Merge branch 'development' into feature/select-children-of-category-w…

…hen-selecting-it

.env.sample

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

app/assets/javascripts/application.js

@@ -12,7 +12,6 @@
 //
 //= require bioportal
 //= require admin/licenses
-//= require bp_notes
 //= require bp_form_complete
 //= require bp_admin
 //= require concepts

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/home.scss

@@ -222,7 +222,7 @@ i.fa.fa-caret-square-o-down {
 .home-statistics-container > div {
   display: flex;
   align-items: start;
-  justify-content: center;
+  justify-content: flex-start;
   flex-wrap: wrap;
 }
 .home-agroportal-figures{

app/assets/stylesheets/ontologies.scss

@@ -2,6 +2,7 @@ $ont-metadata-bg-color: #e2ebf0;
 $widget-table-border-color: #EFEFEF;
 
 
+
 .admin-background{
   a.chip_button_container_clickable{
     color: var(--admin-color) !important;
@@ -314,4 +315,4 @@ $widget-table-border-color: #EFEFEF;
   color: white;
   border-radius: 10px;
   position: relative;
-}
+}

app/assets/stylesheets/taxonomy.scss

@@ -63,7 +63,18 @@
 }
 .taxonomy-card .description{
     color: #666666;
-    padding-bottom: 5px;
+}
+
+.taxonomy-card .descriptionlink svg{
+    margin: 0px 2px;
+    height: 19px;
+}
+
+.taxonomy-card .descriptionlink svg path{
+    fill: #666666;
+}
+.category-link{
+    color: #666666 !important;
 }
 .taxonomy-slice-svg{
     width: 35px;
@@ -98,4 +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/display/taxonomy_card_component.rb

@@ -1,4 +1,5 @@
 class Display::TaxonomyCardComponent < ViewComponent::Base
+  include UrlsHelper
   def initialize(taxonomy: , ontologies_names: )
     @taxonomy = taxonomy
     @ontologies_names = ontologies_names

app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml

@@ -4,12 +4,22 @@
       = "#{@taxonomy.name} (#{@taxonomy.acronym})"
     %a{href: "https://#{@taxonomy.acronym}.#{$UI_URL.sub("https://", "")}"}
       = inline_svg_tag('icons/slices.svg', class: "taxonomy-slice-svg #{@taxonomy.is_slice ? '' : 'd-none'}")
+
+  - if link?(@taxonomy.description)
+    .descriptionlink
+      %a.category-link{href: @taxonomy.description, target: '_blank'}
+        = @taxonomy.description
+        = inline_svg_tag 'icons/external-link.svg'
+
   %a.ontologies{href: "/ontologies?#{@taxonomy.id.split('/')[-2]}=#{@taxonomy.acronym}"}
     = inline_svg_tag('icons/ontology.svg')
     .number-of-ontologies
       = "#{@taxonomy.ontologies.length} ontologies"
-  .description
-    = render TextAreaFieldComponent.new(value: @taxonomy.description)
+
+  - unless link?(@taxonomy.description)
+    .description.mb-1
+      = render TextAreaFieldComponent.new(value: @taxonomy.description)
+
   .ontologies-cards
     - @taxonomy.ontologies.each_with_index do |ontology, index|
       - if index>10

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/agents_controller.rb

@@ -18,7 +18,7 @@ def show
   end
 
   def ajax_agents
-    filters = { query: params[:query], qf: "identifiers_texts^20 acronym_text^15 name_text^10 email_text^10"}
+    filters = { query: "#{params[:query]}*", qf: "identifiers_texts^20 acronym_text^15 name_text^10 email_text^10"}
     @agents = LinkedData::Client::HTTP.get('/search/agents', filters)
     agents_json = @agents.collection.map do |x|
       {

app/controllers/application_controller.rb

@@ -13,7 +13,7 @@
 # Likewise, all the methods added will be available for all controllers.
 
 class ApplicationController < ActionController::Base
-  include InternationalisationHelper
+  include InternationalisationHelper, MultiLanguagesHelper
 
   before_action :set_locale
 
@@ -26,6 +26,9 @@ def set_locale
     I18n.locale = cookies[:locale] || detect_locale
     cookies.permanent[:locale] = I18n.locale if cookies[:locale].nil?
     logger.debug "* Locale set to '#{I18n.locale}'"
+
+    I18n.locale = portal_lang unless portal_language_enabled?(I18n.locale)
+
     session[:locale] = I18n.locale
   end
 
@@ -250,12 +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)
@@ -424,7 +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/collections_controller.rb

@@ -57,12 +57,19 @@ def show_label
 
   def show_members
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id] || params[:ontology]).first
-    @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri')
-    @collection = get_request_collection
+    @submission = @ontology.explore.latest_submission(include: 'uriRegexPattern,preferredNamespaceUri')
     page = params[:page] || '1'
     @auto_click = page.to_s.eql?('1')
-    @page = @collection.explore.members({page: page, language: request_lang})
-    @concepts = @page.collection
+    @collection = get_request_collection(@ontology)
+
+    if @collection
+      @page = @collection.explore.members({ page: page, language: request_lang })
+      @concepts = @page.collection
+    else
+      @page = OpenStruct.new({ nextPage: 1, page: 1 })
+      @concepts = []
+    end
+
     if @ontology.nil?
       ontology_not_found params[:ontology]
     else
@@ -72,14 +79,12 @@ def show_members
 
   private
 
-  def get_request_collection
+  def get_request_collection(ontology = nil)
     params[:id] = request_collection_id
 
-    if params[:id].nil? || params[:id].empty?
-      render plain: t('collections.error_valid_collection')
-      return
-    end
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id] || params[:ontology]).first
+    return nil if params[:id].nil? || params[:id].empty?
+
+    @ontology = ontology || LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id] || params[:ontology]).first
     ontology_not_found(params[:ontology_id]) if @ontology.nil?
     get_collection(@ontology, params[:id])
   end

app/controllers/concepts_controller.rb

@@ -63,8 +63,12 @@ def index
   def show_label
     cls_id = params[:concept] || params[:id]
     ont_id = params[:ontology]
-    pref_label = concept_label(ont_id, cls_id)
-    cls = @ontology.explore.single_class({ language: request_lang, include: 'prefLabel' }, cls_id)
+    pref_label = begin
+                   concept_label(ont_id, cls_id)
+                 rescue
+                   cls_id
+                 end
+    cls = @ontology.explore&.single_class({ language: request_lang, include: 'prefLabel' }, cls_id)
     label = helpers.main_language_label(pref_label)
     link = concept_path(cls_id, ont_id, request_lang)
 

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

@@ -23,11 +23,20 @@ def index
 
     @anal_ont_names = []
     @anal_ont_numbers = []
-    @analytics.sort_by{|ont, count| -count}[0..4].each do |ont, count|
-      @anal_ont_names << ont
-      @anal_ont_numbers << count
+    if @analytics.empty?
+      all_metrics = LinkedData::Client::Models::Metrics.all
+      all_metrics.sort_by{|x| -(x.classes + x.individuals)}[0..4].each do |x|
+        @anal_ont_names << x.id.split('/')[-4]
+        @anal_ont_numbers << (x.classes + x.individuals) || 0
+      end
+    else
+      @analytics.sort_by{|ont, count| -count}[0..4].each do |ont, count|
+        @anal_ont_names << ont
+        @anal_ont_numbers << count
+      end
     end
 
+
   end
 
   def set_cookies
@@ -39,6 +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