update the browse page to use the ontologies metadata search endpoint

app/components/search_input_component/search_input_component_controller.js

@@ -120,7 +120,7 @@ export default class extends Controller {
                 value  = value.toString().split('/').slice(-1)
             }
             const regex = new RegExp('\\b' + key + '\\b', 'gi');
-            string =  string.replace(regex, value.toString())
+            string =  string.replace(regex, value?.toString())
         })
 
         return new DOMParser().parseFromString(string, "text/html").body.firstElementChild

app/controllers/concerns/submission_filter.rb

@@ -10,34 +10,43 @@ def init_filters(params)
     @show_private_only = params[:private_only]&.eql?('true')
     @show_retired = params[:show_retired]&.eql?('true')
     @selected_format = params[:format]
-    @selected_sort_by = params[:sort_by].blank? ? 'visits' : params[:sort_by]
+    @sort_by = params[:sort_by].blank? ? 'visits' : params[:sort_by]
     @search = params[:search]
   end
 
   def submissions_paginate_filter(params)
-    request_params = filters_params(params, page: nil)
+    request_params = filters_params(params, page: params[:page])
+    filter_params = params.permit(@filters.keys).to_h
     init_filters(params)
-    # pagination disabled because is not supported by 4store,
-    # see  https://github.com/ontoportal-lirmm/ontologies_api/issues/25
-    # @page = LinkedData::Client::Models::OntologySubmission.all(request_params)
-    @page = OpenStruct.new(page: 1, next_page: nil)
-    submissions = LinkedData::Client::Models::OntologySubmission.all(request_params)
-    @analytics =  helpers.ontologies_analytics
 
+    @analytics = helpers.ontologies_analytics
+    @ontologies = LinkedData::Client::Models::Ontology.all(include: 'all', also_include_views: @show_views)
     # get fair scores of all ontologies
     @fair_scores = fairness_service_enabled? ? get_fair_score('all') : nil
-    submissions = submissions.reject { |sub| sub.ontology.nil? }.map { |sub| ontology_hash(sub) }
 
-    if @selected_sort_by.eql?('visits')
-      submissions = submissions.sort_by { |x| -x[:popularity] }
-    elsif @selected_sort_by.eql?('fair')
-      submissions = submissions.sort_by { |x| -x[:fairScore] }
-    elsif @selected_sort_by.eql?('notes')
-      submissions = submissions.sort_by { |x| -x[:note_count] }
-    elsif @selected_sort_by.eql?('projects')
-      submissions = submissions.sort_by { |x| -x[:project_count] }
-    end
-    submissions
+    @total_ontologies = @ontologies.size
+    submissions = helpers.search_ontologies(
+      query: @search,
+      status: request_params[:status],
+      show_views: @show_views,
+      private_only: @show_private_only,
+      languages: request_params[:naturalLanguage],
+      page_size: @total_ontologies + 100,
+      formality_level: request_params[:hasFormalityLevel],
+      is_of_type: request_params[:isOfType],
+      groups: request_params[:group], categories: request_params[:hasDomain],
+      formats: request_params[:hasOntologyLanguage]
+    )
+
+    submissions = submissions.reject { |sub| sub.ontology.nil? }.map { |sub| ontology_hash(sub, @ontologies) }
+
+    submissions = sort_submission_by(submissions, @sort_by) if @search.blank?
+
+    @page = paginate_submissions(submissions, request_params[:page].to_i, request_params[:pagesize].to_i)
+
+    count = @page.page.eql?(1) ? count_objects(submissions) : {}
+
+    [@page.collection, @page.totalCount, count, filter_params]
   end
 
   def ontologies_filter_url(filters, page: 1, count: false)
@@ -46,10 +55,44 @@ def ontologies_filter_url(filters, page: 1, count: false)
 
   private
 
+  def paginate_submissions(all_submissions, page, size)
+    current_page = page
+    page_size = size
+
+    start_index = (current_page - 1) * page_size
+    end_index = start_index + page_size - 1
+    next_page = current_page * page_size < all_submissions.size ? current_page + 1 : nil
+    OpenStruct.new(page: current_page, nextPage: next_page, totalCount: all_submissions.size,
+                   collection: all_submissions[start_index..end_index])
+  end
+
+  def sort_submission_by(submissions, sort_by)
+    if sort_by.eql?('visits')
+      submissions = submissions.sort_by { |x| -x[:popularity] }
+    elsif sort_by.eql?('fair')
+      submissions = submissions.sort_by { |x| -x[:fairScore] }
+    elsif sort_by.eql?('notes')
+      submissions = submissions.sort_by { |x| -x[:note_count] }
+    elsif sort_by.eql?('projects')
+      submissions = submissions.sort_by { |x| -x[:project_count] }
+    elsif sort_by.eql?('metrics_classes')
+      submissions = submissions.sort_by { |x| -x[:class_count] }
+    elsif sort_by.eql?('metrics_individuals')
+      submissions = submissions.sort_by { |x| -x[:individual_count] }
+    elsif sort_by.eql?('creationDate')
+      submissions = submissions.sort_by { |x| -x[:creationDate] }
+    elsif sort_by.eql?('released')
+      submissions = submissions.sort_by { |x| -x[:released] }
+    elsif sort_by.eql?('ontology_name')
+      submissions = submissions.sort_by { |x| -x[:name] }
+    end
+    submissions
+  end
+
   def filters_params(params, includes: BROWSE_ATTRIBUTES.join(','), page: 1, pagesize: 5)
     request_params = { display_links: false, display_context: false,
                        include: includes, include_status: 'RDF' }
-    request_params.merge!(page: page, pagesize: pagesize) if page
+    request_params.merge!(page: page.to_i, pagesize: pagesize.to_i) if page
     filters_values_map = {
       categories: :hasDomain,
       groups: :group,
@@ -93,13 +136,21 @@ def filters_params(params, includes: BROWSE_ATTRIBUTES.join(','), page: 1, pages
       end
     end
 
+    unless params[:sort_by].blank?
+      @filters[:sort_by] = params[:sort_by]
+    end
+
+    unless params[:search].blank?
+      @filters[:search] = params[:search]
+    end
+
     request_params.delete(:order_by) if %w[visits fair].include?(request_params[:sort_by].to_s)
     request_params
   end
 
-  def ontology_hash(sub)
+  def ontology_hash(sub, ontologies)
     o = {}
-    ont = sub.ontology
+    ont = ontologies.select { |x| x.acronym.eql?(sub.ontology.acronym) }.first || sub.ontology
 
     add_ontology_attributes(o, ont)
     add_submission_attributes(o, sub)
@@ -144,8 +195,8 @@ def add_submission_attributes(ont_hash, sub)
     ont_hash[:hasFormalityLevel] = sub.hasFormalityLevel
     ont_hash[:isOfType] = sub.isOfType
     ont_hash[:submissionStatusFormatted] = submission_status2string(sub).gsub(/\(|\)/, '')
-    ont_hash[:format] = sub.hasOntologyLanguage
-    ont_hash[:contact] = sub.contact.map(&:name).first unless sub.contact.nil?
+    ont_hash[:format] = sub.hasOntologyLanguage&.split('/').last
+    ont_hash[:contact] = sub.contact.map { |c| c.is_a?(String) ? c.split('|').first : c.name }.first unless sub.contact.nil?
   end
 
   def add_ontology_attributes(ont_hash, ont)
@@ -244,13 +295,8 @@ def object_filter(objects, object_name, name_key = 'acronym')
 
   def count_objects(ontologies)
     objects_count = {}
-    @categories = Rails.cache.fetch('all_categories') do
-      LinkedData::Client::Models::Category.all(display_links: false, display_context: false)
-    end
-
-    @groups = Rails.cache.fetch('all_groups') do
-      LinkedData::Client::Models::Group.all(display_links: false, display_context: false)
-    end
+    @categories = LinkedData::Client::Models::Category.all(display_links: false, display_context: false)
+    @groups = LinkedData::Client::Models::Group.all(display_links: false, display_context: false)
 
     @filters = ontology_filters_init(@categories, @groups)
     object_names = @filters.keys
@@ -265,6 +311,8 @@ def count_objects(ontologies)
       object_names.each do |name|
         values = Array(ontology[name])
         values.each do |v|
+          v.gsub!('http://data.bioontology.org', rest_url)
+
           objects_count[name] = {} unless objects_count[name]
           objects_count[name][v] = (objects_count[name][v] || 0) + 1
         end

app/controllers/ontologies_controller.rb

@@ -43,39 +43,23 @@ def index
   end
 
   def ontologies_filter
-    @ontologies = submissions_paginate_filter(params)
-    @object_count = count_objects(@ontologies)
-
-    update_filters_counts = @object_count.map do |section, values_count|
-      values_count.map do |value, count|
-        replace("count_#{section}_#{value}") do
-          helpers.turbo_frame_tag("count_#{section}_#{value}") do
-            helpers.content_tag(:span, count.to_s, class: "hide-if-loading #{count.zero? ? 'disabled' : ''}")
+    @ontologies, @count, @count_objects, @request_params = submissions_paginate_filter(params)
+    if @page.page.eql?(1)
+      streams = [prepend("ontologies_list_view-page-#{@page.page}", partial: 'ontologies/browser/ontologies')]
+      streams += @count_objects.map do |section, values_count|
+        values_count.map do |value, count|
+          replace("count_#{section}_#{value}") do
+            helpers.turbo_frame_tag("count_#{section}_#{value}") do
+              helpers.content_tag(:span, count.to_s, class: "hide-if-loading #{count.zero? ? 'disabled' : ''}")
+            end
           end
         end
-      end
-    end.flatten
+      end.flatten
+    else
+      streams = [replace("ontologies_list_view-page-#{@page.page}", partial: 'ontologies/browser/ontologies')]
+    end
 
-    count_streams = [
-      replace('ontologies_filter_count_request') do
-        helpers.content_tag(:p, class: "browse-desc-text", style: "margin-bottom: 12px !important;") { "Showing #{@ontologies.size} of #{@analytics.keys.size}" }
-      end
-    ] + update_filters_counts
-
-    streams = if params[:page].nil?
-                [
-                  prepend('ontologies_list_container', partial: 'ontologies/browser/ontologies'),
-                  prepend('ontologies_list_container') {
-                    helpers.turbo_frame_tag("ontologies_filter_count_request") do
-                      helpers.browser_counter_loader
-                    end
-                  }
-                ]
-              else
-                [replace("ontologies_list_view-page-1", partial: 'ontologies/browser/ontologies')]
-              end
-
-    render turbo_stream: streams + count_streams
+    render turbo_stream: streams
   end
 
   def classes
@@ -504,13 +488,6 @@ def properties_hash_values(properties, sub: @submission_latest, custom_labels: {
     properties.map { |x| [x.to_s, [sub.send(x.to_s), custom_labels[x.to_sym]]] }.to_h
   end
 
-  def get_metrics_hash
-    metrics_hash = {}
-    # TODO: Metrics do not return for views on the backend, need to enable include_views param there
-    @metrics = LinkedData::Client::Models::Metrics.all(include_views: true)
-    @metrics.each { |m| metrics_hash[m.links['ontology']] = m }
-    return metrics_hash
-  end
 
   def determine_layout
     case action_name

app/views/ontologies/browser/_ontologies.html.haml

@@ -1,7 +1,11 @@
 = render InfiniteScrollComponent.new(id: 'ontologies_list',
                                     collection: @ontologies,
-                                    next_url: ontologies_filter_url(@filters, page: @page.nextPage),
+                                    next_url: ontologies_filter_url(@request_params, page: @page.nextPage),
                                     current_page: @page.page, next_page: @page.nextPage) do |c|
+
+  - if @page.page.eql?(1)
+    = content_tag(:p, class: "browse-desc-text", style: "margin-bottom: 12px !important;") { "Showing #{@count} of #{@total_ontologies}" }
+
   - ontologies = c.collection
   - ontologies.each do |ontology|
     = render OntologyBrowseCardComponent.new(ontology: ontology)

app/views/ontologies/browser/browse.html.haml

@@ -30,7 +30,7 @@
         });
       });
 
-    %div{data: { controller: "turbo-frame history browse-filters" , "turbo-frame-url-value": "/ontologies_filter", action: "change->browse-filters#dispatchFilterEvent changed->history#updateURL changed->turbo-frame#updateFrame"}}
+    %div{data: { controller: "turbo-frame history browse-filters" , "turbo-frame-url-value": "/ontologies_filter?page=1&#{request.original_url.split('?').last}", action: "change->browse-filters#dispatchFilterEvent changed->history#updateURL changed->turbo-frame#updateFrame"}}
 
       .browse-sub-container
         .browse-first-row{data:{controller: "browse-filters", action: "change->browse-filters#dispatchFilterEvent changed->history#updateURL"}}
@@ -76,15 +76,10 @@
                 %select#format.browse-format-filter{:name => "format"}
                   = options_for_select(@formats, @selected_format)
                 %select#Sort_by.browse-sort-by-filter{:name => "Sort_by"}
-                  = options_for_select(@sorts_options, @selected_sort_by)
+                  = options_for_select(@sorts_options, @sort_by)
           .browse-ontologies
-            = render TurboFrameComponent.new(id:"ontologies_list_container", data:{"turbo-frame-target":"frame", "turbo-frame-url-value": "/ontologies_filter"}) do |container|
-              = turbo_frame_tag "ontologies_filter_count_request" do
-                = browser_counter_loader
-              = render TurboFrameComponent.new(id: "ontologies_list_view-page-1" , src: "/ontologies_filter?page=1&#{request.original_url.split('?').last}") do |list|
-                - list.loader do
-                  - ontologies_browse_skeleton
-              - container.loader do
+            = render TurboFrameComponent.new(id: "ontologies_list_view-page-1" , src: "/ontologies_filter?page=1&#{request.original_url.split('?').last}", data:{"turbo-frame-target":"frame", "turbo-frame-url-value": "/ontologies_filter"}) do |list|
+              - list.loader do
                 = browser_counter_loader
                 - ontologies_browse_skeleton