From c4baf8a4a5e21388f966eb112430154c381468f6 Mon Sep 17 00:00:00 2001
From: Syphax <gs_bouazzouni@esi.dz>
Date: Tue, 17 Dec 2024 05:59:36 +0100
Subject: [PATCH] tmp

---
 app/assets/stylesheets/ontologies.scss        |  4 +-
 app/assets/stylesheets/tree.scss              |  4 +-
 app/components/chip_button_component.rb       | 10 +++
 app/components/chips_component.rb             | 16 ++++
 .../chips_component/chips_component.html.haml |  9 ++
 .../concept_details_component.html.haml       |  8 --
 app/components/rounded_button_component.rb    |  6 +-
 .../rounded_button_component.html.haml        |  4 +-
 app/controllers/concepts_controller.rb        | 17 ++--
 app/controllers/mappings_controller.rb        |  4 +-
 app/controllers/ontologies_controller.rb      |  5 +-
 app/helpers/application_helper.rb             | 73 ++++++++++++----
 app/helpers/concepts_helper.rb                | 14 ++++
 app/helpers/multi_languages_helper.rb         |  4 +-
 app/helpers/ontologies_helper.rb              | 10 +--
 app/javascript/controllers/index.js           |  3 +
 .../controllers/label_ajax_controller.js      | 83 +++++++++++++++++++
 .../controllers/load_chart_controller.js      | 10 +--
 app/views/concepts/_biomixer.html.erb         |  4 +-
 app/views/concepts/_details.html.haml         | 31 +------
 app/views/concepts/_show.html.haml            | 14 ++--
 app/views/ontologies/visualize.html.haml      |  2 +-
 config/initializers/omniauth.rb               |  3 +-
 23 files changed, 238 insertions(+), 100 deletions(-)
 create mode 100644 app/components/chip_button_component.rb
 create mode 100644 app/components/chips_component.rb
 create mode 100644 app/components/chips_component/chips_component.html.haml
 create mode 100644 app/javascript/controllers/label_ajax_controller.js

diff --git a/app/assets/stylesheets/ontologies.scss b/app/assets/stylesheets/ontologies.scss
index e1b23a8db5..0962624704 100644
--- a/app/assets/stylesheets/ontologies.scss
+++ b/app/assets/stylesheets/ontologies.scss
@@ -11,7 +11,6 @@ $ont-show-bg-color: #e9ecef;
 }
 
 .ontologies.show .gutter {
-  background-color: rgba(0, 0, 0, 0.03);
   background-repeat: no-repeat;
   background-position: center;
 
@@ -184,8 +183,9 @@ $ont-show-bg-color: #e9ecef;
 }
 
 #bd_content .sidebar {
-  overflow-x: auto;
   white-space: nowrap;
+  min-height: 70vh;
+  max-height: 90vh;
 }
 
 #search_box:focus {
diff --git a/app/assets/stylesheets/tree.scss b/app/assets/stylesheets/tree.scss
index 82bdffd14f..0697a56b5f 100644
--- a/app/assets/stylesheets/tree.scss
+++ b/app/assets/stylesheets/tree.scss
@@ -2,8 +2,8 @@
 ## TREE VIEW
 *********************/
 #tree_wrapper {
-  max-height: 70vh;
-  overflow-y: scroll;
+  max-height: 75vh;
+  overflow-y: auto;
 }
 
 div.tree_error {
diff --git a/app/components/chip_button_component.rb b/app/components/chip_button_component.rb
new file mode 100644
index 0000000000..316717fe71
--- /dev/null
+++ b/app/components/chip_button_component.rb
@@ -0,0 +1,10 @@
+class ChipButtonComponent < ViewComponent::Base
+    def initialize(url: nil, text: nil, type: "static", disabled: false, tooltip: nil  ,**html_options)
+        @url = url
+        @text = text
+        @type = type
+        @disabled = disabled
+        @tooltip = tooltip
+        @html_options = html_options.merge({href: @url})
+    end
+end
\ No newline at end of file
diff --git a/app/components/chips_component.rb b/app/components/chips_component.rb
new file mode 100644
index 0000000000..624681f812
--- /dev/null
+++ b/app/components/chips_component.rb
@@ -0,0 +1,16 @@
+class ChipsComponent < ViewComponent::Base
+
+    renders_one :count
+    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
+    end
+
+    def checked?
+        @checked
+    end
+end
\ No newline at end of file
diff --git a/app/components/chips_component/chips_component.html.haml b/app/components/chips_component/chips_component.html.haml
new file mode 100644
index 0000000000..f08d5a33dd
--- /dev/null
+++ b/app/components/chips_component/chips_component.html.haml
@@ -0,0 +1,9 @@
+.chips-container{class: @disabled ?  'disabled' : '', 'data-controller': 'tooltip', title: @tooltip}
+  %div
+    %label{:for => "chips-#{@id}-check"}
+      %input{:id => "chips-#{@id}-check", :name => @name, :type => "checkbox", :value => @value, checked: checked?, disabled: @disabled}
+      %span
+        = inline_svg_tag 'check.svg', class: 'chips-check-icon'
+        %div
+          = @label
+        = count
diff --git a/app/components/concept_details_component/concept_details_component.html.haml b/app/components/concept_details_component/concept_details_component.html.haml
index e8c341b8c4..f7af5e94a3 100644
--- a/app/components/concept_details_component/concept_details_component.html.haml
+++ b/app/components/concept_details_component/concept_details_component.html.haml
@@ -22,11 +22,3 @@
 
           - row_hash_properties(bottom_set, @acronym).each do |row|
             - t.add_row(*row)
-
-        - if @concept_id
-          - t.row do |r|
-            - r.td(colspan: 2) do
-              %div.d-flex.justify-content-center.p-2#content_resource_formats
-                - [["json","json-ld-file"], ["xml","rdf-xml-file"] , ["ntriples","ntriples-file"], ["turtle","turtle-file"]].each do |format, icon|
-                  %div.mx-4{data: {controller: "tooltip"}, title: "Export in #{format.upcase}"}
-                    = link_to_format_modal(format, icon)
\ No newline at end of file
diff --git a/app/components/rounded_button_component.rb b/app/components/rounded_button_component.rb
index b2a0ce49c6..46058e3351 100644
--- a/app/components/rounded_button_component.rb
+++ b/app/components/rounded_button_component.rb
@@ -1,10 +1,12 @@
 class RoundedButtonComponent < ViewComponent::Base
-  def initialize(icon: "json.svg", link: "#", size: "small", target: '', title: '')
+  def initialize(id: nil, icon: "json.svg", link: "#", size: "small", target: '', title: '', data: nil)
     @icon = icon
     @link = link
     @size = size
     @target = target
     @title = title
+    @data = data
+    @id = id
   end
 
   def size
@@ -18,4 +20,4 @@ def size
     end
   end
 
-end
\ No newline at end of file
+end
diff --git a/app/components/rounded_button_component/rounded_button_component.html.haml b/app/components/rounded_button_component/rounded_button_component.html.haml
index f5f23aad59..040d6b9a6f 100644
--- a/app/components/rounded_button_component/rounded_button_component.html.haml
+++ b/app/components/rounded_button_component/rounded_button_component.html.haml
@@ -1,2 +1,2 @@
-%a.rounded-button{:href => @link, style: "height:"+size[0]+"; width:"+size[0]+"; border-radius:"+size[2]+";", target:@target, title: @title, 'data-controller':'tooltip'}
-    = inline_svg_tag @icon, style: "transform: scale("+size[1]+");"
+%a.rounded-button{id: @id, :href => @link, style: "height:"+size[0]+"; width:"+size[0]+"; border-radius:"+size[2]+";", target:@target, title: @title, 'data-controller':'tooltip', data: @data}
+    = content || inline_svg_tag(@icon, style: "transform: scale("+size[1]+");")
diff --git a/app/controllers/concepts_controller.rb b/app/controllers/concepts_controller.rb
index 94478c5373..4e22ea63ed 100644
--- a/app/controllers/concepts_controller.rb
+++ b/app/controllers/concepts_controller.rb
@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 class ConceptsController < ApplicationController
-  include MappingsHelper
+  include MappingsHelper, ConceptsHelper
 
   layout 'ontology'
 
@@ -47,17 +47,10 @@ def show
   end
 
   def show_label
-    @ontology = LinkedData::Client::Models::Ontology.find(params[:ontology])
-    @ontology ||= LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
-    not_found unless @ontology
-    # Retrieve a class prefLabel or return the class ID (URI)
-    # - mappings may contain class URIs that are not in bioportal (e.g. obo-xrefs)
-    cls = @ontology.explore.single_class(params[:concept])
-    # TODO: log any cls.errors
-    # TODO: NCBO-402 might be implemented here, but it throws off a lot of ajax result rendering.
-    # cls_label = cls.prefLabel({:use_html => true}) || cls_id
-    cls_label = cls.prefLabel || params[:concept]
-    render plain: cls_label
+  cls_id = params[:concept] || params[:id]  # cls_id should be a full URI
+    ont_id = params[:ontology]  # ont_id could be a full URI or an acronym
+
+    render inline: helpers.main_language_label(concept_label(ont_id, cls_id))
   end
 
   def show_definition
diff --git a/app/controllers/mappings_controller.rb b/app/controllers/mappings_controller.rb
index 1a5e67ab98..8d258ed6b2 100644
--- a/app/controllers/mappings_controller.rb
+++ b/app/controllers/mappings_controller.rb
@@ -4,7 +4,7 @@
 
 class MappingsController < ApplicationController
   include ActionView::Helpers::NumberHelper
-  include MappingStatistics
+  include MappingStatistics,MappingsHelper
 
   layout :determine_layout
   before_action :authorize_and_redirect, only: [:create, :new, :destroy]
@@ -83,7 +83,7 @@ def get_concept_table
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontologyid]).first
     @concept = @ontology.explore.single_class({ full: true }, params[:conceptid])
 
-    @mappings = @concept.explore.mappings
+    @mappings = get_concept_mappings(@concept)
     @type = params[:type]
     @delete_mapping_permission = check_delete_mapping_permission(@mappings)
     render partial: 'mappings/concept_mappings', layout: false
diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb
index 8281af0793..9588de729e 100644
--- a/app/controllers/ontologies_controller.rb
+++ b/app/controllers/ontologies_controller.rb
@@ -143,8 +143,9 @@ def classes
 
     unless @concept.id == "bp_fake_root"
       @notes = @concept.explore.notes
-      @mappings = get_concept_mappings(@concept)
-      @delete_mapping_permission = check_delete_mapping_permission(@mappings)
+      puts 'getting mappings'
+      # @mappings = get_concept_mappings(@concept)
+      # @delete_mapping_permission = check_delete_mapping_permission(@mappings)
     end
     
     update_tab(@ontology, @concept.id)
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index aa9f2bddf5..5341851084 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -3,7 +3,7 @@
 require 'digest/sha1'
 
 module ApplicationHelper
-  include ModalHelper
+  include ModalHelper, MultiLanguagesHelper
 
   RESOLVE_NAMESPACE = {:omv => "http://omv.ontoware.org/2005/05/ontology#", :skos => "http://www.w3.org/2004/02/skos/core#", :owl => "http://www.w3.org/2002/07/owl#",
                        :rdf => "http://www.w3.org/1999/02/22-rdf-syntax-ns#", :rdfs => "http://www.w3.org/2000/01/rdf-schema#", :metadata => "http://data.bioontology.org/metadata/",
@@ -152,10 +152,31 @@ def build_tree(node, string, id, submission)
 
 
   def tree_link_to_concept(li_id:, child:, ontology_acronym:, active_style:, lang: )
-    page_name = ontology_viewer_page_name(ontology_acronym, child.prefLabel, 'Classes')
+    page_name = ontology_viewer_page_name(ontology_acronym, main_language_label(child.prefLabel), 'Classes')
     open = child.expanded? ? "class='open'" : ''
-    href = ontology_acronym.blank? ? '#' :  "/ontologies/#{child.explore.ontology.acronym}/concepts/?id=#{CGI.escape(child.id)}&lang=#{lang}"
-    "<li #{open} id='#{li_id}'><a id='#{CGI.escape(child.id)}' data-bp-ont-page-name='#{page_name}' data-turbo=true data-turbo-frame='concept_show' href='#{href}' #{active_style}> #{child.prefLabel({ use_html: true })}</a>"
+    pref_label_html, tooltip = tree_node_label(child)
+    href = ontology_acronym.blank? ? '#' :  "/ontologies/#{ontology_acronym}/concepts/?id=#{CGI.escape(child.id)}&lang=#{lang}"
+    "<li #{open} id='#{li_id}'><a id='#{CGI.escape(child.id)}' data-bp-ont-page-name='#{page_name}' data-turbo=true data-turbo-frame='concept_show' href='#{href}' #{active_style} title='#{tooltip}'> #{pref_label_html}</a>"
+  end
+
+  def tree_node_label(child)
+    label = begin
+              child.prefLabel || child.label
+            rescue
+              child.id
+            end
+
+    if label.nil?
+      pref_label_html = link_last_part(child.id)
+    else
+      pref_label_lang, pref_label_html = select_language_label(label)
+      pref_label_lang = pref_label_lang.to_s.upcase
+      tooltip = pref_label_lang.eql?("@NONE") ? "" : pref_label_lang
+
+      pref_label_html = "<span class='obsolete_class'>#{pref_label_html.html_safe}</span>".html_safe if child.obsolete?
+    end
+
+    [pref_label_html, tooltip]
   end
 
   def tree_link_to_children(li_id:, child:, ontology_acronym:, lang: )
@@ -351,27 +372,47 @@ def bp_ont_link(ont_acronym)
     "/ontologies/#{ont_acronym}"
   end
 
+
   def bp_class_link(cls_id, ont_acronym)
-    ontology_path(id: ont_acronym, p: 'classes', conceptid: cls_id)
+    "#{bp_ont_link(ont_acronym)}?p=classes&conceptid=#{escape(cls_id)}&language=#{request_lang}"
+  end
+
+  def label_ajax_data_h(cls_id, ont_acronym, ajax_uri, cls_url)
+    { data:
+        {
+          'label-ajax-cls-id-value': cls_id,
+          'label-ajax-ontology-acronym-value': ont_acronym,
+          'label-ajax-ajax-url-value': ajax_uri,
+          'label-ajax-cls-id-url-value': cls_url
+        }
+    }
+  end
+
+  def label_ajax_data(cls_id, ont_acronym, ajax_uri, cls_url)
+    label_ajax_data_h(cls_id, ont_acronym, ajax_uri, cls_url)
+  end
+
+  def label_ajax_link(link, cls_id, ont_acronym, ajax_uri, cls_url, target = nil)
+    data = label_ajax_data(cls_id, ont_acronym, ajax_uri, cls_url)
+    options = {  'data-controller': 'label-ajax' }.merge(data)
+    options = options.merge({ target: target }) if target
+    content_tag(:span, class: 'mx-1') do
+      render ChipButtonComponent.new(url: link, text: cls_id, type: 'clickable', **options)
+    end
   end
 
   def get_link_for_cls_ajax(cls_id, ont_acronym, target = nil)
-    # NOTE: bp_ajax_controller.ajax_process_cls will try to resolve class labels.
-    # Uses 'http' as a more generic attempt to resolve class labels than .include? ont_acronym; the
-    # bp_ajax_controller.ajax_process_cls will try to resolve class labels and
-    # otherwise remove the UNIQUE_SPLIT_STR and the ont_acronym.
-    target = target.nil? ? '' : " target='#{target}' "
-
-    if cls_id.start_with?('http://', 'https://')
-      href_cls = " href='#{bp_class_link(cls_id, ont_acronym)}' "
-      data_cls = " data-cls='#{cls_id}' "
-      data_ont = " data-ont='#{ont_acronym}' "
-      "<a class='cls4ajax' #{data_ont} #{data_cls} #{href_cls} #{target}>#{cls_id}</a>"
+    if cls_id.start_with?('http://') || cls_id.start_with?('https://')
+      link = bp_class_link(cls_id, ont_acronym)
+      ajax_url = "/ajax/classes/label?language=#{request_lang}"
+      cls_url = "/ontologies/#{ont_acronym}?p=classes&conceptid=#{CGI.escape(cls_id)}"
+      label_ajax_link(link, cls_id, ont_acronym, ajax_url , cls_url ,target)
     else
       content_tag(:div, cls_id)
     end
   end
 
+
   def get_link_for_ont_ajax(ont_acronym)
     # Ajax call will replace the acronym with an ontology name (triggered by class='ont4ajax')
     href_ont = " href='#{bp_ont_link(ont_acronym)}' "
diff --git a/app/helpers/concepts_helper.rb b/app/helpers/concepts_helper.rb
index da04a368fb..04986f4214 100644
--- a/app/helpers/concepts_helper.rb
+++ b/app/helpers/concepts_helper.rb
@@ -1,6 +1,20 @@
 # frozen_string_literal: true
 
 module ConceptsHelper
+  include MultiLanguagesHelper
+  def concept_label(ont_id, cls_id)
+    @ontology = LinkedData::Client::Models::Ontology.find(ont_id)
+    @ontology ||= LinkedData::Client::Models::Ontology.find_by_acronym(ont_id).first
+    ontology_not_found(ont_id) unless @ontology
+    # Retrieve a class prefLabel or return the class ID (URI)
+    # - mappings may contain class URIs that are not in bioportal (e.g. obo-xrefs)
+    cls = @ontology.explore.single_class({language: request_lang, include: 'prefLabel'}, cls_id)
+    # TODO: log any cls.errors
+    # TODO: NCBO-402 might be implemented here, but it throws off a lot of ajax result rendering.
+    #cls_label = cls.prefLabel({:use_html => true}) || cls_id
+    cls.prefLabel || cls_id
+  end
+
   def exclude_relation?(relation_to_check, ontology = nil)
     excluded_relations = %w[type rdf:type [R] SuperClass InstanceCount]
 
diff --git a/app/helpers/multi_languages_helper.rb b/app/helpers/multi_languages_helper.rb
index 9504a48095..bd5e38b738 100644
--- a/app/helpers/multi_languages_helper.rb
+++ b/app/helpers/multi_languages_helper.rb
@@ -1,4 +1,5 @@
 module MultiLanguagesHelper
+  include OntologiesHelper
 
   def portal_language_help_text
     t('language.portal_language_help_text')
@@ -110,6 +111,7 @@ def content_languages(submission = @submission || @submission_latest)
       [lang.english_name, lang.alpha2]
     end.compact
 
+    submission_lang << ['All languages', 'all']
     [submission_lang, current_lang]
   end
 
@@ -166,7 +168,7 @@ def display_in_multiple_languages(label)
           Array(value).map do |v|
             content_tag(:div, class: 'definition') do
               concat content_tag(:span, v)
-              concat content_tag(:span, key.upcase, class: 'badge badge-secondary ml-1') unless key.to_s.upcase.eql?('NONE') || key.to_s.upcase.eql?('@NONE')
+              concat content_tag(:span, key.upcase, class: 'badge bg-secondary ml-1') unless key.to_s.upcase.eql?('NONE') || key.to_s.upcase.eql?('@NONE')
             end
           end.join
         end.join)
diff --git a/app/helpers/ontologies_helper.rb b/app/helpers/ontologies_helper.rb
index 67d0c75f84..ad3763bb48 100644
--- a/app/helpers/ontologies_helper.rb
+++ b/app/helpers/ontologies_helper.rb
@@ -10,16 +10,16 @@ def ontology_object_json_link(ontology_acronym, object_type, id)
   end
 
   def render_permalink_link
-    content_tag(:div, class: 'mx-1') do
-      link_to("#classPermalinkModal", class: "class-permalink nav-link", title: t('concepts.permanent_link_class'), aria: { label: t('concepts.permanent_link_class') }, data: { toggle: "modal", current_purl: @current_purl }) do
-        content_tag(:i, '', class: "fas fa-link", aria: { hidden: "true" })
+    content_tag(:div,  class: 'concepts_json_button mx-2') do
+      render RoundedButtonComponent.new(id: 'classPermalink', link: 'javascript:void(0);', title: t('concepts.permanent_link_class'),  data: { 'bs-toggle': "modal", 'bs-target': "#classPermalinkModal", current_purl: @current_purl} ) do
+        inline_svg_tag('icons/copy_link.svg', width: 20, height: 20)
       end
     end
   end
 
   def render_concepts_json_button(link)
     content_tag(:div, class: 'concepts_json_button') do
-      render RoundedButtonComponent.new(link: link, target: '_blank')
+      render RoundedButtonComponent.new(link: link, target: '_blank', title: t('concepts.permanent_link_class'))
     end
   end
 
@@ -250,7 +250,7 @@ def visits_chart_dataset_array(visits_data, fill: true)
         data: x,
         borderWidth: 2,
         borderRadius: 5,
-        borderSkipped: false,
+        borderSkipped: true,
         cubicInterpolationMode: 'monotone',
         tension: 0.4,
         fill: fill
diff --git a/app/javascript/controllers/index.js b/app/javascript/controllers/index.js
index 8933fa1a6e..fdf72f2dca 100644
--- a/app/javascript/controllers/index.js
+++ b/app/javascript/controllers/index.js
@@ -39,3 +39,6 @@ application.register("turbo-frame", TurboFrameController)
 
 import TurboFrameErrorController from "./turbo_frame_error_controller"
 application.register("turbo-frame-error", TurboFrameErrorController)
+
+import LabelAjaxController from "./label_ajax_controller"
+application.register("label-ajax", LabelAjaxController)
diff --git a/app/javascript/controllers/label_ajax_controller.js b/app/javascript/controllers/label_ajax_controller.js
new file mode 100644
index 0000000000..d3cbcfff46
--- /dev/null
+++ b/app/javascript/controllers/label_ajax_controller.js
@@ -0,0 +1,83 @@
+import {Controller} from "@hotwired/stimulus"
+import useAjax from "../mixins/useAjax";
+
+// Connects to data-controller="label-ajax"
+export default class extends Controller {
+    static values = {
+        clsId: String,
+        ontologyAcronym: String,
+        ajaxUrl: String,
+        clsIdUrl: String,
+    }
+
+    connect() {
+        setTimeout(() => {
+            this.linkA = jQuery(this.element);
+
+            if (this.linkA.hasClass('ajax-modified-cls')) {
+                return true
+            }
+
+            this.cls_id = this.clsIdValue;
+            this.ont_acronym = this.ontologyAcronymValue;
+    
+            let ajax_uri = new URL(this.ajaxUrlValue, document.location.origin)
+    
+            ajax_uri.searchParams.set('ontology', this.ont_acronym)
+            ajax_uri.searchParams.set('id', this.cls_id)
+    
+    
+            this.request = useAjax({
+                url: ajax_uri.pathname + ajax_uri.search,
+                timeout: ajax_process_timeout * 1000,
+                success: this.#ajaxSuccess.bind(this),
+                error: this.#ajaxError.bind(this)
+            });
+          },1)
+    }
+
+    abort() {
+        if (this.request) {
+            this.request.abort()
+            this.request = null
+        }
+    }
+
+    disconnect() {
+        this.abort()
+    }
+
+    #ajaxSuccess(data) {
+        data = data.trim();
+        if (typeof data !== "undefined" && data.length > 0 && data.indexOf("http") !== 0) {
+            let cls_name = data
+            let cls_uri = this.clsIdUrlValue
+            this.linkA.html(cls_name);
+            this.linkA.attr('href', cls_uri);
+            this.linkA.addClass('ajax-modified-cls');
+            //find and process any identical classes (low probability)
+            this.#fillIdenticalIds(cls_name, cls_uri)
+        } else {
+            // remove the unique_id separator and the ontology acronym from the href
+            this.linkA.attr('href', this.cls_id);  // it may not be an ontology class, don't use the cls_uri
+            this.linkA.addClass('ajax-modified-cls');
+        }
+    }
+
+    #ajaxError() {
+        this.linkA.addClass('ajax-error')
+    }
+
+    #fillIdenticalIds(cls_name, cls_uri) {
+
+        let unique_id = this.linkA.attr('href');
+        jQuery('a[href="' + unique_id + '"]').each(function () {
+            let link = jQuery(this);
+            if (!link.hasClass('ajax-modified-cls')) {
+                link.html(cls_name);
+                link.attr('href', cls_uri);
+                link.addClass('ajax-modified-cls')
+            }
+        });
+    }
+}
diff --git a/app/javascript/controllers/load_chart_controller.js b/app/javascript/controllers/load_chart_controller.js
index c55b5adbb3..7f34a5e24a 100644
--- a/app/javascript/controllers/load_chart_controller.js
+++ b/app/javascript/controllers/load_chart_controller.js
@@ -57,25 +57,25 @@ export default class extends Controller {
     if (this.indexAxisValue === axe) {
       return {
         border: {
-          display: false
+          display: true
         },
         grid: {
           display: false
         },
         ticks: {
-          beginAtZero: false
+          beginAtZero: true
         }
       }
     } else {
       return {
         border: {
-          display: false
+          display: true
         },
         grid: {
-          display: false
+          display: true
         },
         ticks: {
-          display: false
+          display: true
         }
       }
     }
diff --git a/app/views/concepts/_biomixer.html.erb b/app/views/concepts/_biomixer.html.erb
index 53fbff6a80..84ff4140a2 100644
--- a/app/views/concepts/_biomixer.html.erb
+++ b/app/views/concepts/_biomixer.html.erb
@@ -36,7 +36,7 @@ jQuery(document).data().bp.biomixer_fullscreen.toggle = function(toggle) {
     jQuery("#biomixer_container").css("padding", 0).css("width", jQuery(document).data().bp.biomixer_fullscreen.bio_container_w);
     jQuery("#bd_content").trigger('resize');
   } else {
-    height = jQuery(window).height() - jQuery("#bd_content .cls-info-container").offset().top - 50;
+    height = jQuery(window).height() -  50;
     jQuery("#bd_content .cls-info-container").css("width", "100%").css("height", height);
     jQuery("#bd .bd_content .cls-info-container #contents").css("max-height", height);
     jQuery("#biomixer_container").css("padding", 0).css("width", "100%").css("height", height);
@@ -44,7 +44,7 @@ jQuery(document).data().bp.biomixer_fullscreen.toggle = function(toggle) {
 }
 
 window.onmessage = function(e) {
-  var iframeHeight = jQuery(window).height() - jQuery("#bd_content .cls-info-container").offset().top - 50;
+  var iframeHeight = jQuery(window).height() -  50;
   if (e.data === "biomixer_full_screen_request") {
     if (jQuery(document).data().bp.biomixer_fullscreen.enabled) {
       // make small
diff --git a/app/views/concepts/_details.html.haml b/app/views/concepts/_details.html.haml
index a0b27cb7c7..208b0f5b5b 100644
--- a/app/views/concepts/_details.html.haml
+++ b/app/views/concepts/_details.html.haml
@@ -1,13 +1,8 @@
 = turbo_frame_tag(params[:modal] ? 'application_modal_content' : 'concept_details', class: 'd-block p-2') do
-  - schemes_keys = %w[hasTopConcept topConceptOf]
-  - label_xl_set = %w[skos-xl#prefLabel skos-xl#altLabel skos-xl#hiddenLabel]
-
-
   = render ConceptDetailsComponent.new(id:'concept-details', acronym: @ontology.acronym, concept_id: @concept.id,
                 properties: @concept.properties,
                 top_keys: %w[description comment],
-                bottom_keys: %w[disjoint subclass is_a has_part],
-                exclude_keys: schemes_keys + label_xl_set + ['inScheme', 'narrower']) do |c|
+                bottom_keys: %w[disjoint subclass is_a has_part]) do |c|
 
     - c.header(stripped: true) do |t|
       - t.add_row({th: t('ontology_details.concept.id')}, {td:link_to_with_actions(@concept.id, acronym: @ontology.acronym)})
@@ -32,26 +27,4 @@
       - if @concept.obsolete?
         - t.add_row({th: t('ontology_details.concept.obsolete')}, {td: 'true'})
 
-      - if skos?
-        - unless @concept.memberOf.nil?  || @concept.memberOf.empty?
-          - t.add_row({th: t('ontology_details.concept.member_of')}) do |h|
-            - h.td do
-              - @concept.memberOf.each do |v|
-                %span.m-1
-                  = raw get_link_for_collection_ajax(v, @ontology.acronym, '_blank')
-
-        - unless @concept.inScheme.nil?  || @concept.inScheme.empty?
-          - t.add_row({th: t('ontology_details.concept.in_schemes')}) do |h|
-            - h.td do
-              - @concept.inScheme.each do |v|
-                %span.m-1
-                  = raw get_link_for_scheme_ajax(v, @ontology.acronym, '_blank')
-
-        - t.add_row({th: t('ontology_details.concept.type')} , {td: @concept.type})
-
-
-    - c.add_sections(schemes_keys) do |v|
-      - get_link_for_scheme_ajax(v, @ontology.acronym, '_blank')
-
-    - c.add_sections(label_xl_set) do |v|
-      - get_link_for_label_xl_ajax(v, @ontology.acronym, @concept.id)
+      - t.add_row({th: t('ontology_details.concept.type')} , {td: @concept.type})
diff --git a/app/views/concepts/_show.html.haml b/app/views/concepts/_show.html.haml
index 4a9550638b..399a62cde6 100644
--- a/app/views/concepts/_show.html.haml
+++ b/app/views/concepts/_show.html.haml
@@ -25,14 +25,14 @@
           src:"/ajax/mappings/get_concept_table?ontologyid=#{@ontology.acronym}&conceptid=#{CGI.escape(@concept.id)}")
 
 
-    :javascript
-      jQuery(document).ready(function(){
-        jQuery("#classPermalinkModal").on("shown.bs.modal", function (e) {
-        var currentPurl = jQuery("a.class-permalink").data("current-purl");
+  :javascript
+    jQuery(document).ready(function(){
+      jQuery("#classPermalinkModal").on("shown.bs.modal", function (e) {
+        var currentPurl = jQuery("#classPermalink").data("current-purl");
         jQuery("#purl_input").val(currentPurl);
-        })
+      })
 
-        jQuery("#purl_input").on("click", function () {
+      jQuery("#purl_input").on("click", function () {
         jQuery(this).select();
-        });
       });
+    });
diff --git a/app/views/ontologies/visualize.html.haml b/app/views/ontologies/visualize.html.haml
index c9d407d263..7127dd4d0e 100644
--- a/app/views/ontologies/visualize.html.haml
+++ b/app/views/ontologies/visualize.html.haml
@@ -3,7 +3,7 @@
     - @title = "#{@ontology.name} - #{@concept.prefLabel}"
     %div.tooltip
     %div#bd_content.bd_content.explore.py-3{data:{controller: 'container-splitter'}}
-      %div.sidebar.d-flex.flex-column.pr-2{data:{'container-splitter-target': 'container'}}
+      %div.card.sidebar.d-flex.flex-column.p-1.mx-2{data:{'container-splitter-target': 'container'}}
         %div#qsearch.input-group.pb-2.pe-1
           %span.input-group-text Jump to:
           = text_field_tag("search_box", nil, class: "form-control rounded-end", aria: {label: "Jump to:"},
diff --git a/config/initializers/omniauth.rb b/config/initializers/omniauth.rb
index c7c4027c3e..c0ac6bd0c9 100644
--- a/config/initializers/omniauth.rb
+++ b/config/initializers/omniauth.rb
@@ -1,5 +1,4 @@
 Rails.application.config.middleware.use OmniAuth::Builder do
   Array($OMNIAUTH_PROVIDERS).each do |provider, config|
-    provider config[:strategy] || provider, config[:client_id], config[:client_secret], client_options: {}.merge(config[:client_options].to_h)
   end
-end
\ No newline at end of file
+end