refactor logic so pagy results are returned from query model

app/controllers/groups/samples_controller.rb

@@ -5,14 +5,13 @@ module Groups
   class SamplesController < Groups::ApplicationController
     include Metadata
     include Storable
-    include SamplesQuery
 
     before_action :group, :current_page
     before_action :query, only: %i[index search select]
 
     def index
       @timestamp = DateTime.current
-      @pagy, @samples = pagy_for_samples_query
+      @pagy, @samples = @query.results(action: 'index', limit: params[:limit] || 20, page: params[:page] || 1)
       @has_samples = authorized_samples.count.positive?
     end
 
@@ -26,7 +25,10 @@ def select
 
       respond_to do |format|
         format.turbo_stream do
-          @sample_ids = select_query if params[:select].present?
+          if params[:select].present?
+            @sample_ids = @query.results(action: 'select')
+                                .where(updated_at: ..params[:timestamp].to_datetime).select(:id).pluck(:id)
+          end
         end
       end
     end

app/controllers/projects/samples_controller.rb

@@ -6,15 +6,14 @@ class SamplesController < Projects::ApplicationController # rubocop:disable Metr
     include Metadata
     include ListActions
     include Storable
-    include SamplesQuery
 
     before_action :sample, only: %i[show edit update view_history_version]
     before_action :current_page
     before_action :query, only: %i[index search select]
 
     def index
       @timestamp = DateTime.current
-      @pagy, @samples = pagy_for_samples_query
+      @pagy, @samples = @query.results(action: 'index', limit: params[:limit] || 20, page: params[:page] || 1)
       @has_samples = @project.samples.size.positive?
     end
 
@@ -83,7 +82,10 @@ def select
 
       respond_to do |format|
         format.turbo_stream do
-          @sample_ids = select_query if params[:select].present?
+          if params[:select].present?
+            @sample_ids = @query.results(action: 'select')
+                                .where(updated_at: ..params[:timestamp].to_datetime).select(:id).pluck(:id)
+          end
         end
       end
     end

app/models/sample/query.rb

@@ -4,6 +4,7 @@
 class Sample::Query # rubocop:disable Style/ClassAndModuleChildren
   include ActiveModel::Model
   include ActiveModel::Attributes
+  include Pagy::Backend
 
   ResultTypeError = Class.new(StandardError)
 
@@ -33,28 +34,36 @@ def sort=(value)
 
   def advanced_query?
     # simplified version, will be further implemented when we have the definition of an advanced query
-    false
+    true
   end
 
-  def results(type = :ransack)
-    case type
-    when :ransack
-      ransack_results
-    when :searchkick
-      searchkick_results
-    when :searchkick_pagy
-      searchkick_pagy_results
+  def results(params)
+    case params[:action]
+    when 'index'
+      pagy_results(params[:limit], params[:page])
+    when 'select'
+      advanced_query ? searchkick_results : ransack_results
     else
       raise ResultTypeError, "Unrecognized type: #{type}"
     end
   end
 
   private
 
+  def pagy_results(limit, page)
+    if advanced_query
+      pagy_searchkick(searchkick_pagy_results, limit:, page:)
+    else
+      pagy(ransack_results, limit:, page:)
+    end
+  end
+
   def ransack_results
     return Sample.none unless valid?
 
-    sort_samples.ransack(ransack_params).result
+    samples = sort_samples
+    samples.ransack(ransack_params).result
+    # sort_samples.ransack(ransack_params).result
   end
 
   def searchkick_pagy_results