render DropdownContainerComponent.new(id: "browse-portal-filter", is_open: !request_portals.empty?, title: "Results from external portals") do
+              .browse-filter-checks-container.px-1
+                - federated_portals.each do |key, config|
+                  = group_chip_component(name: "portals", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
 
         .browse-second-row
           .browse-search-bar

From 382582b470564fe1e6d4a7444f0ad64785943c31 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 03:32:25 +0200
Subject: [PATCH 08/72] use federation helpers to get federation ontologies
 information

---
 app/helpers/federation_helper.rb                   |  2 +-
 app/views/ontologies/browser/_ontologies.html.haml | 13 ++++++++++++-
 config/locales/en.yml                              |  2 +-
 config/locales/fr.yml                              |  2 +-
 4 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 0539a40028..10d13ec79c 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -43,7 +43,7 @@ def ontology_portal_color(id)
 
   def ontoportal_ui_link(id)
     portal_key, config =  ontology_portal_config(id)
-    return id  unless portal_key
+    return nil  unless portal_key
 
     ui_link = config[:ui]
     api_link = config[:api]
diff --git a/app/views/ontologies/browser/_ontologies.html.haml b/app/views/ontologies/browser/_ontologies.html.haml
index 3e4d3c130f..fec4643834 100644
--- a/app/views/ontologies/browser/_ontologies.html.haml
+++ b/app/views/ontologies/browser/_ontologies.html.haml
@@ -2,9 +2,20 @@
                                     collection: @ontologies,
                                     next_url: ontologies_filter_url(@filters, page: @page.nextPage),
                                     current_page: @page.page, next_page: @page.nextPage) do |c|
+
+  - if @page.page.eql?(1)
+    = content_tag(:p, class: "browse-desc-text", style: "margin-bottom: 12px !important;") do
+      #{t("ontologies.showing_ontologies_size", ontologies_size: @count, analytics_size: @total_ontologies, portals: request_portals_names.join(', ').html_safe).html_safe} (#{sprintf("%.2f", @time)}s)
+
   - ontologies = c.collection
   - ontologies.each do |ontology|
-    = render OntologyBrowseCardComponent.new(ontology: ontology)
+    - config = ontology_portal_config(ontology[:id])&.last || {}
+
+    = render OntologyBrowseCardComponent.new(ontology: ontology,
+                                             portal_name: config[:name],
+                                             onto_link: ontoportal_ui_link(ontology[:id]),
+                                             text_color: config[:color],
+                                             bg_light_color: config[:'light-color'])
   - c.loader do
     - ontologies_browse_skeleton
   - c.error do
diff --git a/config/locales/en.yml b/config/locales/en.yml
index f437410abb..c03a46fda6 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1092,7 +1092,7 @@ en:
     update_the_current_displayed_content: "will update the current displayed content to all the following submissions:"
     save: Save
   ontologies:
-    showing_ontologies_size: "Showing %{ontologies_size} of %{analytics_size}"
+    showing_ontologies_size: "Showing %{ontologies_size} of %{analytics_size} from %{portals}"
     filters: Filters
     no_license: No license
     view_license: View license
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index 7dbd4254c5..1f9c6e9a74 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1118,7 +1118,7 @@ fr:
     save: Sauvegarder
 
   ontologies:
-    showing_ontologies_size: "Affichage de %{ontologies_size} sur %{analytics_size}"
+    showing_ontologies_size: "Affichage de %{ontologies_size} sur %{analytics_size} de %{portals}"
     filters: Filtres
     no_license: Pas de licence
     view_license: Voir la licence

From 6ab2e86430708e558aa236bb98dd808707e13d45 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 03:33:49 +0200
Subject: [PATCH 09/72] remove the filter using index code from submission
 filter as no used

---
 app/controllers/concerns/submission_filter.rb | 104 ++++++++++++++++--
 1 file changed, 94 insertions(+), 10 deletions(-)

diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index 6cda414068..001634886e 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -28,16 +28,28 @@ def submissions_paginate_filter(params)
     @fair_scores = fairness_service_enabled? ? get_fair_score('all') : nil
     submissions = submissions.reject { |sub| sub.ontology.nil? }.map { |sub| ontology_hash(sub) }
 
-    if @selected_sort_by.eql?('visits')
-      submissions = submissions.sort_by { |x| -x[:popularity] }
-    elsif @selected_sort_by.eql?('fair')
-      submissions = submissions.sort_by { |x| -x[:fairScore] }
-    elsif @selected_sort_by.eql?('notes')
-      submissions = submissions.sort_by { |x| -x[:note_count] }
-    elsif @selected_sort_by.eql?('projects')
-      submissions = submissions.sort_by { |x| -x[:project_count] }
-    end
-    submissions
+    @total_ontologies = @ontologies.size
+
+    params = { query: @search,
+               status: request_params[:status],
+               show_views: @show_views,
+               private_only: @show_private_only,
+               languages: request_params[:naturalLanguage],
+               page_size: @total_ontologies,
+               formality_level: request_params[:hasFormalityLevel],
+               is_of_type: request_params[:isOfType],
+               groups: request_params[:group], categories: request_params[:hasDomain],
+               formats: request_params[:hasOntologyLanguage] }
+
+    submissions = filter_using_data(@ontologies, **params)
+
+    submissions = sort_submission_by(submissions, @sort_by, @search)
+
+    @page = paginate_submissions(submissions, request_params[:page].to_i, request_params[:pagesize].to_i)
+
+    count = @page.page.eql?(1) ? count_objects(submissions) : {}
+
+    [@page.collection, @page.totalCount, count, filter_params]
   end
 
   def ontologies_filter_url(filters, page: 1, count: false)
@@ -46,6 +58,78 @@ def ontologies_filter_url(filters, page: 1, count: false)
 
   private
 
+  def filter_using_data(ontologies, query:, status:, show_views:, private_only:, languages:, page_size:, formality_level:, is_of_type:, groups:, categories:, formats:)
+    submissions = LinkedData::Client::Models::OntologySubmission.all(include: BROWSE_ATTRIBUTES.join(','), also_include_views: true, display_links: false, display_context: false)
+    submissions = ontologies.map { |ont| ontology_hash(ont, submissions) }
+
+    submissions.map do |s|
+      out = ((s.ontology.viewingRestriction.eql?('public') && !private_only) || private_only && s.ontology.viewingRestriction.eql?('private'))
+      out = out && (groups.blank? || (s.ontology.group.map { |x| helpers.link_last_part(x) } & groups.split(',')).any?)
+      out = out && (categories.blank? || (s.ontology.hasDomain.map { |x| helpers.link_last_part(x) } & categories.split(',')).any?)
+      out = out && (status.blank? || status.eql?('alpha,beta,production,retired') || status.split(',').include?(s.status))
+      out = out && (formats.blank? || formats.split(',').any? { |f| s.hasOntologyLanguage.eql?(f) })
+      out = out && (is_of_type.blank? || is_of_type.split(',').any? { |f| helpers.link_last_part(s.isOfType).eql?(f) })
+      out = out && (formality_level.blank? || formality_level.split(',').any? { |f| helpers.link_last_part(s.hasFormalityLevel).eql?(f) })
+      out = out && (languages.blank? || languages.split(',').any? { |f| s.naturalLanguage.any? { |n| helpers.link_last_part(n).eql?(f) } })
+      out = out && (s.ontology.viewOf.blank? || (show_views && !s.ontology.viewOf.blank?))
+
+      out = out && (query.blank? || [s.description, s.ontology.name, s.ontology.acronym].any? { |x| (x|| '').downcase.include?(query.downcase) })
+
+      if out
+        s[:rank] = 0
+
+        next s if query.blank?
+
+        s[:rank] += 3 if s.ontology.acronym && s.ontology.acronym.downcase.include?(query.downcase)
+
+        s[:rank] += 2 if s.ontology.name && s.ontology.name.downcase.include?(query.downcase)
+
+        s[:rank] += 1 if s.description && s.description.downcase.include?(query.downcase)
+
+        s
+      else
+        nil
+      end
+
+    end.compact
+  end
+
+  def paginate_submissions(all_submissions, page, size)
+    current_page = page
+    page_size = size
+
+    start_index = (current_page - 1) * page_size
+    end_index = start_index + page_size - 1
+    next_page = current_page * page_size < all_submissions.size ? current_page + 1 : nil
+    OpenStruct.new(page: current_page, nextPage: next_page, totalCount: all_submissions.size,
+                   collection: all_submissions[start_index..end_index])
+  end
+
+  def sort_submission_by(submissions, sort_by, query = nil)
+    return submissions.sort_by { |x| x[:rank] ? -x[:rank] : 0}  unless query.blank?
+
+    if sort_by.eql?('visits')
+      submissions = submissions.sort_by { |x| -(x[:popularity] || 0) }
+    elsif sort_by.eql?('fair')
+      submissions = submissions.sort_by { |x| -x[:fairScore] }
+    elsif sort_by.eql?('notes')
+      submissions = submissions.sort_by { |x| -x[:note_count] }
+    elsif sort_by.eql?('projects')
+      submissions = submissions.sort_by { |x| -x[:project_count] }
+    elsif sort_by.eql?('metrics_classes')
+      submissions = submissions.sort_by { |x| -x[:class_count] }
+    elsif sort_by.eql?('metrics_individuals')
+      submissions = submissions.sort_by { |x| -x[:individual_count] }
+    elsif sort_by.eql?('creationDate')
+      submissions = submissions.sort_by { |x| x[:creationDate] || '' }.reverse
+    elsif sort_by.eql?('released')
+      submissions = submissions.sort_by { |x| x[:released] || '' }.reverse
+    elsif sort_by.eql?('ontology_name')
+      submissions = submissions.sort_by { |x| -x[:name] }
+    end
+    submissions
+  end
+
   def filters_params(params, includes: BROWSE_ATTRIBUTES.join(','), page: 1, pagesize: 5)
     request_params = { display_links: false, display_context: false,
                        include: includes, include_status: 'RDF' }

From 5f8de42a0f4308ff9bbd40a2eba1790fcf1f0f5f Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 03:35:03 +0200
Subject: [PATCH 10/72] refactor the filter_using_data function to be faster by
 using an hash

---
 app/controllers/concerns/submission_filter.rb | 51 +++++++++----------
 1 file changed, 24 insertions(+), 27 deletions(-)

diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index 001634886e..19c318130c 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -60,31 +60,34 @@ def ontologies_filter_url(filters, page: 1, count: false)
 
   def filter_using_data(ontologies, query:, status:, show_views:, private_only:, languages:, page_size:, formality_level:, is_of_type:, groups:, categories:, formats:)
     submissions = LinkedData::Client::Models::OntologySubmission.all(include: BROWSE_ATTRIBUTES.join(','), also_include_views: true, display_links: false, display_context: false)
+
+    submissions = submissions.map { |x| [x[:ontology][:id], x] }.to_h rescue binding.pry
+
     submissions = ontologies.map { |ont| ontology_hash(ont, submissions) }
 
     submissions.map do |s|
-      out = ((s.ontology.viewingRestriction.eql?('public') && !private_only) || private_only && s.ontology.viewingRestriction.eql?('private'))
-      out = out && (groups.blank? || (s.ontology.group.map { |x| helpers.link_last_part(x) } & groups.split(',')).any?)
-      out = out && (categories.blank? || (s.ontology.hasDomain.map { |x| helpers.link_last_part(x) } & categories.split(',')).any?)
-      out = out && (status.blank? || status.eql?('alpha,beta,production,retired') || status.split(',').include?(s.status))
-      out = out && (formats.blank? || formats.split(',').any? { |f| s.hasOntologyLanguage.eql?(f) })
-      out = out && (is_of_type.blank? || is_of_type.split(',').any? { |f| helpers.link_last_part(s.isOfType).eql?(f) })
-      out = out && (formality_level.blank? || formality_level.split(',').any? { |f| helpers.link_last_part(s.hasFormalityLevel).eql?(f) })
-      out = out && (languages.blank? || languages.split(',').any? { |f| s.naturalLanguage.any? { |n| helpers.link_last_part(n).eql?(f) } })
-      out = out && (s.ontology.viewOf.blank? || (show_views && !s.ontology.viewOf.blank?))
-
-      out = out && (query.blank? || [s.description, s.ontology.name, s.ontology.acronym].any? { |x| (x|| '').downcase.include?(query.downcase) })
+      out = ((s[:ontology].viewingRestriction.eql?('public') && !private_only) || private_only && s[:ontology].viewingRestriction.eql?('private'))
+      out = out && (groups.blank? || (s[:ontology].group.map { |x| helpers.link_last_part(x) } & groups.split(',')).any?)
+      out = out && (categories.blank? || (s[:ontology].hasDomain.map { |x| helpers.link_last_part(x) } & categories.split(',')).any?)
+      out = out && (status.blank? || status.eql?('alpha,beta,production,retired') || status.split(',').include?(s[:status]))
+      out = out && (formats.blank? || formats.split(',').any? { |f| s[:hasOntologyLanguage].eql?(f) })
+      out = out && (is_of_type.blank? || is_of_type.split(',').any? { |f| helpers.link_last_part(s[:isOfType]).eql?(f) })
+      out = out && (formality_level.blank? || formality_level.split(',').any? { |f| helpers.link_last_part(s[:hasFormalityLevel]).eql?(f) })
+      out = out && (languages.blank? || languages.split(',').any? { |f| Array(s[:naturalLanguage]).any? { |n| helpers.link_last_part(n).eql?(f) } })
+      out = out && (s[:ontology].viewOf.blank? || (show_views && !s[:ontology].viewOf.blank?))
+
+      out = out && (query.blank? || [s[:description], s[:ontology].name, s[:ontology].acronym].any? { |x| (x || '').downcase.include?(query.downcase) })
 
       if out
         s[:rank] = 0
 
         next s if query.blank?
 
-        s[:rank] += 3 if s.ontology.acronym && s.ontology.acronym.downcase.include?(query.downcase)
+        s[:rank] += 3 if s[:ontology].acronym && s[:ontology].acronym.downcase.include?(query.downcase)
 
-        s[:rank] += 2 if s.ontology.name && s.ontology.name.downcase.include?(query.downcase)
+        s[:rank] += 2 if s[:ontology].name && s[:ontology].name.downcase.include?(query.downcase)
 
-        s[:rank] += 1 if s.description && s.description.downcase.include?(query.downcase)
+        s[:rank] += 1 if s[:description] && s[:description].downcase.include?(query.downcase)
 
         s
       else
@@ -183,13 +186,15 @@ def filters_params(params, includes: BROWSE_ATTRIBUTES.join(','), page: 1, pages
 
   def ontology_hash(sub)
     o = {}
-    ont = sub.ontology
+    sub = submissions[ont.id]
 
     add_ontology_attributes(o, ont)
     add_submission_attributes(o, sub)
     add_fair_score_metrics(o, ont)
 
-    if sub.metrics
+    o[:hasOntologyLanguage] = sub&.hasOntologyLanguage
+
+    if sub&.metrics && !sub.metrics.is_a?(String)
       o[:class_count] = sub.metrics.classes
       o[:individual_count] = sub.metrics.individuals
     else
@@ -199,18 +204,10 @@ def ontology_hash(sub)
     o[:class_count_formatted] = number_with_delimiter(o[:class_count], delimiter: ',')
     o[:individual_count_formatted] = number_with_delimiter(o[:individual_count], delimiter: ',')
 
-    o[:note_count] = ont.notes.length
-    o[:project_count] = ont.projects.length
+    o[:note_count] = ont.notes&.length || 0
+    o[:project_count] = ont.projects&.length || 0
     o[:popularity] = @analytics[ont.acronym] || 0
-
-    # if o[:type].eql?('ontology_view')
-    #   unless ontologies_hash[ont.viewOf].blank?
-    #     o[:viewOfOnt] = {
-    #       name: ontologies_hash[ont.viewOf].name,
-    #       acronym: ontologies_hash[ont.viewOf].acronym
-    #     }
-    #   end
-    # end
+    o[:rank] = sub ? sub[:rank] : 0
 
     o
   end

From 4dd2740b650fd7c7a1b5ed15efd4abc38d1257f1 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 17:07:37 +0200
Subject: [PATCH 11/72] update the browse analytics cache to change depending
 on portals

---
 app/controllers/concerns/submission_filter.rb | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index 19c318130c..c77100ac1d 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -24,6 +24,12 @@ def submissions_paginate_filter(params)
     submissions = LinkedData::Client::Models::OntologySubmission.all(request_params)
     @analytics =  helpers.ontologies_analytics
 
+    @analytics = Rails.cache.fetch("ontologies_analytics-#{Time.now.year}-#{Time.now.month}-#{request_portals.join('-')}") do
+      helpers.ontologies_analytics
+    end
+
+    @ontologies = LinkedData::Client::Models::Ontology.all(include: 'all', also_include_views: true, display_links: false, display_context: false)
+
     # get fair scores of all ontologies
     @fair_scores = fairness_service_enabled? ? get_fair_score('all') : nil
     submissions = submissions.reject { |sub| sub.ontology.nil? }.map { |sub| ontology_hash(sub) }

From 692c36e9d749877ed9e0850ac3a5cd067c2ec1bb Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 17:09:34 +0200
Subject: [PATCH 12/72] add categories and groups ids on hover to know its
 origin when federated

---
 Gemfile.lock                      | 6 +++---
 app/helpers/application_helper.rb | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 5b3b140032..943e7420f4 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 7664229920b93ca163f1ee96b21e49d1323f843c
+  revision: 0db56d748a1574450ebeb5f67429cd0b766cf932
   branch: feature/federate-multiple-apis
   specs:
     ontologies_api_client (2.2.0)
@@ -421,7 +421,7 @@ GEM
       json
     redcarpet (3.6.0)
     regexp_parser (2.9.0)
-    reline (0.5.5)
+    reline (0.5.6)
       io-console (~> 0.5)
     request_store (1.7.0)
       rack (>= 1.4)
@@ -449,7 +449,7 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.63.4)
+    rubocop (1.63.5)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index cddb64a7e9..3376fa564e 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -32,6 +32,7 @@ def url_to_endpoint(url)
   def resolve_namespaces
     RESOLVE_NAMESPACE
   end
+
   def ontologies_analytics
     data = LinkedData::Client::Analytics.last_month.onts
     data.map{|x| [x[:ont].to_s, x[:views]]}.to_h
@@ -251,7 +252,7 @@ def chips_component(id: , name: , label: , value: , checked: false , tooltip: ni
   end
 
   def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, &block)
-    title ||= object["name"]
+    title ||= "#{object["name"]} (#{object["id"]})"
     value ||= (object["value"] || object["acronym"] || object["id"])
 
     chips_component(id: id || value, name: name, label: object["acronym"],

From 2910b1336e32d83c3b9320249ef07e64a7d351f6 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 9 May 2024 17:11:14 +0200
Subject: [PATCH 13/72] use the last part of ids for browse counts
 independently of its origin

---
 Gemfile.lock                                  |  1 +
 app/controllers/concerns/submission_filter.rb | 24 +++++++++++++++----
 app/controllers/ontologies_controller.rb      | 13 ++++++----
 config/initializers/ontologies_api_client.rb  |  2 +-
 4 files changed, 30 insertions(+), 10 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 943e7420f4..2964125742 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -562,6 +562,7 @@ GEM
     zeitwerk (2.6.13)
 
 PLATFORMS
+  x86_64-linux
   x86_64-linux-musl
 
 DEPENDENCIES
diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index c77100ac1d..cc261412c2 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -186,6 +186,18 @@ def filters_params(params, includes: BROWSE_ATTRIBUTES.join(','), page: 1, pages
       end
     end
 
+    unless params[:sort_by].blank?
+      @filters[:sort_by] = params[:sort_by]
+    end
+
+    unless params[:search].blank?
+      @filters[:search] = params[:search]
+    end
+
+    unless params[:portals].blank?
+      @filters[:portals] = params[:portals]
+    end
+
     request_params.delete(:order_by) if %w[visits fair].include?(request_params[:sort_by].to_s)
     request_params
   end
@@ -212,7 +224,7 @@ def ontology_hash(sub)
 
     o[:note_count] = ont.notes&.length || 0
     o[:project_count] = ont.projects&.length || 0
-    o[:popularity] = @analytics[ont.acronym] || 0
+    o[:popularity] = @analytics[ont.id.to_s] || 0
     o[:rank] = sub ? sub[:rank] : 0
 
     o
@@ -321,11 +333,13 @@ def object_checks(key)
   end
 
   def object_filter(objects, object_name, name_key = 'acronym')
-    checks = object_checks(object_name) || []
-    checks = checks.map { |x| check_id(x, objects, name_key) }.compact
+    checks = params[object_name]&.split(',') || []
+    checks = checks.map { |x| helpers.link_last_part(check_id(x, objects, name_key)) }.compact
 
-    ids = objects.map { |x| x['id'] }
+    objects.uniq! { |x| helpers.link_last_part(x['id']) }
+    ids = objects.map { |x| helpers.link_last_part(x['id']) }
     count = ids.count { |x| checks.include?(x) }
+
     [objects, checks, count]
   end
 
@@ -346,6 +360,8 @@ def count_objects(ontologies)
       object_names.each do |name|
         values = Array(ontology[name])
         values.each do |v|
+          v = helpers.link_last_part(v)
+
           objects_count[name] = {} unless objects_count[name]
           objects_count[name][v] = (objects_count[name][v] || 0) + 1
         end
diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb
index e8f27b3a78..4823273aaa 100644
--- a/app/controllers/ontologies_controller.rb
+++ b/app/controllers/ontologies_controller.rb
@@ -42,11 +42,14 @@ def ontologies_filter
     @ontologies = submissions_paginate_filter(params)
     @object_count = count_objects(@ontologies)
 
-    update_filters_counts = @object_count.map do |section, values_count|
-      values_count.map do |value, count|
-        replace("count_#{section}_#{value}") do
-          helpers.turbo_frame_tag("count_#{section}_#{value}") do
-            helpers.content_tag(:span, count.to_s, class: "hide-if-loading #{count.zero? ? 'disabled' : ''}")
+    if @page.page.eql?(1)
+      streams = [prepend("ontologies_list_view-page-#{@page.page}", partial: 'ontologies/browser/ontologies')]
+      streams += @count_objects.map do |section, values_count|
+        values_count.map do |value, count|
+          replace("count_#{section}_#{link_last_part(value)}") do
+            helpers.turbo_frame_tag("count_#{section}_#{link_last_part(value)}") do
+              helpers.content_tag(:span, count.to_s, class: "hide-if-loading #{count.zero? ? 'disabled' : ''}")
+            end
           end
         end
       end
diff --git a/config/initializers/ontologies_api_client.rb b/config/initializers/ontologies_api_client.rb
index fb2d6f94f2..90ec74ab9c 100644
--- a/config/initializers/ontologies_api_client.rb
+++ b/config/initializers/ontologies_api_client.rb
@@ -7,5 +7,5 @@
   config.debug_client = $DEBUG_RUBY_CLIENT || false
   config.debug_client_keys = $DEBUG_RUBY_CLIENT_KEYS || []
   config.apikey = $API_KEY
-  config.federated_portals = $FEDERATED_PORTALS
+  config.federated_portals = $FEDERATED_PORTALS || []
 end

From cb26cb24aaca764a917e54056bbc67f6902737e2 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Fri, 10 May 2024 17:28:57 +0200
Subject: [PATCH 14/72] remove binding.pry from final federation code

---
 app/controllers/application_controller.rb     | 2 +-
 app/controllers/concerns/submission_filter.rb | 2 +-
 app/helpers/federation_helper.rb              | 2 +-
 config/initializers/ontologies_api_client.rb  | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 4aa6d0e7b9..d049029f9f 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -124,7 +124,7 @@ def domain_ontology_set
       subdomain = host_parts[0].downcase
 
       slices = LinkedData::Client::Models::Slice.all
-      slices_acronyms = slices.map {|s| s.acronym} rescue binding.pry
+      slices_acronyms = slices.map {|s| s.acronym}
 
       # Set custom ontologies if we're on a subdomain that has them
       # Else, make sure user ontologies are set appropriately
diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index cc261412c2..e61aa2be41 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -67,7 +67,7 @@ def ontologies_filter_url(filters, page: 1, count: false)
   def filter_using_data(ontologies, query:, status:, show_views:, private_only:, languages:, page_size:, formality_level:, is_of_type:, groups:, categories:, formats:)
     submissions = LinkedData::Client::Models::OntologySubmission.all(include: BROWSE_ATTRIBUTES.join(','), also_include_views: true, display_links: false, display_context: false)
 
-    submissions = submissions.map { |x| [x[:ontology][:id], x] }.to_h rescue binding.pry
+    submissions = submissions.map { |x| [x[:ontology][:id], x] }.to_h
 
     submissions = ontologies.map { |ont| ontology_hash(ont, submissions) }
 
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 10d13ec79c..fc80e4a2f9 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -1,7 +1,7 @@
 module FederationHelper
 
   def federated_portals
-    $FEDERATED_PORTALS
+    $FEDERATED_PORTALS || {}
   end
 
   def federated_portal_config(name_key)
diff --git a/config/initializers/ontologies_api_client.rb b/config/initializers/ontologies_api_client.rb
index 90ec74ab9c..880ea9fea0 100644
--- a/config/initializers/ontologies_api_client.rb
+++ b/config/initializers/ontologies_api_client.rb
@@ -7,5 +7,5 @@
   config.debug_client = $DEBUG_RUBY_CLIENT || false
   config.debug_client_keys = $DEBUG_RUBY_CLIENT_KEYS || []
   config.apikey = $API_KEY
-  config.federated_portals = $FEDERATED_PORTALS || []
+  config.federated_portals = $FEDERATED_PORTALS || {}
 end

From 7879468de0880576f2142deeca500ab9b8a95f75 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Fri, 10 May 2024 18:25:15 +0200
Subject: [PATCH 15/72] add an error message if one of the external portal is
 down

---
 Gemfile.lock                                       | 6 +++---
 app/controllers/concerns/submission_filter.rb      | 4 +++-
 app/views/ontologies/browser/_ontologies.html.haml | 7 ++++++-
 3 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 2964125742..cf4f1ff835 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 0db56d748a1574450ebeb5f67429cd0b766cf932
+  revision: 1fcf35adcb8955d6b2d48ed08055d31cb00cd3c2
   branch: feature/federate-multiple-apis
   specs:
     ontologies_api_client (2.2.0)
@@ -174,7 +174,7 @@ GEM
     flamegraph (0.9.5)
     globalid (1.2.1)
       activesupport (>= 6.1)
-    graphql (2.3.2)
+    graphql (2.3.3)
       base64
     graphql-client (0.22.0)
       activesupport (>= 3.0)
@@ -349,7 +349,7 @@ GEM
     omniauth-orcid (2.1.1)
       omniauth-oauth2 (~> 1.3)
       ruby_dig (~> 0.0.2)
-    omniauth-rails_csrf_protection (1.0.1)
+    omniauth-rails_csrf_protection (1.0.2)
       actionpack (>= 4.2)
       omniauth (~> 2.0)
     open_uri_redirections (0.2.1)
diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index e61aa2be41..a581f3b7f6 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -30,6 +30,8 @@ def submissions_paginate_filter(params)
 
     @ontologies = LinkedData::Client::Models::Ontology.all(include: 'all', also_include_views: true, display_links: false, display_context: false)
 
+    @ontologies, @errors = @ontologies.partition { |x| !x.errors }
+
     # get fair scores of all ontologies
     @fair_scores = fairness_service_enabled? ? get_fair_score('all') : nil
     submissions = submissions.reject { |sub| sub.ontology.nil? }.map { |sub| ontology_hash(sub) }
@@ -67,7 +69,7 @@ def ontologies_filter_url(filters, page: 1, count: false)
   def filter_using_data(ontologies, query:, status:, show_views:, private_only:, languages:, page_size:, formality_level:, is_of_type:, groups:, categories:, formats:)
     submissions = LinkedData::Client::Models::OntologySubmission.all(include: BROWSE_ATTRIBUTES.join(','), also_include_views: true, display_links: false, display_context: false)
 
-    submissions = submissions.map { |x| [x[:ontology][:id], x] }.to_h
+    submissions = submissions.map { |x| x[:ontology] ? [x[:ontology][:id], x] : nil}.compact.to_h
 
     submissions = ontologies.map { |ont| ontology_hash(ont, submissions) }
 
diff --git a/app/views/ontologies/browser/_ontologies.html.haml b/app/views/ontologies/browser/_ontologies.html.haml
index fec4643834..06d44d362f 100644
--- a/app/views/ontologies/browser/_ontologies.html.haml
+++ b/app/views/ontologies/browser/_ontologies.html.haml
@@ -6,7 +6,12 @@
   - if @page.page.eql?(1)
     = content_tag(:p, class: "browse-desc-text", style: "margin-bottom: 12px !important;") do
       #{t("ontologies.showing_ontologies_size", ontologies_size: @count, analytics_size: @total_ontologies, portals: request_portals_names.join(', ').html_safe).html_safe} (#{sprintf("%.2f", @time)}s)
-
+    - unless @errors.blank?
+      %div.my-1
+        = render Display::AlertComponent.new(type: 'danger') do
+          -  @errors.each do |e|
+            %div
+              = e.errors || e
   - ontologies = c.collection
   - ontologies.each do |ontology|
     - config = ontology_portal_config(ontology[:id])&.last || {}

From f9f4810e2c5f6e094afa6f4cb7b15cf443c423a0 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 29 Aug 2024 22:54:44 +0200
Subject: [PATCH 16/72] display federated results in search page

---
 Gemfile                                       | 2 +-
 Gemfile.lock                                  | 8 ++++++--
 app/controllers/concerns/search_aggregator.rb | 8 ++++----
 app/controllers/search_controller.rb          | 9 +++++++--
 4 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/Gemfile b/Gemfile
index 77f3217de9..c40d042e5b 100644
--- a/Gemfile
+++ b/Gemfile
@@ -92,7 +92,7 @@ gem 'will_paginate', '~> 3.0'
 gem 'inline_svg'
 gem "iso-639", "~> 0.3.6"
 gem "flag-icons-rails", "~> 3.4"
-gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'development'
+gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'feature/federated-search'
 
 # Ruby 2.7.8 pinned gems (to remove when migrating to Ruby >= 3.0)
 gem 'ffi', '~> 1.16.3'
diff --git a/Gemfile.lock b/Gemfile.lock
index 7765c20fdd..b887db6976 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: abea6c217c0ee93bcfd80c47c2af52747365d491
-  branch: development
+  revision: debf991ef77fe6967ffc5e390fad8e4e7455a326
+  branch: feature/federated-search
   specs:
     ontologies_api_client (2.2.0)
       activesupport
@@ -12,6 +12,8 @@ GIT
       lz4-ruby
       multi_json
       oj
+      parallel
+      request_store
       spawnling (= 2.1.5)
 
 GEM
@@ -420,6 +422,8 @@ GEM
     regexp_parser (2.9.2)
     reline (0.5.9)
       io-console (~> 0.5)
+    request_store (1.7.0)
+      rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 5656815b1c..90f2ab77f2 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -24,10 +24,11 @@ module SearchAggregator
     /semanticweb/i
   ]
 
-  def aggregate_results(query, results)
+  def aggregate_results(query, results, is_federate)
     ontologies = aggregate_by_ontology(results)
     grouped_results = add_subordinate_ontologies(query, ontologies)
-    all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false)
+
+    all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false, federate: is_federate)
 
     grouped_results.map do |group|
       format_search_result(group, all_ontologies)
@@ -59,7 +60,7 @@ def search_concept_label(label)
         pref_lab.downcase.include?(@search_query.downcase) || @search_query.downcase.include?(pref_lab.downcase)
       end.first || label.first
     end
-    
+
     label
   end
   def search_result_elem(class_object, ontology_acronym, title)
@@ -229,4 +230,3 @@ def blacklist_cls_id_components(cls_id, blacklist_words)
     stripped_id
   end
 end
-
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index 841f0f948a..8a04b088ba 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -17,10 +17,15 @@ def index
     return if @search_query.empty?
 
     params[:pagesize] = "150"
-    results = LinkedData::Client::Models::Class.search(@search_query, params).collection
+
+    is_federate = params[:federate]
+
+    results = LinkedData::Client::Models::Class.search(@search_query, params)
+
+    results = results.collection unless is_federate
 
     @advanced_options_open = !search_params_empty?
-    @search_results = aggregate_results(@search_query, results)
+    @search_results = aggregate_results(@search_query, results, is_federate)
     @json_url = json_link("#{rest_url}/search", params.permit!.to_h)
   end
 

From e40397351f552ccf59da4537648545189eacab11 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 30 Aug 2024 10:57:35 +0200
Subject: [PATCH 17/72] display federated search results in different colors

---
 .../display/search_result_component.rb          | 17 ++++++++++-------
 .../search_result_component.html.haml           |  5 +++--
 app/controllers/concerns/search_aggregator.rb   | 17 ++++++++++++-----
 app/helpers/federation_helper.rb                |  4 ++++
 4 files changed, 29 insertions(+), 14 deletions(-)

diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb
index 18d56a288e..515485cf25 100644
--- a/app/components/display/search_result_component.rb
+++ b/app/components/display/search_result_component.rb
@@ -5,7 +5,7 @@ class Display::SearchResultComponent < ViewComponent::Base
 
   renders_many :subresults, Display::SearchResultComponent
   renders_many :reuses, Display::SearchResultComponent
-  def initialize(number: 0,title: nil, ontology_acronym: nil ,uri: nil, definition: nil, link: nil,  is_sub_component: false)
+  def initialize(number: 0,title: nil, ontology_acronym: nil ,uri: nil, definition: nil, link: nil,  is_sub_component: false, portal_name: nil, portal_color: nil, portal_light_color: nil)
       @title = title
       @uri = uri
       @definition = definition
@@ -13,6 +13,9 @@ def initialize(number: 0,title: nil, ontology_acronym: nil ,uri: nil, definition
       @is_sub_component = is_sub_component
       @ontology_acronym = ontology_acronym
       @number = number.to_s
+      @portal_name = portal_name
+      @portal_color = portal_color
+      @portal_light_color = portal_light_color
   end
 
   def sub_component_class
@@ -29,9 +32,9 @@ def reuses_id
 
   def details_button
       link_to_modal(nil, "/ajax/class_details?modal=true&ontology=#{@ontology_acronym}&conceptid=#{@uri}&styled=false", data: { show_modal_title_value: @title, show_modal_size_value: 'modal-xl' }) do
-        content_tag(:div, class: 'button') do
+        content_tag(:div, class: 'button', style: @portal_color ? "background-color: #{@portal_light_color} !important" : '') do
           concat inline_svg_tag('icons/details.svg')
-          concat content_tag(:div, class: 'text') { t('search.result_component.details') }
+          concat content_tag(:div, class: 'text', style: @portal_color ? "color: #{@portal_color} !important" : '') { t('search.result_component.details') }
         end
       end
   end
@@ -53,17 +56,17 @@ def mappings_button
 
   def visualize_button
       link_to_modal(nil, "/ajax/biomixer/?ontology=#{@ontology_acronym}&conceptid=#{@uri}", data: { show_modal_title_value: @title, show_modal_size_value: 'modal-xl' }) do
-        content_tag(:div, class: 'button') do
+        content_tag(:div, class: 'button', style: @portal_color ? "background-color: #{@portal_light_color} !important" : '') do
           concat inline_svg_tag('icons/visualize.svg')
-          concat content_tag(:div, class: 'text') { t('search.result_component.visualize') }
+          concat content_tag(:div, class: 'text', style: @portal_color ? "color: #{@portal_color} !important" : '') { t('search.result_component.visualize') }
         end
       end
   end
 
   def reveal_ontologies_button(text,id,icon)
-    content_tag(:div, class: 'button icon-right', 'data-action': "click->reveal-component#toggle", 'data-id': id) do
+    content_tag(:div, class: 'button icon-right', 'data-action': "click->reveal-component#toggle", 'data-id': id, style: @portal_color ? "background-color: #{@portal_light_color} !important" : '') do
       inline_svg_tag(icon) +
-      content_tag(:div, class: 'text') do
+      content_tag(:div, class: 'text', style: @portal_color ? "color: #{@portal_color} !important" : '') do
         text
       end +
       inline_svg_tag("icons/arrow-down.svg")
diff --git a/app/components/display/search_result_component/search_result_component.html.haml b/app/components/display/search_result_component/search_result_component.html.haml
index 9d4d48bc08..ca9b8c1195 100644
--- a/app/components/display/search_result_component/search_result_component.html.haml
+++ b/app/components/display/search_result_component/search_result_component.html.haml
@@ -1,5 +1,5 @@
 .search-result-component{class: sub_component_class, 'data-controller': 'reveal-component'}
-    %a.title{href: @link}
+    %a.title{href: @link, style: @portal_color ? "color: #{@portal_color} !important" : ''}
         = @title
     - if @uri
         .uri
@@ -10,7 +10,8 @@
     .actions
         = details_button
         = visualize_button
-        = mappings_button
+        - unless @portal_name 
+            = mappings_button
         - if subresults?
             = reveal_ontologies_button("#{subresults.size} #{t('search.result_component.more_from_ontology')}", sub_ontologies_id, 'icons/three-dots.svg')
         - if reuses?
diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 90f2ab77f2..54f92563d4 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -1,5 +1,5 @@
 module SearchAggregator
-  include UrlsHelper, MultiLanguagesHelper
+  include UrlsHelper, MultiLanguagesHelper, FederationHelper
   extend ActiveSupport::Concern
   BLACKLIST_FIX_STR = [
     "https://",
@@ -64,18 +64,25 @@ def search_concept_label(label)
     label
   end
   def search_result_elem(class_object, ontology_acronym, title)
-
     label = search_concept_label(class_object.prefLabel)
-
+    internal_class_link = "/ontologies/#{ontology_acronym}?p=classes&conceptid=#{escape(class_object.id)}#{helpers.request_lang&.eql?("ALL") ? '' : "&language="+helpers.request_lang.to_s}"
+    link = is_federation_external_class(class_object) ? class_object.links['ui'] : internal_class_link
+    portal_name = portal_name_from_uri(class_object.links['ui'])
     {
       uri: class_object.id.to_s,
       title: title.empty? ? label : "#{label} - #{title}",
       ontology_acronym: ontology_acronym,
-      link: "/ontologies/#{ontology_acronym}?p=classes&conceptid=#{escape(class_object.id)}#{helpers.request_lang&.eql?("ALL") ? '' : "&language="+helpers.request_lang.to_s}",
-      definition:  class_object.definition
+      link: link,
+      definition:  class_object.definition,
+      portal_name: is_federation_external_class(class_object) ? portal_name : nil,
+      portal_color: is_federation_external_class(class_object) ? federated_portal_color(portal_name) : nil,
+      portal_light_color: is_federation_external_class(class_object) ? federated_portal_light_color(portal_name) : nil
     }
   end
 
+  def is_federation_external_class(class_object)
+    !class_object.links['self'].include?($REST_URL)
+  end
 
   def ontology_name_acronym(ontologies, selected_acronym)
     ontology = ontologies.select { |x| x.acronym.eql?(selected_acronym.split('/').last) }.first
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index fc80e4a2f9..331787213a 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -23,6 +23,10 @@ def federated_portal_light_color(key)
     config[:'light-color'] if config
   end
 
+  def portal_name_from_uri(uri)
+    URI.parse(uri).hostname.split('.').first
+  end
+
 
   def ontology_portal_config(id)
     rest_url = id.split('/')[0..-3].join('/')

From 0ad89fa6392ca3467b71c980f7d787054e4901d5 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 6 Sep 2024 07:34:25 +0200
Subject: [PATCH 18/72] add portals param in federated search

---
 Gemfile.lock                              | 4 ++--
 app/controllers/application_controller.rb | 4 ++++
 app/controllers/ontologies_controller.rb  | 3 ---
 app/controllers/search_controller.rb      | 6 ++++--
 4 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index b887db6976..9fea52aa10 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,10 +1,10 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: debf991ef77fe6967ffc5e390fad8e4e7455a326
+  revision: 230cb4424a296106f918399f58813aafd5306270
   branch: feature/federated-search
   specs:
     ontologies_api_client (2.2.0)
-      activesupport
+      activesupport (~> 7.0.3)
       excon
       faraday
       faraday-excon (~> 2.0.0)
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index dac1c04204..2e38e99c28 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -468,6 +468,10 @@ def json_link(url, optional_params)
     optional_params_str = filtered_params.map { |param, value| "#{param}=#{value}" }.join("&")
     return base_url + optional_params_str + "&apikey=#{$API_KEY}"
   end
+  
+  def set_federated_portals
+    RequestStore.store[:federated_portals] =  params[:portals]&.split(',')
+  end
 
   private
   def not_found_record(exception)
diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb
index 437b5df9eb..4982d367d7 100644
--- a/app/controllers/ontologies_controller.rb
+++ b/app/controllers/ontologies_controller.rb
@@ -559,7 +559,4 @@ def determine_layout
     end
   end
 
-  def set_federated_portals
-    RequestStore.store[:federated_portals] =  params[:portals]&.split(',')
-  end
 end
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index 8a04b088ba..7ac15b8a18 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -18,12 +18,14 @@ def index
 
     params[:pagesize] = "150"
 
-    is_federate = params[:federate]
+    set_federated_portals
+
+    is_federate = params[:federate] || params[:portals]
 
     results = LinkedData::Client::Models::Class.search(@search_query, params)
 
     results = results.collection unless is_federate
-
+    
     @advanced_options_open = !search_params_empty?
     @search_results = aggregate_results(@search_query, results, is_federate)
     @json_url = json_link("#{rest_url}/search", params.permit!.to_h)

From 5db66028117a451945789bf567522dc1062a8bfc Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 6 Sep 2024 13:46:51 +0200
Subject: [PATCH 19/72] add federation checks in search page

---
 Gemfile.lock                                        |  2 +-
 app/components/display/search_result_component.rb   | 10 ++++++++++
 .../search_result_component.html.haml               | 13 +++++++++----
 app/controllers/search_controller.rb                |  5 +++--
 app/views/search/index.html.haml                    |  7 ++++++-
 5 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 9fea52aa10..6b6b5a7256 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 230cb4424a296106f918399f58813aafd5306270
+  revision: 4cff0f52f6a9cc539bfa129c1e989dfc02403541
   branch: feature/federated-search
   specs:
     ontologies_api_client (2.2.0)
diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb
index 515485cf25..1f003d7ac2 100644
--- a/app/components/display/search_result_component.rb
+++ b/app/components/display/search_result_component.rb
@@ -72,4 +72,14 @@ def reveal_ontologies_button(text,id,icon)
       inline_svg_tag("icons/arrow-down.svg")
     end
   end
+
+  def portal_button(name: nil , color: nil , light_color: nil)
+    content_tag(:div, class: 'button icon-right', style: color ? "background-color: #{light_color} !important" : '') do
+      inline_svg_tag('logos/ontoportal.svg') +
+      content_tag(:div, class: 'text', style: color ? "color: #{color} !important" : '') do
+        name.humanize
+      end
+    end
+
+  end
 end
diff --git a/app/components/display/search_result_component/search_result_component.html.haml b/app/components/display/search_result_component/search_result_component.html.haml
index ca9b8c1195..c701099011 100644
--- a/app/components/display/search_result_component/search_result_component.html.haml
+++ b/app/components/display/search_result_component/search_result_component.html.haml
@@ -1,6 +1,9 @@
 .search-result-component{class: sub_component_class, 'data-controller': 'reveal-component'}
-    %a.title{href: @link, style: @portal_color ? "color: #{@portal_color} !important" : ''}
-        = @title
+    %a.title{href: @link, style: @portal_color ? "color: #{@portal_color} !important" : '', target: @portal_color ? "_blank" : ''}
+        .d-flex.align-items-center
+            = @title
+            = inline_svg_tag 'icons/external-link.svg', class: "ml-1 #{@portal_color ? '' : 'd-none'}"
+
     - if @uri
         .uri
             = @uri
@@ -8,14 +11,16 @@
 
         = display_in_multiple_languages(@definition)
     .actions
-        = details_button
-        = visualize_button
         - unless @portal_name 
+            = details_button
+            = visualize_button
             = mappings_button
         - if subresults?
             = reveal_ontologies_button("#{subresults.size} #{t('search.result_component.more_from_ontology')}", sub_ontologies_id, 'icons/three-dots.svg')
         - if reuses?
             = reveal_ontologies_button("#{t('search.result_component.reuses_in')} #{reuses.size} ontologies", reuses_id, 'icons/reuses.svg')
+        - if @portal_name
+            = portal_button(name: @portal_name, color: @portal_color, light_color: @portal_light_color)
     - if subresults?
         .more-from-ontology.d-none{id: sub_ontologies_id}
             .vertical-line
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index 7ac15b8a18..fbd096be62 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -13,6 +13,7 @@ def index
     @advanced_options_open = false
     @search_results = []
     @json_url = json_link("#{rest_url}/search", {})
+    params[:portals] = params[:portals]&.join(',')
 
     return if @search_query.empty?
 
@@ -25,7 +26,7 @@ def index
     results = LinkedData::Client::Models::Class.search(@search_query, params)
 
     results = results.collection unless is_federate
-    
+
     @advanced_options_open = !search_params_empty?
     @search_results = aggregate_results(@search_query, results, is_federate)
     @json_url = json_link("#{rest_url}/search", params.permit!.to_h)
@@ -148,7 +149,7 @@ def search_params
     [
       :ontologies, :categories,
       :also_search_properties, :also_search_obsolete, :also_search_views,
-      :require_exact_match, :require_definition
+      :require_exact_match, :require_definition, :portals
     ]
   end
 
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index 28ecbf2eed..e11944d80b 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -15,7 +15,12 @@
                 = t("search.advanced_options.ontologies")
               .field
                 = ontologies_selector(id:'search_page_ontologies' ,name: 'ontologies[]', selected:  params[:ontologies]&.split(','))
-
+            .filter-container
+              .title 
+                Results from external portals
+              .field.d-flex  
+                - federated_portals.each do |key, config|
+                  = group_chip_component(name: "portals[]", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
           .right
             .filter-container
               .title

From e68d651475a916a69684c2493b54787ced531247 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Mon, 9 Sep 2024 15:57:54 +0200
Subject: [PATCH 20/72] merge federated search results

---
 app/components/display/search_result_component.rb |  3 ++-
 .../search_result_component.html.haml             |  3 ++-
 app/controllers/concerns/search_aggregator.rb     | 15 ++++++++++++++-
 app/controllers/search_controller.rb              |  2 ++
 4 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb
index 1f003d7ac2..990db4d5e8 100644
--- a/app/components/display/search_result_component.rb
+++ b/app/components/display/search_result_component.rb
@@ -5,7 +5,7 @@ class Display::SearchResultComponent < ViewComponent::Base
 
   renders_many :subresults, Display::SearchResultComponent
   renders_many :reuses, Display::SearchResultComponent
-  def initialize(number: 0,title: nil, ontology_acronym: nil ,uri: nil, definition: nil, link: nil,  is_sub_component: false, portal_name: nil, portal_color: nil, portal_light_color: nil)
+  def initialize(number: 0,title: nil, ontology_acronym: nil ,uri: nil, definition: nil, link: nil,  is_sub_component: false, portal_name: nil, portal_color: nil, portal_light_color: nil, other_portals: [])
       @title = title
       @uri = uri
       @definition = definition
@@ -16,6 +16,7 @@ def initialize(number: 0,title: nil, ontology_acronym: nil ,uri: nil, definition
       @portal_name = portal_name
       @portal_color = portal_color
       @portal_light_color = portal_light_color
+      @other_portals = other_portals
   end
 
   def sub_component_class
diff --git a/app/components/display/search_result_component/search_result_component.html.haml b/app/components/display/search_result_component/search_result_component.html.haml
index c701099011..765fb24013 100644
--- a/app/components/display/search_result_component/search_result_component.html.haml
+++ b/app/components/display/search_result_component/search_result_component.html.haml
@@ -8,7 +8,6 @@
         .uri
             = @uri
     - if @definition
-
         = display_in_multiple_languages(@definition)
     .actions
         - unless @portal_name 
@@ -21,6 +20,8 @@
             = reveal_ontologies_button("#{t('search.result_component.reuses_in')} #{reuses.size} ontologies", reuses_id, 'icons/reuses.svg')
         - if @portal_name
             = portal_button(name: @portal_name, color: @portal_color, light_color: @portal_light_color)
+        - @other_portals.each do |p|
+            = portal_button(name: p[:name], color: p[:color], light_color: p[:light_color])
     - if subresults?
         .more-from-ontology.d-none{id: sub_ontologies_id}
             .vertical-line
diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 54f92563d4..f00c785361 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -30,9 +30,22 @@ def aggregate_results(query, results, is_federate)
 
     all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false, federate: is_federate)
 
-    grouped_results.map do |group|
+    search_results = grouped_results.map do |group|
       format_search_result(group, all_ontologies)
     end
+
+    search_results.each do |element|
+      element[:root][:other_portals] = []
+      element[:reuses].reject! do |reuse|
+        if element[:root][:title] == reuse[:root][:title]
+          portal_name = reuse[:root][:portal_name]
+          element[:root][:other_portals] << {name: portal_name, color: federated_portal_color(portal_name), light_color: federated_portal_light_color(portal_name)}
+          true
+        else
+          false
+        end
+      end
+    end
   end
 
   def format_search_result(result, ontologies)
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index fbd096be62..11344aaf10 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -29,6 +29,8 @@ def index
 
     @advanced_options_open = !search_params_empty?
     @search_results = aggregate_results(@search_query, results, is_federate)
+
+
     @json_url = json_link("#{rest_url}/search", params.permit!.to_h)
   end
 

From 065570bedb2834694bbd25d33de90b84f251eeae Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Mon, 9 Sep 2024 16:12:32 +0200
Subject: [PATCH 21/72] show portals names in federated search result chips in
 the form 'AgroPortal' instead of 'agroportal'

---
 app/components/display/search_result_component.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb
index 990db4d5e8..cb67545d30 100644
--- a/app/components/display/search_result_component.rb
+++ b/app/components/display/search_result_component.rb
@@ -78,7 +78,7 @@ def portal_button(name: nil , color: nil , light_color: nil)
     content_tag(:div, class: 'button icon-right', style: color ? "background-color: #{light_color} !important" : '') do
       inline_svg_tag('logos/ontoportal.svg') +
       content_tag(:div, class: 'text', style: color ? "color: #{color} !important" : '') do
-        name.humanize
+        name.humanize.gsub("portal", "Portal")
       end
     end
 

From 2a33a0de48b39ebbcf40c8c50c6f72781273a84d Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Mon, 9 Sep 2024 17:33:41 +0200
Subject: [PATCH 22/72] sort federated search results by string similarity

---
 Gemfile                                       |  3 ++
 Gemfile.lock                                  |  2 +
 app/controllers/concerns/search_aggregator.rb | 38 +++++++++++++------
 3 files changed, 32 insertions(+), 11 deletions(-)

diff --git a/Gemfile b/Gemfile
index c40d042e5b..ae7f2bece0 100644
--- a/Gemfile
+++ b/Gemfile
@@ -88,6 +88,9 @@ gem 'view_component', '~> 2.72'
 # Pagination library for Rails
 gem 'will_paginate', '~> 3.0'
 
+# String similarity
+gem 'string-similarity'
+
 # Render SVG files in Rails views
 gem 'inline_svg'
 gem "iso-639", "~> 0.3.6"
diff --git a/Gemfile.lock b/Gemfile.lock
index 6b6b5a7256..d58dbd3d4b 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -511,6 +511,7 @@ GEM
       net-ssh (>= 2.8.0)
     stimulus-rails (1.3.4)
       railties (>= 6.0.0)
+    string-similarity (2.1.0)
     stringio (3.1.1)
     strscan (3.1.0)
     temple (0.10.3)
@@ -621,6 +622,7 @@ DEPENDENCIES
   simplecov-cobertura
   sprockets-rails
   stimulus-rails
+  string-similarity
   terser
   turbo-rails
   tzinfo-data
diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index f00c785361..7faebfd424 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -1,5 +1,6 @@
 module SearchAggregator
   include UrlsHelper, MultiLanguagesHelper, FederationHelper
+  require 'string-similarity'
   extend ActiveSupport::Concern
   BLACKLIST_FIX_STR = [
     "https://",
@@ -34,18 +35,11 @@ def aggregate_results(query, results, is_federate)
       format_search_result(group, all_ontologies)
     end
 
-    search_results.each do |element|
-      element[:root][:other_portals] = []
-      element[:reuses].reject! do |reuse|
-        if element[:root][:title] == reuse[:root][:title]
-          portal_name = reuse[:root][:portal_name]
-          element[:root][:other_portals] << {name: portal_name, color: federated_portal_color(portal_name), light_color: federated_portal_light_color(portal_name)}
-          true
-        else
-          false
-        end
-      end
+    if is_federate
+      search_results = merge_federated_results(search_results)
+      search_results = sort_results_by_string_similarity(query, search_results)
     end
+    search_results
   end
 
   def format_search_result(result, ontologies)
@@ -249,4 +243,26 @@ def blacklist_cls_id_components(cls_id, blacklist_words)
 
     stripped_id
   end
+
+  def merge_federated_results(search_results)
+    search_results.each do |element|
+      element[:root][:other_portals] = []
+      element[:reuses].reject! do |reuse|
+        if element[:root][:title] == reuse[:root][:title]
+          portal_name = reuse[:root][:portal_name]
+          element[:root][:other_portals] << {name: portal_name, color: federated_portal_color(portal_name), light_color: federated_portal_light_color(portal_name)}
+          true
+        else
+          false
+        end
+      end
+    end
+  end
+
+  def sort_results_by_string_similarity(query, search_results)
+    search_results = search_results.sort_by do |entry|
+      root_similarity = String::Similarity.cosine(query, entry[:root][:title].split('-').first.gsub(" ", "").downcase)
+      -root_similarity
+    end
+  end
 end

From 62e1cc0c88990e147f18df7332cc024266b4e60e Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 12 Sep 2024 10:27:20 +0200
Subject: [PATCH 23/72] fix merge development to federated search issues

---
 Gemfile.lock                          |  2 +-
 app/helpers/federation_helper.rb      |  4 +++
 config/bioportal_config_env.rb.sample | 44 +++++++++++++++++++++++++++
 3 files changed, 49 insertions(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 79da59cb25..9da7889567 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 4cff0f52f6a9cc539bfa129c1e989dfc02403541
+  revision: 929920411203d25c57e3fd5e264200764181ca3e
   branch: feature/federated-search
   specs:
     ontologies_api_client (2.2.0)
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index afd60dfa00..d4470c44c4 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -21,6 +21,10 @@ def federated_portal_config(name_key)
     federated_portals[name_key.to_sym]
   end
 
+  def portal_name_from_uri(uri)
+    URI.parse(uri).hostname.split('.').first
+  end
+
   def federated_portal_name(key)
     config = federated_portal_config(key)
     config ? config[:name] : key
diff --git a/config/bioportal_config_env.rb.sample b/config/bioportal_config_env.rb.sample
index 352805b196..7ea55f59d0 100644
--- a/config/bioportal_config_env.rb.sample
+++ b/config/bioportal_config_env.rb.sample
@@ -213,6 +213,50 @@ $HOME_PAGE_LOGOS = [
 
 
 # Federation configuration
+$FEDERATED_PORTALS = {
+  bioportal: {
+    name: "BioPortal",
+    api: 'https://data.bioontology.org/',
+    ui: 'https://bioportal.bioontology.org/',
+    apikey: '8b5b7825-538d-40e0-9e9e-5ab9274a9aeb',
+    color: '#234979',
+    'light-color': '#E9F2FA',
+  },
+  agroportal: {
+    name: "AgroPortal",
+    api: 'https://data.agroportal.lirmm.fr',
+    ui: 'https://agroportal.lirmm.fr',
+    apikey: '1de0a270-29c5-4dda-b043-7c3580628cd5',
+    color: '#349696',
+    'light-color': '#F1F6FA',
+  },
+  ecoportal: {
+    name: "EcoPortal",
+    api: 'https://data.ecoportal.lifewatch.eu/',
+    ui: 'https://ecoportal.lifewatch.eu',
+    apikey: "43a437ba-a437-4bf0-affd-ab520e584719",
+    color: '#2076C9',
+    'light-color': '#E9F2FA',
+  },
+  # earthportal: {
+  #   name: 'EarthPortal',
+  #   api: 'https://earthportal.eu:8443/',
+  #   ui: 'https://earthportal.eu',
+  #   apikey: "c9147279-954f-41bd-b068-da9b0c441288",
+  #   color: '#404696',
+  #   'light-color': '#404696'
+  # },
+  biodivportal: {
+    name: "BioDivPortal",
+    api: 'https://data.biodivportal.gfbio.org/',
+    ui: 'https://biodivportal.gfbio.org/',
+    apikey: "47a57aa3-7b54-4f34-b695-dbb5f5b7363e",
+    color: '#349696',
+    'light-color': '#EBF5F5',
+  }
+}
+
+
 $PORTALS_INSTANCES = [
   {
     name: 'AgroPortal',

From 07f0e44cffee8dd699740e62516888599761e2cd Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 12 Sep 2024 10:42:34 +0200
Subject: [PATCH 24/72] clean search result component

---
 app/components/display/search_result_component.rb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb
index cb67545d30..74f0e725b2 100644
--- a/app/components/display/search_result_component.rb
+++ b/app/components/display/search_result_component.rb
@@ -33,9 +33,9 @@ def reuses_id
 
   def details_button
       link_to_modal(nil, "/ajax/class_details?modal=true&ontology=#{@ontology_acronym}&conceptid=#{@uri}&styled=false", data: { show_modal_title_value: @title, show_modal_size_value: 'modal-xl' }) do
-        content_tag(:div, class: 'button', style: @portal_color ? "background-color: #{@portal_light_color} !important" : '') do
+        content_tag(:div, class: 'button') do
           concat inline_svg_tag('icons/details.svg')
-          concat content_tag(:div, class: 'text', style: @portal_color ? "color: #{@portal_color} !important" : '') { t('search.result_component.details') }
+          concat content_tag(:div, class: 'text') { t('search.result_component.details') }
         end
       end
   end
@@ -57,9 +57,9 @@ def mappings_button
 
   def visualize_button
       link_to_modal(nil, "/ajax/biomixer/?ontology=#{@ontology_acronym}&conceptid=#{@uri}", data: { show_modal_title_value: @title, show_modal_size_value: 'modal-xl' }) do
-        content_tag(:div, class: 'button', style: @portal_color ? "background-color: #{@portal_light_color} !important" : '') do
+        content_tag(:div, class: 'button') do
           concat inline_svg_tag('icons/visualize.svg')
-          concat content_tag(:div, class: 'text', style: @portal_color ? "color: #{@portal_color} !important" : '') { t('search.result_component.visualize') }
+          concat content_tag(:div, class: 'text') { t('search.result_component.visualize') }
         end
       end
   end

From 2e5dd7b82c5983a14da16abc9ee00e719647c7a6 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 12 Sep 2024 10:57:23 +0200
Subject: [PATCH 25/72] internationalize: results from other portals in search
 and browse page

---
 app/views/ontologies/browser/browse.html.haml | 2 +-
 app/views/search/index.html.haml              | 2 +-
 config/locales/en.yml                         | 5 ++++-
 config/locales/fr.yml                         | 4 +++-
 4 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
index fd9777e3a8..e0695e73d8 100644
--- a/app/views/ontologies/browser/browse.html.haml
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -72,7 +72,7 @@
                               %span.show-if-loading
                                 = render LoaderComponent.new(small:true)
           %div{data:{controller: "show-filter-count browse-filters", action: "change->show-filter-count#updateCount change->browse-filters#dispatchFilterEvent"}, id: "portals_filter_container"}
-            = render DropdownContainerComponent.new(id: "browse-portal-filter", is_open: !request_portals.empty?, title: "Results from external portals") do
+            = render DropdownContainerComponent.new(id: "browse-portal-filter", is_open: !request_portals.empty?, title: t('federation.results_from_external_portals')) do
               .browse-filter-checks-container.px-1
                 - federated_portals.each do |key, config|
                   = group_chip_component(name: "portals", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index e11944d80b..b8895ced4a 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -17,7 +17,7 @@
                 = ontologies_selector(id:'search_page_ontologies' ,name: 'ontologies[]', selected:  params[:ontologies]&.split(','))
             .filter-container
               .title 
-                Results from external portals
+                = t('federation.results_from_external_portals')
               .field.d-flex  
                 - federated_portals.each do |key, config|
                   = group_chip_component(name: "portals[]", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 79ae1583e5..fb54a1cef2 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1496,4 +1496,7 @@ en:
   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.
-    show_sub_categories: Show sub categories
\ No newline at end of file
+    show_sub_categories: Show sub categories
+
+  federation:
+    results_from_external_portals: Results from external portals
\ No newline at end of file
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index f044708cb8..34c68bafa8 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1535,4 +1535,6 @@ fr:
   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.
-    show_sub_categories: Afficher les sous-catégories
\ No newline at end of file
+    show_sub_categories: Afficher les sous-catégories
+  federation:
+    results_from_external_portals: Résultats provenant de portails externes

From d1b228a60064180cbd56b29fdc3b6084fde504e3 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 12 Sep 2024 21:52:14 +0200
Subject: [PATCH 26/72] fix performance issue in federated search

---
 Gemfile.lock                                  |  2 +-
 app/controllers/concerns/search_aggregator.rb |  2 +-
 config/bioportal_config_env.rb.sample         | 22 +++++++++++++++----
 3 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 9da7889567..79da59cb25 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 929920411203d25c57e3fd5e264200764181ca3e
+  revision: 4cff0f52f6a9cc539bfa129c1e989dfc02403541
   branch: feature/federated-search
   specs:
     ontologies_api_client (2.2.0)
diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 7eefdd5a3d..4e2ac084bc 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -29,7 +29,7 @@ def aggregate_results(query, results, is_federate)
     ontologies = aggregate_by_ontology(results)
     grouped_results = add_subordinate_ontologies(query, ontologies)
 
-    all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false, federate: is_federate)
+    all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false)
 
     search_results = grouped_results.map do |group|
       format_search_result(group, all_ontologies)
diff --git a/config/bioportal_config_env.rb.sample b/config/bioportal_config_env.rb.sample
index 7ea55f59d0..9036b0e875 100644
--- a/config/bioportal_config_env.rb.sample
+++ b/config/bioportal_config_env.rb.sample
@@ -262,7 +262,7 @@ $PORTALS_INSTANCES = [
     name: 'AgroPortal',
     api: 'https://data.agroportal.lirmm.fr',
     ui: 'https://agroportal.lirmm.fr/',
-    color: '#349696',
+    color: '#3CB371',
     apikey: '1de0a270-29c5-4dda-b043-7c3580628cd5',
     'light-color': '#F1F6FA',
   },
@@ -277,14 +277,17 @@ $PORTALS_INSTANCES = [
   {
     name: 'SIFR BioPortal',
     ui: 'https://bioportal.lirmm.fr/',
+    api: 'https://data.bioportal.lirmm.fr/',
+    apikey: '1de0a270-29c5-4dda-b043-7c3580628cd5',
     color: '#74a9cb',
+    'light-color': '#E9F2FA',
   },
   {
     name: 'EcoPortal',
     ui: 'https://ecoportal.lifewatch.eu/',
     api: 'https://data.ecoportal.lifewatch.eu/',
     apikey: "43a437ba-a437-4bf0-affd-ab520e584719",
-    color: '#0d508a',
+    color: '#2076C9',
     'light-color': '#E9F2FA',
   },
   {
@@ -300,26 +303,37 @@ $PORTALS_INSTANCES = [
   {
     name: 'IndustryPortal',
     ui: 'http://industryportal.enit.fr',
+    api: 'https://data.industryportal.enit.fr/',
+    apikey: '019adb70-1d64-41b7-8f6e-8f7e5eb54942',
     color: '#1c0f5d',
+    'light-color': '#F0F5F6',
   },
   {
     name: 'EarthPortal',
     ui: 'https://earthportal.eu/',
     api: 'https://data.earthportal.eu/',
     apikey: "c9147279-954f-41bd-b068-da9b0c441288",
-    color: '#1e2251',
+    color: '#404696',
     'light-color': '#F0F5F6'
   },
+  {
+    name: 'TestPortal',
+    ui: 'https://testportal.lirmm.fr/',
+    api: 'https://data.testportal.lirmm.fr/',
+    color: '#74a9cb',
+    apikey: '1de0a270-29c5-4dda-b043-7c3580628cd5',
+  },
   {
     name: 'BiodivPortal',
     ui: 'https://biodivportal.gfbio.org/',
     api: 'https://data.biodivportal.gfbio.org/',
     apikey: "47a57aa3-7b54-4f34-b695-dbb5f5b7363e",
-    color: '#33691B',
+    color: '#349696',
     'light-color': '#EBF5F5',
   }
 ]
 
+
 $ONTOPORTAL_WEBSITE_LINK = "https://ontoportal.org/"
 $ONTOPORTAL_GITHUB_REPO = "https://github.com/ontoportal"
 

From bb96959cc197966493a3b3346df1f07ed8bb5a92 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 13 Sep 2024 10:06:15 +0200
Subject: [PATCH 27/72] merge results using class id and ontology acronym

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

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 4e2ac084bc..3626cf0fd9 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -248,7 +248,7 @@ def merge_federated_results(search_results)
     search_results.each do |element|
       element[:root][:other_portals] = []
       element[:reuses].reject! do |reuse|
-        if element[:root][:title] == reuse[:root][:title]
+        if (element[:root][:ontology_acronym] == reuse[:root][:ontology_acronym]) && (element[:root][:uri] == reuse[:root][:uri])
           portal_name = reuse[:root][:portal_name]
           element[:root][:other_portals] << {name: portal_name, color: federated_portal_color(portal_name), light_color: federated_portal_light_color(portal_name)}
           true

From edb6937c1a52632523ca7d6427e5589d9c063c74 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 13 Sep 2024 10:11:18 +0200
Subject: [PATCH 28/72] extract federation enabled into a helper in federated
 search

---
 app/controllers/concerns/search_aggregator.rb | 4 ++--
 app/controllers/search_controller.rb          | 6 ++----
 app/helpers/federation_helper.rb              | 4 ++++
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 3626cf0fd9..6a849dad1e 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -25,7 +25,7 @@ module SearchAggregator
     /semanticweb/i
   ]
 
-  def aggregate_results(query, results, is_federate)
+  def aggregate_results(query, results)
     ontologies = aggregate_by_ontology(results)
     grouped_results = add_subordinate_ontologies(query, ontologies)
 
@@ -35,7 +35,7 @@ def aggregate_results(query, results, is_federate)
       format_search_result(group, all_ontologies)
     end
 
-    if is_federate
+    if federatation_enabled?
       search_results = merge_federated_results(search_results)
       search_results = sort_results_by_string_similarity(query, search_results)
     end
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index 11344aaf10..ba4a2f104f 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -21,14 +21,12 @@ def index
 
     set_federated_portals
 
-    is_federate = params[:federate] || params[:portals]
-
     results = LinkedData::Client::Models::Class.search(@search_query, params)
 
-    results = results.collection unless is_federate
+    results = results.collection unless federatation_enabled?
 
     @advanced_options_open = !search_params_empty?
-    @search_results = aggregate_results(@search_query, results, is_federate)
+    @search_results = aggregate_results(@search_query, results)
 
 
     @json_url = json_link("#{rest_url}/search", params.permit!.to_h)
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index d4470c44c4..6950ba3ae2 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -98,4 +98,8 @@ def request_portals_names
       content_tag(:span, federated_portal_name(name), style: color ? "color: #{color}" :  "", class: color ? "" : "text-primary")
     end.compact
   end
+
+  def federatation_enabled?
+    params[:federate] || params[:portals]
+  end
 end

From d986607888a7ba33d5cd65a74fc8d71b2424b18d Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 13 Sep 2024 10:21:08 +0200
Subject: [PATCH 29/72] refactor search result elem function

---
 app/controllers/concerns/search_aggregator.rb | 20 +++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 6a849dad1e..359c1f8f48 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -72,18 +72,22 @@ def search_concept_label(label)
   end
   def search_result_elem(class_object, ontology_acronym, title)
     label = search_concept_label(class_object.prefLabel)
-    internal_class_link = "/ontologies/#{ontology_acronym}?p=classes&conceptid=#{escape(class_object.id)}#{helpers.request_lang&.eql?("ALL") ? '' : "&language="+helpers.request_lang.to_s}"
-    link = is_federation_external_class(class_object) ? class_object.links['ui'] : internal_class_link
-    portal_name = portal_name_from_uri(class_object.links['ui'])
+    request_lang = helpers.request_lang&.eql?("ALL") ? '' : "&language=#{helpers.request_lang}"
+    internal_class_link = "/ontologies/#{ontology_acronym}?p=classes&conceptid=#{escape(class_object.id)}#{request_lang}"
+
+    is_external = is_federation_external_class(class_object)
+    link = is_external ? class_object.links['ui'] : internal_class_link
+    portal_name = is_external ? portal_name_from_uri(class_object.links['ui']) : nil
+
     {
       uri: class_object.id.to_s,
-      title: title.nil? || title.empty? ? "#{label} - #{ontology_acronym}" : "#{label} - #{title}",
+      title: title.to_s.empty? ? "#{label} - #{ontology_acronym}" : "#{label} - #{title}",
       ontology_acronym: ontology_acronym,
       link: link,
-      definition:  class_object.definition,
-      portal_name: is_federation_external_class(class_object) ? portal_name : nil,
-      portal_color: is_federation_external_class(class_object) ? federated_portal_color(portal_name) : nil,
-      portal_light_color: is_federation_external_class(class_object) ? federated_portal_light_color(portal_name) : nil
+      definition: class_object.definition,
+      portal_name: portal_name,
+      portal_color: is_external ? federated_portal_color(portal_name) : nil,
+      portal_light_color: is_external ? federated_portal_light_color(portal_name) : nil
     }
   end
 

From d285722bf886089b779e01a02c3bdcc8bd1cf45f Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 13 Sep 2024 10:26:10 +0200
Subject: [PATCH 30/72] add realtime benchmark for search federated search

---
 app/controllers/search_controller.rb | 13 +++++--------
 app/views/search/index.html.haml     |  2 +-
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index ba4a2f104f..df014dd6ea 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -20,15 +20,12 @@ def index
     params[:pagesize] = "150"
 
     set_federated_portals
-
-    results = LinkedData::Client::Models::Class.search(@search_query, params)
-
-    results = results.collection unless federatation_enabled?
-
+    @time = Benchmark.realtime do
+      results = LinkedData::Client::Models::Class.search(@search_query, params)
+      results = results.collection unless federatation_enabled?
+      @search_results = aggregate_results(@search_query, results)
+    end
     @advanced_options_open = !search_params_empty?
-    @search_results = aggregate_results(@search_query, results)
-
-
     @json_url = json_link("#{rest_url}/search", params.permit!.to_h)
   end
 
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index b8895ced4a..fdfeccd99e 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -40,7 +40,7 @@
         .search-page-options{class:  @search_results.empty? ? 'justify-content-end': ''}
           - unless @search_results.empty?
             .search-page-number-of-results
-              = "#{t('search.match_in')} #{@search_results.length} #{t('search.ontologies')}"
+              = "#{t('search.match_in')} #{@search_results.length} #{t('search.ontologies')} (#{sprintf("%.2f", @time)}s)"
           %div.d-flex
             .search-page-json.mx-4.mt-1
               = search_json_link

From 4d0f827160850dfc2675eba6a70c95942381a3a2 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 13 Sep 2024 11:08:36 +0200
Subject: [PATCH 31/72] add portal names and colors in top of federated search
 results

---
 app/views/search/index.html.haml | 2 +-
 config/locales/en.yml            | 3 ++-
 config/locales/fr.yml            | 1 +
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index fdfeccd99e..8702df407a 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -40,7 +40,7 @@
         .search-page-options{class:  @search_results.empty? ? 'justify-content-end': ''}
           - unless @search_results.empty?
             .search-page-number-of-results
-              = "#{t('search.match_in')} #{@search_results.length} #{t('search.ontologies')} (#{sprintf("%.2f", @time)}s)"
+              = "#{t('search.match_in')} #{@search_results.length} #{t('search.ontologies')} #{t('federation.from')} #{request_portals_names.join(', ').html_safe} (#{sprintf("%.2f", @time)}s)".html_safe
           %div.d-flex
             .search-page-json.mx-4.mt-1
               = search_json_link
diff --git a/config/locales/en.yml b/config/locales/en.yml
index fb54a1cef2..2c994a3d37 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1499,4 +1499,5 @@ en:
     show_sub_categories: Show sub categories
 
   federation:
-    results_from_external_portals: Results from external portals
\ No newline at end of file
+    results_from_external_portals: Results from external portals
+    from: from
\ No newline at end of file
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index 34c68bafa8..2a47f018a6 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1538,3 +1538,4 @@ fr:
     show_sub_categories: Afficher les sous-catégories
   federation:
     results_from_external_portals: Résultats provenant de portails externes
+    from: de

From 6f716856332fb12d0e4eb82cf25aa9d92ef8129c Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 13 Sep 2024 20:39:01 +0200
Subject: [PATCH 32/72] make sort by string similarity not case sensitive

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

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 359c1f8f48..7961740c9b 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -265,7 +265,7 @@ def merge_federated_results(search_results)
 
   def sort_results_by_string_similarity(query, search_results)
     search_results = search_results.sort_by do |entry|
-      root_similarity = String::Similarity.cosine(query, entry[:root][:title].split('-').first.gsub(" ", "").downcase)
+      root_similarity = String::Similarity.cosine(query.downcase, entry[:root][:title].split('-').first.gsub(" ", "").downcase)
       -root_similarity
     end
   end

From fc8ec7e9e6909616daf91965f15b7f7a33f7001b Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 20 Sep 2024 12:58:04 +0200
Subject: [PATCH 33/72] remove duplicated federation configuration

---
 config/bioportal_config_env.rb.sample | 46 ---------------------------
 1 file changed, 46 deletions(-)

diff --git a/config/bioportal_config_env.rb.sample b/config/bioportal_config_env.rb.sample
index 9036b0e875..f3c50f6b39 100644
--- a/config/bioportal_config_env.rb.sample
+++ b/config/bioportal_config_env.rb.sample
@@ -211,52 +211,6 @@ $HOME_PAGE_LOGOS = [
     }
 ]
 
-
-# Federation configuration
-$FEDERATED_PORTALS = {
-  bioportal: {
-    name: "BioPortal",
-    api: 'https://data.bioontology.org/',
-    ui: 'https://bioportal.bioontology.org/',
-    apikey: '8b5b7825-538d-40e0-9e9e-5ab9274a9aeb',
-    color: '#234979',
-    'light-color': '#E9F2FA',
-  },
-  agroportal: {
-    name: "AgroPortal",
-    api: 'https://data.agroportal.lirmm.fr',
-    ui: 'https://agroportal.lirmm.fr',
-    apikey: '1de0a270-29c5-4dda-b043-7c3580628cd5',
-    color: '#349696',
-    'light-color': '#F1F6FA',
-  },
-  ecoportal: {
-    name: "EcoPortal",
-    api: 'https://data.ecoportal.lifewatch.eu/',
-    ui: 'https://ecoportal.lifewatch.eu',
-    apikey: "43a437ba-a437-4bf0-affd-ab520e584719",
-    color: '#2076C9',
-    'light-color': '#E9F2FA',
-  },
-  # earthportal: {
-  #   name: 'EarthPortal',
-  #   api: 'https://earthportal.eu:8443/',
-  #   ui: 'https://earthportal.eu',
-  #   apikey: "c9147279-954f-41bd-b068-da9b0c441288",
-  #   color: '#404696',
-  #   'light-color': '#404696'
-  # },
-  biodivportal: {
-    name: "BioDivPortal",
-    api: 'https://data.biodivportal.gfbio.org/',
-    ui: 'https://biodivportal.gfbio.org/',
-    apikey: "47a57aa3-7b54-4f34-b695-dbb5f5b7363e",
-    color: '#349696',
-    'light-color': '#EBF5F5',
-  }
-}
-
-
 $PORTALS_INSTANCES = [
   {
     name: 'AgroPortal',

From f7a4e47cea483cf30a772265f2e1ebd14e267081 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 20 Sep 2024 13:24:13 +0200
Subject: [PATCH 34/72] extract portal button in home page to federation
 helper, fix the style of it and make it clickable

---
 Gemfile.lock                                          |  3 ++-
 app/assets/stylesheets/components/search_result.scss  |  1 +
 app/components/display/search_result_component.rb     | 11 +----------
 .../search_result_component.html.haml                 |  4 ++--
 app/controllers/concerns/search_aggregator.rb         |  3 ++-
 app/helpers/federation_helper.rb                      |  9 +++++++++
 6 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 45a8917875..4cc820671e 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -555,6 +555,7 @@ GEM
     zeitwerk (2.6.18)
 
 PLATFORMS
+  x86_64-linux
   x86_64-linux-musl
 
 DEPENDENCIES
@@ -630,4 +631,4 @@ DEPENDENCIES
   will_paginate (~> 3.0)
 
 BUNDLED WITH
-   2.4.22
+   2.3.23
diff --git a/app/assets/stylesheets/components/search_result.scss b/app/assets/stylesheets/components/search_result.scss
index fc99288618..494b66fe75 100644
--- a/app/assets/stylesheets/components/search_result.scss
+++ b/app/assets/stylesheets/components/search_result.scss
@@ -52,6 +52,7 @@
 }
 .search-result-component .actions .button svg{
   width: 16px;
+  height: 16px;
 }
 
 .search-result-component .actions .button svg path{
diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb
index 74f0e725b2..3896bc94f3 100644
--- a/app/components/display/search_result_component.rb
+++ b/app/components/display/search_result_component.rb
@@ -2,6 +2,7 @@ class Display::SearchResultComponent < ViewComponent::Base
   include UrlsHelper
   include ModalHelper
   include MultiLanguagesHelper
+  include FederationHelper
 
   renders_many :subresults, Display::SearchResultComponent
   renders_many :reuses, Display::SearchResultComponent
@@ -73,14 +74,4 @@ def reveal_ontologies_button(text,id,icon)
       inline_svg_tag("icons/arrow-down.svg")
     end
   end
-
-  def portal_button(name: nil , color: nil , light_color: nil)
-    content_tag(:div, class: 'button icon-right', style: color ? "background-color: #{light_color} !important" : '') do
-      inline_svg_tag('logos/ontoportal.svg') +
-      content_tag(:div, class: 'text', style: color ? "color: #{color} !important" : '') do
-        name.humanize.gsub("portal", "Portal")
-      end
-    end
-
-  end
 end
diff --git a/app/components/display/search_result_component/search_result_component.html.haml b/app/components/display/search_result_component/search_result_component.html.haml
index 765fb24013..80f7274673 100644
--- a/app/components/display/search_result_component/search_result_component.html.haml
+++ b/app/components/display/search_result_component/search_result_component.html.haml
@@ -19,9 +19,9 @@
         - if reuses?
             = reveal_ontologies_button("#{t('search.result_component.reuses_in')} #{reuses.size} ontologies", reuses_id, 'icons/reuses.svg')
         - if @portal_name
-            = portal_button(name: @portal_name, color: @portal_color, light_color: @portal_light_color)
+            = portal_button(name: @portal_name, color: @portal_color, light_color: @portal_light_color, link: @link)
         - @other_portals.each do |p|
-            = portal_button(name: p[:name], color: p[:color], light_color: p[:light_color])
+            = portal_button(name: p[:name], color: p[:color], light_color: p[:light_color], link: p[:link])
     - if subresults?
         .more-from-ontology.d-none{id: sub_ontologies_id}
             .vertical-line
diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 7961740c9b..a14e2bf088 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -254,7 +254,8 @@ def merge_federated_results(search_results)
       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]
-          element[:root][:other_portals] << {name: portal_name, color: federated_portal_color(portal_name), light_color: federated_portal_light_color(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}
           true
         else
           false
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 6950ba3ae2..58c4e2aea7 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -102,4 +102,13 @@ def request_portals_names
   def federatation_enabled?
     params[:federate] || params[:portals]
   end
+
+  def portal_button(name: nil , color: nil , light_color: nil, link: nil, tooltip: nil)
+    content_tag(:a, href: link, target: '_blank', 'data-controller': 'tooltip', title: tooltip, class: 'button icon-right', style: color ? "background-color: #{light_color} !important" : '') do
+      inline_svg_tag('logos/ontoportal.svg') +
+      content_tag(:div, class: 'text', style: color ? "color: #{color} !important" : '') do
+        name.humanize.gsub("portal", "Portal")
+      end
+    end
+  end
 end

From f8742b6109975bdcc8c70aecefdb110d077a2367 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Mon, 23 Sep 2024 13:42:31 +0200
Subject: [PATCH 35/72] fix icons colors in federation

---
 .../display/search_result_component.rb         |  4 ++--
 .../search_result_component.html.haml          |  4 ++--
 app/helpers/federation_helper.rb               |  2 +-
 .../controllers/federation_controller.js       | 18 ++++++++++++++++++
 app/javascript/controllers/index.js            |  5 ++++-
 5 files changed, 27 insertions(+), 6 deletions(-)
 create mode 100644 app/javascript/controllers/federation_controller.js

diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb
index 3896bc94f3..e8da14a353 100644
--- a/app/components/display/search_result_component.rb
+++ b/app/components/display/search_result_component.rb
@@ -67,11 +67,11 @@ def visualize_button
 
   def reveal_ontologies_button(text,id,icon)
     content_tag(:div, class: 'button icon-right', 'data-action': "click->reveal-component#toggle", 'data-id': id, style: @portal_color ? "background-color: #{@portal_light_color} !important" : '') do
-      inline_svg_tag(icon) +
+      inline_svg_tag(icon, class: "federated-icon-#{@portal_name}") +
       content_tag(:div, class: 'text', style: @portal_color ? "color: #{@portal_color} !important" : '') do
         text
       end +
-      inline_svg_tag("icons/arrow-down.svg")
+      inline_svg_tag("icons/arrow-down.svg", class: "federated-icon-#{@portal_name}")
     end
   end
 end
diff --git a/app/components/display/search_result_component/search_result_component.html.haml b/app/components/display/search_result_component/search_result_component.html.haml
index 80f7274673..446ada6408 100644
--- a/app/components/display/search_result_component/search_result_component.html.haml
+++ b/app/components/display/search_result_component/search_result_component.html.haml
@@ -1,8 +1,8 @@
-.search-result-component{class: sub_component_class, 'data-controller': 'reveal-component'}
+.search-result-component{class: sub_component_class, 'data-controller': 'reveal-component federation', 'data-federation-config-value': federated_portals.to_h.to_json}
     %a.title{href: @link, style: @portal_color ? "color: #{@portal_color} !important" : '', target: @portal_color ? "_blank" : ''}
         .d-flex.align-items-center
             = @title
-            = inline_svg_tag 'icons/external-link.svg', class: "ml-1 #{@portal_color ? '' : 'd-none'}"
+            = inline_svg_tag 'icons/external-link.svg', class: "ml-1 federated-icon-#{@portal_name} #{@portal_color ? '' : 'd-none'}"
 
     - if @uri
         .uri
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 58c4e2aea7..d1b027d296 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -105,7 +105,7 @@ def federatation_enabled?
 
   def portal_button(name: nil , color: nil , light_color: nil, link: nil, tooltip: nil)
     content_tag(:a, href: link, target: '_blank', 'data-controller': 'tooltip', title: tooltip, class: 'button icon-right', style: color ? "background-color: #{light_color} !important" : '') do
-      inline_svg_tag('logos/ontoportal.svg') +
+      inline_svg_tag('logos/ontoportal.svg', class: "federated-icon-#{name}") +
       content_tag(:div, class: 'text', style: color ? "color: #{color} !important" : '') do
         name.humanize.gsub("portal", "Portal")
       end
diff --git a/app/javascript/controllers/federation_controller.js b/app/javascript/controllers/federation_controller.js
new file mode 100644
index 0000000000..31f104feb3
--- /dev/null
+++ b/app/javascript/controllers/federation_controller.js
@@ -0,0 +1,18 @@
+import { Controller } from "@hotwired/stimulus"
+
+// Connects to data-controller="federation"
+export default class extends Controller {
+    static values = {
+        config: Object,
+      }
+    connect() {
+        const style = document.createElement('style');
+        let styles = '';
+        Object.entries(this.configValue).forEach(([key, portal]) => {
+            styles += `.federated-icon-${key} path { fill: ${portal.color} !important; }\n`;
+        });
+        style.innerHTML = styles;
+        document.head.appendChild(style);
+    }
+  }
+  
\ No newline at end of file
diff --git a/app/javascript/controllers/index.js b/app/javascript/controllers/index.js
index 24f39bf453..68d74a48a5 100644
--- a/app/javascript/controllers/index.js
+++ b/app/javascript/controllers/index.js
@@ -105,4 +105,7 @@ import MappingsController from "./mappings_visualization_controller"
 application.register('mappings', MappingsController)
 
 import ConceptsJsonButtonController from "./concepts_json_button_controller.js"
-application.register('concepts-json', ConceptsJsonButtonController)
\ No newline at end of file
+application.register('concepts-json', ConceptsJsonButtonController)
+
+import FederationController from "./federation_controller"
+application.register('federation', FederationController)
\ No newline at end of file

From 52e9b27ffd876fe8754d933d034c89bccbfbd10e Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 27 Sep 2024 10:39:44 +0200
Subject: [PATCH 36/72] display a message in the federated search results when
 a portal is not responding

---
 Gemfile.lock                         | 4 ++--
 app/controllers/search_controller.rb | 9 ++++++++-
 app/helpers/federation_helper.rb     | 5 +++++
 app/views/search/index.html.haml     | 2 ++
 4 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 4cc820671e..bb422e95fa 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 4cff0f52f6a9cc539bfa129c1e989dfc02403541
+  revision: 929920411203d25c57e3fd5e264200764181ca3e
   branch: feature/federated-search
   specs:
     ontologies_api_client (2.2.0)
@@ -631,4 +631,4 @@ DEPENDENCIES
   will_paginate (~> 3.0)
 
 BUNDLED WITH
-   2.3.23
+   2.4.22
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index df014dd6ea..b14aded69b 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -22,7 +22,14 @@ def index
     set_federated_portals
     @time = Benchmark.realtime do
       results = LinkedData::Client::Models::Class.search(@search_query, params)
-      results = results.collection unless federatation_enabled?
+      if federatation_enabled?
+        @federation_errors = results[:errors].map{|e| find_portal_name_by_api(e.split(' ').last.gsub('search', ''))}
+        @federation_errors = @federation_errors.map{ |p| "#{p} is not responding. " }.join(' ')
+        
+        results = results[:results]
+      else
+        results = results.collection
+      end
       @search_results = aggregate_results(@search_query, results)
     end
     @advanced_options_open = !search_params_empty?
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index d1b027d296..536592a994 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -111,4 +111,9 @@ def portal_button(name: nil , color: nil , light_color: nil, link: nil, tooltip:
       end
     end
   end
+
+  def find_portal_name_by_api(api_url)
+    portal = federated_portals.values.find { |portal| portal[:api] == api_url }
+    portal ? portal[:name] : nil
+  end
 end
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index 8702df407a..39be354543 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -54,6 +54,8 @@
                 =inline_svg_tag 'icons/hide.svg'
               .text
                 = t('search.hide_advanced_options')
+    - unless @federation_errors.blank?
+      = render Display::AlertComponent.new(message: @federation_errors, type: "warning")
     - if @search_results
       .search-page-results-container
         - number = 0

From bf5fe76436249256ce0cdf65f0edf3f7f3cbdf69 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 27 Sep 2024 14:01:22 +0200
Subject: [PATCH 37/72] disable input chips in federated search page for the
 portals that are not responding

---
 .../controllers/federation_controller.js      | 38 ++++++++++++++++---
 app/views/search/index.html.haml              |  4 +-
 2 files changed, 34 insertions(+), 8 deletions(-)

diff --git a/app/javascript/controllers/federation_controller.js b/app/javascript/controllers/federation_controller.js
index 31f104feb3..9a072819e4 100644
--- a/app/javascript/controllers/federation_controller.js
+++ b/app/javascript/controllers/federation_controller.js
@@ -5,14 +5,40 @@ export default class extends Controller {
     static values = {
         config: Object,
       }
+    static targets = ['chips']
     connect() {
-        const style = document.createElement('style');
-        let styles = '';
-        Object.entries(this.configValue).forEach(([key, portal]) => {
-            styles += `.federated-icon-${key} path { fill: ${portal.color} !important; }\n`;
+      this.#initIconsStyle()
+      this.#initInputChips()
+    }
+    #initIconsStyle(){
+      const style = document.createElement('style');
+      let styles = '';
+      Object.entries(this.configValue).forEach(([key, portal]) => {
+          styles += `.federated-icon-${key} path { fill: ${portal.color} !important; }\n`;
+      });
+      style.innerHTML = styles;
+      document.head.appendChild(style);
+    }
+
+    #initInputChips(){
+      for (const key in this.configValue) {
+        $.ajax({
+          url: this.configValue[key].api,
+          type: 'GET',
+          success: function(response) {
+              console.log('working');
+          },
+          error: function() {
+              let chipsInputs = this.chipsTarget.querySelectorAll('input') 
+              Array.from(chipsInputs).forEach(input => {
+                if (input.value === this.configValue[key].name.toLowerCase()) {
+                    input.disabled = true; 
+                    input.parentNode.style.opacity = '0.5'
+                }
+              });
+          }.bind(this)
         });
-        style.innerHTML = styles;
-        document.head.appendChild(style);
+      }
     }
   }
   
\ No newline at end of file
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index 39be354543..795db68522 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -15,10 +15,10 @@
                 = t("search.advanced_options.ontologies")
               .field
                 = ontologies_selector(id:'search_page_ontologies' ,name: 'ontologies[]', selected:  params[:ontologies]&.split(','))
-            .filter-container
+            .filter-container{'data-controller': 'federation', 'data-federation-config-value': federated_portals.to_h.to_json}
               .title 
                 = t('federation.results_from_external_portals')
-              .field.d-flex  
+              .field.d-flex{'data-federation-target': 'chips'}  
                 - federated_portals.each do |key, config|
                   = group_chip_component(name: "portals[]", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
           .right

From 3366fca5cc6cf1d193680fd6dd1001e63a191bc3 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 27 Sep 2024 14:49:15 +0200
Subject: [PATCH 38/72] show tooltip for disabled input chips in the federated
 search

---
 app/javascript/controllers/federation_controller.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/app/javascript/controllers/federation_controller.js b/app/javascript/controllers/federation_controller.js
index 9a072819e4..e88e0a1680 100644
--- a/app/javascript/controllers/federation_controller.js
+++ b/app/javascript/controllers/federation_controller.js
@@ -33,7 +33,9 @@ export default class extends Controller {
               Array.from(chipsInputs).forEach(input => {
                 if (input.value === this.configValue[key].name.toLowerCase()) {
                     input.disabled = true; 
-                    input.parentNode.style.opacity = '0.5'
+                    input.parentNode.style.opacity = '0.5';
+                    input.parentNode.setAttribute('data-controller', 'tooltip');
+                    input.parentNode.setAttribute('title', `${this.configValue[key].name} is currently down`);
                 }
               });
           }.bind(this)

From d2177f9194d876bba2d372759ae4c6d7add94bf1 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Tue, 1 Oct 2024 15:35:02 +0200
Subject: [PATCH 39/72] clean search controller federation code

---
 Gemfile.lock                         |  2 +-
 app/controllers/search_controller.rb | 11 +++--------
 2 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index bb422e95fa..46607df0af 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 929920411203d25c57e3fd5e264200764181ca3e
+  revision: f6b39981b3dda17e911c497762681d15210a4ad2
   branch: feature/federated-search
   specs:
     ontologies_api_client (2.2.0)
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index b14aded69b..222e2a3c0e 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -22,14 +22,9 @@ def index
     set_federated_portals
     @time = Benchmark.realtime do
       results = LinkedData::Client::Models::Class.search(@search_query, params)
-      if federatation_enabled?
-        @federation_errors = results[:errors].map{|e| find_portal_name_by_api(e.split(' ').last.gsub('search', ''))}
-        @federation_errors = @federation_errors.map{ |p| "#{p} is not responding. " }.join(' ')
-        
-        results = results[:results]
-      else
-        results = results.collection
-      end
+      @federation_errors = results[:errors].map{|e| find_portal_name_by_api(e.split(' ').last.gsub('search', ''))}
+      @federation_errors = @federation_errors.map{ |p| "#{p} is not responding. " }.join(' ')
+      results = results[:results]
       @search_results = aggregate_results(@search_query, results)
     end
     @advanced_options_open = !search_params_empty?

From 5c7d43496a805452b456d7a26e121759f629b3fb Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Tue, 1 Oct 2024 22:52:36 +0200
Subject: [PATCH 40/72] update ontologies api ruby client to the latest version
 of federated search

---
 Gemfile.lock | 41 ++++++++++++++++++++---------------------
 1 file changed, 20 insertions(+), 21 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 46607df0af..cf29740310 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,10 +1,10 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: f6b39981b3dda17e911c497762681d15210a4ad2
+  revision: d2134bf8738c82c5bbf7971d7295873f8c6d953a
   branch: feature/federated-search
   specs:
     ontologies_api_client (2.2.0)
-      activesupport (~> 7.0.3)
+      activesupport (~> 7.0.4)
       excon
       faraday
       faraday-excon (~> 2.0.0)
@@ -150,14 +150,14 @@ GEM
     debug (1.9.2)
       irb (~> 1.10)
       reline (>= 0.3.8)
-    deepl-rb (2.5.3)
+    deepl-rb (3.0.1)
     diff-lcs (1.5.1)
     docile (1.4.1)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
     erubi (1.13.0)
     erubis (2.7.0)
-    excon (0.111.0)
+    excon (0.112.0)
     execjs (2.9.1)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
@@ -176,7 +176,7 @@ GEM
       sass-rails
     globalid (1.2.1)
       activesupport (>= 6.1)
-    graphql (2.3.14)
+    graphql (2.3.16)
       base64
       fiber-storage
     graphql-client (0.23.0)
@@ -203,7 +203,7 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.7)
       domain_name (~> 0.5)
-    i18n (1.14.5)
+    i18n (1.14.6)
       concurrent-ruby (~> 1.0)
     i18n-tasks (0.9.37)
       activesupport (>= 4.0.2)
@@ -225,7 +225,7 @@ GEM
       activesupport (>= 3.0)
       nokogiri (>= 1.6)
     io-console (0.7.2)
-    irb (1.14.0)
+    irb (1.14.1)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
     iso-639 (0.3.6)
@@ -245,7 +245,7 @@ GEM
       bindata
       faraday (~> 2.0)
       faraday-follow_redirects
-    jwt (2.8.2)
+    jwt (2.9.1)
       base64
     language_server-protocol (3.17.0.3)
     launchy (3.0.1)
@@ -302,7 +302,7 @@ GEM
       time
     net-http (0.3.2)
       uri
-    net-imap (0.4.15)
+    net-imap (0.4.16)
       date
       net-protocol
     net-pop (0.1.2)
@@ -317,7 +317,7 @@ GEM
       net-protocol
     net-ssh (7.2.3)
     netrc (0.11.0)
-    newrelic_rpm (9.13.0)
+    newrelic_rpm (9.14.0)
     nio4r (2.7.3)
     nokogiri (1.15.6-x86_64-linux)
       racc (~> 1.4)
@@ -328,7 +328,7 @@ GEM
       rack (>= 1.2, < 4)
       snaky_hash (~> 2.0)
       version_gem (~> 1.1)
-    oj (3.16.5)
+    oj (3.16.6)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omniauth (2.1.2)
@@ -338,8 +338,8 @@ GEM
     omniauth-github (2.0.1)
       omniauth (~> 2.0)
       omniauth-oauth2 (~> 1.8)
-    omniauth-google-oauth2 (1.1.3)
-      jwt (>= 2.0)
+    omniauth-google-oauth2 (1.2.0)
+      jwt (>= 2.9)
       oauth2 (~> 2.0)
       omniauth (~> 2.0)
       omniauth-oauth2 (~> 1.8)
@@ -369,7 +369,7 @@ GEM
     psych (5.1.2)
       stringio
     public_suffix (5.1.1)
-    puma (5.6.8)
+    puma (5.6.9)
       nio4r (~> 2.0)
     racc (1.8.1)
     rack (2.2.9)
@@ -429,8 +429,8 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.7)
-    rouge (4.3.0)
+    rexml (3.3.8)
+    rouge (4.4.0)
     rspec-core (3.13.1)
       rspec-support (~> 3.13.0)
     rspec-expectations (3.13.3)
@@ -458,7 +458,7 @@ GEM
       rubocop-ast (>= 1.32.2, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.32.2)
+    rubocop-ast (1.32.3)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
@@ -522,13 +522,12 @@ GEM
     time (0.4.0)
       date
     timeout (0.4.1)
-    turbo-rails (2.0.6)
+    turbo-rails (2.0.10)
       actionpack (>= 6.0.0)
-      activejob (>= 6.0.0)
       railties (>= 6.0.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.5.0)
+    unicode-display_width (2.6.0)
     uri (0.13.1)
     version_gem (1.1.4)
     view_component (2.83.0)
@@ -540,7 +539,7 @@ GEM
       activemodel (>= 6.0.0)
       bindex (>= 0.4.0)
       railties (>= 6.0.0)
-    webmock (3.23.1)
+    webmock (3.24.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)

From cb8276d8d8d0143e7f023b3e1960bd12fcdfebff Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 2 Oct 2024 10:46:51 +0200
Subject: [PATCH 41/72] fix federated browse icons colors

---
 .../ontology_browse_card_component.html.haml                   | 3 ++-
 app/views/ontologies/browser/browse.html.haml                  | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
index 6a08ccc836..be22043169 100644
--- a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
+++ b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
@@ -7,7 +7,8 @@
             = ontology[:name]+" ("+ontology[:acronym]+")"
             = private_ontology_icon(ontology[:private])
             - if external_ontology?
-              = render Display::InfoTooltipComponent.new(text: "Federated ontology from #{ontology[:sources].map{|x| link_to(x,x)}.join(', ')}", icon: 'external-link.svg')
+              %div{class: "federated-icon-#{@portal_name&.downcase} d-inline"}
+                = render Display::InfoTooltipComponent.new(text: "Federated ontology from #{ontology[:sources].map{|x| link_to(x,x)}.join(', ')}", icon: 'external-link.svg')
             - if session[:user]&.admin?
               - ontology_status = status_string(ontology)
               = render Display::InfoTooltipComponent.new(text: ontology_status, icon: submission_status_icons(ontology_status))
diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
index e0695e73d8..b0abb8cf94 100644
--- a/app/views/ontologies/browser/browse.html.haml
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -1,5 +1,5 @@
 .browse-center
-  .browse-container
+  .browse-container{'data-controller': 'federation', 'data-federation-config-value': federated_portals.to_h.to_json}
     .container.align-alert
       - if session[:user]&.admin?
         %div{style:'width: 70%;'}

From d320de2b14c4607969d65a78d24786b3ae4a5ca3 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 2 Oct 2024 10:47:11 +0200
Subject: [PATCH 42/72] add tooltip for portal button in federated search

---
 .../search_result_component/search_result_component.html.haml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/components/display/search_result_component/search_result_component.html.haml b/app/components/display/search_result_component/search_result_component.html.haml
index 446ada6408..0693686deb 100644
--- a/app/components/display/search_result_component/search_result_component.html.haml
+++ b/app/components/display/search_result_component/search_result_component.html.haml
@@ -19,9 +19,9 @@
         - if reuses?
             = reveal_ontologies_button("#{t('search.result_component.reuses_in')} #{reuses.size} ontologies", reuses_id, 'icons/reuses.svg')
         - if @portal_name
-            = portal_button(name: @portal_name, color: @portal_color, light_color: @portal_light_color, link: @link)
+            = portal_button(name: @portal_name, color: @portal_color, light_color: @portal_light_color, link: @link, tooltip: "Source #{@portal_name.humanize.gsub("portal", "Portal")}")
         - @other_portals.each do |p|
-            = portal_button(name: p[:name], color: p[:color], light_color: p[:light_color], link: p[:link])
+            = portal_button(name: p[:name], color: p[:color], light_color: p[:light_color], link: p[:link], tooltip: "Source #{p[:name].humanize.gsub("portal", "Portal")}")
     - if subresults?
         .more-from-ontology.d-none{id: sub_ontologies_id}
             .vertical-line

From 02ce7cb4d631a03995be80fb80886b352cd88796 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 2 Oct 2024 11:04:13 +0200
Subject: [PATCH 43/72] open external ontologies links in new tab in federated
 browse

---
 .../ontology_browse_card_component.html.haml                    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
index be22043169..75d8a43c02 100644
--- a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
+++ b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
@@ -3,7 +3,7 @@
     .d-flex
       .browse-ontology-description
         .browse-ontology-title-bar
-          %a.browse-ontology-title{:href => onto_link, data: {'turbo': 'false'} , style: style_text}
+          %a.browse-ontology-title{:href => onto_link, data: {'turbo': 'false'} , style: style_text, target: external_ontology? ? '_blank' : ''}
             = ontology[:name]+" ("+ontology[:acronym]+")"
             = private_ontology_icon(ontology[:private])
             - if external_ontology?

From cd83029f8f9d8025bf8785f3c50353276eddbf37 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 2 Oct 2024 17:29:36 +0200
Subject: [PATCH 44/72] use portal button helper in federated browse

---
 Gemfile.lock                                  | 11 ++++---
 .../stylesheets/application.css.scss.erb      |  1 +
 .../stylesheets/components/search_result.scss |  2 +-
 app/assets/stylesheets/federation.scss        | 31 +++++++++++++++++++
 .../ontology_browse_card_component.html.haml  | 10 ++----
 app/helpers/federation_helper.rb              |  4 +--
 6 files changed, 43 insertions(+), 16 deletions(-)
 create mode 100644 app/assets/stylesheets/federation.scss

diff --git a/Gemfile.lock b/Gemfile.lock
index cf29740310..0dd52ad941 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -150,7 +150,7 @@ GEM
     debug (1.9.2)
       irb (~> 1.10)
       reline (>= 0.3.8)
-    deepl-rb (3.0.1)
+    deepl-rb (3.0.2)
     diff-lcs (1.5.1)
     docile (1.4.1)
     domain_name (0.6.20240107)
@@ -287,9 +287,10 @@ GEM
     marcel (1.0.4)
     matrix (0.4.2)
     method_source (1.1.0)
-    mime-types (3.5.2)
+    mime-types (3.6.0)
+      logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0903)
+    mime-types-data (3.2024.1001)
     mini_mime (1.1.5)
     minitest (5.25.1)
     msgpack (1.7.2)
@@ -315,7 +316,7 @@ GEM
       net-ssh (>= 5.0.0, < 8.0.0)
     net-smtp (0.5.0)
       net-protocol
-    net-ssh (7.2.3)
+    net-ssh (7.3.0)
     netrc (0.11.0)
     newrelic_rpm (9.14.0)
     nio4r (2.7.3)
@@ -436,7 +437,7 @@ GEM
     rspec-expectations (3.13.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-mocks (3.13.1)
+    rspec-mocks (3.13.2)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-rails (7.0.1)
diff --git a/app/assets/stylesheets/application.css.scss.erb b/app/assets/stylesheets/application.css.scss.erb
index c5b6723fb3..52b88a0a6d 100755
--- a/app/assets/stylesheets/application.css.scss.erb
+++ b/app/assets/stylesheets/application.css.scss.erb
@@ -60,6 +60,7 @@
 @import "tools";
 @import "portal_configuration";
 @import "taxonomy";
+@import "federation";
 
 /* Bootstrap and Font Awesome */
 @import "bootstrap";
diff --git a/app/assets/stylesheets/components/search_result.scss b/app/assets/stylesheets/components/search_result.scss
index 494b66fe75..f5d8510458 100644
--- a/app/assets/stylesheets/components/search_result.scss
+++ b/app/assets/stylesheets/components/search_result.scss
@@ -41,7 +41,7 @@
   display: flex;
   justify-content: center;
   align-items: center;
-  border-radius: 4px;
+  border-radius: 5px;
   background-color: var(--light-color);
   padding: 5px 13px;
   margin-right: 10px;
diff --git a/app/assets/stylesheets/federation.scss b/app/assets/stylesheets/federation.scss
new file mode 100644
index 0000000000..6bb893e251
--- /dev/null
+++ b/app/assets/stylesheets/federation.scss
@@ -0,0 +1,31 @@
+.federation-portal-button{
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    border-radius: 5px;
+    background-color: var(--light-color);
+    padding: 5px 13px;
+    margin-right: 0px;
+    height: 100%;
+}
+
+
+.federation-portal-button:hover{
+    cursor: pointer;
+}
+
+.federation-portal-button svg{
+    width: 16px;
+    height: 16px;
+}
+.federation-portal-button svg path{
+    fill: var(--primary-color);
+}
+
+.federation-portal-button .text{
+    color: var(--primary-color);
+    margin-left: 8px;
+}
+.federation-portal-button.icon-right .text{
+    margin:0 8px;
+}
\ No newline at end of file
diff --git a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
index 75d8a43c02..6b6791710c 100644
--- a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
+++ b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
@@ -78,14 +78,8 @@
         - ontology[:sources].each do |id|
           - config = ontology_portal_config(id)&.last || internal_portal_config(id) || {}
           - unless config.blank?
-            %div.mx-1{title: content_tag(:div, "Source #{config[:name]}"), data:{controller: 'tooltip', 'tooltip-interactive-value': 'true'}}
-              = render ChipButtonComponent.new(type: "clickable" , style: style_bg) do
-                = link_to ontoportal_ui_link(id), target: '_top' do
-                  %span.d-inline
-                    %span.mr-1
-                      = inline_svg 'logo-white.svg', width: "20", height: "20"
-                    %span
-                      = config[:name]
+            %span{style: "padding: 3px 0; margin-right: 0.25rem;"}
+              = portal_button(name: config[:name], color: @text_color, light_color: @bg_light_color, link: ontoportal_ui_link(id), tooltip: "Source #{config[:name]}")
 
       - if session[:user]&.admin?
         %div.mx-1{title: content_tag(:div, debug(ontology), style: 'height: 300px; overflow: scroll'), data:{controller: 'tooltip', 'tooltip-interactive-value': 'true'}}
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 536592a994..2d852ae9ba 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -104,8 +104,8 @@ def federatation_enabled?
   end
 
   def portal_button(name: nil , color: nil , light_color: nil, link: nil, tooltip: nil)
-    content_tag(:a, href: link, target: '_blank', 'data-controller': 'tooltip', title: tooltip, class: 'button icon-right', style: color ? "background-color: #{light_color} !important" : '') do
-      inline_svg_tag('logos/ontoportal.svg', class: "federated-icon-#{name}") +
+    content_tag(:a, href: link, target: '_blank', 'data-controller': 'tooltip', title: tooltip, class: 'federation-portal-button button icon-right', style: color ? "background-color: #{light_color} !important" : '') do
+      inline_svg_tag('logos/ontoportal.svg', class: "federated-icon-#{name.downcase}") +
       content_tag(:div, class: 'text', style: color ? "color: #{color} !important" : '') do
         name.humanize.gsub("portal", "Portal")
       end

From aacfd566cc735dcc434a25e7a46e64a098cebff0 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 3 Oct 2024 18:00:49 +0200
Subject: [PATCH 45/72] cache federation status call

---
 app/helpers/federation_helper.rb | 37 ++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 2d852ae9ba..7412989fa5 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -116,4 +116,41 @@ def find_portal_name_by_api(api_url)
     portal = federated_portals.values.find { |portal| portal[:api] == api_url }
     portal ? portal[:name] : nil
   end
+
+  def federation_portals_status
+    federation_apis = federated_portals.map { |p| [ p.first , p.last[:api] ] }
+
+    tmp_portals_up = Rails.cache.read('federation_portals_up')
+    if tmp_portals_up
+      return tmp_portals_up
+    else
+      portals_up = []
+      federation_apis.each do |portal|
+        begin
+          conn = Faraday.new(url: portal.last) do |f|
+            f.request  :url_encoded
+            f.adapter  Faraday.default_adapter
+            f.options.timeout = 20
+            f.options.open_timeout = 20
+          end
+          response = conn.get
+          if response.success?
+            parsed_response = JSON.parse(response.body)
+            # todo: check if the response is a correct response
+            portals_up << portal.first
+          else
+            raise "API call failed with status #{response.status}"
+          end
+
+        rescue => e
+          # timout or error
+        end
+        Rails.cache.write('federation_portals_up', portals_up, expires_in: 2.hours)
+      end
+
+      return portals_up
+
+    end
+
+  end
 end

From d17c31b9b1b47cc4284817220225defab622dea5 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 3 Oct 2024 18:38:44 +0200
Subject: [PATCH 46/72] update chip helpers to support disabled state

---
 app/assets/stylesheets/components/chips.scss |  2 +-
 app/components/chips_component.rb            |  5 +++--
 app/helpers/components_helper.rb             | 20 ++++++++++----------
 app/helpers/inputs_helper.rb                 |  6 +++---
 4 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/app/assets/stylesheets/components/chips.scss b/app/assets/stylesheets/components/chips.scss
index ac1a2a939f..e120ced177 100644
--- a/app/assets/stylesheets/components/chips.scss
+++ b/app/assets/stylesheets/components/chips.scss
@@ -32,7 +32,7 @@
 
 }
 .chips-container.disabled div label > span, .chips-container div label span:has(span.disabled){
-  background-color: #f8f9fa !important;
+  opacity: 60%;
 }
 
 .chips-container div label input[type="checkbox"]:checked ~ span{
diff --git a/app/components/chips_component.rb b/app/components/chips_component.rb
index 624681f812..b97ddb3bbc 100644
--- a/app/components/chips_component.rb
+++ b/app/components/chips_component.rb
@@ -1,16 +1,17 @@
 class ChipsComponent < ViewComponent::Base
 
     renders_one :count
-    def initialize(id:nil, name:,  label: nil, value: nil, checked: false, tooltip: nil)
+    def initialize(id:nil, name:,  label: nil, value: nil, checked: false, tooltip: nil, disabled: false)
         @id = id || name
         @name = name
         @value = value || 'true'
         @checked = checked
         @label = label || @value
         @tooltip = tooltip
+        @disabled = disabled
     end
 
     def checked?
         @checked
     end
-end
\ No newline at end of file
+end
diff --git a/app/helpers/components_helper.rb b/app/helpers/components_helper.rb
index 210e4ab57c..1cb32afc1d 100644
--- a/app/helpers/components_helper.rb
+++ b/app/helpers/components_helper.rb
@@ -1,19 +1,19 @@
 module ComponentsHelper
   include TermsReuses
 
-  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, &block)
+  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, disabled: false, &block)
     content_tag(:div, data: { controller: 'tooltip' }, title: tooltip) do
-      check_input(id: id, name: name, value: value, label: label, checked: checked, &block)
+      check_input(id: id, name: name, value: value, label: label, checked: checked, disabled: disabled, &block)
     end
   end
 
-  def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, &block)
+  def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, disabled: false, &block)
     title ||= object["name"]
     value ||= (object["value"] || object["acronym"] || object["id"])
 
     chips_component(id: id || value, name: name, label: object["acronym"],
                     checked: checked,
-                    value: value, tooltip: title, &block)
+                    value: value, tooltip: title, disabled: disabled, &block)
   end
   alias  :category_chip_component :group_chip_component
 
@@ -29,7 +29,7 @@ def check_resolvability_container(url)
       end
     end
   end
-  
+
   def search_page_input_component(name:, value: nil, placeholder: , button_icon: 'icons/search.svg', type: 'text', &block)
     content_tag :div, class: 'search-page-input-container', data: { controller: 'reveal' } do
       search_input = content_tag :div, class: 'search-page-input' do
@@ -63,7 +63,7 @@ def paginated_list_component(id:, results:, next_page_url:, child_url:, child_tu
           end
         end)
       end
-      
+
       concepts = c.collection
       if concepts && !concepts.empty?
         concepts.each do |concept|
@@ -104,7 +104,7 @@ def copy_link_to_clipboard(url, show_content: false)
   end
 
 
-  def generated_link_to_clipboard(url, acronym) 
+  def generated_link_to_clipboard(url, acronym)
     url = "#{$UI_URL}/ontologies/#{acronym}/#{link_last_part(url)}"
     content_tag(:span, id: "generate_portal_link", style: 'display: inline-block;') do
       render ClipboardComponent.new(icon: 'icons/copy_link.svg', title: "#{t("components.copy_portal_uri", portal_name: portal_name)} #{link_to(url)}", message: url, show_content: false)
@@ -123,7 +123,7 @@ def htaccess_tag(acronym)
   def link_to_with_actions(link_to_tag, acronym: nil, url: nil, copy: true, check_resolvability: true, generate_link: true, generate_htaccess: false)
     tag = link_to_tag
     url = link_to_tag if url.nil?
-    
+
     tag += content_tag(:span, class: 'mx-1') do
       concat copy_link_to_clipboard(url) if copy
       concat generated_link_to_clipboard(url, acronym) if generate_link
@@ -136,11 +136,11 @@ def link_to_with_actions(link_to_tag, acronym: nil, url: nil, copy: true, check_
 
   def tree_component(root, selected, target_frame:, sub_tree: false, id: nil, auto_click: false, submission: nil, &child_data_generator)
     root.children.sort! { |a, b| (a.prefLabel || a.id).downcase <=> (b.prefLabel || b.id).downcase }
-    
+
     render TreeViewComponent.new(id: id, sub_tree: sub_tree, auto_click: auto_click) do |tree_child|
       root.children.each do |child|
         children_link, data, href = child_data_generator.call(child)
-  
+
         if children_link.nil? || data.nil? || href.nil?
           raise ArgumentError, t('components.error_block')
         end
diff --git a/app/helpers/inputs_helper.rb b/app/helpers/inputs_helper.rb
index cd4782b6f3..242de76990 100644
--- a/app/helpers/inputs_helper.rb
+++ b/app/helpers/inputs_helper.rb
@@ -28,8 +28,8 @@ def number_input(name: , label: '', value: )
                                       value: value)
   end
 
-  def check_input(id:, name:, value:, label: '', checked: false, &block)
-    render ChipsComponent.new(name: name, id: id, label: label, value: value, checked: checked) do |c|
+  def check_input(id:, name:, value:, label: '', checked: false, disabled: false, &block)
+    render ChipsComponent.new(name: name, id: id, label: label, value: value, checked: checked, disabled: disabled) do |c|
       if block_given?
         capture(c, &block)
       end
@@ -82,4 +82,4 @@ def attribute_error(attr)
   def input_error_message(name)
     attribute_error(method_name(name))
   end
-end
\ No newline at end of file
+end

From 7ca635953fdd177d2fbf1b84d76a7a4a3c1ab2e0 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 3 Oct 2024 18:39:25 +0200
Subject: [PATCH 47/72] use turbo frame for federation input chips, and use
 federation portals status to disable non working portals

---
 app/controllers/home_controller.rb            |  7 ++++++
 .../controllers/federation_controller.js      | 23 -------------------
 .../home/federation_portals_status.html.haml  |  6 +++++
 app/views/search/index.html.haml              | 10 ++++----
 config/routes.rb                              |  1 +
 5 files changed, 19 insertions(+), 28 deletions(-)
 create mode 100644 app/views/home/federation_portals_status.html.haml

diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb
index d7e4beeb31..c0856acbbb 100644
--- a/app/controllers/home_controller.rb
+++ b/app/controllers/home_controller.rb
@@ -166,6 +166,13 @@ def annotator_recommender_form
     end
   end
 
+  def federation_portals_status
+    @acronym = params[:acronym]
+    @key = params[:key]
+    @checked = params[:checked].eql?('true')
+    render 'home/federation_portals_status'
+  end
+
   private
 
   # Dr. Musen wants 5 specific groups to appear first, sorted by order of importance.
diff --git a/app/javascript/controllers/federation_controller.js b/app/javascript/controllers/federation_controller.js
index e88e0a1680..7551f3d04b 100644
--- a/app/javascript/controllers/federation_controller.js
+++ b/app/javascript/controllers/federation_controller.js
@@ -8,7 +8,6 @@ export default class extends Controller {
     static targets = ['chips']
     connect() {
       this.#initIconsStyle()
-      this.#initInputChips()
     }
     #initIconsStyle(){
       const style = document.createElement('style');
@@ -20,27 +19,5 @@ export default class extends Controller {
       document.head.appendChild(style);
     }
 
-    #initInputChips(){
-      for (const key in this.configValue) {
-        $.ajax({
-          url: this.configValue[key].api,
-          type: 'GET',
-          success: function(response) {
-              console.log('working');
-          },
-          error: function() {
-              let chipsInputs = this.chipsTarget.querySelectorAll('input') 
-              Array.from(chipsInputs).forEach(input => {
-                if (input.value === this.configValue[key].name.toLowerCase()) {
-                    input.disabled = true; 
-                    input.parentNode.style.opacity = '0.5';
-                    input.parentNode.setAttribute('data-controller', 'tooltip');
-                    input.parentNode.setAttribute('title', `${this.configValue[key].name} is currently down`);
-                }
-              });
-          }.bind(this)
-        });
-      }
-    }
   }
   
\ No newline at end of file
diff --git a/app/views/home/federation_portals_status.html.haml b/app/views/home/federation_portals_status.html.haml
new file mode 100644
index 0000000000..972dc987fe
--- /dev/null
+++ b/app/views/home/federation_portals_status.html.haml
@@ -0,0 +1,6 @@
+- portal_up = federation_portals_status.include?(@key.to_sym)
+= render TurboFrameComponent.new(id:"federation_portals_status_#{@key}") do |container|
+    %div{style: "cursor: default;"}
+        = group_chip_component(name: "portals[]", object: { "acronym" => @acronym, "value" => @key }, checked: @checked, title: "#{!portal_up ? "#{@key.humanize.gsub('portal', 'Portal')} is currently down" : ''}", disabled: !portal_up)
+
+-# TODO put the portal is down tooltip message in local lang files
\ No newline at end of file
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index 795db68522..3649f2934b 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -1,4 +1,4 @@
-.search-page-container
+.search-page-container{data: {turbo_frame: 'federation_portals_status'}}
   .search-page-subcontainer{'data-controller': 'reveal-component'}
     = form_tag(search_path, method: :get,data:{turbo: true, controller: 'form-url', action: 'submit->form-url#submit'}) do
       = search_page_input_component(placeholder: t('search.search_place_holder'), name: "q", value: @search_query) do
@@ -15,12 +15,13 @@
                 = t("search.advanced_options.ontologies")
               .field
                 = ontologies_selector(id:'search_page_ontologies' ,name: 'ontologies[]', selected:  params[:ontologies]&.split(','))
-            .filter-container{'data-controller': 'federation', 'data-federation-config-value': federated_portals.to_h.to_json}
+            .filter-container
               .title 
                 = t('federation.results_from_external_portals')
-              .field.d-flex{'data-federation-target': 'chips'}  
+              .field.d-flex 
                 - federated_portals.each do |key, config|
-                  = group_chip_component(name: "portals[]", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
+                  = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}")
+                    
           .right
             .filter-container
               .title
@@ -76,4 +77,3 @@
       .browse-empty-illustration
         %img{:src => "#{asset_path("empty-box.svg")}"}
         %p No result was found
-          
\ No newline at end of file
diff --git a/config/routes.rb b/config/routes.rb
index b28c26ec02..226b6d0ca5 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -131,6 +131,7 @@
   end
 
   get '' => 'home#index'
+  get 'home/federation_portals_status', to: 'home#federation_portals_status'
 
   match 'sparql_proxy', to: 'admin#sparql_endpoint', via: [:get, :post]
 

From aa7913c68eeab01581bc81a60db72e7a3e9c98f2 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 3 Oct 2024 19:14:28 +0200
Subject: [PATCH 48/72] add skelton loading animation for federation input
 chips

---
 app/assets/stylesheets/components/chips.scss | 38 +++++++++++++++++++-
 app/helpers/application_helper.rb            | 12 ++++++-
 app/views/search/index.html.haml             |  5 +--
 3 files changed, 51 insertions(+), 4 deletions(-)

diff --git a/app/assets/stylesheets/components/chips.scss b/app/assets/stylesheets/components/chips.scss
index e120ced177..770a41a3f9 100644
--- a/app/assets/stylesheets/components/chips.scss
+++ b/app/assets/stylesheets/components/chips.scss
@@ -42,4 +42,40 @@
 
 .chips-container div label input[type="checkbox"]:checked ~ span .chips-check-icon{
     display:unset;
-}
\ No newline at end of file
+}
+
+.chips-container.loading div {
+    cursor: default;
+    opacity: 0.6; 
+}
+
+.chips-container .skeleton {
+    width: 80px; 
+    height: 36px; 
+    background-color: #e0e0e0; 
+    border-radius: 5px; 
+    animation: shimmer 4s infinite; 
+    position: relative; 
+    overflow: hidden; 
+}
+
+@keyframes shimmer {
+    0% {
+        background-position: -200px 0; 
+    }
+    100% {
+        background-position: 200px 0; 
+    }
+}
+
+.chips-container .skeleton::before {
+    content: '';
+    position: absolute;
+    top: 0;
+    left: 0;
+    width: 100%;
+    height: 100%;
+    background: linear-gradient(90deg, rgba(255, 255, 255, 0.2) 0%, rgba(255, 255, 255, 0.6) 50%, rgba(255, 255, 255, 0.2) 100%);
+    animation: shimmer 4s infinite; 
+    border-radius: 5px; 
+}
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 0f0a6f0c9d..ffc71d919b 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -154,7 +154,7 @@ def link_last_part(url)
   def at_slice?
     !@subdomain_filter.nil? && !@subdomain_filter[:active].nil? && @subdomain_filter[:active] == true
   end
-  
+
   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"
@@ -547,4 +547,14 @@ def categories_select(id: nil, name: nil, selected: 'None')
     categories_for_select = LinkedData::Client::Models::Category.all.map{|x| ["#{x.name} (#{x.acronym})", x.id]}.unshift(["None", ''])
     render Input::SelectComponent.new(id: id, name: name, value: categories_for_select, selected: selected)
   end
+
+  def chips_skelton
+    content_tag(:div, class: 'chips-container loading') do
+      content_tag(:div) do
+        content_tag(:label) do
+          content_tag(:span, '', class: 'skeleton')
+        end
+      end
+    end
+  end
 end
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index 3649f2934b..eb8f5e4736 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -20,8 +20,9 @@
                 = t('federation.results_from_external_portals')
               .field.d-flex 
                 - federated_portals.each do |key, config|
-                  = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}")
-                    
+                  = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
+                    - container.loader do
+                      = chips_skelton
           .right
             .filter-container
               .title

From bf8224fe1d18209943d7dfa0d7627914821f9db6 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 4 Oct 2024 10:16:16 +0200
Subject: [PATCH 49/72] cache federation input chips separately

---
 app/controllers/home_controller.rb            |  3 +-
 app/helpers/federation_helper.rb              | 52 +++++++++----------
 .../home/federation_portals_status.html.haml  |  3 +-
 3 files changed, 27 insertions(+), 31 deletions(-)

diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb
index c0856acbbb..b1b2d6e9d3 100644
--- a/app/controllers/home_controller.rb
+++ b/app/controllers/home_controller.rb
@@ -4,7 +4,7 @@ class HomeController < ApplicationController
   layout :determine_layout
 
 
-  include FairScoreHelper
+  include FairScoreHelper, FederationHelper
 
   def index
     @analytics = helpers.ontologies_analytics
@@ -170,6 +170,7 @@ def federation_portals_status
     @acronym = params[:acronym]
     @key = params[:key]
     @checked = params[:checked].eql?('true')
+    @portal_up = federation_portal_status(portal_name: @key.downcase.to_sym)
     render 'home/federation_portals_status'
   end
 
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 7412989fa5..0d7527fb50 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -117,39 +117,35 @@ def find_portal_name_by_api(api_url)
     portal ? portal[:name] : nil
   end
 
-  def federation_portals_status
-    federation_apis = federated_portals.map { |p| [ p.first , p.last[:api] ] }
+  def federation_portal_status(portal_name: nil)
+    portal_api = federated_portals[portal_name][:api]
+    tmp_portal_up = Rails.cache.read("federation_portal_up_#{portal_name}")
 
-    tmp_portals_up = Rails.cache.read('federation_portals_up')
-    if tmp_portals_up
-      return tmp_portals_up
+    if !tmp_portal_up.nil?
+      return tmp_portal_up
     else
-      portals_up = []
-      federation_apis.each do |portal|
-        begin
-          conn = Faraday.new(url: portal.last) do |f|
-            f.request  :url_encoded
-            f.adapter  Faraday.default_adapter
-            f.options.timeout = 20
-            f.options.open_timeout = 20
-          end
-          response = conn.get
-          if response.success?
-            parsed_response = JSON.parse(response.body)
-            # todo: check if the response is a correct response
-            portals_up << portal.first
-          else
-            raise "API call failed with status #{response.status}"
-          end
-
-        rescue => e
-          # timout or error
+      portal_up = false
+      begin
+        conn = Faraday.new(url: portal_api) do |f|
+          f.request  :url_encoded
+          f.adapter  Faraday.default_adapter
+          f.options.timeout = 20
+          f.options.open_timeout = 20
+        end
+        response = conn.get
+        if response.success?
+          parsed_response = JSON.parse(response.body)
+          # todo: check if the response is a correct response
+          portal_up = true
+        else
+          raise "API call failed with status #{response.status}"
         end
-        Rails.cache.write('federation_portals_up', portals_up, expires_in: 2.hours)
-      end
 
-      return portals_up
+      rescue => e
 
+      end
+      Rails.cache.write("federation_portal_up_#{portal_name}", portal_up, expires_in: 2.hours)
+      return portal_up
     end
 
   end
diff --git a/app/views/home/federation_portals_status.html.haml b/app/views/home/federation_portals_status.html.haml
index 972dc987fe..ecd73b11f8 100644
--- a/app/views/home/federation_portals_status.html.haml
+++ b/app/views/home/federation_portals_status.html.haml
@@ -1,6 +1,5 @@
-- portal_up = federation_portals_status.include?(@key.to_sym)
 = render TurboFrameComponent.new(id:"federation_portals_status_#{@key}") do |container|
     %div{style: "cursor: default;"}
-        = group_chip_component(name: "portals[]", object: { "acronym" => @acronym, "value" => @key }, checked: @checked, title: "#{!portal_up ? "#{@key.humanize.gsub('portal', 'Portal')} is currently down" : ''}", disabled: !portal_up)
+        = group_chip_component(name: "portals[]", object: { "acronym" => @acronym, "value" => @key }, checked: @checked, title: "#{!@portal_up ? "#{@key.humanize.gsub('portal', 'Portal')} is currently down" : ''}", disabled: !@portal_up)
 
 -# TODO put the portal is down tooltip message in local lang files
\ No newline at end of file

From d15ae626f2a2164f08b3f9d4e7a30eb60d461a8d Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 4 Oct 2024 11:39:30 +0200
Subject: [PATCH 50/72] use cached federation input chips in browse page

---
 app/assets/stylesheets/browse.scss                 | 12 ++++++++++++
 app/controllers/home_controller.rb                 |  1 +
 app/views/home/federation_portals_status.html.haml |  2 +-
 app/views/ontologies/browser/browse.html.haml      | 11 ++++++-----
 app/views/search/index.html.haml                   |  2 +-
 5 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/app/assets/stylesheets/browse.scss b/app/assets/stylesheets/browse.scss
index 2dc96db265..0cd58df72b 100644
--- a/app/assets/stylesheets/browse.scss
+++ b/app/assets/stylesheets/browse.scss
@@ -451,6 +451,18 @@
   margin-top: 10px;
 }
 
+.browse-federation-input-chips{
+  display: flex;
+  flex-wrap: wrap;
+  margin: 0 15px 15px 15px;
+  div {
+    flex-grow: 1;
+  }
+
+  label{
+    display: grid;
+  }
+}
 
 @media only screen and (max-width: 1250px) {
   .browse-first-row {
diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb
index b1b2d6e9d3..da0166fcac 100644
--- a/app/controllers/home_controller.rb
+++ b/app/controllers/home_controller.rb
@@ -167,6 +167,7 @@ def annotator_recommender_form
   end
 
   def federation_portals_status
+    @name = params[:name]
     @acronym = params[:acronym]
     @key = params[:key]
     @checked = params[:checked].eql?('true')
diff --git a/app/views/home/federation_portals_status.html.haml b/app/views/home/federation_portals_status.html.haml
index ecd73b11f8..d8621ee3cf 100644
--- a/app/views/home/federation_portals_status.html.haml
+++ b/app/views/home/federation_portals_status.html.haml
@@ -1,5 +1,5 @@
 = render TurboFrameComponent.new(id:"federation_portals_status_#{@key}") do |container|
     %div{style: "cursor: default;"}
-        = group_chip_component(name: "portals[]", object: { "acronym" => @acronym, "value" => @key }, checked: @checked, title: "#{!@portal_up ? "#{@key.humanize.gsub('portal', 'Portal')} is currently down" : ''}", disabled: !@portal_up)
+        = group_chip_component(name: @name, object: { "acronym" => @acronym, "value" => @key }, checked: @checked, title: "#{!@portal_up ? "#{@key.humanize.gsub('portal', 'Portal')} is currently down" : ''}", disabled: !@portal_up)
 
 -# TODO put the portal is down tooltip message in local lang files
\ No newline at end of file
diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
index b0abb8cf94..ef5156d97c 100644
--- a/app/views/ontologies/browser/browse.html.haml
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -71,11 +71,12 @@
                               = turbo_frame_tag "count_#{key}_#{link_last_part(object["id"])}", busy: true
                               %span.show-if-loading
                                 = render LoaderComponent.new(small:true)
-          %div{data:{controller: "show-filter-count browse-filters", action: "change->show-filter-count#updateCount change->browse-filters#dispatchFilterEvent"}, id: "portals_filter_container"}
-            = render DropdownContainerComponent.new(id: "browse-portal-filter", is_open: !request_portals.empty?, title: t('federation.results_from_external_portals')) do
-              .browse-filter-checks-container.px-1
-                - federated_portals.each do |key, config|
-                  = group_chip_component(name: "portals", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
+          = render DropdownContainerComponent.new(id: "browse-portal-filter", is_open: !request_portals.empty?, title: t('federation.results_from_external_portals')) do
+            .px-1.browse-federation-input-chips
+              - federated_portals.each do |key, config|
+                = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?name=portals&key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
+                  - container.loader do
+                    = chips_skelton
 
         .browse-second-row
           .browse-search-bar
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index eb8f5e4736..a36f8d83ce 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -20,7 +20,7 @@
                 = t('federation.results_from_external_portals')
               .field.d-flex 
                 - federated_portals.each do |key, config|
-                  = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
+                  = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?name=portals[]&key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
                     - container.loader do
                       = chips_skelton
           .right

From 6f989f6e9112fa69c5cbdbfc6e9753f9c4330c55 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 4 Oct 2024 11:49:31 +0200
Subject: [PATCH 51/72] fix browse page federation inputs section title style

---
 app/assets/stylesheets/browse.scss            |  7 +++++++
 app/views/ontologies/browser/browse.html.haml | 13 +++++++------
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/app/assets/stylesheets/browse.scss b/app/assets/stylesheets/browse.scss
index 0cd58df72b..a55292bde0 100644
--- a/app/assets/stylesheets/browse.scss
+++ b/app/assets/stylesheets/browse.scss
@@ -463,6 +463,13 @@
     display: grid;
   }
 }
+.browse-federation-input-chip-container{
+  p{
+    font-size: 14px;
+    font-weight: 400;
+    color: #666666;
+  }
+}
 
 @media only screen and (max-width: 1250px) {
   .browse-first-row {
diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
index ef5156d97c..01e127d966 100644
--- a/app/views/ontologies/browser/browse.html.haml
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -71,12 +71,13 @@
                               = turbo_frame_tag "count_#{key}_#{link_last_part(object["id"])}", busy: true
                               %span.show-if-loading
                                 = render LoaderComponent.new(small:true)
-          = render DropdownContainerComponent.new(id: "browse-portal-filter", is_open: !request_portals.empty?, title: t('federation.results_from_external_portals')) do
-            .px-1.browse-federation-input-chips
-              - federated_portals.each do |key, config|
-                = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?name=portals&key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
-                  - container.loader do
-                    = chips_skelton
+          .browse-federation-input-chip-container                    
+            = render DropdownContainerComponent.new(id: "browse-portal-filter", is_open: !request_portals.empty?, title: t('federation.results_from_external_portals')) do
+              .px-1.browse-federation-input-chips
+                - federated_portals.each do |key, config|
+                  = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?name=portals&key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
+                    - container.loader do
+                      = chips_skelton
 
         .browse-second-row
           .browse-search-bar

From 3d2a63c294736cd56a717d0e9e4ccd17c96e4ac7 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Fri, 4 Oct 2024 13:00:28 +0200
Subject: [PATCH 52/72] initialize federation portals input chips in the home
 page (asynch in the background)

---
 app/views/home/index.html.haml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/app/views/home/index.html.haml b/app/views/home/index.html.haml
index fd32acc016..006e5a70fe 100644
--- a/app/views/home/index.html.haml
+++ b/app/views/home/index.html.haml
@@ -230,6 +230,13 @@
         %a{href:logo[:url], target: "_blanc"}
           %img{src: asset_path(logo[:img_src])}
 
+-# This section is hidden, used to initialize the cache of federation portals status
+.d-none
+  - federated_portals.each do |key, config|
+    = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?name=portals[]&key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
+      - container.loader do
+        = chips_skelton
+
 :javascript
   function submitAnnotator(){
   document.getElementById("annotator_submit").click()

From 701879ad70675c3cef06f1c28815b645181b8c80 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Mon, 7 Oct 2024 16:07:33 +0200
Subject: [PATCH 53/72] clean federated search aggregator code

---
 Gemfile                                       | 2 +-
 app/controllers/concerns/search_aggregator.rb | 5 +----
 app/helpers/federation_helper.rb              | 4 ++++
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/Gemfile b/Gemfile
index 683672fb59..768984099f 100644
--- a/Gemfile
+++ b/Gemfile
@@ -88,7 +88,7 @@ gem 'view_component', '~> 2.72'
 # Pagination library for Rails
 gem 'will_paginate', '~> 3.0'
 
-# String similarity
+# String similarity, used by federated search to rank results
 gem 'string-similarity'
 
 # Render SVG files in Rails views
diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index a14e2bf088..3d7e52b2a1 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -85,16 +85,13 @@ def search_result_elem(class_object, ontology_acronym, title)
       ontology_acronym: ontology_acronym,
       link: link,
       definition: class_object.definition,
+      # Used for federation:
       portal_name: portal_name,
       portal_color: is_external ? federated_portal_color(portal_name) : nil,
       portal_light_color: is_external ? federated_portal_light_color(portal_name) : nil
     }
   end
 
-  def is_federation_external_class(class_object)
-    !class_object.links['self'].include?($REST_URL)
-  end
-
   def ontology_name_acronym(ontologies, selected_acronym)
     ontology = ontologies.select { |x| x.acronym.eql?(selected_acronym.split('/').last) }.first
     "#{ontology.name} (#{ontology.acronym})" if ontology
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 0d7527fb50..698daaee64 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -103,6 +103,10 @@ def federatation_enabled?
     params[:federate] || params[:portals]
   end
 
+  def is_federation_external_class(class_object)
+    !class_object.links['self'].include?($REST_URL)
+  end
+
   def portal_button(name: nil , color: nil , light_color: nil, link: nil, tooltip: nil)
     content_tag(:a, href: link, target: '_blank', 'data-controller': 'tooltip', title: tooltip, class: 'federation-portal-button button icon-right', style: color ? "background-color: #{light_color} !important" : '') do
       inline_svg_tag('logos/ontoportal.svg', class: "federated-icon-#{name.downcase}") +

From 965cab561b82a07ff46e706a7eeb00d1b753354e Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Mon, 7 Oct 2024 16:22:07 +0200
Subject: [PATCH 54/72] move chip skelton to components helper

---
 app/helpers/application_helper.rb | 10 ----------
 app/helpers/components_helper.rb  | 11 ++++++++++-
 2 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index ffc71d919b..ef2daf6b20 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -547,14 +547,4 @@ def categories_select(id: nil, name: nil, selected: 'None')
     categories_for_select = LinkedData::Client::Models::Category.all.map{|x| ["#{x.name} (#{x.acronym})", x.id]}.unshift(["None", ''])
     render Input::SelectComponent.new(id: id, name: name, value: categories_for_select, selected: selected)
   end
-
-  def chips_skelton
-    content_tag(:div, class: 'chips-container loading') do
-      content_tag(:div) do
-        content_tag(:label) do
-          content_tag(:span, '', class: 'skeleton')
-        end
-      end
-    end
-  end
 end
diff --git a/app/helpers/components_helper.rb b/app/helpers/components_helper.rb
index 0241c111fb..8aa36fc3d4 100644
--- a/app/helpers/components_helper.rb
+++ b/app/helpers/components_helper.rb
@@ -10,7 +10,7 @@ def alert_component(message, type: "info")
     render Display::AlertComponent.new(type: type, message: message)
   end
 
-  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, disabled: false, &block)   
+  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, disabled: false, &block)
     content_tag(:div, data: { controller: 'tooltip' }, title: tooltip) do
       check_input(id: id, name: name, value: value, label: label, checked: checked, disabled: disabled, &block)
     end
@@ -288,5 +288,14 @@ def form_cancel_button
     end
   end
 
+  def chips_skelton
+    content_tag(:div, class: 'chips-container loading') do
+      content_tag(:div) do
+        content_tag(:label) do
+          content_tag(:span, '', class: 'skeleton')
+        end
+      end
+    end
+  end
 
 end

From f3cb39bbc89bd86cb73928efb53cf7a2bf716bb4 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Mon, 7 Oct 2024 16:22:33 +0200
Subject: [PATCH 55/72] internationalize portal is not responding message

---
 Gemfile                              | 2 ++
 app/controllers/search_controller.rb | 2 +-
 app/helpers/federation_helper.rb     | 2 +-
 config/locales/en.yml                | 3 ++-
 config/locales/fr.yml                | 2 ++
 5 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/Gemfile b/Gemfile
index 768984099f..140d8debf6 100644
--- a/Gemfile
+++ b/Gemfile
@@ -93,6 +93,8 @@ gem 'string-similarity'
 
 # Render SVG files in Rails views
 gem 'inline_svg'
+
+# ISO language codes and flags
 gem "iso-639", "~> 0.3.6"
 gem "flag-icons-rails", "~> 3.4"
 gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'feature/federated-search'
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index 222e2a3c0e..bceee9b3f8 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -23,7 +23,7 @@ def index
     @time = Benchmark.realtime do
       results = LinkedData::Client::Models::Class.search(@search_query, params)
       @federation_errors = results[:errors].map{|e| find_portal_name_by_api(e.split(' ').last.gsub('search', ''))}
-      @federation_errors = @federation_errors.map{ |p| "#{p} is not responding. " }.join(' ')
+      @federation_errors = @federation_errors.map{ |p| "#{p} #{t('federation.not_responding')} " }.join(' ')
       results = results[:results]
       @search_results = aggregate_results(@search_query, results)
     end
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 698daaee64..8dfad433f3 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -100,7 +100,7 @@ def request_portals_names
   end
 
   def federatation_enabled?
-    params[:federate] || params[:portals]
+    params[:portals]
   end
 
   def is_federation_external_class(class_object)
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 10ce6d9f26..e99e3420c6 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1505,4 +1505,5 @@ en:
 
   federation:
     results_from_external_portals: Results from external portals
-    from: from
\ No newline at end of file
+    from: from
+    not_responding: is not responding.
\ No newline at end of file
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index edcfb71842..d5b33a5d7c 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1543,3 +1543,5 @@ fr:
   federation:
     results_from_external_portals: Résultats provenant de portails externes
     from: de
+    not_responding: ne répond pas.
+

From fba0daf43b8550b5d8fca16721cc26ae8b131a8e Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Mon, 7 Oct 2024 16:29:18 +0200
Subject: [PATCH 56/72] clean federation portal status cache method

---
 app/helpers/federation_helper.rb | 34 ++++++++++----------------------
 1 file changed, 10 insertions(+), 24 deletions(-)

diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 8dfad433f3..5f9a50b595 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -122,35 +122,21 @@ def find_portal_name_by_api(api_url)
   end
 
   def federation_portal_status(portal_name: nil)
-    portal_api = federated_portals[portal_name][:api]
-    tmp_portal_up = Rails.cache.read("federation_portal_up_#{portal_name}")
-
-    if !tmp_portal_up.nil?
-      return tmp_portal_up
-    else
+    Rails.cache.fetch("federation_portal_up_#{portal_name}", expires_in: 2.hours) do
+      portal_api = federated_portals[portal_name][:api]
       portal_up = false
       begin
-        conn = Faraday.new(url: portal_api) do |f|
-          f.request  :url_encoded
-          f.adapter  Faraday.default_adapter
+        response = Faraday.new(url: portal_api) do |f|
+          f.request :url_encoded
+          f.adapter Faraday.default_adapter
           f.options.timeout = 20
           f.options.open_timeout = 20
-        end
-        response = conn.get
-        if response.success?
-          parsed_response = JSON.parse(response.body)
-          # todo: check if the response is a correct response
-          portal_up = true
-        else
-          raise "API call failed with status #{response.status}"
-        end
-
-      rescue => e
-
+        end.head
+        portal_up = response.success?
+      rescue StandardError => e
+        Rails.logger.error("Error checking portal status for #{portal_name}: #{e.message}")
       end
-      Rails.cache.write("federation_portal_up_#{portal_name}", portal_up, expires_in: 2.hours)
-      return portal_up
+      portal_up
     end
-
   end
 end

From b4f78166a5146b304dded1db491dfc5b017e0ecc Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Tue, 8 Oct 2024 23:42:31 +0200
Subject: [PATCH 57/72] clean federation stimulus controller code

---
 app/javascript/controllers/federation_controller.js | 1 -
 app/views/ontologies/browser/browse.html.haml       | 4 ++--
 app/views/search/index.html.haml                    | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/app/javascript/controllers/federation_controller.js b/app/javascript/controllers/federation_controller.js
index 7551f3d04b..432e5b5d72 100644
--- a/app/javascript/controllers/federation_controller.js
+++ b/app/javascript/controllers/federation_controller.js
@@ -5,7 +5,6 @@ export default class extends Controller {
     static values = {
         config: Object,
       }
-    static targets = ['chips']
     connect() {
       this.#initIconsStyle()
     }
diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
index 01e127d966..05152ac363 100644
--- a/app/views/ontologies/browser/browse.html.haml
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -1,5 +1,5 @@
 .browse-center
-  .browse-container{'data-controller': 'federation', 'data-federation-config-value': federated_portals.to_h.to_json}
+  .browse-container
     .container.align-alert
       - if session[:user]&.admin?
         %div{style:'width: 70%;'}
@@ -88,7 +88,7 @@
                   = options_for_select(@formats, @selected_format)
                 %select#Sort_by.browse-sort-by-filter{:name => "Sort_by"}
                   = options_for_select(@sorts_options, @sort_by)
-          .browse-ontologies
+          .browse-ontologies{'data-controller': 'federation', 'data-federation-config-value': federated_portals.to_h.to_json}
             = render TurboFrameComponent.new(id: "ontologies_list_view-page-1" , src: "/ontologies_filter?page=1&#{request.original_url.split('?').last}", data:{"turbo-frame-target":"frame", "turbo-frame-url-value": "/ontologies_filter"}) do |list|
               - list.loader do
                 = browser_counter_loader
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index a36f8d83ce..22a5752be3 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -1,4 +1,4 @@
-.search-page-container{data: {turbo_frame: 'federation_portals_status'}}
+.search-page-container
   .search-page-subcontainer{'data-controller': 'reveal-component'}
     = form_tag(search_path, method: :get,data:{turbo: true, controller: 'form-url', action: 'submit->form-url#submit'}) do
       = search_page_input_component(placeholder: t('search.search_place_holder'), name: "q", value: @search_query) do

From 2a21b8cec6161cb99a6278a1730029efd94037d1 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Tue, 8 Oct 2024 23:44:41 +0200
Subject: [PATCH 58/72] display federated browse errors as warning instead of
 danger (orange instead of red)

---
 app/views/ontologies/browser/_ontologies.html.haml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/ontologies/browser/_ontologies.html.haml b/app/views/ontologies/browser/_ontologies.html.haml
index 3ca8685bc0..cadbb85168 100644
--- a/app/views/ontologies/browser/_ontologies.html.haml
+++ b/app/views/ontologies/browser/_ontologies.html.haml
@@ -8,7 +8,7 @@
       #{t("ontologies.showing_ontologies_size", ontologies_size: @count, analytics_size: @total_ontologies, portals: request_portals_names.join(', ').html_safe).html_safe} (#{sprintf("%.2f", @time)}s)
     - unless @errors.blank?
       %div.my-1
-        = render Display::AlertComponent.new(type: 'danger') do
+        = render Display::AlertComponent.new(type: 'warning') do
           -  @errors.each do |e|
             %div
               = e.errors || e

From b037ab3e08f3cf47c4d6db45582a2f51e6d9275b Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 9 Oct 2024 00:13:57 +0200
Subject: [PATCH 59/72] remove related code to fedrated portals status to put
 it in another PR

---
 app/assets/stylesheets/browse.scss            | 19 ----------
 app/assets/stylesheets/components/chips.scss  | 38 +------------------
 app/components/chips_component.rb             |  3 +-
 app/controllers/home_controller.rb            |  9 -----
 app/helpers/components_helper.rb              | 18 ++-------
 app/helpers/federation_helper.rb              | 18 ---------
 app/helpers/inputs_helper.rb                  |  4 +-
 .../home/federation_portals_status.html.haml  |  5 ---
 app/views/home/index.html.haml                |  7 ----
 app/views/ontologies/browser/browse.html.haml |  6 +--
 app/views/search/index.html.haml              |  4 +-
 config/routes.rb                              |  1 -
 12 files changed, 11 insertions(+), 121 deletions(-)
 delete mode 100644 app/views/home/federation_portals_status.html.haml

diff --git a/app/assets/stylesheets/browse.scss b/app/assets/stylesheets/browse.scss
index a55292bde0..2dc96db265 100644
--- a/app/assets/stylesheets/browse.scss
+++ b/app/assets/stylesheets/browse.scss
@@ -451,25 +451,6 @@
   margin-top: 10px;
 }
 
-.browse-federation-input-chips{
-  display: flex;
-  flex-wrap: wrap;
-  margin: 0 15px 15px 15px;
-  div {
-    flex-grow: 1;
-  }
-
-  label{
-    display: grid;
-  }
-}
-.browse-federation-input-chip-container{
-  p{
-    font-size: 14px;
-    font-weight: 400;
-    color: #666666;
-  }
-}
 
 @media only screen and (max-width: 1250px) {
   .browse-first-row {
diff --git a/app/assets/stylesheets/components/chips.scss b/app/assets/stylesheets/components/chips.scss
index 770a41a3f9..267fbb00db 100644
--- a/app/assets/stylesheets/components/chips.scss
+++ b/app/assets/stylesheets/components/chips.scss
@@ -32,7 +32,7 @@
 
 }
 .chips-container.disabled div label > span, .chips-container div label span:has(span.disabled){
-  opacity: 60%;
+    background-color: #f8f9fa !important;
 }
 
 .chips-container div label input[type="checkbox"]:checked ~ span{
@@ -43,39 +43,3 @@
 .chips-container div label input[type="checkbox"]:checked ~ span .chips-check-icon{
     display:unset;
 }
-
-.chips-container.loading div {
-    cursor: default;
-    opacity: 0.6; 
-}
-
-.chips-container .skeleton {
-    width: 80px; 
-    height: 36px; 
-    background-color: #e0e0e0; 
-    border-radius: 5px; 
-    animation: shimmer 4s infinite; 
-    position: relative; 
-    overflow: hidden; 
-}
-
-@keyframes shimmer {
-    0% {
-        background-position: -200px 0; 
-    }
-    100% {
-        background-position: 200px 0; 
-    }
-}
-
-.chips-container .skeleton::before {
-    content: '';
-    position: absolute;
-    top: 0;
-    left: 0;
-    width: 100%;
-    height: 100%;
-    background: linear-gradient(90deg, rgba(255, 255, 255, 0.2) 0%, rgba(255, 255, 255, 0.6) 50%, rgba(255, 255, 255, 0.2) 100%);
-    animation: shimmer 4s infinite; 
-    border-radius: 5px; 
-}
diff --git a/app/components/chips_component.rb b/app/components/chips_component.rb
index b97ddb3bbc..b92080d79c 100644
--- a/app/components/chips_component.rb
+++ b/app/components/chips_component.rb
@@ -1,14 +1,13 @@
 class ChipsComponent < ViewComponent::Base
 
     renders_one :count
-    def initialize(id:nil, name:,  label: nil, value: nil, checked: false, tooltip: nil, disabled: false)
+    def initialize(id:nil, name:,  label: nil, value: nil, checked: false, tooltip: nil)
         @id = id || name
         @name = name
         @value = value || 'true'
         @checked = checked
         @label = label || @value
         @tooltip = tooltip
-        @disabled = disabled
     end
 
     def checked?
diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb
index da0166fcac..bc9531e562 100644
--- a/app/controllers/home_controller.rb
+++ b/app/controllers/home_controller.rb
@@ -166,15 +166,6 @@ def annotator_recommender_form
     end
   end
 
-  def federation_portals_status
-    @name = params[:name]
-    @acronym = params[:acronym]
-    @key = params[:key]
-    @checked = params[:checked].eql?('true')
-    @portal_up = federation_portal_status(portal_name: @key.downcase.to_sym)
-    render 'home/federation_portals_status'
-  end
-
   private
 
   # Dr. Musen wants 5 specific groups to appear first, sorted by order of importance.
diff --git a/app/helpers/components_helper.rb b/app/helpers/components_helper.rb
index 8aa36fc3d4..efef766868 100644
--- a/app/helpers/components_helper.rb
+++ b/app/helpers/components_helper.rb
@@ -10,19 +10,19 @@ def alert_component(message, type: "info")
     render Display::AlertComponent.new(type: type, message: message)
   end
 
-  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, disabled: false, &block)
+  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, &block)
     content_tag(:div, data: { controller: 'tooltip' }, title: tooltip) do
-      check_input(id: id, name: name, value: value, label: label, checked: checked, disabled: disabled, &block)
+      check_input(id: id, name: name, value: value, label: label, checked: checked, &block)
     end
   end
 
-  def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, disabled: false, &block)
+  def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, &block)
     title ||= object["name"]
     value ||= (object["value"] || object["acronym"] || object["id"])
 
     chips_component(id: id || value, name: name, label: object["acronym"],
                     checked: checked,
-                    value: value, tooltip: title, disabled: disabled, &block)
+                    value: value, tooltip: title, &block)
   end
   alias  :category_chip_component :group_chip_component
 
@@ -288,14 +288,4 @@ def form_cancel_button
     end
   end
 
-  def chips_skelton
-    content_tag(:div, class: 'chips-container loading') do
-      content_tag(:div) do
-        content_tag(:label) do
-          content_tag(:span, '', class: 'skeleton')
-        end
-      end
-    end
-  end
-
 end
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 5f9a50b595..52b40e2465 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -121,22 +121,4 @@ def find_portal_name_by_api(api_url)
     portal ? portal[:name] : nil
   end
 
-  def federation_portal_status(portal_name: nil)
-    Rails.cache.fetch("federation_portal_up_#{portal_name}", expires_in: 2.hours) do
-      portal_api = federated_portals[portal_name][:api]
-      portal_up = false
-      begin
-        response = Faraday.new(url: portal_api) do |f|
-          f.request :url_encoded
-          f.adapter Faraday.default_adapter
-          f.options.timeout = 20
-          f.options.open_timeout = 20
-        end.head
-        portal_up = response.success?
-      rescue StandardError => e
-        Rails.logger.error("Error checking portal status for #{portal_name}: #{e.message}")
-      end
-      portal_up
-    end
-  end
 end
diff --git a/app/helpers/inputs_helper.rb b/app/helpers/inputs_helper.rb
index 242de76990..94b677ccd2 100644
--- a/app/helpers/inputs_helper.rb
+++ b/app/helpers/inputs_helper.rb
@@ -28,8 +28,8 @@ def number_input(name: , label: '', value: )
                                       value: value)
   end
 
-  def check_input(id:, name:, value:, label: '', checked: false, disabled: false, &block)
-    render ChipsComponent.new(name: name, id: id, label: label, value: value, checked: checked, disabled: disabled) do |c|
+  def check_input(id:, name:, value:, label: '', checked: false, &block)
+    render ChipsComponent.new(name: name, id: id, label: label, value: value, checked: checked) do |c|
       if block_given?
         capture(c, &block)
       end
diff --git a/app/views/home/federation_portals_status.html.haml b/app/views/home/federation_portals_status.html.haml
deleted file mode 100644
index d8621ee3cf..0000000000
--- a/app/views/home/federation_portals_status.html.haml
+++ /dev/null
@@ -1,5 +0,0 @@
-= render TurboFrameComponent.new(id:"federation_portals_status_#{@key}") do |container|
-    %div{style: "cursor: default;"}
-        = group_chip_component(name: @name, object: { "acronym" => @acronym, "value" => @key }, checked: @checked, title: "#{!@portal_up ? "#{@key.humanize.gsub('portal', 'Portal')} is currently down" : ''}", disabled: !@portal_up)
-
--# TODO put the portal is down tooltip message in local lang files
\ No newline at end of file
diff --git a/app/views/home/index.html.haml b/app/views/home/index.html.haml
index 006e5a70fe..fd32acc016 100644
--- a/app/views/home/index.html.haml
+++ b/app/views/home/index.html.haml
@@ -230,13 +230,6 @@
         %a{href:logo[:url], target: "_blanc"}
           %img{src: asset_path(logo[:img_src])}
 
--# This section is hidden, used to initialize the cache of federation portals status
-.d-none
-  - federated_portals.each do |key, config|
-    = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?name=portals[]&key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
-      - container.loader do
-        = chips_skelton
-
 :javascript
   function submitAnnotator(){
   document.getElementById("annotator_submit").click()
diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml
index 05152ac363..0bb240dcc3 100644
--- a/app/views/ontologies/browser/browse.html.haml
+++ b/app/views/ontologies/browser/browse.html.haml
@@ -73,11 +73,9 @@
                                 = render LoaderComponent.new(small:true)
           .browse-federation-input-chip-container                    
             = render DropdownContainerComponent.new(id: "browse-portal-filter", is_open: !request_portals.empty?, title: t('federation.results_from_external_portals')) do
-              .px-1.browse-federation-input-chips
+              .browse-filter-checks-container.px-1
                 - federated_portals.each do |key, config|
-                  = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?name=portals&key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
-                    - container.loader do
-                      = chips_skelton
+                  = group_chip_component(name: "portals", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
 
         .browse-second-row
           .browse-search-bar
diff --git a/app/views/search/index.html.haml b/app/views/search/index.html.haml
index 22a5752be3..d5f117cf13 100644
--- a/app/views/search/index.html.haml
+++ b/app/views/search/index.html.haml
@@ -20,9 +20,7 @@
                 = t('federation.results_from_external_portals')
               .field.d-flex 
                 - federated_portals.each do |key, config|
-                  = render TurboFrameComponent.new(id: "federation_portals_status_#{key}", src: "home/federation_portals_status?name=portals[]&key=#{key}&acronym=#{config[:name]}&checked=#{request_portals.include?(key.to_s)}") do |container|
-                    - container.loader do
-                      = chips_skelton
+                  = group_chip_component(name: "portals[]", object: { "acronym" => config[:name], "value" => key }, checked: request_portals.include?(key.to_s), title: '')
           .right
             .filter-container
               .title
diff --git a/config/routes.rb b/config/routes.rb
index 226b6d0ca5..b28c26ec02 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -131,7 +131,6 @@
   end
 
   get '' => 'home#index'
-  get 'home/federation_portals_status', to: 'home#federation_portals_status'
 
   match 'sparql_proxy', to: 'admin#sparql_endpoint', via: [:get, :post]
 

From 69fe323011da48be904b469d586f465d81938b9b Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 9 Oct 2024 01:46:54 +0200
Subject: [PATCH 60/72] use the key "collection" instead of "results" in
 federated search result hash to maintain the endpoint expected schema

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

diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index bceee9b3f8..5cfd4c59a1 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -24,7 +24,7 @@ def index
       results = LinkedData::Client::Models::Class.search(@search_query, params)
       @federation_errors = results[:errors].map{|e| find_portal_name_by_api(e.split(' ').last.gsub('search', ''))}
       @federation_errors = @federation_errors.map{ |p| "#{p} #{t('federation.not_responding')} " }.join(' ')
-      results = results[:results]
+      results = results[:collection]
       @search_results = aggregate_results(@search_query, results)
     end
     @advanced_options_open = !search_params_empty?

From 71f92bfa2bbc12a980c94f949e67d00fc2ccdc9b Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 9 Oct 2024 19:16:36 +0200
Subject: [PATCH 61/72] method to get the canonical portal for an ontology
 using pullLocation

---
 app/helpers/federation_helper.rb | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 52b40e2465..528ec50b62 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -121,4 +121,25 @@ def find_portal_name_by_api(api_url)
     portal ? portal[:name] : nil
   end
 
+  def canonical_portal(ontologies)
+    portals = federated_portals.map{|portal| portal.first}
+    portal_counts = Hash.new(0)
+    # Count occurrences of each portal in the pull_location URL
+    ontologies.each do |ontology|
+      portals.each do |portal|
+        if ontology[:pullLocation]&.include?(portal.to_s)
+          portal_counts[portal] += 1
+        end
+      end
+    end
+    # Determine the portal with the most occurrences
+    canonical_portal = portal_counts.max_by { |_, count| count }&.first
+
+    canonical_portal
+  end
+
+  def ontology_from_portal(ontologies, portal)
+    ontologies.select{|o| o[:id].include?(portal.to_s)}.first
+  end
+
 end

From 108ed98c0c1ff89d352c999d63fd0aa030e989bd Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 9 Oct 2024 19:17:11 +0200
Subject: [PATCH 62/72] display federated ontologies in browse page based on
 the canonical portal

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

diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index b37beeb8d4..579996ceb0 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -71,7 +71,7 @@ def merge_by_acronym(submissions)
       if ontologies.size.eql?(1)
         ontology = ontologies.first
       else
-        ontology = ontologies.select { |x| helpers.internal_ontology?(x[:id]) }.first || ontologies.first
+        ontology = ontologies.select { |x| helpers.internal_ontology?(x[:id]) }.first || ontology_from_portal(ontologies, canonical_portal(ontologies))
       end
 
       ontology[:sources] = ontologies.map { |x| x[:id] }

From 2f4c8c4d2ee07013b52f6a0df0fb5eabd86157f4 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 16 Oct 2024 20:57:59 +0200
Subject: [PATCH 63/72] clean canonical portal function in federation helper

---
 app/helpers/federation_helper.rb | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 19847f5999..d06e96f7b0 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -125,18 +125,17 @@ def federation_external_class?(class_object)
 
 
   def canonical_portal(ontologies)
-    portals = federated_portals.map{|portal| portal.first}
     portal_counts = Hash.new(0)
     # Count occurrences of each portal in the pull_location URL
-      portals.each do |portal|
-        if ontology[:pullLocation]&.include?(portal.to_s)
     ontologies.each do |ontology|
+      federated_portals.keys.each do |portal|
+        if ontology[:pullLocation]&.include?(portal.to_s)
           portal_counts[portal] += 1
-      end
         end
+      end
     end
-    canonical_portal = portal_counts.max_by { |_, count| count }&.first
     # Determine the portal with the most occurrences
+    canonical_portal = portal_counts.max_by { |_, count| count }&.first
 
     canonical_portal
   end

From 61d8cfd30dcc4576adb2d3775b3850aaaecfc037 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 16 Oct 2024 21:05:25 +0200
Subject: [PATCH 64/72] extract canonical portal ontology choice in a function
 for clarity

---
 app/controllers/concerns/submission_filter.rb | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index 579996ceb0..fd7becd364 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -71,7 +71,7 @@ def merge_by_acronym(submissions)
       if ontologies.size.eql?(1)
         ontology = ontologies.first
       else
-        ontology = ontologies.select { |x| helpers.internal_ontology?(x[:id]) }.first || ontology_from_portal(ontologies, canonical_portal(ontologies))
+        ontology = canonical_portal_ontology(ontologies)
       end
 
       ontology[:sources] = ontologies.map { |x| x[:id] }
@@ -80,6 +80,10 @@ def merge_by_acronym(submissions)
     merged_submissions
   end
 
+  def canonical_portal_ontology(ontologies)
+    ontologies.select { |x| helpers.internal_ontology?(x[:id]) }.first || ontology_from_portal(ontologies, canonical_portal(ontologies))
+  end
+
   def filter_submissions(ontologies, query:, status:, show_views:, private_only:, languages:, page_size:, formality_level:, is_of_type:, groups:, categories:, formats:)
     submissions = LinkedData::Client::Models::OntologySubmission.all(include: BROWSE_ATTRIBUTES.join(','), also_include_views: true, display_links: false, display_context: false)
 

From 4dbba55e415d9752c245635807cff384d240773a Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Thu, 17 Oct 2024 16:41:11 +0200
Subject: [PATCH 65/72] display search page results based on the canonical
 portal of the ontology

---
 app/controllers/concerns/search_aggregator.rb |  4 +++
 app/helpers/federation_helper.rb              | 31 +++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index e8a72a74ed..2a77e4dbef 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -31,12 +31,16 @@ def aggregate_results(query, results)
 
     all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false)
 
+    all_submissions = LinkedData::Client::Models::OntologySubmission.all(include: 'pullLocation', include_views: true, display_links: false, display_context: false)
+
     search_results = grouped_results.map do |group|
       format_search_result(group, all_ontologies)
     end
 
     search_results = merge_sort_federated_results(query, search_results) if federation_enabled?
 
+    search_results = apply_canonical_portal(search_results, all_submissions)
+
     search_results
   end
 
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index d06e96f7b0..01c84e0148 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -140,6 +140,37 @@ def canonical_portal(ontologies)
     canonical_portal
   end
 
+  def apply_canonical_portal(search_results, all_submissions)
+    search_results.each do |result|
+      next if result[:root][:portal_name].nil? || result[:root][:other_portals].blank?
+
+      root_link = result[:root][:link].split('?').first
+      candidates = [result[:root][:link]] + result[:root][:other_portals].map { |p| p[:link].split('?').first }
+
+      portal_counts = Hash.new(0)
+      candidates.each do |candidate|
+        submission = all_submissions.find { |s| s.id.split('/')[0...-2].join('/') == candidate }
+
+        federated_portals.keys.each do |portal|
+          portal_counts[portal] += 1 if submission&.include?(portal.to_s)
+        end
+      end
+
+      canonical_portal = portal_counts.max_by { |_, count| count }&.first
+      next if canonical_portal.nil? || result[:root][:portal_name].eql?(canonical_portal.to_s)
+
+      canonical_portal_result = result[:root][:other_portals].find { |r| r[:name] == canonical_portal.to_s }
+      swap_portal_attributes(result[:root], canonical_portal_result) if canonical_portal_result
+    end
+  end
+
+  def swap_portal_attributes(root_portal, new_portal)
+    root_portal[:link], new_portal[:link] = new_portal[:link], root_portal[:link]
+    root_portal[:portal_name], new_portal[:portal_name] = new_portal[:portal_name], root_portal[:portal_name]
+    root_portal[:portal_color], new_portal[:portal_color] = new_portal[:portal_color], root_portal[:portal_color]
+    root_portal[:portal_light_color], new_portal[:portal_light_color] = new_portal[:portal_light_color], root_portal[:portal_light_color]
+  end
+
   def ontology_from_portal(ontologies, portal)
     ontologies.select{|o| o[:id].include?(portal.to_s)}.first
   end

From 1d748c8e72f71c6300552923a8573cd31cd73ae6 Mon Sep 17 00:00:00 2001
From: Syphax <gs_bouazzouni@esi.dz>
Date: Tue, 22 Oct 2024 08:05:48 +0200
Subject: [PATCH 66/72] move federation canonical to federation helper

---
 app/controllers/concerns/submission_filter.rb | 10 +-------
 app/helpers/federation_helper.rb              | 23 ++++++++++++-------
 2 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
index fd7becd364..c35fadd950 100644
--- a/app/controllers/concerns/submission_filter.rb
+++ b/app/controllers/concerns/submission_filter.rb
@@ -68,21 +68,13 @@ def ontologies_with_filters_url(filters, page: 1, count: false)
   def merge_by_acronym(submissions)
     merged_submissions = []
     submissions.group_by { |x| x[:ontology]&.acronym }.each do |acronym, ontologies|
-      if ontologies.size.eql?(1)
-        ontology = ontologies.first
-      else
-        ontology = canonical_portal_ontology(ontologies)
-      end
-
+      ontology = canonical_ontology(ontologies)
       ontology[:sources] = ontologies.map { |x| x[:id] }
       merged_submissions << ontology
     end
     merged_submissions
   end
 
-  def canonical_portal_ontology(ontologies)
-    ontologies.select { |x| helpers.internal_ontology?(x[:id]) }.first || ontology_from_portal(ontologies, canonical_portal(ontologies))
-  end
 
   def filter_submissions(ontologies, query:, status:, show_views:, private_only:, languages:, page_size:, formality_level:, is_of_type:, groups:, categories:, formats:)
     submissions = LinkedData::Client::Models::OntologySubmission.all(include: BROWSE_ATTRIBUTES.join(','), also_include_views: true, display_links: false, display_context: false)
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 01c84e0148..67d4a40eae 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -123,8 +123,20 @@ def federation_external_class?(class_object)
     !class_object.links['self'].include?($REST_URL)
   end
 
+  def canonical_ontology(ontologies)
+    if ontologies.size.eql?(1)
+      ontologies.first
+    else
+      internal_ontology = ontologies.select { |x| helpers.internal_ontology?(x[:id]) }.first
+      if internal_ontology
+        internal_ontology
+      else
+        external_canonical_ontology_portal(ontologies)
+      end
+    end
+  end
 
-  def canonical_portal(ontologies)
+  def external_canonical_ontology_portal(ontologies)
     portal_counts = Hash.new(0)
     # Count occurrences of each portal in the pull_location URL
     ontologies.each do |ontology|
@@ -135,16 +147,15 @@ def canonical_portal(ontologies)
       end
     end
     # Determine the portal with the most occurrences
-    canonical_portal = portal_counts.max_by { |_, count| count }&.first
+    portal = portal_counts.max_by { |_, count| count }&.first
 
-    canonical_portal
+    ontologies.select{|o| o[:id].include?(portal.to_s)}.first
   end
 
   def apply_canonical_portal(search_results, all_submissions)
     search_results.each do |result|
       next if result[:root][:portal_name].nil? || result[:root][:other_portals].blank?
 
-      root_link = result[:root][:link].split('?').first
       candidates = [result[:root][:link]] + result[:root][:other_portals].map { |p| p[:link].split('?').first }
 
       portal_counts = Hash.new(0)
@@ -171,8 +182,4 @@ def swap_portal_attributes(root_portal, new_portal)
     root_portal[:portal_light_color], new_portal[:portal_light_color] = new_portal[:portal_light_color], root_portal[:portal_light_color]
   end
 
-  def ontology_from_portal(ontologies, portal)
-    ontologies.select{|o| o[:id].include?(portal.to_s)}.first
-  end
-
 end

From 6a2aba4e000da760930d2dd2ed74047575f77121 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 23 Oct 2024 10:00:48 +0200
Subject: [PATCH 67/72] clean swap portal attributes function in federation
 helper

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

diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 67d4a40eae..db99831d18 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -176,10 +176,9 @@ def apply_canonical_portal(search_results, all_submissions)
   end
 
   def swap_portal_attributes(root_portal, new_portal)
-    root_portal[:link], new_portal[:link] = new_portal[:link], root_portal[:link]
-    root_portal[:portal_name], new_portal[:portal_name] = new_portal[:portal_name], root_portal[:portal_name]
-    root_portal[:portal_color], new_portal[:portal_color] = new_portal[:portal_color], root_portal[:portal_color]
-    root_portal[:portal_light_color], new_portal[:portal_light_color] = new_portal[:portal_light_color], root_portal[:portal_light_color]
+    [:link, :portal_name, :portal_color, :portal_light_color].each do |attribute|
+      root_portal[attribute], new_portal[attribute] = new_portal[attribute], root_portal[attribute]
+    end
   end
 
 end

From a5c855f1ccda48b17c8d3fcae75cfaffeafb8ec1 Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 23 Oct 2024 11:06:39 +0200
Subject: [PATCH 68/72] fix and clean apply canincal portal function

---
 app/helpers/federation_helper.rb | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index db99831d18..38453c7360 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -141,9 +141,7 @@ def external_canonical_ontology_portal(ontologies)
     # Count occurrences of each portal in the pull_location URL
     ontologies.each do |ontology|
       federated_portals.keys.each do |portal|
-        if ontology[:pullLocation]&.include?(portal.to_s)
-          portal_counts[portal] += 1
-        end
+        portal_counts[portal] += 1 if ontology[:pullLocation]&.include?(portal.to_s)
       end
     end
     # Determine the portal with the most occurrences
@@ -156,14 +154,18 @@ def apply_canonical_portal(search_results, all_submissions)
     search_results.each do |result|
       next if result[:root][:portal_name].nil? || result[:root][:other_portals].blank?
 
-      candidates = [result[:root][:link]] + result[:root][:other_portals].map { |p| p[:link].split('?').first }
+      candidates = [result[:root][:link].split('?').first] + result[:root][:other_portals].map { |p| p[:link].split('?').first }
 
       portal_counts = Hash.new(0)
+
       candidates.each do |candidate|
-        submission = all_submissions.find { |s| s.id.split('/')[0...-2].join('/') == candidate }
 
-        federated_portals.keys.each do |portal|
-          portal_counts[portal] += 1 if submission&.include?(portal.to_s)
+        submission = all_submissions.find { |s| s.id&.include?(candidate.split('/').last) }
+
+        if submission
+          federated_portals.keys.each do |portal|
+            portal_counts[portal] += 1 if submission[:pullLocation]&.include?(portal.to_s)
+          end
         end
       end
 
@@ -173,6 +175,7 @@ def apply_canonical_portal(search_results, all_submissions)
       canonical_portal_result = result[:root][:other_portals].find { |r| r[:name] == canonical_portal.to_s }
       swap_portal_attributes(result[:root], canonical_portal_result) if canonical_portal_result
     end
+    return search_results
   end
 
   def swap_portal_attributes(root_portal, new_portal)

From 8b2182f10e8d50262b620bcf989a6e7ccc3499ac Mon Sep 17 00:00:00 2001
From: Bilel KIHAL <kb_kihal@esi.dz>
Date: Wed, 23 Oct 2024 11:18:55 +0200
Subject: [PATCH 69/72] extract count portals into a separate function from
 external_canonical_ontology_portal function + apply_canonical_portal function

---
 app/helpers/federation_helper.rb | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 38453c7360..4ba324c0e1 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -136,17 +136,19 @@ def canonical_ontology(ontologies)
     end
   end
 
-  def external_canonical_ontology_portal(ontologies)
+  def count_portals(ontologies_list)
     portal_counts = Hash.new(0)
-    # Count occurrences of each portal in the pull_location URL
-    ontologies.each do |ontology|
+    ontologies_list.each do |ontology|
       federated_portals.keys.each do |portal|
         portal_counts[portal] += 1 if ontology[:pullLocation]&.include?(portal.to_s)
       end
     end
-    # Determine the portal with the most occurrences
-    portal = portal_counts.max_by { |_, count| count }&.first
+    portal_counts
+  end
 
+  def external_canonical_ontology_portal(ontologies)
+    portal_counts = count_portals(ontologies)
+    portal = portal_counts.max_by { |_, count| count }&.first
     ontologies.select{|o| o[:id].include?(portal.to_s)}.first
   end
 
@@ -156,19 +158,14 @@ def apply_canonical_portal(search_results, all_submissions)
 
       candidates = [result[:root][:link].split('?').first] + result[:root][:other_portals].map { |p| p[:link].split('?').first }
 
-      portal_counts = Hash.new(0)
-
+      ontologies_list = []
       candidates.each do |candidate|
-
         submission = all_submissions.find { |s| s.id&.include?(candidate.split('/').last) }
-
-        if submission
-          federated_portals.keys.each do |portal|
-            portal_counts[portal] += 1 if submission[:pullLocation]&.include?(portal.to_s)
-          end
-        end
+        ontologies_list << submission if submission
       end
 
+      portal_counts = count_portals(ontologies_list)
+
       canonical_portal = portal_counts.max_by { |_, count| count }&.first
       next if canonical_portal.nil? || result[:root][:portal_name].eql?(canonical_portal.to_s)
 

From 55d0b716707e17451b797a7786201a99c5559a93 Mon Sep 17 00:00:00 2001
From: Syphax <gs_bouazzouni@esi.dz>
Date: Wed, 23 Oct 2024 21:27:11 +0200
Subject: [PATCH 70/72] put again search canonical logic the search_aggregator
 file and refactor the code

---
 app/controllers/concerns/search_aggregator.rb | 40 ++++++++++--
 app/helpers/federation_helper.rb              | 62 +++++--------------
 2 files changed, 53 insertions(+), 49 deletions(-)

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index b2f19a3438..870bf50667 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -39,9 +39,7 @@ def aggregate_results(query, results)
 
     search_results = merge_sort_federated_results(query, search_results) if federation_enabled?
 
-    search_results = apply_canonical_portal(search_results, all_submissions)
-
-    search_results
+    swap_canonical_portal_results_first(search_results, all_submissions)
   end
 
   def format_search_result(result, ontologies)
@@ -255,7 +253,13 @@ def merge_federated_results(search_results)
         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}
+          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]
+          }
           true
         else
           false
@@ -264,6 +268,34 @@ def merge_federated_results(search_results)
     end
   end
 
+  def swap_canonical_portal_results_first(search_results, all_submissions)
+    search_results.each do |result|
+      next if result[:root][:portal_name].nil? || result[:root][:other_portals].blank?
+
+      result_ontology_ids = [result[:root][:ontology_id]] + result[:root][:other_portals].map { |p| p[:ontology_id] }
+
+      result_submissions = all_submissions.select do |submission|
+        result_ontology_ids.any? { |ontology_id| submission.id.include?(ontology_id) }
+      end
+
+      canonical_portal = most_referred_portal(result_submissions)
+      is_internal_ontology = result[:root][:portal_name].eql?(canonical_portal.to_s)
+
+      next if canonical_portal.nil? || is_internal_ontology
+
+      canonical_portal_result = result[:root][:other_portals].find { |r| r[:name] == canonical_portal.to_s }
+      swap_portal_attributes(result[:root], canonical_portal_result) if canonical_portal_result
+    end
+    search_results
+  end
+
+
+  def swap_portal_attributes(root_portal, new_portal)
+    [:link, :portal_name, :portal_color, :portal_light_color].each do |attribute|
+      root_portal[attribute], new_portal[attribute] = new_portal[attribute], root_portal[attribute]
+    end
+  end
+
   def sort_results_by_string_similarity(query, search_results)
     search_results = search_results.sort_by do |entry|
       root_similarity = String::Similarity.cosine(query.downcase, entry[:root][:title].split('-').first.gsub(" ", "").downcase)
diff --git a/app/helpers/federation_helper.rb b/app/helpers/federation_helper.rb
index 136be8b615..135cae2883 100644
--- a/app/helpers/federation_helper.rb
+++ b/app/helpers/federation_helper.rb
@@ -148,51 +148,6 @@ def canonical_ontology(ontologies)
     end
   end
 
-  def count_portals(ontologies_list)
-    portal_counts = Hash.new(0)
-    ontologies_list.each do |ontology|
-      federated_portals.keys.each do |portal|
-        portal_counts[portal] += 1 if ontology[:pullLocation]&.include?(portal.to_s)
-      end
-    end
-    portal_counts
-  end
-
-  def external_canonical_ontology_portal(ontologies)
-    portal_counts = count_portals(ontologies)
-    portal = portal_counts.max_by { |_, count| count }&.first
-    ontologies.select{|o| o[:id].include?(portal.to_s)}.first
-  end
-
-  def apply_canonical_portal(search_results, all_submissions)
-    search_results.each do |result|
-      next if result[:root][:portal_name].nil? || result[:root][:other_portals].blank?
-
-      candidates = [result[:root][:link].split('?').first] + result[:root][:other_portals].map { |p| p[:link].split('?').first }
-
-      ontologies_list = []
-      candidates.each do |candidate|
-        submission = all_submissions.find { |s| s.id&.include?(candidate.split('/').last) }
-        ontologies_list << submission if submission
-      end
-
-      portal_counts = count_portals(ontologies_list)
-
-      canonical_portal = portal_counts.max_by { |_, count| count }&.first
-      next if canonical_portal.nil? || result[:root][:portal_name].eql?(canonical_portal.to_s)
-
-      canonical_portal_result = result[:root][:other_portals].find { |r| r[:name] == canonical_portal.to_s }
-      swap_portal_attributes(result[:root], canonical_portal_result) if canonical_portal_result
-    end
-    return search_results
-  end
-
-  def swap_portal_attributes(root_portal, new_portal)
-    [:link, :portal_name, :portal_color, :portal_light_color].each do |attribute|
-      root_portal[attribute], new_portal[attribute] = new_portal[attribute], root_portal[attribute]
-    end
-  end
-
   def federation_portal_status(portal_name: nil)
     Rails.cache.fetch("federation_portal_up_#{portal_name}", expires_in: 2.hours) do
       portal_api = federated_portals&.dig(portal_name,:api)
@@ -248,6 +203,7 @@ def init_federation_portals_status
       federation_input_chips
     end
   end
+
   def federated_search_counts(search_results)
     ids = search_results.map do |result|
       result.dig(:root, :ontology_id) || rest_url
@@ -276,4 +232,20 @@ def counts_ontology_ids_by_portal_name(portals_ids)
 
     counts
   end
+
+  def external_canonical_ontology_portal(ontologies)
+    canonical_portal = most_referred_portal(ontologies)
+    ontologies.select{|o| o[:id].include?(canonical_portal.to_s)}.first
+  end
+
+  def most_referred_portal(ontology_submissions)
+    portal_counts = Hash.new(0)
+    ontology_submissions.each do |submission|
+      federated_portals.keys.each do |portal|
+        portal_counts[portal] += 1 if submission[:pullLocation]&.include?(portal.to_s)
+      end
+    end
+    portal_counts.max_by { |_, count| count }&.first
+  end
+
 end

From a86ba778d8783d03756f373dc339501fb704b38c Mon Sep 17 00:00:00 2001
From: Syphax <gs_bouazzouni@esi.dz>
Date: Wed, 23 Oct 2024 21:30:47 +0200
Subject: [PATCH 71/72] do the search canonical logic only if enabled

---
 app/controllers/concerns/search_aggregator.rb | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
index 870bf50667..24cc2b292c 100644
--- a/app/controllers/concerns/search_aggregator.rb
+++ b/app/controllers/concerns/search_aggregator.rb
@@ -31,15 +31,17 @@ def aggregate_results(query, results)
 
     all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false)
 
-    all_submissions = LinkedData::Client::Models::OntologySubmission.all(include: 'pullLocation', include_views: true, display_links: false, display_context: false)
 
     search_results = grouped_results.map do |group|
       format_search_result(group, all_ontologies)
     end
 
-    search_results = merge_sort_federated_results(query, search_results) if federation_enabled?
+    if federation_enabled?
+      search_results = merge_sort_federated_results(query, search_results) if federation_enabled?
+      search_results = swap_canonical_portal_results_first(search_results)
+    end
 
-    swap_canonical_portal_results_first(search_results, all_submissions)
+    search_results
   end
 
   def format_search_result(result, ontologies)
@@ -268,7 +270,9 @@ def merge_federated_results(search_results)
     end
   end
 
-  def swap_canonical_portal_results_first(search_results, all_submissions)
+  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)
+
     search_results.each do |result|
       next if result[:root][:portal_name].nil? || result[:root][:other_portals].blank?
 

From 5a533f1c37310f9de5cd5565533fba252db062e6 Mon Sep 17 00:00:00 2001
From: Syphax <gs_bouazzouni@esi.dz>
Date: Wed, 23 Oct 2024 21:45:12 +0200
Subject: [PATCH 72/72] fix rest_hostname raising an exception that REST_URI
 does not exist

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

diff --git a/app/helpers/urls_helper.rb b/app/helpers/urls_helper.rb
index b193f0a084..2c149e29d4 100644
--- a/app/helpers/urls_helper.rb
+++ b/app/helpers/urls_helper.rb
@@ -5,7 +5,7 @@ def url_to_endpoint(url)
         endpoint
     end
     def rest_hostname
-        extract_hostname(REST_URI)
+        extract_hostname($REST_URL)
     end
 
     def extract_hostname(url)