tmp

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 {

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 {

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

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

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

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)

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
+end

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]+");")

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

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

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)

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)}' "

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]
 

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)

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

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)