Merge remote-tracking branch 'ontoportal-lirmm/master'

Align to 3.0.2 of AgroPortal

.env.sample

@@ -10,6 +10,8 @@ API_KEY=
 
 UI_THEME=ontoportal
 
+TWITTER_NEWS=
+
 BIOMIXER_URL=
 BIOMIXER_APIKEY=
 

app/assets/stylesheets/components/tree_view.scss

@@ -35,7 +35,6 @@ padding:0;
 a.tree-link {
     display: inline-block;
     padding: 5px;
-    word-break: break-all;
     text-wrap: wrap;
     color: var(--primary-color) !important;
 }

app/assets/stylesheets/taxonomy.scss

@@ -109,4 +109,23 @@
     background-color: var(--primary-color);
 }
 
+.taxonomy-empty-illustration{
+    display: flex;
+    flex-direction: column;
+    align-items: center;
+    justify-content: center;
+    width: 100%;
+    .browse-empty-illustration {
+        margin-top: 40px;
+    }
+}
+
+
+.taxonomy-empty-illustration-text{
+    color: var(--gray-color);
+
+}
+.taxonomy-empty-illustration-button{
+    width: 168px;
+}
 

app/components/federated_portal_button_component.rb

@@ -2,6 +2,7 @@
 
 class FederatedPortalButtonComponent < ViewComponent::Base
   attr_reader :name, :tooltip, :link, :color, :light_color
+  include UrlsHelper
 
   def initialize(name:, link:, color:, tooltip:, light_color:)
     @name = name
@@ -10,4 +11,8 @@ def initialize(name:, link:, color:, tooltip:, light_color:)
     @color = color
     @light_color = light_color
   end
+
+  def internal?
+    !link?(@link)
+  end
 end

app/components/federated_portal_button_component/federated_portal_button_component.html.haml

@@ -1,7 +1,7 @@
 %span{'data-controller': 'federation-portals-colors',
       'data-federation-portals-colors-color-value': color,
       'data-federation-portals-colors-portal-name-value': name.downcase}
-%a{ href: link, target: '_blank', 'data-controller' => 'tooltip', title: tooltip, class: 'federation-portal-button button icon-right', style: color ? "background-color: #{light_color} !important" : '' }
+%a{ href: link, target: internal? ? '_top' : '_blank', 'data-controller' => 'tooltip', title: tooltip, class: 'federation-portal-button button icon-right', style: color ? "background-color: #{light_color} !important" : '' }
   = inline_svg_tag('logos/ontoportal.svg', class: "federated-icon-#{name.downcase}")
   %div{ class: 'text', style: color ? "color: #{color} !important" : '' }
     = name.humanize.gsub("portal", "Portal")

app/controllers/admin/categories_controller.rb

@@ -11,6 +11,15 @@ class Admin::CategoriesController < ApplicationController
 
   def index
     @categories = _categories
+
+    @parents_list = Hash.new { |hash, key| hash[key] = [] }
+    @categories.each do |category|
+      category.parentCategory.each do |parent|
+        @parents_list[parent] << category.acronym
+      end
+    end
+
+
   end
 
   def new

app/controllers/application_controller.rb

@@ -27,7 +27,7 @@ def set_locale
     cookies.permanent[:locale] = I18n.locale if cookies[:locale].nil?
     logger.debug "* Locale set to '#{I18n.locale}'"
 
-    I18n.locale = portal_lang if portal_language_enabled?(I18n.locale)
+    I18n.locale = portal_lang unless portal_language_enabled?(I18n.locale)
 
     session[:locale] = I18n.locale
   end
@@ -253,12 +253,15 @@ def authorize_and_redirect
   end
 
   def authorize_admin
-    admin = session[:user] && session[:user].admin?
-    redirect_to_home unless admin
+    redirect_to_home unless current_user_admin?
   end
 
   def current_user_admin?
-    session[:user] && session[:user].admin?
+    session[:user]&.admin? || current_login_as_admin?
+  end
+
+  def current_login_as_admin?
+    session[:admin_user]&.admin?
   end
 
   def ontology_restricted?(acronym)
@@ -427,7 +430,7 @@ 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

app/controllers/concerns/search_aggregator.rb

@@ -251,18 +251,21 @@ def blacklist_cls_id_components(cls_id, blacklist_words)
   def merge_federated_results(search_results)
     search_results.each do |element|
       element[:root][:other_portals] = []
-
-      element[:reuses].reject! do |reuse|
-        element_ontology_id = element[:root][:ontology_id].split('/').last
-        element_uri = element[:root][:uri]
-        reuse_ontology_id = reuse[:root][:ontology_id].split('/').last
-        reuse_uri = reuse[:root][:uri]
-
-        if element_ontology_id == reuse_ontology_id && element_uri == reuse_uri
-          element[:root][:other_portals] << build_other_portal_entry(reuse)
-          true
-        else
-          false
+      element_ontology_id = element[:root][:ontology_id].split('/').last
+      element_uri = element[:root][:uri]
+      [element[:reuses], search_results].each do |collection|
+        collection.reject! do |entry|
+          next if entry == element
+
+          entry_ontology_id = entry[:root][:ontology_id].split('/').last
+          entry_uri = entry[:root][:uri]
+
+          if element_ontology_id == entry_ontology_id && element_uri == entry_uri
+            element[:root][:other_portals] << build_other_portal_entry(entry)
+            true
+          else
+            false
+          end
         end
       end
     end

app/controllers/home_controller.rb

@@ -48,6 +48,8 @@ def portal_config
     @config = $PORTALS_INSTANCES.select { |x| x[:name].downcase.eql?((params[:portal] || helpers.portal_name).downcase) }.first
     if @config && @config[:api]
       @portal_config = LinkedData::Client::Models::Ontology.top_level_links(@config[:api]).to_h
+      @color = @portal_config[:color].present? ? @portal_config[:color] : @config[:color]
+      @name = @portal_config[:title].present? ? @portal_config[:title] : @config[:name]
     else
       @portal_config = {}
     end

app/controllers/ontologies_controller.rb

@@ -60,17 +60,20 @@ def ontologies_filter
         end
       end.flatten
 
-      unless request_portals.empty?
+      if federated_request?
         streams += [
           replace('categories_refresh_for_federation') do
-            key = "categories"
+            key = 'categories'
             objects, checked_values, _ = @filters[key.to_sym]
+            objects = keep_only_root_categories(objects)
+
             helpers.browse_filter_section_body(checked_values: checked_values,
                                                key: key, objects: objects,
                                                counts: @count_objects[key.to_sym])
           end
         ]
       end
+
     else
       streams = [replace("ontologies_list_view-page-#{@page.page}", partial: 'ontologies/browser/ontologies')]
     end
@@ -583,4 +586,9 @@ def search_first_instance_id
     return !results.blank? ? results.first[:name] : nil
   end
 
+  def keep_only_root_categories(categories)
+    categories.select do |category|
+      category.id.start_with?(rest_url) || category.parentCategory.blank?
+    end
+  end
 end

app/controllers/taxonomy_controller.rb

@@ -32,8 +32,9 @@ def nest_categories_children(categories)
       category_index[category[:id]] = category
     end
     categories.each do |category|
-      category[:parentCategory].each do |parent_id|
+      category[:parentCategory]&.each do |parent_id|
         parent = category_index[parent_id]
+        next if parent.nil?
         parent[:children] ||= []
         parent[:children] << category
       end

app/controllers/users_controller.rb

@@ -226,6 +226,7 @@ def unescape_id
 
   def verify_owner
     return if current_user_admin?
+
     if session[:user].nil? || (!session[:user].id.eql?(params[:id]) && !session[:user].username.eql?(params[:id]))
       redirect_to controller: 'login', action: 'index', redirect: "/accounts/#{params[:id]}"
     end

app/helpers/application_helper.rb

@@ -452,4 +452,13 @@ def categories_select(id: nil, name: nil, selected: 'None')
     render Input::SelectComponent.new(id: id, name: name, value: categories_for_select, selected: selected, multiple: true)
   end
 
+  def category_is_parent?(parents_list, category)
+    is_parent = parents_list.keys.include?(category.id)
+    parent_error_message = t('admin.categories.category_used_parent')
+    parents_list[category.id].each do |c|
+      parent_error_message = "#{parent_error_message} #{c}"
+    end
+    [is_parent,parent_error_message]
+  end
+
 end

app/helpers/components_helper.rb

@@ -274,8 +274,8 @@ def properties_dropdown(id, title, tooltip, properties, is_open: false, &block)
     end
   end
 
-  def regular_button(id, value, variant: "secondary", state: "regular", size: "slim", &block)
-    render Buttons::RegularButtonComponent.new(id:id, value: value, variant: variant, state: state, size: size) do |btn|
+  def regular_button(id, value, variant: "secondary", state: "regular", size: "slim", href: nil, &block)
+    render Buttons::RegularButtonComponent.new(id:id, value: value, variant: variant, state: state, size: size, href: href) do |btn|
       capture(btn, &block) if block_given?
     end
   end

app/helpers/fair_score_helper.rb

@@ -5,7 +5,7 @@ def user_apikey
   end
 
   def fairness_service_enabled?
-    !$FAIRNESS_DISABLED
+    $FAIRNESS_DISABLED == 'false' || !$FAIRNESS_DISABLED
   end
 
   def get_fairness_service_url(apikey = user_apikey)

app/helpers/federation_helper.rb

@@ -3,6 +3,11 @@ module FederationHelper
 
   def federated_portals
     $FEDERATED_PORTALS ||= LinkedData::Client.settings.federated_portals
+    $FEDERATED_PORTALS.each do |key, portal|
+      portal[:ui] += "/" unless portal[:ui].end_with?("/")
+      portal[:api] += "/" unless portal[:api].end_with?("/")
+    end
+    $FEDERATED_PORTALS
   end
 
   def internal_portal_config(id)
@@ -53,13 +58,17 @@ def ontology_portal_color(id)
   end
 
   def ontoportal_ui_link(id)
+    if id.include?($REST_URL)
+      return id.gsub($REST_URL,'')
+    end
+
     portal_key, config = ontology_portal_config(id)
     return nil unless portal_key
 
     ui_link = config[:ui]
     api_link = config[:api]
 
-    id.gsub(api_link, "#{ui_link}/") rescue id
+    id.gsub(api_link, "#{ui_link}") rescue id
   end
 
   def internal_ontology?(id)
@@ -210,14 +219,18 @@ def init_federation_portals_status
   end
 
   def federated_search_counts(search_results)
-    ids = search_results.map do |result|
-      result.dig(:root, :ontology_id) || rest_url
-    end
+    ids = search_results.flat_map do |result|
+      ontology_id = result.dig(:root, :ontology_id) || rest_url
+      other_portal_ids = result.dig(:root, :other_portals)&.map { |portal| portal[:link].split('?').first } || []
+      [ontology_id] + other_portal_ids
+    end.uniq
     counts_ontology_ids_by_portal_name(ids)
   end
 
   def federated_browse_counts(ontologies)
-    ids = ontologies.map { |ontology| ontology[:id] }
+    ids = ontologies.flat_map do |ontology|
+      [ontology[:id]] + (ontology[:sources] || [])
+    end.uniq
     counts_ontology_ids_by_portal_name(ids)
   end
 
@@ -230,8 +243,9 @@ def counts_ontology_ids_by_portal_name(portals_ids)
       counts[current_portal.downcase] += 1 if id.include?(current_portal.to_s.downcase)
 
       federation_portals.each do |portal|
-        portal_api = federated_portals[portal.downcase.to_sym][:api]
-        counts[portal.downcase] += 1 if id.include?(portal_api)
+        portal_api = federated_portals[portal.downcase.to_sym][:api].sub(/^https?:\/\//, '')
+        portal_ui = federated_portals[portal.downcase.to_sym][:ui].sub(/^https?:\/\//, '')
+        counts[portal.downcase] += 1 if (id.include?(portal_api) || id.include?(portal_ui))
       end
     end
 

app/helpers/instances_helper.rb

@@ -52,7 +52,7 @@ def link_to_class(ontology_acronym, conceptid)
 
   def link_to_property(property, ontology_acronym)
     link_to extract_label_from(property),
-            ontology_path(ontology_acronym, p: 'properties'),
+            ontology_path(ontology_acronym, p: 'properties', propertyid: property),
             { target: '_blank'}
   end
 

app/views/admin/categories/_category.html.haml

@@ -1,5 +1,6 @@
 %tr.human{:id => category.id.split('/').last}
-  - count = category.ontologies&.size || 0
+  - count = category.ontologies&.size || 0 
+  - is_parent, parent_error_message = category_is_parent?(@parents_list, category)
   %td
     %div{style: 'width: 250px'}
       %div.text-truncate{title: category.name}
@@ -18,8 +19,11 @@
         = link_to_modal(nil, edit_admin_category_path(category.id.split('/').last), data: {show_modal_title_value:  category.name}) do
           = t('admin.categories.edit_button')
       %span
-        - if count.zero?
-          = button_to t('admin.categories.delete'), CGI.unescape(admin_category_path(category.id.split('/').last)), method: :delete, class: 'btn btn-link',  form: {data: { turbo: true, turbo_confirm: t('admin.categories.turbo_confirm'), turbo_frame: '_top'}}
-        - else
+        - if !count.zero?
           %span{data: { controller: 'tooltip' }, title: t('admin.categories.info_error_delete')}
             = link_to t('admin.categories.delete'), "", class: 'btn btn-link disabled'
+        - elsif is_parent
+          %span{data: { controller: 'tooltip' }, title: parent_error_message}
+            = link_to t('admin.categories.delete'), "", class: 'btn btn-link disabled'
+        - else
+          = button_to t('admin.categories.delete'), CGI.unescape(admin_category_path(category.id.split('/').last)), method: :delete, class: 'btn btn-link',  form: {data: { turbo: true, turbo_confirm: t('admin.categories.turbo_confirm'), turbo_frame: '_top'}}

app/views/home/index.html.haml

@@ -165,15 +165,15 @@
             %a{:href => "/landscape#fairness_assessment"}
               %div.home-fair-details
                 %p= t('home.fair_details')
-
-      .home-sub-section-right
-        %h4= t('home.twitter_news')
-        %hr.home-section-line
-        .home-card.home-twitter-news
-          %a.twitter-timeline{"data-height" => "360", :href => "https://twitter.com/lagroportal?ref_src=twsrc%5Etfw"}
-            .home-twitter-loader
-              = render LoaderComponent.new(type: 'pulsing')
-          %script{:async => "", :charset => "utf-8", :src => "https://platform.twitter.com/widgets.js"}
+      - if !$TWITTER_NEWS.blank?
+        .home-sub-section-right
+          %h4= t('home.twitter_news')
+          %hr.home-section-line
+          .home-card.home-twitter-news
+            %a.twitter-timeline{"data-height" => "360", :href => $TWITTER_NEWS}
+              .home-twitter-loader
+                = render LoaderComponent.new(type: 'pulsing')
+            %script{:async => "", :charset => "utf-8", :src => "https://platform.twitter.com/widgets.js"}
 
   - if slices_enabled?
     .home-section