Merge branch 'master' into feature/migrate-ruby-3

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 23ae179ca9e6aa858b4ceabc454876ff9a65420b
+  revision: f5b82f304abaf6f0a4ee671729120973084189e5
   branch: development
   specs:
     ontologies_api_client (2.2.0)
@@ -104,7 +104,8 @@ GEM
       autoprefixer-rails (>= 9.1.0)
       popper_js (>= 1.14.3, < 2)
       sassc-rails (>= 2.0.0)
-    brakeman (5.4.1)
+    brakeman (7.0.0)
+      racc
     bugsnag (6.27.1)
       concurrent-ruby (~> 1.0)
     builder (3.3.0)
@@ -124,11 +125,11 @@ GEM
       capistrano-bundler (>= 1.1, < 3)
     capistrano-yarn (2.0.2)
       capistrano (~> 3.0)
-    capybara (3.39.2)
+    capybara (3.40.0)
       addressable
       matrix
       mini_mime (>= 0.1.3)
-      nokogiri (~> 1.8)
+      nokogiri (~> 1.11)
       rack (>= 1.6.0)
       rack-test (>= 0.6.3)
       regexp_parser (>= 1.5, < 3.0)
@@ -146,7 +147,7 @@ GEM
       bigdecimal
       rexml
     crass (1.0.6)
-    css_parser (1.17.1)
+    css_parser (1.21.0)
       addressable
     csv (3.3.2)
     dalli (3.2.8)
@@ -155,7 +156,7 @@ GEM
       irb (~> 1.10)
       reline (>= 0.3.8)
     deepl-rb (3.2.0)
-    diff-lcs (1.5.1)
+    diff-lcs (1.6.0)
     docile (1.4.1)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
@@ -197,7 +198,8 @@ GEM
       railties (>= 5.1)
     hashdiff (1.1.2)
     hashie (5.0.0)
-    highline (2.1.0)
+    highline (3.1.2)
+      reline
     html2haml (2.3.0)
       erubis (~> 2.7.0)
       haml (>= 4.0)
@@ -222,7 +224,7 @@ GEM
       terminal-table (>= 1.5.1)
     i18n-tasks-csv (1.1)
       i18n-tasks (~> 0.9)
-    importmap-rails (2.0.3)
+    importmap-rails (2.1.0)
       actionpack (>= 6.0.0)
       activesupport (>= 6.0.0)
       railties (>= 6.0.0)
@@ -244,7 +246,7 @@ GEM
       railties (>= 3.2.16)
     jsbundling-rails (1.3.1)
       railties (>= 6.0.0)
-    json (2.9.1)
+    json (2.10.1)
     json-jwt (1.16.7)
       activesupport (>= 4.2)
       aes_key_wrap
@@ -266,10 +268,11 @@ GEM
       letter_opener (~> 1.7)
       railties (>= 5.2)
       rexml
+    lint_roller (1.1.0)
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    logger (1.6.5)
+    logger (1.6.6)
     loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
@@ -298,10 +301,10 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2025.0107)
+    mime-types-data (3.2025.0204)
     mini_mime (1.1.5)
     minitest (5.25.4)
-    msgpack (1.7.5)
+    msgpack (1.8.0)
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.4.1)
@@ -311,7 +314,7 @@ GEM
       time
     net-http (0.3.2)
       uri
-    net-imap (0.4.18)
+    net-imap (0.5.6)
       date
       net-protocol
     net-pop (0.1.2)
@@ -322,7 +325,7 @@ GEM
       net-ssh (>= 2.6.5, < 8.0.0)
     net-sftp (4.0.0)
       net-ssh (>= 5.0.0, < 8.0.0)
-    net-smtp (0.5.0)
+    net-smtp (0.5.1)
       net-protocol
     net-ssh (7.3.0)
     netrc (0.11.0)
@@ -372,7 +375,7 @@ GEM
       omniauth (~> 2.0)
     ostruct (0.6.1)
     parallel (1.26.3)
-    parser (3.3.7.0)
+    parser (3.3.7.1)
       ast (~> 2.4.1)
       racc
     popper_js (1.16.1)
@@ -385,11 +388,11 @@ GEM
     psych (5.2.3)
       date
       stringio
-    public_suffix (5.1.1)
+    public_suffix (6.0.1)
     puma (5.6.9)
       nio4r (~> 2.0)
     racc (1.8.1)
-    rack (2.2.10)
+    rack (2.2.11)
     rack-protection (3.2.0)
       base64 (>= 0.1.0)
       rack (~> 2.2, >= 2.2.4)
@@ -430,7 +433,7 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.11.1)
       ffi (~> 1.0)
-    rdoc (6.11.0)
+    rdoc (6.12.0)
       psych (>= 4.0.0)
     recaptcha (5.9.0)
       json
@@ -447,15 +450,15 @@ GEM
       netrc (~> 0.8)
     rexml (3.4.0)
     rouge (4.5.1)
-    rspec-core (3.13.2)
+    rspec-core (3.13.3)
       rspec-support (~> 3.13.0)
     rspec-expectations (3.13.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-mocks (3.13.2)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-rails (7.1.0)
+    rspec-rails (7.1.1)
       actionpack (>= 7.0)
       activesupport (>= 7.0)
       railties (>= 7.0)
@@ -464,9 +467,10 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.2)
-    rubocop (1.71.1)
+    rubocop (1.72.0)
       json (~> 2.3)
-      language_server-protocol (>= 3.17.0)
+      language_server-protocol (~> 3.17.0.2)
+      lint_roller (~> 1.1.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
@@ -493,7 +497,9 @@ GEM
       sprockets (> 3.0)
       sprockets-rails
       tilt
-    selenium-webdriver (4.9.0)
+    selenium-webdriver (4.28.0)
+      base64 (~> 0.2)
+      logger (~> 1.4)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
@@ -518,16 +524,17 @@ GEM
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       sprockets (>= 3.0.0)
-    sshkit (1.23.2)
+    sshkit (1.24.0)
       base64
+      logger
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
       ostruct
     stimulus-rails (1.3.4)
       railties (>= 6.0.0)
     string-similarity (2.1.0)
-    stringio (3.1.2)
+    stringio (3.1.3)
     temple (0.10.3)
     terminal-table (4.0.0)
       unicode-display_width (>= 1.1.1, < 4)
@@ -558,7 +565,7 @@ GEM
       activemodel (>= 6.0.0)
       bindex (>= 0.4.0)
       railties (>= 6.0.0)
-    webmock (3.24.0)
+    webmock (3.25.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)

app/assets/stylesheets/concepts.scss

@@ -167,3 +167,11 @@ div.synonym-change-request button {
   margin-top: -4px;
 }
 
+.concept_details_component{
+  .chip-button-component-container{
+    word-break: break-word !important;
+    overflow-wrap: break-word !important;
+    white-space: normal !important;
+  }
+}
+

app/controllers/application_controller.rb

@@ -326,7 +326,7 @@ def get_class(params)
         # TODO_REV: Support views? Replace old view call: @ontology.top_level_classes(view)
         @roots = @ontology.explore.roots(concept_schemes: params[:concept_schemes]) rescue nil
 
-        if @roots.nil? || response_error?(@roots) || @roots.compact&.empty?
+        if @roots.blank? || response_error?(@roots) || @roots.compact&.empty?
           LOG.add :debug, t('application.missing_roots_for_ontology', acronym: @ontology.acronym)
           classes = @ontology.explore.classes.collection
           @concept = classes.first.explore.self(full: true) if classes&.first

app/controllers/concepts_controller.rb

@@ -23,7 +23,7 @@ def show
     redirect_to(ontology_path(id: params[:ontology], p: 'classes', conceptid: params[:id], lang: request_lang)) and return unless turbo_frame_request?
 
     @submission = get_ontology_submission_ready(@ontology)
-    @concept = @ontology.explore.single_class({full: true, language: request_lang}, params[:id])
+    @concept = @ontology.explore.single_class({ full: true, language: request_lang }, params[:id])
     @instances_concept_id = @concept.id
 
     concept_not_found(params[:id]) if @concept.nil?
@@ -40,22 +40,21 @@ def index
       return
     end
 
-    # Note that find_by_acronym includes views by default
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
-
-    @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri')
-
-    @concept = @ontology.explore.single_class({dispay: 'prefLabel'}, params[:id])
-
-    concept_not_found(params[:id]) if @concept.nil?
+    @submission = LinkedData::Client::Models::Ontology.explore(params[:ontology])
+                                                      .latest_submission
+                                                      .get(include: 'uriRegexPattern,preferredNamespaceUri')
     @schemes = params[:concept_schemes].split(',')
 
-    @concept.children = @concept.explore.children(pagesize: 750, concept_schemes: Array(@schemes).join(','), language: request_lang, display: 'prefLabel,obsolete,hasChildren').collection || []
+    @concept = LinkedData::Client::Models::Class.new(values: { id: params[:id] })
 
+    @concept.children = LinkedData::Client::Models::Ontology.explore(params[:ontology])
+                                                            .classes(params[:id])
+                                                            .children
+                                                            .get(pagesize: 750, concept_schemes: Array(@schemes).join(','), language: request_lang, display: 'prefLabel,obsolete,hasChildren').collection || []
     render turbo_stream: [
       replace(helpers.child_id(@concept) + '_open_link') { TreeLinkComponent.tree_close_icon },
       replace(helpers.child_id(@concept) + '_childs') do
-        helpers.concepts_tree_component(@concept, @concept, @ontology.acronym, Array(@schemes), request_lang, sub_tree: true, submission: @submission)
+        helpers.concepts_tree_component(@concept, @concept, params[:ontology], Array(@schemes), request_lang, sub_tree: true, submission: @submission)
       end
     ]
   end
@@ -84,11 +83,11 @@ def show_definition
 
   def show_tree
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
-    @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri')
+    @submission = @ontology.explore.latest_submission(include: 'uriRegexPattern,preferredNamespaceUri')
     if @ontology.nil? || @ontology.errors
       ontology_not_found(params[:ontology])
     else
-      get_class(params) #application_controller
+      get_class(params) # application_controller
 
       not_found(t('concepts.missing_roots')) if @root.nil?
 
@@ -109,8 +108,8 @@ def show_date_sorted_list
       auto_click = page.to_s.eql?('1')
       params = {
         page: page,
-        sortby:'modified,created',
-        order:'desc,desc',
+        sortby: 'modified,created',
+        order: 'desc,desc',
         display: 'prefLabel,modified,created',
         language: request_lang
       }
@@ -142,32 +141,27 @@ def details
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
     ontology_not_found(params[:ontology]) if @ontology.nil?
 
-    @concept = @ontology.explore.single_class({full: true}, CGI.unescape(params[:conceptid]))
+    @concept = @ontology.explore.single_class({ full: true }, CGI.unescape(params[:conceptid]))
     concept_not_found(CGI.unescape(params[:conceptid])) if @concept.nil? || @concept.errors
     @container_id = params[:modal] ? 'application_modal_content' : 'concept_details'
 
     render :partial => "details"
   end
 
-
   def biomixer
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
     ontology_not_found(params[:ontology]) if @ontology.nil?
 
-    @concept = @ontology.explore.single_class({full: true}, params[:conceptid])
+    @concept = @ontology.explore.single_class({ full: true }, params[:conceptid])
     concept_not_found(params[:conceptid]) if @concept.nil?
 
     render partial: "biomixer", layout: false
   end
 
-
   private
 
-
-
-
   def filter_concept_with_no_date(concepts)
-    concepts.filter { |c| !concept_date(c).nil?}
+    concepts.filter { |c| !concept_date(c).nil? }
   end
 
   def concepts_to_years_months(concepts)

app/helpers/federation_helper.rb

@@ -118,7 +118,7 @@ def federation_error?(response)
   end
 
   def federation_error(response)
-    federation_errors = response[:errors].map { |e| ontology_portal_name(e.split(' ').last.gsub('search', '')) }
+    federation_errors = response[:errors].map { |e| e.split(' ').last }
     federation_errors.map { |p| "#{p} #{t('federation.not_responding')} " }.join(' ')
   end
 

app/helpers/home_helper.rb

@@ -24,8 +24,8 @@ def format_number_abbreviated(number)
     end
   end
 
-  def portal_config_tooltip(portal_name, &block)
-    portal_id = portal_name&.downcase
+  def portal_config_tooltip(portal, &block)
+    portal_id = portal&.downcase
     title = if (federation_portal_status(portal_name: portal_id) || portal_id.eql?(portal_name&.downcase))
       render(
         TurboFrameComponent.new(

app/helpers/multi_languages_helper.rb

@@ -166,7 +166,7 @@ def main_language_label(label)
   end
 
   # @param label String | Array | OpenStruct
-  def display_in_multiple_languages(label, show_max: 5, style_as_badge: false)
+  def display_in_multiple_languages(label, style_as_badge: false, show_max: 5)
     if label.blank?
       return render Display::AlertComponent.new(message: t('ontology_details.concept.no_preferred_name_for_selected_language'),
                                                 type: "warning",