From e0ceaa44cd57154110617f9be01b35c45cff322d Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 8 Aug 2023 14:01:32 +0200
Subject: [PATCH 01/12] Fix column resizing for existing inventories with no
 colSize data [SCI-8984]

---
 .../javascripts/repositories/repository_datatable.js      | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/app/assets/javascripts/repositories/repository_datatable.js b/app/assets/javascripts/repositories/repository_datatable.js
index 0b5a17802..9cd32cbde 100644
--- a/app/assets/javascripts/repositories/repository_datatable.js
+++ b/app/assets/javascripts/repositories/repository_datatable.js
@@ -185,7 +185,7 @@ var RepositoryDatatable = (function(global) {
     $('#saveRecord').attr('disabled', false);
     $(TABLE_WRAPPER_ID).find('tr').removeClass('blocked');
 
-    if (TABLE.ColSizes) {
+    if (TABLE.ColSizes && TABLE.ColSizes.filter((s) => !!s).length > 0) {
       $(TABLE_WRAPPER_ID).find('.table').addClass('table--resizable-columns');
     }
 
@@ -558,7 +558,9 @@ var RepositoryDatatable = (function(global) {
 
           state.ColSizes = data;
 
-          $(TABLE_WRAPPER_ID).find('.table').addClass('table--resizable-columns');
+          if (data.length > 0) {
+            $(TABLE_WRAPPER_ID).find('.table').addClass('table--resizable-columns');
+          }
 
           updateColSizeMap(state);
 
@@ -743,7 +745,7 @@ var RepositoryDatatable = (function(global) {
             if (json.state.columns[7]) json.state.columns[7].visible = archived;
             if (json.state.search) delete json.state.search;
 
-            if (json.state.ColSizes) {
+            if (json.state.ColSizes && json.state.ColSizes.length > 0) {
               $(TABLE_WRAPPER_ID).find('.table').addClass('table--resizable-columns');
               TABLE.ColSizes = json.state.ColSizes;
               updateColSizeMap(json.state);

From e01c3682b4551d9311c1c9c16ed57644e2d7408c Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Wed, 9 Aug 2023 13:54:31 +0200
Subject: [PATCH 02/12] Fix handling of result table metadata for project
 exports [SCI-9000] (#5943)

---
 .../reports/elements/_my_module_result_table_element.html.erb   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/reports/elements/_my_module_result_table_element.html.erb b/app/views/reports/elements/_my_module_result_table_element.html.erb
index 9d093570c..e40d27282 100644
--- a/app/views/reports/elements/_my_module_result_table_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_table_element.html.erb
@@ -25,7 +25,7 @@
   </div>
   <div class="report-element-body">
     <input type="hidden" class="hot-table-contents" value="<%= table.contents_utf_8 %>" />
-    <input type="hidden" class="hot-table-metadata" value="<%= table.metadata.to_json %>" />
+    <input type="hidden" class="hot-table-metadata" value="<%= table.metadata ? table.metadata.to_json : nil %>" />
     <div class="hot-table-container"></div>
     <table class="report-common-table-format"></table>
   </div>

From 348d467d02f07d49151d5a081340ba9c8215079b Mon Sep 17 00:00:00 2001
From: Giga Chubinidze <giga@scinote.net>
Date: Thu, 10 Aug 2023 22:26:45 +0400
Subject: [PATCH 03/12] Non team owner user does not have access to archive
 inventory [SCI-8955]

---
 app/views/repositories/_view_archived_btn.html.erb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/app/views/repositories/_view_archived_btn.html.erb b/app/views/repositories/_view_archived_btn.html.erb
index 3be64c929..c47897a70 100644
--- a/app/views/repositories/_view_archived_btn.html.erb
+++ b/app/views/repositories/_view_archived_btn.html.erb
@@ -1,5 +1,4 @@
-<div class="content-pane flexible <%= params[:archived] ? :archived : :active %> repositories-index"
-      data-readonly="<%= !can_manage_team?(current_team) %>">
+<div class="content-pane flexible <%= params[:archived] ? :archived : :active %> repositories-index">
   <div class="content-header">
     <div class="title-row">
       <h1 data-view-mode="active"><%= t('libraries.index.head_title') %></h1>

From 26eba7da647cdacca72b6df86e4cfc995bbe559a Mon Sep 17 00:00:00 2001
From: Giga Chubinidze <giga@scinote.net>
Date: Thu, 10 Aug 2023 22:41:39 +0400
Subject: [PATCH 04/12] Smart annotation modal- inventories are out of modal
 [SCI-9001]

---
 app/views/shared/smart_annotation/_menu.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/shared/smart_annotation/_menu.html.erb b/app/views/shared/smart_annotation/_menu.html.erb
index ec9d3a77b..74a1d9d5d 100644
--- a/app/views/shared/smart_annotation/_menu.html.erb
+++ b/app/views/shared/smart_annotation/_menu.html.erb
@@ -12,7 +12,7 @@
     <div class="tab-pane" role="tabpanel" id="exp-tab-<%= at_who_key %>" data-object-type="EXPERIMENT"></div>
     <div class="tab-pane" role="tabpanel" id="tsk-tab-<%= at_who_key %>" data-object-type="TASK"></div>
     <div class="tab-pane rep-tab" role="tabpanel" id="rep-tab-<%= at_who_key %>" data-object-type="REPOSITORY"><% if repositories.length > 1 %>
-      <div class=sci-btn-group>
+      <div class="sci-btn-group flex-wrap">
       <% repositories.each do |repository| %>
         <button class="btn btn-light repository-object" data-object-id="<%= repository.id %>">
           <% if repository.shared_with?(current_team) %>

From 5332cbc78888e300f404d416b23c0cc372816f7f Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Fri, 11 Aug 2023 15:31:29 +0200
Subject: [PATCH 05/12] Pass user by id instead of serialized object for
 deleyed jobs [SCI-9053]

---
 .../access_permissions/experiments_controller.rb       |  4 ++--
 .../access_permissions/projects_controller.rb          |  4 ++--
 .../api/service/projects_json_export_controller.rb     |  2 +-
 app/controllers/experiments_controller.rb              |  2 +-
 app/controllers/reports_controller.rb                  |  4 ++--
 app/controllers/repositories_controller.rb             |  4 ++--
 app/controllers/teams_controller.rb                    |  2 +-
 app/helpers/notifications_helper.rb                    |  2 +-
 app/jobs/hide_repository_reminders_job.rb              |  3 ++-
 app/jobs/my_modules/copy_content_job.rb                |  3 ++-
 app/jobs/projects_json_export_job.rb                   |  3 ++-
 app/jobs/reports/docx_job.rb                           |  5 +++--
 app/jobs/reports/pdf_job.rb                            |  5 +++--
 app/jobs/repositories_export_job.rb                    |  4 ++--
 .../user_assignments/generate_user_assignments_job.rb  |  4 ++--
 .../user_assignments/project_group_assignment_job.rb   |  8 ++++----
 app/jobs/user_assignments/propagate_assignment_job.rb  |  6 +++---
 app/mailers/app_mailer.rb                              |  8 ++++----
 app/models/concerns/assignable.rb                      |  2 +-
 app/models/experiment.rb                               |  4 ++--
 app/models/project.rb                                  |  2 +-
 app/models/team_zip_export.rb                          |  4 ++--
 app/models/zip_export.rb                               |  3 ++-
 app/services/experiments/move_to_project_service.rb    |  2 +-
 ...em_notification_in_communication_channel_service.rb |  2 +-
 app/services/repository_zip_export.rb                  |  2 +-
 app/services/team_importer.rb                          |  4 ++--
 .../create_team_user_assignments_service.rb            |  2 +-
 .../remove_team_user_assignments_service.rb            |  2 +-
 .../user_assignments/generate_user_assignments_job.rb  |  4 ++--
 .../user_assignments/propagate_assignment_job_spec.rb  |  8 ++++----
 spec/models/project_member_spec.rb                     |  4 ++--
 test/mailers/previews/app_mailer_preview.rb            | 10 +++++-----
 33 files changed, 67 insertions(+), 61 deletions(-)

diff --git a/app/controllers/access_permissions/experiments_controller.rb b/app/controllers/access_permissions/experiments_controller.rb
index a2eb3286f..7b11ba4ca 100644
--- a/app/controllers/access_permissions/experiments_controller.rb
+++ b/app/controllers/access_permissions/experiments_controller.rb
@@ -29,9 +29,9 @@ module AccessPermissions
 
       UserAssignments::PropagateAssignmentJob.perform_later(
         @experiment,
-        @user_assignment.user,
+        @user_assignment.user.id,
         @user_assignment.user_role,
-        current_user
+        current_user.id
       )
 
       log_change_activity
diff --git a/app/controllers/access_permissions/projects_controller.rb b/app/controllers/access_permissions/projects_controller.rb
index 90ca466d6..4d84406d2 100644
--- a/app/controllers/access_permissions/projects_controller.rb
+++ b/app/controllers/access_permissions/projects_controller.rb
@@ -174,9 +174,9 @@ module AccessPermissions
     def propagate_job(user_assignment, destroy: false)
       UserAssignments::PropagateAssignmentJob.perform_later(
         @project,
-        user_assignment.user,
+        user_assignment.user.id,
         user_assignment.user_role,
-        current_user,
+        current_user.id,
         destroy: destroy
       )
     end
diff --git a/app/controllers/api/service/projects_json_export_controller.rb b/app/controllers/api/service/projects_json_export_controller.rb
index f5a421b70..f6b0e2fa1 100644
--- a/app/controllers/api/service/projects_json_export_controller.rb
+++ b/app/controllers/api/service/projects_json_export_controller.rb
@@ -10,7 +10,7 @@ module Api
         valid_url?(projects_json_export_params[:callback_url])
         ProjectsJsonExportJob.perform_later(projects_json_export_params[:task_ids],
                                             projects_json_export_params[:callback_url],
-                                            current_user)
+                                            current_user.id)
         render json: { status: :ok }, status: :accepted
       end
 
diff --git a/app/controllers/experiments_controller.rb b/app/controllers/experiments_controller.rb
index 662e7f6a5..32542e5a2 100644
--- a/app/controllers/experiments_controller.rb
+++ b/app/controllers/experiments_controller.rb
@@ -502,7 +502,7 @@ class ExperimentsController < ApplicationController
           }.merge(new_my_module.get_new_position)
         )
         new_my_module.designated_users << current_user
-        MyModules::CopyContentJob.perform_later(current_user, my_module.id, new_my_module.id)
+        MyModules::CopyContentJob.perform_later(current_user.id, my_module.id, new_my_module.id)
       end
       @experiment.workflowimg.purge
     end
diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index 64f825e04..fcb96d473 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -184,7 +184,7 @@ class ReportsController < ApplicationController
     log_activity(:generate_docx_report)
 
     ensure_report_template!
-    Reports::DocxJob.perform_later(@report.id, current_user, root_url)
+    Reports::DocxJob.perform_later(@report.id, current_user.id, root_url)
     render json: {
       message: I18n.t('projects.reports.index.generation.accepted_message')
     }
@@ -399,7 +399,7 @@ class ReportsController < ApplicationController
     log_activity(:generate_pdf_report)
 
     ensure_report_template!
-    Reports::PdfJob.perform_later(@report.id, current_user)
+    Reports::PdfJob.perform_later(@report.id, current_user.id)
   end
 
   def ensure_report_template!
diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index 2977f1828..67ccc98fb 100644
--- a/app/controllers/repositories_controller.rb
+++ b/app/controllers/repositories_controller.rb
@@ -108,7 +108,7 @@ class RepositoriesController < ApplicationController
     end
 
     # offload the rest to background job
-    HideRepositoryRemindersJob.perform_later(@repository, current_user)
+    HideRepositoryRemindersJob.perform_later(@repository, current_user.id)
 
     render json: { status: :ok }, status: :accepted
   end
@@ -349,7 +349,7 @@ class RepositoriesController < ApplicationController
     repositories = Repository.viewable_by_user(current_user, current_team).where(id: params[:repository_ids])
     if repositories.present? && current_user.has_available_exports?
       current_user.increase_daily_exports_counter!
-      RepositoriesExportJob.perform_later(repositories.pluck(:id), current_user, current_team)
+      RepositoriesExportJob.perform_later(repositories.pluck(:id), current_user.id, current_team)
       render json: { message: t('zip_export.export_request_success') }
     else
       render json: { message: t('zip_export.export_error') }, status: :unprocessable_entity
diff --git a/app/controllers/teams_controller.rb b/app/controllers/teams_controller.rb
index f0bf65cff..e532bf12b 100644
--- a/app/controllers/teams_controller.rb
+++ b/app/controllers/teams_controller.rb
@@ -132,7 +132,7 @@ class TeamsController < ApplicationController
     options = { team: @team }
     zip = TeamZipExport.create(user: current_user)
     zip.generate_exportable_zip(
-      current_user,
+      current_user.id,
       ids,
       :teams,
       options
diff --git a/app/helpers/notifications_helper.rb b/app/helpers/notifications_helper.rb
index 208456ac2..5cce5d3e6 100644
--- a/app/helpers/notifications_helper.rb
+++ b/app/helpers/notifications_helper.rb
@@ -1,6 +1,6 @@
 module NotificationsHelper
   def send_email_notification(user, notification)
-    AppMailer.delay.notification(user, notification)
+    AppMailer.delay.notification(user.id, notification)
   end
 
   # generate assignment notification
diff --git a/app/jobs/hide_repository_reminders_job.rb b/app/jobs/hide_repository_reminders_job.rb
index b72a6b2e8..d50a16948 100644
--- a/app/jobs/hide_repository_reminders_job.rb
+++ b/app/jobs/hide_repository_reminders_job.rb
@@ -3,7 +3,8 @@
 class HideRepositoryRemindersJob < ApplicationJob
   queue_as :high_priority
 
-  def perform(repository, user)
+  def perform(repository, user_id)
+    user = User.find(user_id)
     hidden_reminder_repository_cell_ids =
       HiddenRepositoryCellReminder.joins(repository_cell: { repository_row: :repository })
                                   .where(user: user)
diff --git a/app/jobs/my_modules/copy_content_job.rb b/app/jobs/my_modules/copy_content_job.rb
index abd3ab4d4..01a7db461 100644
--- a/app/jobs/my_modules/copy_content_job.rb
+++ b/app/jobs/my_modules/copy_content_job.rb
@@ -2,7 +2,8 @@
 
 module MyModules
   class CopyContentJob < ApplicationJob
-    def perform(user, source_my_module_id, target_my_module_id)
+    def perform(user_id, source_my_module_id, target_my_module_id)
+      user = User.find(user_id)
       target_my_module = MyModule.find(target_my_module_id)
       MyModule.transaction do
         MyModule.find(source_my_module_id).copy_content(user, target_my_module)
diff --git a/app/jobs/projects_json_export_job.rb b/app/jobs/projects_json_export_job.rb
index f65bdec24..4b7c95519 100644
--- a/app/jobs/projects_json_export_job.rb
+++ b/app/jobs/projects_json_export_job.rb
@@ -1,7 +1,8 @@
 # frozen_string_literal: true
 
 class ProjectsJsonExportJob < ApplicationJob
-  def perform(task_ids, callback, user)
+  def perform(task_ids, callback, user_id)
+    user = User.find(user_id)
     projects_json_export_service = ProjectsJsonExportService.new(task_ids,
                                                                  callback,
                                                                  user)
diff --git a/app/jobs/reports/docx_job.rb b/app/jobs/reports/docx_job.rb
index 893845ec9..53fa27ba3 100644
--- a/app/jobs/reports/docx_job.rb
+++ b/app/jobs/reports/docx_job.rb
@@ -21,7 +21,7 @@ module Reports
         else
           Rails.application.routes.url_helpers.reports_path(team: report.team.id)
         end
-      user = job.arguments.second
+      user = User.find(job.arguments.second)
       notification = Notification.create(
         type_of: :deliver_error,
         title: I18n.t('projects.reports.index.generation.error_docx_notification_title'),
@@ -33,8 +33,9 @@ module Reports
       Rails.logger.error("Couldn't generate DOCX for Report with id: #{report.id}. Error:\n #{error}")
     end
 
-    def perform(report_id, user, root_url)
+    def perform(report_id, user_id, root_url)
       report = Report.find(report_id)
+      user = User.find(user_id)
       file = Tempfile.new(['report', '.docx'])
       begin
         I18n.backend.date_format = user.settings[:date_format]
diff --git a/app/jobs/reports/pdf_job.rb b/app/jobs/reports/pdf_job.rb
index 8e5c53699..22d22b614 100644
--- a/app/jobs/reports/pdf_job.rb
+++ b/app/jobs/reports/pdf_job.rb
@@ -25,7 +25,7 @@ module Reports
         else
           Rails.application.routes.url_helpers.reports_path(team: report.team.id)
         end
-      user = job.arguments.second
+      user = User.find(job.arguments.second)
       notification = Notification.create(
         type_of: :deliver_error,
         title: I18n.t('projects.reports.index.generation.error_pdf_notification_title'),
@@ -39,8 +39,9 @@ module Reports
 
     PREVIEW_EXTENSIONS = %w(docx pdf).freeze
 
-    def perform(report_id, user)
+    def perform(report_id, user_id)
       report = Report.find(report_id)
+      user = User.find(user_id)
       file = Tempfile.new(['report', '.pdf'], binmode: true)
       begin
         template =
diff --git a/app/jobs/repositories_export_job.rb b/app/jobs/repositories_export_job.rb
index 35bdcf601..33ddd3662 100644
--- a/app/jobs/repositories_export_job.rb
+++ b/app/jobs/repositories_export_job.rb
@@ -3,8 +3,8 @@
 class RepositoriesExportJob < ApplicationJob
   include StringUtility
 
-  def perform(repository_ids, user, team)
-    @user = user
+  def perform(repository_ids, user_id, team)
+    @user = User.find(user_id)
     @team = team
     @repositories = Repository.viewable_by_user(@user, @team).where(id: repository_ids).order(:id)
     zip_input_dir = FileUtils.mkdir_p(Rails.root.join("tmp/temp_zip_#{Time.now.to_i}")).first
diff --git a/app/jobs/user_assignments/generate_user_assignments_job.rb b/app/jobs/user_assignments/generate_user_assignments_job.rb
index 20c0934d9..db4bc6af1 100644
--- a/app/jobs/user_assignments/generate_user_assignments_job.rb
+++ b/app/jobs/user_assignments/generate_user_assignments_job.rb
@@ -4,8 +4,8 @@ module UserAssignments
   class GenerateUserAssignmentsJob < ApplicationJob
     queue_as :high_priority
 
-    def perform(object, assigned_by)
-      @assigned_by = assigned_by
+    def perform(object, assigned_by_id)
+      @assigned_by = User.find_by(id: assigned_by_id)
       ActiveRecord::Base.transaction do
         case object
         when Experiment
diff --git a/app/jobs/user_assignments/project_group_assignment_job.rb b/app/jobs/user_assignments/project_group_assignment_job.rb
index 0b12b4d7c..9c9334ebe 100644
--- a/app/jobs/user_assignments/project_group_assignment_job.rb
+++ b/app/jobs/user_assignments/project_group_assignment_job.rb
@@ -4,9 +4,9 @@ module UserAssignments
   class ProjectGroupAssignmentJob < ApplicationJob
     queue_as :high_priority
 
-    def perform(team, project, assigned_by)
+    def perform(team, project, assigned_by_id)
       @team = team
-      @assigned_by = assigned_by
+      @assigned_by = User.find_by(id: assigned_by_id)
 
       return unless project.visible?
 
@@ -27,9 +27,9 @@ module UserAssignments
           # make sure all related experiments and my modules are assigned
           UserAssignments::PropagateAssignmentJob.perform_later(
             project,
-            user,
+            user.id,
             project.default_public_user_role || UserRole.find_predefined_viewer_role,
-            @assigned_by
+            @assigned_by.id
           )
         end
       end
diff --git a/app/jobs/user_assignments/propagate_assignment_job.rb b/app/jobs/user_assignments/propagate_assignment_job.rb
index 338b0f335..7babd336a 100644
--- a/app/jobs/user_assignments/propagate_assignment_job.rb
+++ b/app/jobs/user_assignments/propagate_assignment_job.rb
@@ -4,10 +4,10 @@ module UserAssignments
   class PropagateAssignmentJob < ApplicationJob
     queue_as :high_priority
 
-    def perform(resource, user, user_role, assigned_by, options = {})
-      @user = user
+    def perform(resource, user_id, user_role, assigned_by_id, options = {})
+      @user = User.find(user_id)
       @user_role = user_role
-      @assigned_by = assigned_by
+      @assigned_by = User.find_by(id: assigned_by_id)
       @destroy = options.fetch(:destroy, false)
       @remove_from_team = options.fetch(:remove_from_team, false)
       @resource = resource
diff --git a/app/mailers/app_mailer.rb b/app/mailers/app_mailer.rb
index be7010a96..ca8d81410 100644
--- a/app/mailers/app_mailer.rb
+++ b/app/mailers/app_mailer.rb
@@ -7,8 +7,8 @@ class AppMailer < Devise::Mailer
   default from: ENV['MAIL_FROM']
   default reply: ENV['MAIL_REPLYTO']
 
-  def notification(user, notification, opts = {})
-    @user = user
+  def notification(user_id, notification, opts = {})
+    @user = User.find(user_id)
     @notification = notification
     subject =
       if notification.deliver?
@@ -23,8 +23,8 @@ class AppMailer < Devise::Mailer
     mail(headers)
   end
 
-  def system_notification(user, system_notification, opts = {})
-    @user = user
+  def system_notification(user_id, system_notification, opts = {})
+    @user = User.find(user_id)
     @system_notification = system_notification
 
     headers = {
diff --git a/app/models/concerns/assignable.rb b/app/models/concerns/assignable.rb
index e2a856c16..afcea0ae8 100644
--- a/app/models/concerns/assignable.rb
+++ b/app/models/concerns/assignable.rb
@@ -73,7 +73,7 @@ module Assignable
         user_role: role
       )
 
-      UserAssignments::GenerateUserAssignmentsJob.perform_later(self, created_by)
+      UserAssignments::GenerateUserAssignmentsJob.perform_later(self, created_by.id)
     end
   end
 end
diff --git a/app/models/experiment.rb b/app/models/experiment.rb
index ae5573e59..81ade333b 100644
--- a/app/models/experiment.rb
+++ b/app/models/experiment.rb
@@ -353,7 +353,7 @@ class Experiment < ApplicationRecord
 
       # regenerate user assignments
       my_module.user_assignments.destroy_all
-      UserAssignments::GenerateUserAssignmentsJob.perform_later(my_module, current_user)
+      UserAssignments::GenerateUserAssignmentsJob.perform_later(my_module, current_user.id)
 
       Activities::CreateActivityService.call(activity_type: :move_task,
                                              owner: current_user,
@@ -410,7 +410,7 @@ class Experiment < ApplicationRecord
 
             # regenerate user assignments
             m.user_assignments.destroy_all
-            UserAssignments::GenerateUserAssignmentsJob.new(m, current_user).perform_now
+            UserAssignments::GenerateUserAssignmentsJob.new(m, current_user.id).perform_now
 
             # Add activity
             Activities::CreateActivityService.call(
diff --git a/app/models/project.rb b/app/models/project.rb
index 398cd5481..00d199828 100644
--- a/app/models/project.rb
+++ b/app/models/project.rb
@@ -341,7 +341,7 @@ class Project < ApplicationRecord
     UserAssignments::ProjectGroupAssignmentJob.perform_later(
       team,
       self,
-      last_modified_by || created_by
+      last_modified_by&.id || created_by&.id
     )
   end
 
diff --git a/app/models/team_zip_export.rb b/app/models/team_zip_export.rb
index 6632f3737..31e231575 100644
--- a/app/models/team_zip_export.rb
+++ b/app/models/team_zip_export.rb
@@ -6,8 +6,8 @@ require 'csv'
 class TeamZipExport < ZipExport
   include StringUtility
 
-  def generate_exportable_zip(user, data, type, options = {})
-    @user = user
+  def generate_exportable_zip(user_id, data, type, options = {})
+    @user = User.find(user_id)
     zip_input_dir = FileUtils.mkdir_p(
       File.join(Rails.root, "tmp/temp_zip_#{Time.now.to_i}")
     ).first
diff --git a/app/models/zip_export.rb b/app/models/zip_export.rb
index 292d8d413..a76d51c4e 100644
--- a/app/models/zip_export.rb
+++ b/app/models/zip_export.rb
@@ -45,7 +45,8 @@ class ZipExport < ApplicationRecord
     end
   end
 
-  def generate_exportable_zip(user, data, type, options = {})
+  def generate_exportable_zip(user_id, data, type, options = {})
+    user = User.find(user_id)
     I18n.backend.date_format = user.settings[:date_format] || Constants::DEFAULT_DATE_FORMAT
     zip_input_dir = FileUtils.mkdir_p(File.join(Rails.root, "tmp/temp_zip_#{Time.now.to_i}")).first
     tmp_zip_dir = FileUtils.mkdir_p(File.join(Rails.root, 'tmp/zip-ready')).first
diff --git a/app/services/experiments/move_to_project_service.rb b/app/services/experiments/move_to_project_service.rb
index 6252768d4..29556cdb9 100644
--- a/app/services/experiments/move_to_project_service.rb
+++ b/app/services/experiments/move_to_project_service.rb
@@ -118,7 +118,7 @@ module Experiments
         user_role: @project.user_assignments.find_by(user: @user).user_role
       )
 
-      UserAssignments::GenerateUserAssignmentsJob.perform_later(object, @user)
+      UserAssignments::GenerateUserAssignmentsJob.perform_later(object, @user.id)
     end
 
     def clean_up_user_my_modules(my_module)
diff --git a/app/services/notifications/handle_system_notification_in_communication_channel_service.rb b/app/services/notifications/handle_system_notification_in_communication_channel_service.rb
index c4c84a9d5..eed050bc8 100644
--- a/app/services/notifications/handle_system_notification_in_communication_channel_service.rb
+++ b/app/services/notifications/handle_system_notification_in_communication_channel_service.rb
@@ -14,7 +14,7 @@ module Notifications
     def call
       @system_notification.user_system_notifications.find_each do |usn|
         user = usn.user
-        AppMailer.delay.system_notification(user, @system_notification) if user.system_message_email_notification
+        AppMailer.delay.system_notification(user.id, @system_notification) if user.system_message_email_notification
       end
 
       self
diff --git a/app/services/repository_zip_export.rb b/app/services/repository_zip_export.rb
index c40bda2c7..9bd8b5d05 100644
--- a/app/services/repository_zip_export.rb
+++ b/app/services/repository_zip_export.rb
@@ -30,7 +30,7 @@ module RepositoryZipExport
 
     zip = ZipExport.create(user: current_user)
     zip.generate_exportable_zip(
-      current_user,
+      current_user.id,
       to_csv(rows, params[:header_ids], current_user, repository, nil, params[:my_module_id].present?),
       :repositories
     )
diff --git a/app/services/team_importer.rb b/app/services/team_importer.rb
index 060a751dc..b42f1657e 100644
--- a/app/services/team_importer.rb
+++ b/app/services/team_importer.rb
@@ -188,9 +188,9 @@ class TeamImporter
 
         # handle the permissions for newly created experiment
         user = User.find(user_id)
-        UserAssignments::GenerateUserAssignmentsJob.perform_now(experiment, user)
+        UserAssignments::GenerateUserAssignmentsJob.perform_now(experiment, user.id)
         experiment.my_modules.find_each do |my_module|
-          UserAssignments::GenerateUserAssignmentsJob.perform_now(my_module, user)
+          UserAssignments::GenerateUserAssignmentsJob.perform_now(my_module, user.id)
         end
         puts "Imported experiment: #{experiment.id}"
         return experiment
diff --git a/app/services/user_assignments/create_team_user_assignments_service.rb b/app/services/user_assignments/create_team_user_assignments_service.rb
index f4dfc60e9..e12c86f20 100644
--- a/app/services/user_assignments/create_team_user_assignments_service.rb
+++ b/app/services/user_assignments/create_team_user_assignments_service.rb
@@ -24,7 +24,7 @@ module UserAssignments
         UserAssignments::ProjectGroupAssignmentJob.perform_later(
           @team,
           project,
-          @assigned_by
+          @assigned_by.id
         )
       end
     end
diff --git a/app/services/user_assignments/remove_team_user_assignments_service.rb b/app/services/user_assignments/remove_team_user_assignments_service.rb
index ecce6874c..53baaab3f 100644
--- a/app/services/user_assignments/remove_team_user_assignments_service.rb
+++ b/app/services/user_assignments/remove_team_user_assignments_service.rb
@@ -10,7 +10,7 @@ module UserAssignments
     def call
       @team.projects.find_each do |project|
         UserAssignments::PropagateAssignmentJob
-          .perform_now(project, @user, nil, nil, destroy: true, remove_from_team: true)
+          .perform_now(project, @user.id, nil, nil, destroy: true, remove_from_team: true)
       end
       remove_repositories_assignments
       remove_protocols_assignments
diff --git a/spec/jobs/user_assignments/generate_user_assignments_job.rb b/spec/jobs/user_assignments/generate_user_assignments_job.rb
index 8a07f1b91..795888efa 100644
--- a/spec/jobs/user_assignments/generate_user_assignments_job.rb
+++ b/spec/jobs/user_assignments/generate_user_assignments_job.rb
@@ -30,7 +30,7 @@ module UserAssignments
         end
 
         it 'assigns the same role as the user had on project level' do
-          described_class.perform_now(experiment, user_one)
+          described_class.perform_now(experiment, user_one.id)
           user_two_assignment = UserAssignment.find_by(user: user_two, assignable: experiment)
           user_three_assignment = UserAssignment.find_by(user: user_three, assignable: experiment)
           expect(user_two_assignment.user_role).to eq viewer_role
@@ -49,7 +49,7 @@ module UserAssignments
         end
 
         it 'assigns the same role as the user had on project level' do
-          described_class.perform_now(my_module, user_one)
+          described_class.perform_now(my_module, user_one.id)
           user_two_assignment = UserAssignment.find_by(user: user_two, assignable: my_module)
           user_three_assignment = UserAssignment.find_by(user: user_three, assignable: my_module)
           expect(user_two_assignment.user_role).to eq viewer_role
diff --git a/spec/jobs/user_assignments/propagate_assignment_job_spec.rb b/spec/jobs/user_assignments/propagate_assignment_job_spec.rb
index 5b654f2ed..eb8da07fd 100644
--- a/spec/jobs/user_assignments/propagate_assignment_job_spec.rb
+++ b/spec/jobs/user_assignments/propagate_assignment_job_spec.rb
@@ -19,12 +19,12 @@ module UserAssignments
     describe 'perform' do
       it 'propagates the user assignments to project child object' do
         expect {
-          described_class.perform_now(project, user_two, technician_role, user_one)
+          described_class.perform_now(project, user_two.id, technician_role, user_one.id)
         }.to change(UserAssignment, :count).by(4)
       end
 
       it 'propagates the user assignments to project child object with the same role' do
-        described_class.perform_now(project, user_two, technician_role, user_one)
+        described_class.perform_now(project, user_two.id, technician_role, user_one.id)
         [
           UserAssignment.find_by(user: user_two, assignable: experiment_one),
           UserAssignment.find_by(user: user_two, assignable: experiment_two),
@@ -53,7 +53,7 @@ module UserAssignments
                                        user_role: owner_role,
                                        assigned_by: user_one,
                                        assigned: :manually
-        described_class.perform_now(project, user_two, technician_role, user_one)
+        described_class.perform_now(project, user_two.id, technician_role, user_one.id)
         expect(experiment_assignment.reload.user_role).to eq owner_role
       end
 
@@ -64,7 +64,7 @@ module UserAssignments
                                        user_role: owner_role,
                                        assigned_by: user_one,
                                        assigned: :automatically
-        described_class.perform_now(project, user_two, technician_role, user_one)
+        described_class.perform_now(project, user_two.id, technician_role, user_one.id)
         expect(experiment_assignment.reload.user_role).to eq technician_role
       end
     end
diff --git a/spec/models/project_member_spec.rb b/spec/models/project_member_spec.rb
index b9bfd3236..3c46ca189 100644
--- a/spec/models/project_member_spec.rb
+++ b/spec/models/project_member_spec.rb
@@ -30,7 +30,7 @@ describe ProjectMember, type: :model do
     it 'triggers the UserAssignments::PropagateAssignmentJob job' do
       subject.user_role_id = normal_user_role.id
       expect(UserAssignments::PropagateAssignmentJob).to receive(:perform_later).with(
-        project, user, normal_user_role, user
+        project, user.id, normal_user_role, user.id
       )
       subject.update
     end
@@ -74,7 +74,7 @@ describe ProjectMember, type: :model do
 
     it 'triggers the UserAssignments::PropagateAssignmentJob job' do
       expect(UserAssignments::PropagateAssignmentJob).to receive(:perform_later).with(
-        project, user, owner_role, user, destroy: true
+        project, user.id, owner_role, user.id, destroy: true
       )
       subject.destroy
     end
diff --git a/test/mailers/previews/app_mailer_preview.rb b/test/mailers/previews/app_mailer_preview.rb
index c728d926b..35ac5b2c1 100644
--- a/test/mailers/previews/app_mailer_preview.rb
+++ b/test/mailers/previews/app_mailer_preview.rb
@@ -17,7 +17,7 @@ class AppMailerPreview < ActionMailer::Preview
 
   def assignment_notification
     AppMailer.notification(
-      fake_user,
+      fake_user.id,
       Notification.new(
         type_of: :assignment,
         title: I18n.t(
@@ -40,7 +40,7 @@ class AppMailerPreview < ActionMailer::Preview
     user = User.first
     user = fake_user if user.blank?
     AppMailer.notification(
-      user,
+      user.id,
       Notification.new(
         type_of: :recent_changes,
         title: I18n.t(
@@ -60,7 +60,7 @@ class AppMailerPreview < ActionMailer::Preview
   # <b>DEPRECATED:</b> Please use <tt>system_notification</tt> instead.
   def system_message_notification
     AppMailer.notification(
-      fake_user,
+      fake_user.id,
       Notification.new(
         type_of: :system_message,
         title: 'SciNote 9.1 released!',
@@ -72,7 +72,7 @@ class AppMailerPreview < ActionMailer::Preview
 
   def delivery_notification
     AppMailer.notification(
-      fake_user,
+      fake_user.id,
       Notification.new(
         type_of: :deliver,
         title: 'Your requested export package is ready!',
@@ -86,7 +86,7 @@ class AppMailerPreview < ActionMailer::Preview
   def system_notification
     sn = FactoryBot.build(:system_notification)
     user = FactoryBot.build(:user)
-    AppMailer.system_notification(user, sn)
+    AppMailer.system_notification(user.id, sn)
   end
 
   private

From 1d21b404793689f64174c7dadb9518c3242c9546 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Wed, 16 Aug 2023 14:12:47 +0200
Subject: [PATCH 06/12] Fix long project and task names in report [SCI-9061]

---
 app/assets/stylesheets/reports_print.scss | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/app/assets/stylesheets/reports_print.scss b/app/assets/stylesheets/reports_print.scss
index 252962c63..bc7308000 100644
--- a/app/assets/stylesheets/reports_print.scss
+++ b/app/assets/stylesheets/reports_print.scss
@@ -42,24 +42,20 @@ div.print-report {
   .report-project-header-element {
     & > .report-element-body .project-name {
       color: $color-black;
-      white-space: nowrap;
     }
 
     &:hover > .report-element-body .project-name {
       color: $color-black;
-      white-space: nowrap;
     }
   }
 
   .report-module-element:hover {
     & > .report-element-body .module-name {
       color: $color-black;
-      white-space: nowrap;
     }
 
     &:hover > .report-element-body .module-name {
       color: $color-black;
-      white-space: nowrap;
     }
   }
 

From 5e29523c6150cfb1d26f89ba6b5026e7e5890333 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Wed, 16 Aug 2023 14:34:42 +0200
Subject: [PATCH 07/12] Fix calls of user assignment propagation jobs with
 optional assigned_by [SCI-9053]

---
 app/jobs/user_assignments/project_group_assignment_job.rb       | 2 +-
 .../user_assignments/create_team_user_assignments_service.rb    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/jobs/user_assignments/project_group_assignment_job.rb b/app/jobs/user_assignments/project_group_assignment_job.rb
index 9c9334ebe..b507ba027 100644
--- a/app/jobs/user_assignments/project_group_assignment_job.rb
+++ b/app/jobs/user_assignments/project_group_assignment_job.rb
@@ -29,7 +29,7 @@ module UserAssignments
             project,
             user.id,
             project.default_public_user_role || UserRole.find_predefined_viewer_role,
-            @assigned_by.id
+            @assigned_by&.id
           )
         end
       end
diff --git a/app/services/user_assignments/create_team_user_assignments_service.rb b/app/services/user_assignments/create_team_user_assignments_service.rb
index e12c86f20..d4630f46f 100644
--- a/app/services/user_assignments/create_team_user_assignments_service.rb
+++ b/app/services/user_assignments/create_team_user_assignments_service.rb
@@ -24,7 +24,7 @@ module UserAssignments
         UserAssignments::ProjectGroupAssignmentJob.perform_later(
           @team,
           project,
-          @assigned_by.id
+          @assigned_by&.id
         )
       end
     end

From 450f5df8ea3b95cc11c8d03ab6c024ffa2c502c4 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Thu, 17 Aug 2023 11:20:26 +0200
Subject: [PATCH 08/12] Allow export of archived inventories [SCI-9060]

---
 app/services/toolbars/repositories_service.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/services/toolbars/repositories_service.rb b/app/services/toolbars/repositories_service.rb
index fa88a79dd..ffcd1c296 100644
--- a/app/services/toolbars/repositories_service.rb
+++ b/app/services/toolbars/repositories_service.rb
@@ -21,7 +21,7 @@ module Toolbars
       return [] if @repositories.none?
 
       if @archived_state
-        [restore_action, delete_action]
+        [export_action, restore_action, delete_action]
       else
         [rename_action, duplicate_action, export_action, archive_action, share_action]
       end.compact

From b07432a4444bf9fb1668b168be5321c01aff4ce7 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Thu, 17 Aug 2023 14:20:44 +0200
Subject: [PATCH 09/12] Add checks for metadata on protocol import [SCI-9064]

---
 app/assets/javascripts/protocols/import_export/eln_table.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/assets/javascripts/protocols/import_export/eln_table.js b/app/assets/javascripts/protocols/import_export/eln_table.js
index 9258f5ea7..40777bde0 100644
--- a/app/assets/javascripts/protocols/import_export/eln_table.js
+++ b/app/assets/javascripts/protocols/import_export/eln_table.js
@@ -48,14 +48,14 @@ function generateElnTable(content, tableMetadata) {
 
     for (let j = 0; j < numCols; j += 1) {
       let cellData = '';
-      let cellClass = getMetadataCellValue(tableMetadata.cells, i - 1, j - 1);
+      let cellClass = tableMetadata ? getMetadataCellValue(tableMetadata.cells, i - 1, j - 1) : '';
 
       if (i > 0 && j > 0 && tableData.data[i - 1][j - 1] !== null) {
         cellData = tableData.data[i - 1][j - 1];
       } else if (i === 0 && j !== 0) {
-        cellData = tableMetadata.plateTemplate ? j.toString() : colName(j - 1);
+        cellData = tableMetadata && tableMetadata.plateTemplate ? j.toString() : colName(j - 1);
       } else if (j === 0 && i !== 0) {
-        cellData = tableMetadata.plateTemplate ? colName(i - 1) : i.toString();
+        cellData = tableMetadata && tableMetadata.plateTemplate ? colName(i - 1) : i.toString();
       }
 
       tableCells = `${tableCells}<td ${cellClass ? `class="${cellClass}"` : ''}>${cellData}</td>`;

From 622a8766bb911aa7d8d366ab3ed763c22f4c091b Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Wed, 16 Aug 2023 14:55:59 +0200
Subject: [PATCH 10/12] Hide results title if results not selected [SCI-9062]

---
 app/views/reports/elements/_my_module_element.html.erb | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/app/views/reports/elements/_my_module_element.html.erb b/app/views/reports/elements/_my_module_element.html.erb
index bb6c1c479..4284bffac 100644
--- a/app/views/reports/elements/_my_module_element.html.erb
+++ b/app/views/reports/elements/_my_module_element.html.erb
@@ -66,9 +66,11 @@
     <% end %>
 
 
-    <div class="results-title-name">
-      <%= t('projects.reports.elements.module.results') %>
-    </div><br>
+    <% if %w(file_results table_results text_results).any? { |k| @settings.dig('task', k) } %>
+      <div class="results-title-name">
+        <%= t('projects.reports.elements.module.results') %>
+      </div><br>
+    <% end %>
 
     <% order_results_for_report(my_module.results, @settings.dig('task', 'result_order')).each do |result| %>
       <% if result.is_asset && @settings.dig('task', 'file_results') %>

From 37e1c4615269b474f1f08fa23f83a1081d0eb247 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Fri, 18 Aug 2023 11:35:24 +0200
Subject: [PATCH 11/12] Hide result title in docx [SCI-9062]

---
 app/services/reports/docx/draw_my_module.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/services/reports/docx/draw_my_module.rb b/app/services/reports/docx/draw_my_module.rb
index 7f0f5380e..8b1080d17 100644
--- a/app/services/reports/docx/draw_my_module.rb
+++ b/app/services/reports/docx/draw_my_module.rb
@@ -70,7 +70,7 @@ module Reports::Docx::DrawMyModule
       draw_step(step)
     end
 
-    @docx.h4 I18n.t('Results') if my_module.results.any?
+    @docx.h4 I18n.t('Results') if my_module.results.any? && (%w(file_results table_results text_results).any? { |k| @settings.dig('task', k) })
     order_results_for_report(my_module.results, @settings.dig('task', 'result_order')).each do |result|
       if result.is_asset && @settings.dig('task', 'file_results')
         draw_result_asset(result, @settings)

From 10a0ba97396502cc5ee1403280ddd640c5271b5f Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Mon, 21 Aug 2023 14:09:05 +0200
Subject: [PATCH 12/12] Bump version to 1.28.0.1

---
 VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION b/VERSION
index cfc730712..6ee34ec94 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.28.0
+1.28.0.1