Merge branch 'development' into feature/federate-search-page

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

@@ -11,9 +11,12 @@
   .description
     = render TextAreaFieldComponent.new(value: @taxonomy.description)
   .ontologies-cards
-    - @taxonomy.ontologies.each do |ontology|
+    - @taxonomy.ontologies.each_with_index do |ontology, index|
+      - if index>10
+        = render ChipButtonComponent.new(url: "/ontologies?#{@taxonomy.id.split('/')[-2]}=#{@taxonomy.acronym}", text: "...", tooltip:"See all ontologies ...", type: "clickable")
+        - break
       = render ChipButtonComponent.new(url: "/ontologies/#{ontology.split('/').last}", text: ontology.split('/').last, tooltip: @ontologies_names[ontology], type: "clickable")
-
+    
   - if @taxonomy.children
     .taxonomy-children-reveal{'data-action': "click->reveal-component#toggle", 'data-id': reveal_id}
       .text

app/components/tab_item_component.rb

@@ -44,12 +44,8 @@ def page_name
   end
 
   def call
-    if title && !title.empty?
-      link_to(title, @path, id: "#{item_id}_tab", class: "#{active_class} tab-link", 'data-json-link': @json_link)
-    else
-      link_to(@path, id: "#{item_id}_tab", class: "#{active_class} tab-link", 'data-json-link': @json_link) do
-        content
-      end
+    link_to(@path, id: "#{item_id}_tab", class: "#{active_class} tab-link", 'data-json-link': @json_link) do
+      (title && !title.empty?) ? title.html_safe : content
     end
   end
 

app/controllers/collections_controller.rb

@@ -37,9 +37,12 @@ def index
   end
 
   def show
-    redirect_to(ontology_path(id: params[:ontology_id], p: 'collections', collectionid: params[:id], lang: request_lang)) and return unless turbo_frame_request?
+
+    redirect_to(ontology_path(id: params[:ontology], p: 'collections', collectionid: params[:id], lang: request_lang)) and return unless turbo_frame_request?
 
     @collection = get_request_collection
+
+    render partial: "collections/show"
   end
 
   def show_label

app/controllers/instances_controller.rb

@@ -41,7 +41,7 @@ def show
 
     redirect_to(ontology_path(id: params[:ontology], p: 'instances', instanceid: params[:id] || params[:instanceid], lang: request_lang)) and return unless turbo_frame_request?
 
-    render partial: 'instances/details', layout: nil
+    render partial: 'show'
   end
 
   private

app/controllers/ontologies_controller.rb

@@ -192,7 +192,8 @@ def instances
   def schemes
     @schemes = get_schemes(@ontology)
     scheme_id = params[:schemeid] || @submission_latest.URI || nil
-    @scheme = get_scheme(@ontology, scheme_id) if scheme_id
+    @scheme = scheme_id ? get_scheme(@ontology, scheme_id) : @schemes.first
+
 
     render partial: 'ontologies/sections/schemes', layout: 'ontology_viewer'
   end

app/controllers/schemes_controller.rb

@@ -32,9 +32,11 @@ def index
   end
 
   def show
-    redirect_to(ontology_path(id: params[:ontology_id], p: 'schemes', schemeid: params[:id],lang: request_lang)) and return unless turbo_frame_request?
+    redirect_to(ontology_path(id: params[:ontology], p: 'schemes', schemeid: params[:id],lang: request_lang)) and return unless turbo_frame_request?
 
     @scheme = get_request_scheme
+
+    render partial: "schemes/show"
   end
 
   def show_label

app/helpers/collections_helper.rb

@@ -4,7 +4,7 @@ module CollectionsHelper
   def get_collections(ontology, add_colors: false)
     collections = ontology.explore.collections(language: request_lang)
     generate_collections_colors(collections) if add_colors
-    collections
+    collections.sort_by{ |x| x.prefLabel }
   end
 
   def get_collection(ontology, collection_uri)

app/helpers/components_helper.rb

@@ -1,7 +1,16 @@
 module ComponentsHelper
   include TermsReuses
 
-  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, disabled: false, &block)
+  def tab_item_component(container_tabs:, title:, path:, selected: false, json_link: "", &content)
+    container_tabs.item(title: title.html_safe, path: path, selected: selected, json_link: json_link)
+    container_tabs.item_content { capture(&content) }
+  end
+
+  def alert_component(message, type: "info")
+    render Display::AlertComponent.new(type: type, message: message)
+  end
+
+  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, disabled: false, &block)   
     content_tag(:div, data: { controller: 'tooltip' }, title: tooltip) do
       check_input(id: id, name: name, value: value, label: label, checked: checked, disabled: disabled, &block)
     end

app/helpers/ontologies_helper.rb

@@ -530,6 +530,51 @@ def language_selector_hidden_tag(section)
                      data: { controller: "language-change", 'language-change-section-value': section, action: "change->language-change#dispatchLangChangeEvent" }
   end
 
+  def ontology_object_json_link(ontology_acronym, object_type, id)
+    "#{rest_url}/ontologies/#{ontology_acronym}/#{object_type}/#{escape(id)}?display=all&apikey=#{get_apikey}"
+  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" })
+      end
+    end
+  end
+
+  def render_concepts_json_button(link)
+    content_tag(:div, class: 'concepts_json_button') do
+      render RoundedButtonComponent.new(link: link, target: '_blank')
+    end
+  end
+
+
+  def ontology_object_details_component(frame_id: , ontology_id:, objects_title:, object:, &block)
+    render TurboFrameComponent.new(id: frame_id, data: {"turbo-frame-target": "frame"}) do
+      return if !object.present?
+      return alert_component(object.errors.join) if object.errors
+
+      ontology_object_tabs_component(ontology_id: ontology_id, objects_title: objects_title, object_id: object["@id"]) do |tabs|
+        tab_item_component(container_tabs: tabs, title: t('concepts.details'), path: '#details', selected: true) do
+          capture(&block)
+        end
+      end
+    end
+  end
+
+  def ontology_object_tabs_component(ontology_id:, objects_title:, object_id:, &block)
+    resource_url = ontology_object_json_link(ontology_id, objects_title, object_id)
+    render TabsContainerComponent.new(type: 'outline') do |c|
+      concat(c.pinned_right do
+        content_tag(:div, '', 'data-concepts-json-target': 'button') do
+          concat(render_permalink_link) if $PURL_ENABLED
+          concat(render_concepts_json_button(resource_url))
+        end
+      end)
+
+      capture(c, &block)
+    end
+  end
 
 
   def display_complex_text(definitions)

app/views/annotator/index.html.haml

@@ -27,7 +27,7 @@
                 = render(ChipsComponent.new(name: 'exclude_synonyms', label: t('annotator.exclude_synonyms'), checked: params[:exclude_synonyms]))
 
             .select-ontologies
-              = ontologies_selector(id:'annotator_page_ontologies', label: 'Select ontologies' ,name: 'ontologies[]', selected: params[:ontologies]&.split(','))
+              = ontologies_selector(id:'annotator_page_ontologies', label: t('annotator.select_ontologies') ,name: 'ontologies[]', selected: params[:ontologies]&.split(','))
             = show_advanced_options_button(text: t('show_advanced_options'), init: @advanced_options_open)
             = hide_advanced_options_button(text: t('hide_advanced_options'), init: @advanced_options_open)
         .more-advanced-options{'data-reveal-component-target': 'item', class: "#{@advanced_options_open ? '' : 'd-none'}"}

app/views/collections/_show.html.haml

@@ -0,0 +1,14 @@
+= ontology_object_details_component(frame_id: "collection", ontology_id:  @ontology.acronym, objects_title:  "collections", object: @collection) do
+  = render ConceptDetailsComponent.new(id:'collection-label', acronym: @ontology.acronym, concept_id: @collection.id,
+                      properties: @collection.properties,
+                      top_keys: %w[created modified comment note],
+                      bottom_keys: [],
+                      exclude_keys: %w[member]) do |c|
+    - c.header(stripped: true) do |t|
+      - t.add_row({th: t("collections.id")}, {td: link_to_with_actions(@collection["@id"], acronym: @ontology.acronym)})
+      - t.add_row({th: t("collections.preferred_name")}, {td: display_in_multiple_languages(get_collection_label(@collection))})
+      - t.add_row({th: t("collections.members_count")}) do |r|
+        - r.td do
+          = link_to @collection["memberCount"],  "/ontologies/" + @ontology.acronym + "/?p=classes&sub_menu=list&concept_collections=" + @collection["@id"], 'data-turbo-frame':'_top'
+      - t.add_row({th: t("collections.type")}, {td: @collection["@type"]})
+

app/views/concepts/_show.html.haml

@@ -4,63 +4,32 @@
       = t('concepts.use_jump_to')
   - else
     %div{'data-controller': 'concepts-json', 'data-action': 'click->concepts-json#update'}
-      = render TabsContainerComponent.new(type:'outline') do |c|
-        - c.pinned_right do
-          - if $PURL_ENABLED
-            %div.mx-1
-              = 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
-                %i{class: "fas fa-link", aria: {hidden: "true"}}
-          %div{'data-concepts-json-target': 'button'}
-            .concepts_json_button
-              = render RoundedButtonComponent.new(link: "#{@ontology.id}/classes/#{escape(@concept.id)}?display=all&apikey=#{get_apikey}", target:'_blank')
+      = ontology_object_tabs_component(ontology_id: @ontology.acronym, objects_title: "classes", object_id: @concept.id) do |c|
         - apikey = "apikey=#{get_apikey}"
         - baseClassUrl = "#{@ontology.id}/classes/#{escape(@concept.id)}"
-        - c.item(title: t('concepts.details'), path: '#details', selected: true, json_link: "#{baseClassUrl}?#{apikey}&display=all")
-
-        - unless skos?
-          - c.item(id: 'instances', path: '#instances', json_link: "#{baseClassUrl}/instances?#{apikey}") do
-            = t('concepts.instances')
-            (
-            %span#concept_instances_sorted_list_count
-            )
-
-        - c.item(title: t('concepts.visualization'), path: '#visualization')
-
-        - c.item(id: 'notes', path: '#notes', json_link: "#{baseClassUrl}/notes?#{apikey}") do
-          = t('concepts.notes')
-          %span#note_count_wrapper
-            (
-            %span#note_count= @notes.length
-            )
-        - c.item(id: 'mappings', path: '#mappings', json_link: "#{baseClassUrl}/mappings?#{apikey}") do
-          .d-flex
-            #{t('concepts.mappings')}
-            (
-            = concept_mappings_loader(ontology_acronym: @ontology.acronym, concept_id: @concept.id)
-            )
-
-        - if @enable_ontolobridge
-          - c.item(title: t('concepts.new_term_requests'), path: '#request_term')
-
-        - c.item_content do
+        - tab_item_component(container_tabs: c, title: t('concepts.details'), path: '#details', selected: true, json_link: "#{baseClassUrl}?#{apikey}&display=all") do
           = render :partial =>'/concepts/details'
 
         - unless skos?
-          - c.item_content do
+          - count_span = content_tag(:span, "#{t('concepts.instances')} (#{content_tag(:span, "", id: 'concept_instances_sorted_list_count')})".html_safe)
+          - tab_item_component(container_tabs: c, title: count_span, path: '#instances', json_link: "#{baseClassUrl}/instances?#{apikey}") do
             = render :partial =>'instances/instances' , locals: {id: "class-instances-data-table"}
-        - c.item_content do
+
+
+        - tab_item_component(container_tabs: c, title: t('concepts.visualization'), path: '#visualization') do
           = render :partial =>'/concepts/biomixer'
 
-        - c.item_content do
+
+        - count_span = content_tag(:span, "#{t('concepts.notes')} (#{content_tag(:span, @notes.length, id: 'note_count')})".html_safe)
+        - tab_item_component(container_tabs: c, title: count_span, path: '#notes', json_link: "#{baseClassUrl}/notes?#{apikey}") do
           = render :partial =>'/notes/list'
 
-        - c.item_content do
+
+        - count_span = content_tag(:span, "#{t('concepts.mappings')} (#{content_tag(:span, concept_mappings_loader(ontology_acronym: @ontology.acronym, concept_id: @concept.id))})".html_safe, class: "d-flex")
+        - tab_item_component(container_tabs: c, title: count_span, path: '#mappings', json_link: "#{baseClassUrl}/mappings?#{apikey}") do
           = render TurboFrameComponent.new(id:'concept_mappings',
           src:"/ajax/mappings/get_concept_table?ontologyid=#{@ontology.acronym}&conceptid=#{CGI.escape(@concept.id)}")
 
-        - if @enable_ontolobridge
-          - c.item_content do
-            = render :partial =>'/concepts/request_term'
 
     :javascript
       jQuery(document).ready(function(){

app/views/home/cookies.html.haml

@@ -10,4 +10,4 @@
       %div
         = link_button_component(id:'accept-cookie-selector', value: t('cookies_modal.accept_button'), href: cookies_path(cookies: true), size: "slim", variant: 'primary')
       %div.cookie-privacy-link
-        = link_to t('cookies_modal.privacy_link'), $FOOTER_LINKS.dig(:sections, :agreements, :privacy_policy)
+        = link_to t('cookies_modal.privacy_link'), "#{$FOOTER_LINKS.dig(:sections, :agreements, :privacy_policy)}#{t('cookies_modal.privacy_policy_anchor')}"

app/views/instances/_instances.html.haml

@@ -9,7 +9,7 @@
 
     - if params[:p].eql?('instances')
       %div#prop_contents{data: {'container-splitter-target': 'container'}}
-        = render partial: 'instances/details'
+        = render partial: 'instances/show'
 
 
 

app/views/instances/_show.html.haml

@@ -0,0 +1,22 @@
+= ontology_object_details_component(frame_id: params['modal'].eql?('true') ? modal_frame_id : "instance_show", ontology_id:  @ontology.acronym, objects_title:  "instances", object: @instance) do
+  = render ConceptDetailsComponent.new(id: 'instance-details', acronym: @ontology.acronym, concept_id: @instance["@id"]) do |c|
+    - c.header(stripped: true) do |t|
+      - t.add_row({ th: t("instances.id") }, { td: link_to_with_actions(@instance["@id"], acronym: @ontology.acronym) })
+
+      - label = @instance['label'] || @instance['prefLabel']
+      - t.add_row({ th: t('instances.label') }, { td: label.join(', ').html_safe }) unless label.blank?
+
+      - types = @instance.types.reject { |x| x['NamedIndividual'] }
+      - unless types.empty?
+        - t.add_row({ th: t('instances.type') }) do |r|
+          - r.td do
+            = types.map { |cls| link_to_class(@ontology.acronym, cls) }.join(', ').html_safe
+
+      - filter_properties = %w[http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/2000/01/rdf-schema#label http://www.w3.org/2004/02/skos/core#prefLabel]
+      - properties = @instance[:properties].to_h.reject { |k, _| filter_properties.include?(k.to_s) }
+      - properties.each do |prop, values|
+        - if values.present?
+          - t.add_row({ th: link_to_property(prop, @ontology.acronym) }, { td: values.map { |value| instance_property_value(value, @ontology.acronym) }.join(', ').html_safe })
+
+
+

app/views/layouts/_footer.html.haml

@@ -20,8 +20,10 @@
           %h2
             = t("layout.footer."+key.to_s)
           %div
+
             - section_links.each do |section , link|
-              %a{:href => link, :target => "_blank"}
+              - anchor = I18n.t("layout.footer.#{section}_anchor", default: "")
+              %a{:href => "#{link}#{anchor}", :target => "_blank"}
                 = t("layout.footer."+section.to_s)
 
 

app/views/ontologies/sections/_collections.html.haml

@@ -1,17 +1,15 @@
 = render TurboFrameComponent.new(id: "collections", data: {"turbo-frame-target": "frame"} ) do
-  - if no_collections?
-    = no_collections_alert
-  - else
-    %div.ont-collections{data:{controller: 'container-splitter'}}
-      %div#collectionsTree.card.sidebar{data:{'container-splitter-target': 'container'}}
+  %div.ont-collections{data:{controller: 'container-splitter'}}
+    %div#collectionsTree.card.sidebar{data:{'container-splitter-target': 'container'}}
+      - if no_collections?
+        = no_collections_alert
+      - else
         = tree_container_component(id: "collections_sorted_list_view-page-1",
                                  placeholder: t('ontologies.sections.collections_search_placeholder',  acronym: @ontology.acronym),
                                  frame_url:  "/ontologies/#{@ontology.acronym}/collections",
                                  tree_url: "/ontologies/#{@ontology.acronym}/collections?#{request.original_url.split('?')[1]}")
-
-      %div#collection_contents{data:{'container-splitter-target': 'container'}}
-        = render TurboFrameComponent.new(id: 'collection') do
-          - if @collection
-            = render partial: 'collections/collection', locals: {collection: @collection}
+    %div#collection_contents{data:{'container-splitter-target': 'container'}}
+      = render TurboFrameComponent.new(id: 'collection') do
+        = render partial: 'collections/show'
 
 

app/views/ontologies/sections/_schemes.html.haml

@@ -11,7 +11,7 @@
 
     %div#scheme_contents{data:{'container-splitter-target': 'container'}}
       = render TurboFrameComponent.new(id:'scheme') do
-        = render partial: 'schemes/scheme', locals: {scheme: @scheme}
+        = render partial: 'schemes/show'