Feat: Sample::Query form object

app/components/samples/table_component.html.erb

@@ -33,27 +33,15 @@
                     "w-4 h-4 mr-2.5 text-primary-600 bg-slate-100 border-slate-300 rounded focus:ring-primary-500 dark:focus:ring-primary-600 dark:ring-offset-slate-800 focus:ring-2 dark:bg-slate-700 dark:border-slate-600" %>
                 <% end %>
 
-                <% if column == :attachments_updated_at %>
-                  <%= render Ransack::SortComponent.new(
-                    ransack_obj: @q,
-                    label: t(".#{column}"),
-                    url: helpers.sorting_url(@q, :attachments_updated_at_nulls_last),
-                    field: :attachments_updated_at_nulls_last,
-                    data: {
-                      turbo_action: "replace",
-                    },
-                  ) %>
-                <% else %>
-                  <%= render Ransack::SortComponent.new(
-                    ransack_obj: @q,
-                    label: t(".#{column}"),
-                    url: helpers.sorting_url(@q, column),
-                    field: column,
-                    data: {
-                      turbo_action: "replace",
-                    },
-                  ) %>
-                <% end %>
+                <%= render SortComponent.new(
+                  sort: @search_params[:sort],
+                  label: t(".#{column}"),
+                  url: sort_url(column),
+                  field: column,
+                  data: {
+                    turbo_action: "replace",
+                  },
+                ) %>
               <% end %>
             <% end %>
             <% @metadata_fields.each do |field| %>
@@ -62,11 +50,10 @@
               scope: 'col',
               classes: class_names('px-3 py-3')
             ) do %>
-                <%= render Ransack::SortComponent.new(
-                  ransack_obj: @q,
+                <%= render SortComponent.new(
+                  sort: @search_params[:sort],
                   label: field,
-                  url:
-                    helpers.sorting_url(@q, URI.encode_www_form_component("metadata_#{field}")),
+                  url: sort_url("metadata_#{field}"),
                   field: "metadata_#{field}",
                   data: {
                     turbo_action: "replace",
@@ -127,7 +114,7 @@
                         ) %>
                       </span>
                     <% end %>
-                  <% elsif column == :project %>
+                  <% elsif column == :project_id %>
                     <%= link_to sample.project.puid,
                     project_samples_path(sample.project),
                     data: {

app/components/samples/table_component.rb

@@ -7,12 +7,11 @@ module Samples
   class TableComponent < Component
     include Ransack::Helpers::FormHelper
 
-    # rubocop:disable Naming/MethodParameterName,Metrics/ParameterLists
+    # rubocop:disable Metrics/ParameterLists
     def initialize(
       samples,
       namespace,
       pagy,
-      q,
       has_samples: true,
       abilities: {},
       metadata_fields: [],
@@ -24,7 +23,6 @@ def initialize(
       @samples = samples
       @namespace = namespace
       @pagy = pagy
-      @q = q
       @has_samples = has_samples
       @abilities = abilities
       @metadata_fields = metadata_fields
@@ -34,9 +32,11 @@ def initialize(
       @renders_row_actions = @row_actions.select { |_key, value| value }.count.positive?
       @system_arguments = system_arguments
 
+      @sort_key, @sort_direction = search_params[:sort].split
+
       @columns = columns
     end
-    # rubocop:enable Naming/MethodParameterName,Metrics/ParameterLists
+    # rubocop:enable Metrics/ParameterLists
 
     def system_arguments
       { tag: 'div' }.deep_merge(@system_arguments).tap do |args|
@@ -77,11 +77,26 @@ def select_samples_url(**)
       end
     end
 
+    def sort_url(field)
+      sort_string = if field.to_s == @sort_key && @sort_direction == 'asc'
+                      "#{field} desc"
+                    else
+                      "#{field} asc"
+                    end
+
+      if @namespace.type == 'Group'
+        group_samples_url(@namespace, q: { sort: sort_string }, limit: @pagy.limit)
+      else
+        namespace_project_samples_url(@namespace.parent, @namespace.project, q: { sort: sort_string },
+                                                                             limit: @pagy.limit)
+      end
+    end
+
     private
 
     def columns
       columns = %i[puid name]
-      columns << :project if @namespace.type == 'Group'
+      columns << :project_id if @namespace.type == 'Group'
       columns += %i[created_at updated_at attachments_updated_at]
       columns
     end

app/components/sort_component.html.erb

@@ -0,0 +1,4 @@
+<%= render Viral::BaseComponent.new(tag: 'a', href: url, type: "button", classes: class_names('inline-flex items-center'), **system_arguments) do %>
+  <%= label %>
+  <span class="flex-grow-0 ml-2 flex items-center"><%= viral_icon(name: icon, classes: "w-4 h-4 inline-block") %></span>
+<% end %>

app/components/sort_component.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+# Component for sort in table headers
+class SortComponent < Component
+  attr_reader :label, :field, :url, :system_arguments
+
+  def initialize(sort:, label:, url:, field:, **system_arguments)
+    @sort_key, @sort_direction = sort.split
+    @label = label
+    @url = url
+    @field = field
+    @system_arguments = system_arguments
+  end
+
+  def icon
+    return unless @sort_key.to_s == URI.encode_www_form_component(@field.to_s)
+
+    @sort_direction == 'asc' ? 'arrow_up' : 'arrow_down'
+  end
+end

app/controllers/concerns/storable.rb

@@ -18,6 +18,7 @@ def store(session_key, value)
   # @param value [Hash] the value to merge with the existing value in the session.
   def update_store(search_key, value)
     session[search_key] = (session[search_key] || {}).merge(value)
+    session[search_key].reject! { |_, val| val.blank? || val == [''] }
     get_store(search_key)
   end
 

app/controllers/groups/samples_controller.rb

@@ -7,12 +7,11 @@
     include Storable
 
     before_action :group, :current_page
-    before_action :process_samples, only: %i[index search select]
-    include Sortable
+    before_action :query, only: %i[index search select]
 
     def index
       @timestamp = DateTime.current
-      @pagy, @samples = pagy_with_metadata_sort(@q.result)
+      @pagy, @samples = pagy(@query.results, limit: params[:limit] || 20)
       @has_samples = authorized_samples.count.positive?
     end
 
@@ -22,12 +21,12 @@
 
     def select
       authorize! @group, to: :sample_listing?
-      @selected_sample_ids = []
+      @sample_ids = []
 
       respond_to do |format|
         format.turbo_stream do
           if params[:select].present?
-            @selected_sample_ids = @q.result.where(updated_at: ..params[:timestamp].to_datetime).select(:id).pluck(:id)
+            @sample_ids = @query.results.where(updated_at: ..params[:timestamp].to_datetime).select(:id).pluck(:id)
           end
         end
       end
@@ -39,6 +38,10 @@
       @group = Group.find_by_full_path(params[:group_id]) # rubocop:disable Rails/DynamicFindBy
     end
 
+    def authorized_projects
+      authorized_scope(Project, type: :relation, as: :group_projects, scope_options: { group: @group })
+    end
+
     def authorized_samples
       authorized_scope(Sample, type: :relation, as: :namespace_samples,
                                scope_options: { namespace: @group }).includes(project: { namespace: [{ parent: :route },
@@ -71,20 +74,21 @@
       fields_for_namespace(namespace: @group, show_fields: @search_params && @search_params[:metadata].to_i == 1)
     end
 
-    def process_samples
+    def query
       authorize! @group, to: :sample_listing?
+
       @search_params = search_params
       set_metadata_fields
-      query_parser = Irida::SearchSyntax::Ransack.new(text: :name_or_puid_cont, metadata_fields: @fields)
-      @parsed_params = query_parser.parse(@search_params.fetch(:name_or_puid_cont, nil))
-      @q = authorized_samples.ransack(@search_params.except(:name_or_puid_cont).merge(@parsed_params))
+
+      @query = Sample::Query.new(@search_params.except(:metadata).merge({ project_ids: authorized_projects.select(:id) }))
     end
 
     def search_params
       updated_params = update_store(search_key, params[:q].present? ? params[:q].to_unsafe_h : {})
 
-      if updated_params[:metadata].to_i.zero? && updated_params[:s].present? && updated_params[:s].match?(/metadata_/)
-        updated_params[:s] = default_sort
+      if !updated_params.key?(:sort) ||
+         (updated_params[:metadata].to_i.zero? && updated_params[:sort]&.match?(/metadata_/))
+        updated_params[:sort] = 'updated_at desc'
         update_store(search_key, updated_params)
       end
       updated_params

app/controllers/projects/samples_controller.rb

@@ -9,12 +9,11 @@ class SamplesController < Projects::ApplicationController # rubocop:disable Metr
 
     before_action :sample, only: %i[show edit update view_history_version]
     before_action :current_page
-    before_action :process_samples, only: %i[index search select]
-    include Sortable
+    before_action :query, only: %i[index search select]
 
     def index
       @timestamp = DateTime.current
-      @pagy, @samples = pagy_with_metadata_sort(@q.result)
+      @pagy, @samples = pagy(@query.results, limit: params[:limit] || 20)
       @has_samples = @project.samples.size.positive?
     end
 
@@ -79,12 +78,12 @@ def update
 
     def select
       authorize! @project, to: :sample_listing?
-      @samples = []
+      @sample_ids = []
 
       respond_to do |format|
         format.turbo_stream do
           if params[:select].present?
-            @samples = @q.result.where(updated_at: ..params[:timestamp].to_datetime).select(:id)
+            @sample_ids = @query.results.where(updated_at: ..params[:timestamp].to_datetime).select(:id).pluck(:id)
           end
         end
       end
@@ -138,22 +137,22 @@ def search_key
       :"#{controller_name}_#{@project.id}_search_params"
     end
 
-    def process_samples
+    def query
       authorize! @project, to: :sample_listing?
 
       @search_params = search_params
-
       set_metadata_fields
-      query_parser = Irida::SearchSyntax::Ransack.new(text: :name_or_puid_cont, metadata_fields: @fields)
-      @parsed_params = query_parser.parse(@search_params.fetch(:name_or_puid_cont, nil))
-      @q = load_samples.ransack(@search_params.except(:name_or_puid_cont).merge(@parsed_params))
+
+      @query = Sample::Query.new(@search_params.except(:metadata).merge({ project_ids: [@project.id] }))
     end
 
     def search_params
-      updated_params = update_store(search_key, params[:q].present? ? params[:q].to_unsafe_h : {})
+      updated_params = update_store(search_key,
+                                    params[:q].present? ? params[:q].to_unsafe_h : {}).with_indifferent_access
 
-      if updated_params[:metadata].to_i.zero? && updated_params[:s].present? && updated_params[:s].match?(/metadata_/)
-        updated_params[:s] = default_sort
+      if !updated_params.key?(:sort) ||
+         (updated_params[:metadata].to_i.zero? && updated_params[:sort]&.match?(/metadata_/))
+        updated_params[:sort] = 'updated_at desc'
         update_store(search_key, updated_params)
       end
       updated_params

app/models/sample/query.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+# model to represent sample search form
+class Sample::Query # rubocop:disable Style/ClassAndModuleChildren
+  include ActiveModel::Model
+  include ActiveModel::Attributes
+
+  attribute :column, :string
+  attribute :direction, :string
+  attribute :name_or_puid_cont, :string
+  attribute :name_or_puid_in, default: -> { [] }
+  attribute :project_ids, default: -> { [] }
+  attribute :sort, :string, default: 'updated_at desc'
+
+  validates :direction, inclusion: { in: %w[asc desc] }
+  validates :project_ids, length: { minimum: 1 }
+
+  def initialize(...)
+    super
+    self.sort = sort
+  end
+
+  def sort=(value)
+    super
+    column, direction = sort.split
+    assign_attributes(column:, direction:)
+  end
+
+  def results
+    return Sample.none unless valid?
+
+    sort_samples.ransack(ransack_params).result
+  end
+
+  private
+
+  def ransack_params
+    {
+      name_or_puid_cont: name_or_puid_cont,
+      name_or_puid_in: name_or_puid_in
+    }.compact
+  end
+
+  def sort_samples(scope = Sample.where(project_id: project_ids))
+    if column.starts_with? 'metadata_'
+      field = column.gsub('metadata_', '')
+      scope.order(Sample.metadata_sort(field, direction))
+    else
+      scope.order("#{column} #{direction}")
+    end
+  end
+end

app/views/groups/samples/_table.html.erb

@@ -3,15 +3,14 @@
   samples,
   group,
   pagy,
-  @q,
   has_samples: @has_samples,
   abilities: {
     select_samples:
       allowed_to?(:submit_workflow?, group) ||
         allowed_to?(:export_data?, group),
   },
   metadata_fields: @fields,
-  search_params: @parsed_params,
+  search_params: @search_params,
   empty: {
     title: t(:"groups.samples.table.no_samples"),
     description: t(:"groups.samples.table.no_associated_samples"),