Add archived and deleted repositories to reports [SCI-5781] (#3387)

* Add archived and deleted repositories to reports [SCI-5781]

* Small markup fix [SCI-5781]

app/assets/javascripts/reports/new.js

@@ -975,7 +975,7 @@ function reportHandsonTableConverter() {
     reportData.report = {
       name: $('.report-name').val(),
       description: $('#projectDescription').val(),
-      settings: { task: { protocol: {} } }
+      settings: { task: { protocol: {} }, deleted_repositories: [] }
     };
     // Project
     reportData.project_id = dropdownSelector.getValues('#projectSelector');
@@ -1032,7 +1032,7 @@ function reportHandsonTableConverter() {
         reportData.project_content.tasks[experimentId].push(parseInt(myModule.value, 10));
       });
     });
-    $.each($('.task-contents-container .repositories-contents .sci-checkbox:checked'), function(i, e) {
+    $.each($('.task-contents-container .repositories-contents .repositories-setting:checked'), function(i, e) {
       reportData.project_content.repositories.push(parseInt(e.value, 10));
     });
 
@@ -1046,6 +1046,9 @@ function reportHandsonTableConverter() {
     $.each($('.task-contents-container .content-element .task-setting'), function(i, e) {
       reportData.report.settings.task[e.value] = e.checked;
     });
+    $.each($('.task-contents-container .repositories-contents .deleted-repositories-setting:checked'), function(i, e) {
+      reportData.report.settings.deleted_repositories.push(parseInt(e.value, 10));
+    });
 
     reportData.report.settings.task.result_order = dropdownSelector.getValues('#taskResultsOrder');
 

app/controllers/reports_controller.rb

@@ -30,6 +30,7 @@ class ReportsController < ApplicationController
 
   before_action :check_manage_permissions, only: BEFORE_ACTION_METHODS
   before_action :switch_team_with_param, only: :index
+  before_action :load_repositories, only: %i(new edit)
 
   after_action :generate_pdf_report, only: %i(create update generate_pdf)
 
@@ -51,7 +52,6 @@ class ReportsController < ApplicationController
   # Report grouped by modules
   def new
     @templates = Extends::REPORT_TEMPLATES
-    @repositories = Repository.accessible_by_teams(current_team).active.select(:id, :name).order(:name)
     @report = current_team.reports.new
   end
 
@@ -114,7 +114,6 @@ class ReportsController < ApplicationController
     @edit = true
     @templates = Extends::REPORT_TEMPLATES
     @active_template = @report.settings[:template]
-    @repositories = Repository.accessible_by_teams(current_team).active.select(:id, :name).order(:name)
     @report.settings = Report::DEFAULT_SETTINGS if @report.settings.blank?
 
     @project_contents = {
@@ -495,6 +494,16 @@ class ReportsController < ApplicationController
   include StringUtility
   AvailableRepository = Struct.new(:id, :name)
 
+  def load_repositories
+    @repositories = Repository.accessible_by_teams(current_team).order(:name)
+    @deleted_repositories = RepositorySnapshot.where(team: current_team)
+                                              .group(:parent_id, :name)
+                                              .where.not(
+                                                original_repository: Repository.accessible_by_teams(current_team)
+                                              )
+                                              .select(:parent_id, :name)
+  end
+
   def load_vars
     @report = current_team.reports.find_by(id: params[:id])
     render_404 unless @report

app/services/report_actions/report_content.rb

@@ -14,7 +14,7 @@ module ReportActions
       @report = report
       @template_values = template_values
       @repositories = Repository.accessible_by_teams(report.project.team)
-                                .where(id: @content['repositories']).active
+                                .where(id: @content['repositories'])
     end
 
     def save_with_content

app/services/reports/docx/draw_my_module.rb

@@ -88,6 +88,14 @@ module Reports::Docx::DrawMyModule
       end
     end
 
+    @settings['deleted_repositories']&.each do |repo|
+      draw_my_module_repository(nil,
+                                my_module,
+                                my_module.repository_snapshots
+                                         .where(parent_id: repo)
+                                         .find_by(selected: true))
+    end
+
     @docx.p
     subject.children.active.each do |child|
       public_send("draw_#{child.type_of}", child)

app/services/reports/docx/draw_my_module_repository.rb

@@ -1,10 +1,12 @@
 # frozen_string_literal: true
 
 module Reports::Docx::DrawMyModuleRepository
-  def draw_my_module_repository(subject)
-    my_module = subject.my_module
-    repository = subject.repository
-    return unless can_read_experiment?(@user, my_module.experiment) && can_read_repository?(@user, repository)
+  def draw_my_module_repository(subject, my_module = nil, snapshot = nil)
+    my_module ||= subject&.my_module
+    repository = subject&.repository
+    repository = assigned_repository_or_snapshot(my_module, repository&.id, nil, snapshot)
+    return unless can_read_experiment?(@user, my_module.experiment) &&
+                  (can_read_repository?(@user, repository) || repository.is_a?(RepositorySnapshot))
 
     repository_data = my_module.repository_docx_json(repository)
 

app/views/reports/elements/_my_module_element.html.erb

@@ -98,6 +98,10 @@
         <%= render partial: 'reports/elements/my_module_result_text_element.html.erb', locals: { result: result, export_all: export_all } %>
       <% end %>
     <% end %>
+
+    <% @settings['deleted_repositories']&.each do |repo| %>
+      <%= render partial: 'reports/elements/my_module_repository_element.html.erb', locals: { repository_snapshot: my_module.repository_snapshots.where(parent_id: repo).find_by(selected: true), export_all: export_all, my_module: my_module } %>
+    <% end %>
   </div>
 
   <% if defined?(children) %>

app/views/reports/elements/_my_module_repository_element.html.erb

@@ -1,6 +1,7 @@
 <% my_module ||= @my_module %>
-<% element_id ||= repository&.id %>
+<% repository ||= nil %>
 <% repository_snapshot ||= nil %>
+<% element_id ||= repository&.id %>
 <% repository ||= assigned_repository_or_snapshot(my_module, element_id, repository, repository_snapshot) %>
 <% timestamp = Time.current + 1.year - 1.days %>
 <% rows_json = my_module.repository_json_hot(repository, :desc) %>

app/views/reports/wizard/_third_step.html.erb

@@ -73,6 +73,24 @@
                   <span class="sci-checkbox-label"></span>
                 </span>
                 <%= repository.name %>
+                <% unless repository.active? %>
+                  <span class="archived">
+                    <%= t("projects.reports.wizard.third_step.archived") %>
+                  </span>
+                <% end %>
+                <div class="divider"></div>
+              </li>
+            <% end %>
+            <% @deleted_repositories.each do |repository| %>
+              <li>
+                <span class="sci-checkbox-container">
+                  <input type="checkbox" class="sci-checkbox deleted-repositories-setting" value="<%= repository.parent_id %>" <%= 'checked' if report.new_record? || report.settings.dig(:deleted_repositories).include?(repository.parent_id) %> />
+                  <span class="sci-checkbox-label"></span>
+                </span>
+                <%= repository.name %>
+                <span class="deleted">
+                  <%= t("projects.reports.wizard.third_step.deleted") %>
+                </span>
                 <div class="divider"></div>
               </li>
             <% end %>

config/locales/en.yml

@@ -586,6 +586,8 @@ en:
           results_comments: "Include all result comments"
           additional_content: "Additional content"
           task_activity: "Include task activity"
+          archived: "[archived]"
+          deleted: "[deleted]"
 
       new:
         report_name_placeholder: "Name your report"