Merge to master: Sync with release 3.0.3 of AgroPortal

app/components/concept_details_component.rb

@@ -10,14 +10,14 @@ class ConceptDetailsComponent < ViewComponent::Base
 
   attr_reader :concept_properties
 
-  def initialize(id:, acronym:, concept_id: nil , properties: nil, top_keys: [], bottom_keys: [], exclude_keys: [])
+  def initialize(id:, acronym:, concept_id: nil, properties: nil, top_keys: [], bottom_keys: [], exclude_keys: [])
     @acronym = acronym
     @properties = properties
     @top_keys = top_keys
     @bottom_keys = bottom_keys
     @exclude_keys = exclude_keys
     @id = id
-    @concept_id=concept_id
+    @concept_id = concept_id
 
     @concept_properties = concept_properties2hash(@properties) if @properties
   end
@@ -55,8 +55,8 @@ def row_hash_properties(properties_set, ontology_acronym, &block)
       end
 
       out << [
-        { th:  content_tag(:span, remove_owl_notation(key), title: url, 'data-controller': 'tooltip') },
-        { td: content_tag(:span, ajax_links.join.html_safe) }
+        { th: content_tag(:span, remove_owl_notation(key), title: url, 'data-controller': 'tooltip') },
+        { td: list_items_component(max_items: 5) { |r| ajax_links.map { |val| r.container { val.html_safe } } } }
       ]
     end
     out
@@ -81,7 +81,7 @@ def filter_properties(top_keys, bottom_keys, exclude_keys, concept_properties)
   private
 
   def link_to_format_modal(format, icon)
-    link_to_modal(nil, "/ontologies/#{@acronym}/#{escape(@concept_id)}/serialize/#{format}",{ id: "resource_content_#{format}", data: {show_modal_title_value: @concept_id, show_modal_size_value: 'modal-xl'}}) do
+    link_to_modal(nil, "/ontologies/#{@acronym}/#{escape(@concept_id)}/serialize/#{format}", { id: "resource_content_#{format}", data: { show_modal_title_value: @concept_id, show_modal_size_value: 'modal-xl' } }) do
       inline_svg("icons/#{icon}.svg", width: '50px', height: '50px')
     end
   end

app/components/list_items_show_more_component.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+class ListItemsShowMoreComponent < ViewComponent::Base
+  renders_many :containers
+
+  def initialize(max_items: 10)
+    super
+    @max_items = max_items - 1
+  end
+
+end

app/components/list_items_show_more_component/list_items_show_more_component.html.haml

@@ -0,0 +1,14 @@
+%div{data: {controller: 'reveal-component'}}
+  - containers[..@max_items].each do |item|
+    = item
+
+  - if (@max_items + 1) < containers.size
+    - Array(containers[@max_items+1..]).each do |item|
+      %span{'data-reveal-component-target': "item", class: 'd-none'}
+        = item
+    %div{'data-reveal-component-target': "showButton", 'data-action': "click->reveal-component#show" }
+      %span.btn-link
+        See more
+    %div.d-none{'data-reveal-component-target': "hideButton", 'data-action': "click->reveal-component#hide" }
+      %span.btn-link
+        See less

app/controllers/ontologies_controller.rb

@@ -588,6 +588,7 @@ def search_first_instance_id
 
   def keep_only_root_categories(categories)
     categories.select do |category|
+      next unless category.id
       category.id.start_with?(rest_url) || category.parentCategory.blank?
     end
   end

app/controllers/users_controller.rb

@@ -40,6 +40,7 @@ def show
     @user_ontologies ||= []
 
     @admin_ontologies = @ontologies.select {|o| o.administeredBy.include? @user.id }
+    @accessed_ontologies = @ontologies.select {|o| o.acl.include? @user.id }
 
     projects = LinkedData::Client::Models::Project.all;
     @user_projects = projects.select {|p| p.creator.include? @user.id }

app/helpers/application_helper.rb

@@ -460,4 +460,31 @@ def category_is_parent?(parents_list, category)
     [is_parent,parent_error_message]
   end
 
+  def categories_with_children(categories)
+    parent_to_children = Hash.new { |hash, key| hash[key] = [] }
+    categories.each do |category|
+      next unless category.parentCategory
+      category.parentCategory.each do |parent_id|
+        parent_acronym = id_to_acronym(parent_id)
+        child_acronym = id_to_acronym(category.id)
+        parent_to_children[parent_acronym] << child_acronym
+      end
+    end
+    parent_to_children
+  end
+
+  def categories_with_parents(categories_children)
+    categories_parents = Hash.new { |hash, key| hash[key] = [] }
+    categories_children.each do |child, parents|
+      parents.each do |parent|
+        categories_parents[parent] << child
+      end
+    end
+    categories_parents
+  end
+
+  def id_to_acronym(id)
+    id.split('/').last
+  end
+
 end

app/helpers/components_helper.rb

@@ -25,6 +25,11 @@ def chips_component(id: , name: , label: , value: , checked: false , tooltip: ni
       check_input(id: id, name: name, value: value, label: label, checked: checked, disabled: disabled, &block)
     end
   end
+  def list_items_component(max_items:, &block)
+    render ListItemsShowMoreComponent.new(max_items: max_items) do |r|
+      capture(r, &block)
+    end
+  end
 
   def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, disabled: false, &block)
     title ||= object["name"]
@@ -111,7 +116,7 @@ def resolvability_check_tag(url)
   end
 
   def rounded_button_component(link)
-    render RoundedButtonComponent.new(link: link, target: '_blank',size: 'small',title: t("components.go_to_api"))
+    render RoundedButtonComponent.new(link: link, target: '_blank', size: 'small', title: t("components.go_to_api"))
   end
 
   def copy_link_to_clipboard(url, show_content: false)

app/helpers/federation_helper.rb

@@ -163,7 +163,7 @@ def canonical_ontology(ontologies)
   end
 
   def federation_portal_status(portal_name: nil)
-    Rails.cache.fetch("federation_portal_up_#{portal_name}", expires_in: 2.hours) do
+    Rails.cache.fetch("federation_portal_up_#{portal_name}", expires_in: 10.minutes) do
       portal_api = federated_portals&.dig(portal_name,:api)
       return false unless portal_api
       portal_up = false
@@ -260,8 +260,8 @@ def external_canonical_ontology_portal(ontologies)
   def most_referred_portal(ontology_submissions)
     portal_counts = Hash.new(0)
     ontology_submissions.each do |submission|
-      federated_portals.keys.each do |portal|
-        portal_counts[portal] += 1 if submission[:pullLocation]&.include?(portal.to_s)
+      request_portals.each do |portal|
+        portal_counts[portal.downcase] += 1 if submission[:pullLocation]&.include?(portal.downcase)
       end
     end
     portal_counts.max_by { |_, count| count }&.first

app/helpers/home_helper.rb

@@ -26,7 +26,7 @@ def format_number_abbreviated(number)
 
   def portal_config_tooltip(portal_name, &block)
     portal_id = portal_name&.downcase
-    title = if federation_portal_status(portal_name: portal_id)
+    title = if (federation_portal_status(portal_name: portal_id) || portal_id.eql?(portal_name&.downcase))
       render(
         TurboFrameComponent.new(
           id: "portal_config_tooltip_#{portal_id}",

app/helpers/multi_languages_helper.rb

@@ -1,4 +1,5 @@
 module MultiLanguagesHelper
+  include OntologiesHelper, ComponentsHelper
   def portal_lang
     session[:locale] || 'en'
   end
@@ -172,15 +173,15 @@ def display_in_multiple_languages(label)
                                                 closable: true)
     end
 
-
-
     label = label.to_h.reject { |key, _| %i[links context].include?(key) } if label.is_a?(OpenStruct)
 
     if label.is_a?(String)
       content_tag(:p, label)
     elsif label.is_a?(Array)
-      content_tag(:div) do
-        raw(label.map { |x| content_tag(:div, x) }.join)
+      list_items_component(max_items: show_max) do |r|
+        label.map do |x|
+          r.container { content_tag(:span, x, class: style_as_badge ? 'badge bg-secondary' : '').html_safe }
+        end
       end
     else
       content_tag(:div) do

app/helpers/ontologies_helper.rb

@@ -1,6 +1,5 @@
 require 'iso-639'
 module OntologiesHelper
-
   REST_URI = $REST_URL
   API_KEY = $API_KEY
   LANGUAGE_FILTERABLE_SECTIONS = %w[classes schemes collections instances properties].freeze
@@ -801,10 +800,6 @@ def submission_languages(submission = @submission)
     Array(submission&.naturalLanguage).map { |natural_language| natural_language["iso639"] && natural_language.split('/').last }.compact
   end
 
-  def id_to_acronym(id)
-    id.split('/').last
-  end
-
   def browse_taxonomy_tooltip(taxonomy_type)
     return nil unless taxonomy_type.eql?("categories") || taxonomy_type.eql?("groups")
 
@@ -817,9 +812,10 @@ def browse_taxonomy_tooltip(taxonomy_type)
   def browse_chip_filter(key:, object:, values:, countable: true, count: nil)
     title = (key.to_s.eql?("categories") || key.to_s.eql?("groups")) ? nil : ''
     checked = values.any? { |obj| [link_last_part(object["id"]), link_last_part(object["value"])].include?(obj) }
-
-    group_chip_component(name: key, object: object, checked: checked, title: title) do |c|
-      c.count { browse_chip_count_badge(key: key, id: object["id"], count: count) } if countable
+    content_tag(:div, (key.to_s.eql?("categories") ? { 'data-action' => 'click->parent-categories-selector#check' } : {})) do
+      group_chip_component(name: key, object: object, checked: checked, title: title) do |c|
+        c.count { browse_chip_count_badge(key: key, id: object["id"], count: count) } if countable
+      end
     end
   end
 

app/helpers/submission_inputs_helper.rb

@@ -1,7 +1,7 @@
 module SubmissionInputsHelper
 
   class SubmissionMetadataInput
-    include MetadataHelper
+    include MetadataHelper, ApplicationHelper
 
     def initialize(attribute_key:, attr_metadata:, submission: nil, label: nil)
       @attribute_key = attribute_key
@@ -128,14 +128,21 @@ def ontology_administered_by_input(ontology = @ontology, users_list = @user_sele
 
   def ontology_categories_input(ontology = @ontology, categories = @categories)
     categories ||= LinkedData::Client::Models::Category.all(display_links: false, display_context: false)
+    categories_children = categories_with_children(categories)
+    categories_parents = categories_with_parents(categories_children)
 
     render Input::InputFieldComponent.new(name: '', label: 'Categories') do
-      content_tag(:div, class: 'upload-ontology-chips-container') do
+      content_tag(:div, class: 'upload-ontology-chips-container', 'data-controller': 'parent-categories-selector',
+      'data-parent-categories-selector-categories-children-value': "#{categories_children.to_json}",
+      'data-parent-categories-selector-categories-parents-value': "#{categories_parents.to_json}",
+      'data-parent-categories-selector-target': "chips") do
         hidden_field_tag('ontology[hasDomain][]') +
-          categories.map do |category|
+        categories.map do |category|
+          content_tag(:div, 'data-action': 'click->parent-categories-selector#check') do
             category_chip_component(id: category[:acronym], name: "ontology[hasDomain][]",
                                     object: category, value: category[:id],
                                     checked: ontology.hasDomain&.any? { |x| x.eql?(category[:id]) })
+            end
           end.join.html_safe
       end
     end

app/javascript/controllers/index.js

@@ -100,3 +100,6 @@ application.register('mappings', MappingsController)
 
 import ConceptsJsonButtonController from "./concepts_json_button_controller.js"
 application.register('concepts-json', ConceptsJsonButtonController)
+
+import ParentCategoriesSelectorController from "./parent_categories_selector_controller.js"
+application.register('parent-categories-selector', ParentCategoriesSelectorController)

app/javascript/controllers/parent_categories_selector_controller.js

@@ -0,0 +1,53 @@
+import { Controller } from "@hotwired/stimulus"
+
+// Connects to data-controller="parent-categories-selector"
+export default class extends Controller {
+    static targets = ['chips']
+    static values = { categoriesChildren: Object, categoriesParents: Object}
+
+    check(event) {
+        const input = event.currentTarget.querySelector('input');
+        const allInputs = this.chipsTarget.querySelectorAll('input');
+        const parents = this.categoriesChildrenValue;
+        const children = this.categoriesParentsValue;
+        const browseLogic = !this.hasCategoriesParentsValue;
+
+        // Browse page logic: 
+            // - Selecting a category will auto select all its children
+            // - Deselecting a category will auto deselect all its children
+        // Upload/Edit forms logic: 
+            // - Selecting a category will auto select its parents
+            // - Deselecting a category will auto deselect its children
+
+        const inputAcronym = this.#id_to_acronym(input.value);
+
+        if (browseLogic) {
+            if (inputAcronym in parents) {
+                const parentChildren = parents[inputAcronym];
+                this.#toggleInputState(allInputs, i => parentChildren.includes(this.#id_to_acronym(i.value)), input.checked);
+            }
+        } else {
+            if (inputAcronym in parents) {
+                const parentChildren = parents[inputAcronym];
+                this.#toggleInputState(allInputs, i => parentChildren.includes(this.#id_to_acronym(i.value)), false);
+            }
+            if (inputAcronym in children) {
+                const childParents = children[inputAcronym];
+                this.#toggleInputState(allInputs, i => childParents.includes(this.#id_to_acronym(i.value)), true);
+            }
+        }
+    }
+
+    #toggleInputState(inputs, condition, state) {
+        inputs.forEach(input => {
+            if (condition(input)) {
+                input.checked = state;
+                input.dispatchEvent(new Event('change', { bubbles: true }));
+            }
+        });
+    }
+
+    #id_to_acronym(id){
+        return id.split('/').pop();
+    }
+}

app/javascript/controllers/turbo_frame_controller.js

@@ -30,8 +30,12 @@ export default class extends Controller {
             }
 
             this.urlValue = this.#updatedPageUrl(data)
-
+            
             this.frame.src  = this.urlValue
+
+            requestAnimationFrame(() => {
+                this.frame.setAttribute('busy', 'true');
+            });
         }
     }
 

app/views/concepts/_details.html.haml

@@ -19,8 +19,7 @@
         - t.add_row({th: t('ontology_details.concept.synonyms')}) do |h|
           - h.td do
             %div.d-flex
-              %div.d-flex
-                = display_in_multiple_languages(@concept.synonym)
+              = display_in_multiple_languages(@concept.synonym, style_as_badge: true, show_max: 5)
               %div.synonym-change-request
                 = add_synonym_button
                 = remove_synonym_button