From 452547564e0c610642ba8c37a691e7e8f4ef3490 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 30 Jul 2024 10:41:06 +0200
Subject: [PATCH 01/96] Enable protocol template renaming [SCI-10851]

---
 app/controllers/protocols_controller.rb | 1 -
 app/models/protocol.rb                  | 8 --------
 config/locales/en.yml                   | 1 -
 3 files changed, 10 deletions(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index b0ade7fb4..63a782d59 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -909,7 +909,6 @@ class ProtocolsController < ApplicationController
   end
 
   def set_inline_name_editing
-    return unless @protocol.initial_draft?
     return unless can_manage_protocol_draft_in_repository?(@protocol)
 
     @inline_editable_title_config = {
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index a1a69b3d8..f26da6f07 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -70,12 +70,10 @@ class Protocol < ApplicationRecord
   with_options if: :in_repository_published_version? do
     validates :parent, presence: true
     validate :parent_type_constraint
-    validate :versions_same_name_constraint
   end
   with_options if: :in_repository_draft? do
     # Only one draft can exist for each protocol
     validate :ensure_single_draft
-    validate :versions_same_name_constraint
   end
   with_options if: -> { in_repository? && !parent && !archived_changed?(from: false) } do |protocol|
     # Active protocol must have unique name inside its team
@@ -797,12 +795,6 @@ class Protocol < ApplicationRecord
     end
   end
 
-  def versions_same_name_constraint
-    if parent.present? && !parent.name.eql?(name)
-      errors.add(:base, I18n.t('activerecord.errors.models.protocol.wrong_version_name'))
-    end
-  end
-
   def version_number_constraint
     if Protocol.where(protocol_type: Protocol::REPOSITORY_TYPES)
                .where.not(id: id)
diff --git a/config/locales/en.yml b/config/locales/en.yml
index a6e68a6b6..9eb819df6 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -166,7 +166,6 @@ en:
         protocol:
           unchangable: "Published protocols can not be changed!"
           wrong_parent_type: "Protocol can only be linked to published protocol!"
-          wrong_version_name: "Protocol versions should have same name!"
           wrong_version_number: "Protocol version number should be sequential!"
           wrong_parent_draft_number: "Procol can have only 1 draft"
           attributes:

From 5841fbdda13c22953818324e90e56bd90d924dd3 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Fri, 9 Aug 2024 12:01:05 +0200
Subject: [PATCH 02/96] Add basic support for custom templates docx [SCI-10967]

---
 Gemfile                                       |   4 +-
 Gemfile.lock                                  |  18 +-
 app/assets/javascripts/reports/new.js         |  79 +++++++-
 .../repositories_input_component.html.erb     |  11 +
 .../reports/repositories_input_component.rb   |  18 ++
 app/controllers/reports_controller.rb         |  42 +++-
 app/jobs/reports/docx_job.rb                  |   2 +
 app/services/reports/docx.rb                  |  18 +-
 app/services/reports/docx/draw_my_module.rb   |  26 +--
 app/services/reports/docx/draw_results.rb     |  30 +++
 app/services/reports/docx/draw_step.rb        |   2 +-
 app/services/reports/docx/private_methods.rb  |  10 -
 .../reports/docx/repository_helper.rb         |   4 +-
 .../reports/template_values_editor.html.erb   |  75 ++++---
 .../docx_templates/custom_template/docx.rb    | 188 ++++++++++++++++++
 .../custom_template/edit.html.erb             |  57 ++++++
 .../docx_templates/custom_template/name.txt   |   1 +
 .../docx_templates/scinote_template/docx.rb   |  19 ++
 .../docx_templates/scinote_template/name.txt  |   1 +
 app/views/reports/wizard/_first_step.html.erb |   4 +-
 .../_project_template_selector.html.erb       |  12 ++
 config/initializers/extends.rb                |   1 +
 config/initializers/report_templates.rb       |  14 ++
 config/locales/en.yml                         |   4 +-
 config/routes.rb                              |   1 +
 25 files changed, 553 insertions(+), 88 deletions(-)
 create mode 100644 app/components/reports/repositories_input_component.html.erb
 create mode 100644 app/components/reports/repositories_input_component.rb
 create mode 100644 app/services/reports/docx/draw_results.rb
 create mode 100644 app/views/reports/docx_templates/custom_template/docx.rb
 create mode 100644 app/views/reports/docx_templates/custom_template/edit.html.erb
 create mode 100644 app/views/reports/docx_templates/custom_template/name.txt
 create mode 100644 app/views/reports/docx_templates/scinote_template/docx.rb
 create mode 100644 app/views/reports/docx_templates/scinote_template/name.txt

diff --git a/Gemfile b/Gemfile
index 675d300cf..453dea286 100644
--- a/Gemfile
+++ b/Gemfile
@@ -47,8 +47,8 @@ gem 'aspector' # Aspect-oriented programming for Rails
 gem 'auto_strip_attributes', '~> 2.1' # Removes unnecessary whitespaces AR
 gem 'bcrypt', '~> 3.1.10'
 # gem 'caracal'
-gem 'caracal',
-    git: 'https://github.com/scinote-eln/caracal.git', branch: 'rubyzip2' # Build docx report
+# gem 'caracal', git: 'https://github.com/scinote-eln/caracal.git', branch: 'rubyzip2' # Build docx report
+gem 'caracal_the_curve', '~> 1.4', '>= 1.4.6'
 gem 'caxlsx' # Build XLSX files
 gem 'deface', '~> 1.9'
 gem 'down', '~> 5.0'
diff --git a/Gemfile.lock b/Gemfile.lock
index dc2d6db14..5a29368f2 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -22,16 +22,6 @@ GIT
       docile (>= 1.1.0)
       rails (>= 4)
 
-GIT
-  remote: https://github.com/scinote-eln/caracal.git
-  revision: f8e4c279adfee7801eb1024e1d6a18bb06c9c76a
-  branch: rubyzip2
-  specs:
-    caracal (1.4.1)
-      nokogiri (~> 1.6)
-      rubyzip (>= 2.3)
-      tilt (>= 1.4)
-
 GIT
   remote: https://github.com/scinote-eln/img2zpl
   revision: 23d61cfc3e90ac4caa62dd08546fa0d7590a5140
@@ -227,6 +217,10 @@ GEM
     capybara-email (3.0.2)
       capybara (>= 2.4, < 4.0)
       mail
+    caracal_the_curve (1.4.6)
+      nokogiri (~> 1.6)
+      rubyzip (>= 1.1.0, < 3.0)
+      tilt (>= 1.4)
     case_transform (0.2)
       activesupport
     caxlsx (4.0.0)
@@ -725,7 +719,7 @@ GEM
     tailwindcss-rails (2.4.0-x86_64-linux)
       railties (>= 6.0.0)
     thor (1.3.1)
-    tilt (2.2.0)
+    tilt (2.4.0)
     timecop (0.9.6)
     timeout (0.4.1)
     turbolinks (5.2.1)
@@ -805,7 +799,7 @@ DEPENDENCIES
   canaid!
   capybara
   capybara-email
-  caracal!
+  caracal_the_curve (~> 1.4, >= 1.4.6)
   caxlsx
   cssbundling-rails
   cucumber-rails
diff --git a/app/assets/javascripts/reports/new.js b/app/assets/javascripts/reports/new.js
index a7aba901e..ad280af9f 100644
--- a/app/assets/javascripts/reports/new.js
+++ b/app/assets/javascripts/reports/new.js
@@ -1036,6 +1036,7 @@ function reportHandsonTableConverter() {
 
     // Settings
     reportData.report.settings.template = dropdownSelector.getValues('#templateSelector');
+    reportData.report.settings.docx_template = dropdownSelector.getValues('#docxTemplateSelector');
     reportData.report.settings.all_tasks = $('.project-contents-container .select-all-my-modules-checkbox')
       .prop('checked');
     $.each($('.task-contents-container .content-element .protocol-setting'), function(i, e) {
@@ -1254,7 +1255,8 @@ function reportHandsonTableConverter() {
 
   function reCheckContinueButton() {
     if (dropdownSelector.getValues('#projectSelector').length > 0
-          && dropdownSelector.getValues('#templateSelector').length > 0) {
+          && dropdownSelector.getValues('#templateSelector').length > 0
+          && dropdownSelector.getValues('#docxTemplateSelector').length > 0) {
       $('.continue-button').attr('disabled', false);
     } else {
       $('.continue-button').attr('disabled', true);
@@ -1276,9 +1278,12 @@ function reportHandsonTableConverter() {
         }
         if (dropdownSelector.getValues('#projectSelector').length > 0) {
           dropdownSelector.enableSelector('#templateSelector');
+          dropdownSelector.enableSelector('#docxTemplateSelector');
         } else {
           dropdownSelector.selectValues('#templateSelector', '');
           dropdownSelector.disableSelector('#templateSelector');
+          dropdownSelector.selectValues('#docxTemplateSelector', '');
+          dropdownSelector.disableSelector('#docxTemplateSelector');
         }
         reCheckContinueButton();
       }
@@ -1292,12 +1297,12 @@ function reportHandsonTableConverter() {
       disableSearch: true,
       onSelect: function() {
         if (dropdownSelector.getValues('#templateSelector').length === 0) {
-          $('.report-template-values-container').html('').addClass('hidden');
+          $('.report-template-values-container.pdf').html('').addClass('hidden');
           reCheckContinueButton();
           return;
         }
 
-        let filledFieldsCount = $('.report-template-values-container')
+        let filledFieldsCount = $('.report-template-values-container.pdf')
           .find('input.sci-input-field, textarea.sci-input-field').filter(function() {
             return !!this.value;
           }).length;
@@ -1311,9 +1316,39 @@ function reportHandsonTableConverter() {
       }
     });
 
+    dropdownSelector.init('#docxTemplateSelector', {
+      singleSelect: true,
+      closeOnSelect: true,
+      noEmptyOption: true,
+      selectAppearance: 'simple',
+      disableSearch: true,
+      onSelect: function() {
+        if (dropdownSelector.getValues('#docxTemplateSelector').length === 0) {
+          $('.report-template-values-container.docx').html('').addClass('hidden');
+          reCheckContinueButton();
+          return;
+        }
+
+        let filledFieldsCount = $('.report-template-values-container.docx')
+          .find('input.sci-input-field, textarea.sci-input-field').filter(function() {
+            return !!this.value;
+          }).length;
+
+        if (filledFieldsCount === 0) {
+          loadDocxTemplate();
+        } else {
+          $('#templateReportWarningModal').modal('show');
+        }
+        reCheckContinueButton();
+      }
+    });
+
     if (dropdownSelector.getValues('#templateSelector').length > 0) {
       loadTemplate();
     }
+    if (dropdownSelector.getValues('#docxTemplateSelector').length > 0) {
+      loadDocxTemplate();
+    }
   }
 
   function loadTemplate() {
@@ -1325,8 +1360,38 @@ function reportHandsonTableConverter() {
 
     $('#templateSelector').data('selected-template', template);
     $.get($('#templateSelector').data('valuesEditorPath'), params, function(result) {
-      $('.report-template-values-container').removeClass('hidden');
-      $('.report-template-values-container').html(result.html);
+      $('.report-template-values-container.pdf').removeClass('hidden');
+      $('.report-template-values-container.pdf').html(result.html);
+
+      $('.section').each(function() {
+        var section = $(this);
+        var collapseButton = section.find('.sn-icon-down');
+        var valuesContainer = section.find('.values-container');
+
+        if (valuesContainer.children().length === 0) {
+          collapseButton.hide();
+        }
+      });
+
+      $('.report-template-value-dropdown').each(function() {
+        dropdownSelector.init($(this), {
+          noEmptyOption: true
+        });
+      });
+    });
+  }
+
+  function loadDocxTemplate() {
+    let template = $('#docxTemplateSelector').val();
+    let params = {
+      project_id: dropdownSelector.getValues('#projectSelector'),
+      template: template
+    };
+
+    $('#docxTemplateSelector').data('selected-template', template);
+    $.get($('#docxTemplateSelector').data('valuesEditorPath'), params, function(result) {
+      $('.report-template-values-container.docx').removeClass('hidden');
+      $('.report-template-values-container.docx').html(result.html);
 
       $('.section').each(function() {
         var section = $(this);
@@ -1448,7 +1513,9 @@ function reportHandsonTableConverter() {
     .on('hide.bs.modal', function() {
       if (!$('#templateReportWarningModal').hasClass('skip-hide-event')) {
         let previousTemplate = $('#templateSelector').data('selected-template');
+        let previousDocxTemplate = $('#docxTemplateSelector').data('selected-template');
         dropdownSelector.selectValues('#templateSelector', previousTemplate);
+        dropdownSelector.selectValues('#docxTemplateSelector', previousDocxTemplate);
       }
       $('#templateReportWarningModal').removeClass('skip-hide-event');
     });
@@ -1461,7 +1528,7 @@ function reportHandsonTableConverter() {
 
   $('#reportWizardEditWarning').modal('show');
   $('.experiment-contents').sortable();
-  
+
   initNameContainerFocus();
   initGenerateButton();
   initReportWizard();
diff --git a/app/components/reports/repositories_input_component.html.erb b/app/components/reports/repositories_input_component.html.erb
new file mode 100644
index 000000000..9906b3b2c
--- /dev/null
+++ b/app/components/reports/repositories_input_component.html.erb
@@ -0,0 +1,11 @@
+<% if @editing %>
+  <div class="sci-select-container">
+    <%= label_tag @name, @label %>
+    <%= select_tag @name, options_from_collection_for_select(@repositories, :id, :name, @value), placeholder: @placeholder, class: 'sci-input-field report-template-value-dropdown', data: { type: 'RepositoriesInputComponent' }, multiple: true %>
+  </div>
+<% else %>
+  <% @project_members.where(id: @value).each do |member| %>
+    <%= member.public_send(@displayed_field) %>
+    <br>
+  <% end %>
+<% end %>
diff --git a/app/components/reports/repositories_input_component.rb b/app/components/reports/repositories_input_component.rb
new file mode 100644
index 000000000..c7909d8c7
--- /dev/null
+++ b/app/components/reports/repositories_input_component.rb
@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+module Reports
+  class RepositoriesInputComponent < TemplateValueComponent
+    def initialize(report:, name:, label:, placeholder: nil, editing: true, displayed_field: :name)
+      super(report: report, name: name, label: label, placeholder: placeholder, editing: editing)
+
+      live_repositories = Repository.accessible_by_teams(report.team).sort_by { |r| r.name.downcase }
+      snapshots_of_deleted = RepositorySnapshot.left_outer_joins(:original_repository)
+                                               .where(team: report.team)
+                                               .where.not(original_repository: live_repositories)
+                                               .select('DISTINCT ON ("repositories"."parent_id") "repositories".*')
+                                               .sort_by { |r| r.name.downcase }
+      @repositories = live_repositories + snapshots_of_deleted
+      @displayed_field = displayed_field
+    end
+  end
+end
diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index c148511f3..2e5b20a39 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -7,13 +7,13 @@ class ReportsController < ApplicationController
   before_action :load_vars, only: %i(edit update document_preview generate_pdf generate_docx status
                                      save_pdf_to_inventory_modal save_pdf_to_inventory_item)
   before_action :load_vars_nested, only: %i(create edit update generate_pdf
-                                            generate_docx new_template_values project_contents)
+                                            generate_docx new_template_values new_docx_template_values project_contents)
   before_action :load_wizard_vars, only: %i(new edit)
   before_action :load_available_repositories, only: %i(index save_pdf_to_inventory_modal available_repositories)
   before_action :check_project_read_permissions, only: %i(create edit update generate_pdf
-                                                          generate_docx new_template_values project_contents)
+                                                          generate_docx new_template_values new_docx_template_values project_contents)
   before_action :check_read_permissions, except: %i(index new create edit update destroy actions_toolbar generate_pdf
-                                                    generate_docx new_template_values project_contents
+                                                    generate_docx new_template_values project_contents new_docx_template_values
                                                     available_repositories)
   before_action :check_create_permissions, only: %i(new create)
   before_action :check_manage_permissions, only: %i(edit update generate_pdf generate_docx)
@@ -37,6 +37,7 @@ class ReportsController < ApplicationController
   # Report grouped by modules
   def new
     @templates = Extends::REPORT_TEMPLATES
+    @docx_templates = Extends::DOCX_REPORT_TEMPLATES
     @report = current_team.reports.new
   end
 
@@ -73,6 +74,39 @@ class ReportsController < ApplicationController
     end
   end
 
+  def new_docx_template_values
+    if Extends::DOCX_REPORT_TEMPLATES.key?(params[:template]&.to_sym)
+      template = params[:template]
+    else
+      return render_404
+    end
+
+    report = current_team.reports.where(project: @project).find_by(id: params[:report_id])
+    if report.present?
+      return render_403 unless can_manage_report?(report)
+    else
+      return render_403 unless can_create_reports?(current_team)
+
+      report = current_team.reports.new(project: @project)
+    end
+
+    if lookup_context.any_templates?("reports/docx_templates/#{template}/edit")
+      render json: {
+        html: render_to_string(
+          template: "reports/docx_templates/#{template}/edit",
+          layout: 'reports/template_values_editor',
+          locals: { report: report },
+          formats: :html
+        )
+      }
+    else
+      render json: {
+        html: render_to_string(partial: 'reports/wizard/no_template_values',
+                               formats: :html)
+      }
+    end
+  end
+
   # Creating new report from the _save modal of the new page
   def create
     @report = Report.new(report_params)
@@ -102,6 +136,7 @@ class ReportsController < ApplicationController
   def edit
     @edit = true
     @active_template = @report.settings[:template]
+    @active_docx_template = @report.settings[:docx_template]
     @report.settings = Report::DEFAULT_SETTINGS if @report.settings.blank?
 
     @project_contents = {
@@ -312,6 +347,7 @@ class ReportsController < ApplicationController
 
   def load_wizard_vars
     @templates = Extends::REPORT_TEMPLATES
+    @docx_templates = Extends::DOCX_REPORT_TEMPLATES
     live_repositories = Repository.accessible_by_teams(current_team).sort_by { |r| r.name.downcase }
     snapshots_of_deleted = RepositorySnapshot.left_outer_joins(:original_repository)
                                              .where(team: current_team)
diff --git a/app/jobs/reports/docx_job.rb b/app/jobs/reports/docx_job.rb
index 51043ff37..1165653eb 100644
--- a/app/jobs/reports/docx_job.rb
+++ b/app/jobs/reports/docx_job.rb
@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require 'caracal'
+
 module Reports
   class DocxJob < ApplicationJob
     extend InputSanitizeHelper
diff --git a/app/services/reports/docx.rb b/app/services/reports/docx.rb
index 7a0251371..46445f338 100644
--- a/app/services/reports/docx.rb
+++ b/app/services/reports/docx.rb
@@ -2,6 +2,10 @@
 
 # rubocop:disable  Style/ClassAndModuleChildren
 
+Dir[Rails.root.join('app/views/reports/docx_templates/**/docx.rb')].each do |file|
+  require file
+end
+
 class Reports::Docx
   include ActionView::Helpers::TextHelper
   include ActionView::Helpers::UrlHelper
@@ -26,15 +30,23 @@ class Reports::Docx
     @link_style = {}
     @color = {}
     @scinote_url = options[:scinote_url][0..-2]
+    @template = @settings[:docx_template] || 'scinote_template'
+
+    extend "#{@template.camelize}Docx".constantize
   end
 
   def draw
     initial_document_load
 
-    @report.root_elements.each do |subject|
-      public_send("draw_#{subject.type_of}", subject)
-    end
+    prepare_docx
+
     @docx
   end
+
+  private
+
+  def get_template_value(name)
+    @report.report_template_values.find_by(name: name)&.value
+  end
 end
 # rubocop:enable  Style/ClassAndModuleChildren
diff --git a/app/services/reports/docx/draw_my_module.rb b/app/services/reports/docx/draw_my_module.rb
index ddfefd7df..e85ccf701 100644
--- a/app/services/reports/docx/draw_my_module.rb
+++ b/app/services/reports/docx/draw_my_module.rb
@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module Reports::Docx::DrawMyModule
-  def draw_my_module(subject)
+  def draw_my_module(subject, without_results: false, without_repositories: false)
     color = @color
     link_style = @link_style
     scinote_url = @scinote_url
@@ -70,30 +70,12 @@ module Reports::Docx::DrawMyModule
       draw_step(step)
     end
 
-    if my_module.results.any? && (%w(file_results table_results text_results).any? { |k| @settings.dig('task', k) })
-      @docx.h4 I18n.t('Results')
-      order_results_for_report(my_module.results, @settings.dig('task', 'result_order')).each do |result|
-        @docx.p do
-          text result.name.presence || I18n.t('projects.reports.unnamed'), italic: true
-          text "  #{I18n.t('search.index.archived')} ", bold: true if result.archived?
-          text I18n.t('projects.reports.elements.result.user_time',
-                      timestamp: I18n.l(result.created_at, format: :full),
-                      user: result.user.full_name), color: color[:gray]
-        end
-        draw_result_asset(result, @settings) if @settings.dig('task', 'file_results')
-        result.result_orderable_elements.each do |element|
-          if @settings.dig('task', 'table_results') && element.orderable_type == 'ResultTable'
-            draw_result_table(element)
-          elsif @settings.dig('task', 'text_results') && element.orderable_type == 'ResultText'
-            draw_result_text(element)
-          end
-        end
-        draw_result_comments(result) if @settings.dig('task', 'result_comments')
-      end
-    end
+    draw_results(my_module) unless without_results
 
     @docx.p
     subject.children.active.each do |child|
+      next if without_repositories && child.type_of == 'my_module_repository'
+
       public_send("draw_#{child.type_of}", child)
     end
 
diff --git a/app/services/reports/docx/draw_results.rb b/app/services/reports/docx/draw_results.rb
new file mode 100644
index 000000000..0baedb9cf
--- /dev/null
+++ b/app/services/reports/docx/draw_results.rb
@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+module Reports::Docx::DrawResults
+  def draw_results(my_module)
+    color = @color
+    return unless can_read_my_module?(@user, my_module)
+
+    if my_module.results.any? && (%w(file_results table_results text_results).any? { |k| @settings.dig('task', k) })
+      @docx.h4 I18n.t('Results')
+      order_results_for_report(my_module.results, @settings.dig('task', 'result_order')).each do |result|
+        @docx.p do
+          text result.name.presence || I18n.t('projects.reports.unnamed'), italic: true
+          text "  #{I18n.t('search.index.archived')} ", bold: true if result.archived?
+          text I18n.t('projects.reports.elements.result.user_time',
+                      timestamp: I18n.l(result.created_at, format: :full),
+                      user: result.user.full_name), color: color[:gray]
+        end
+        draw_result_asset(result, @settings) if @settings.dig('task', 'file_results')
+        result.result_orderable_elements.each do |element|
+          if @settings.dig('task', 'table_results') && element.orderable_type == 'ResultTable'
+            draw_result_table(element)
+          elsif @settings.dig('task', 'text_results') && element.orderable_type == 'ResultText'
+            draw_result_text(element)
+          end
+        end
+        draw_result_comments(result) if @settings.dig('task', 'result_comments')
+      end
+    end
+  end
+end
diff --git a/app/services/reports/docx/draw_step.rb b/app/services/reports/docx/draw_step.rb
index c6cc90660..6d4e27da6 100644
--- a/app/services/reports/docx/draw_step.rb
+++ b/app/services/reports/docx/draw_step.rb
@@ -7,7 +7,7 @@ module Reports::Docx::DrawStep
     user = (step.completed? && step.last_modified_by) || step.user
     timestamp = step.completed ? step.completed_on : step.created_at
     @docx.p
-    @docx.h5(
+    @docx.h4(
       "#{I18n.t('projects.reports.elements.step.step_pos', pos: step.position_plus_one)} #{step.name}"
     )
     @docx.p do
diff --git a/app/services/reports/docx/private_methods.rb b/app/services/reports/docx/private_methods.rb
index 8e5db9780..1136bc635 100644
--- a/app/services/reports/docx/private_methods.rb
+++ b/app/services/reports/docx/private_methods.rb
@@ -16,16 +16,6 @@ module Reports::Docx::PrivateMethods
       bottom  Constants::REPORT_DOCX_MARGIN_BOTTOM
     end
 
-    @docx.page_numbers true, align: :right
-
-    insert_logo
-
-    @docx.p do
-      text I18n.t('projects.reports.new.generate_PDF.generated_on', timestamp: I18n.l(Time.zone.now, format: :full))
-    end
-
-    @docx.hr
-
     generate_html_styles
   end
 
diff --git a/app/services/reports/docx/repository_helper.rb b/app/services/reports/docx/repository_helper.rb
index f24065fd9..50b693891 100644
--- a/app/services/reports/docx/repository_helper.rb
+++ b/app/services/reports/docx/repository_helper.rb
@@ -4,7 +4,7 @@ module Reports::Docx::RepositoryHelper
   include InputSanitizeHelper
   include ActionView::Helpers::NumberHelper
 
-  def prepare_row_columns(repository_data, my_module, repository)
+  def prepare_row_columns(repository_data, my_module = nil, repository = nil)
     result = [repository_data[:headers]]
     repository_data[:rows].each do |record|
       row = []
@@ -16,7 +16,7 @@ module Reports::Docx::RepositoryHelper
       cell_values = {}
       custom_cells = record.repository_cells
       custom_cells.each do |cell|
-        if cell.value.instance_of? RepositoryStockValue
+        if cell.value.instance_of?(RepositoryStockValue) && my_module
           if repository.is_a?(RepositorySnapshot)
             consumed_stock = record.repository_stock_consumption_cell&.value&.formatted || 0
             cell_values[cell.repository_column_id] = consumed_stock
diff --git a/app/views/layouts/reports/template_values_editor.html.erb b/app/views/layouts/reports/template_values_editor.html.erb
index 1f9352e83..225c32a4a 100644
--- a/app/views/layouts/reports/template_values_editor.html.erb
+++ b/app/views/layouts/reports/template_values_editor.html.erb
@@ -17,32 +17,57 @@
   <%= t('projects.reports.wizard.first_step.values_editor.description') %>
 </div>
 
-<div class="section">
-  <h1>
-    <i class="sn-icon sn-icon-down " data-toggle="collapse" href="#headerContainer" aria-expanded="false"></i>
-    <%= t('projects.reports.wizard.first_step.values_editor.header') %>
-  </h1>
-  <div class="values-container collapse in" id="headerContainer">
-    <%= yield :header %>
-  </div>
-</div>
+<%
+  toc = yield :toc
+  header = yield :header
+  cover = yield :cover
+  footer = yield :footer
+%>
 
-<div class="section">
-  <h1>
-    <i class="sn-icon sn-icon-down " data-toggle="collapse" href="#coverContainer" aria-expanded="false"></i>
-    <%= t('projects.reports.wizard.first_step.values_editor.cover') %>
-  </h1>
-  <div class="values-container collapse in" id="coverContainer">
-    <%= yield :cover %>
+<% if toc.present? %>
+  <div class="section">
+    <h1>
+      <i class="sn-icon sn-icon-down " data-toggle="collapse" href="#tocContainer" aria-expanded="false"></i>
+      <%= t('projects.reports.wizard.first_step.values_editor.toc') %>
+    </h1>
+    <div class="values-container collapse in" id="tocContainer">
+      <%= toc %>
+    </div>
   </div>
-</div>
+<% end %>
 
-<div class="section">
-  <h1>
-    <i class="sn-icon sn-icon-down " data-toggle="collapse" href="#footerContainer" aria-expanded="false"></i>
-    <%= t('projects.reports.wizard.first_step.values_editor.footer') %>
-  </h1>
-  <div class="values-container collapse in" id="footerContainer">
-    <%= yield :footer %>
+<% if header.present? %>
+  <div class="section">
+    <h1>
+      <i class="sn-icon sn-icon-down " data-toggle="collapse" href="#headerContainer" aria-expanded="false"></i>
+      <%= t('projects.reports.wizard.first_step.values_editor.header') %>
+    </h1>
+    <div class="values-container collapse in" id="headerContainer">
+      <%= yield header %>
+    </div>
   </div>
-</div>
+<% end %>
+
+<% if cover.present? %>
+  <div class="section">
+    <h1>
+      <i class="sn-icon sn-icon-down " data-toggle="collapse" href="#coverContainer" aria-expanded="false"></i>
+      <%= t('projects.reports.wizard.first_step.values_editor.cover') %>
+    </h1>
+    <div class="values-container collapse in" id="coverContainer">
+      <%= cover %>
+    </div>
+  </div>
+<% end %>
+
+<% if footer.present? %>
+  <div class="section">
+    <h1>
+      <i class="sn-icon sn-icon-down " data-toggle="collapse" href="#footerContainer" aria-expanded="false"></i>
+      <%= t('projects.reports.wizard.first_step.values_editor.footer') %>
+    </h1>
+    <div class="values-container collapse in" id="footerContainer">
+      <%= footer %>
+    </div>
+  </div>
+<% end %>
diff --git a/app/views/reports/docx_templates/custom_template/docx.rb b/app/views/reports/docx_templates/custom_template/docx.rb
new file mode 100644
index 000000000..b2e16276a
--- /dev/null
+++ b/app/views/reports/docx_templates/custom_template/docx.rb
@@ -0,0 +1,188 @@
+# frozen_string_literal: true
+
+module CustomTemplateDocx
+  def prepare_docx
+    report_name = get_template_value('custom_docx_report_name')
+    report_number = get_template_value('custom_docx_report_number')
+
+    @project_members = @report.project&.users
+
+    report_authors = @project_members.where(id: get_template_value('custom_docx_author[]')).pluck(:full_name).join(', ')
+    report_reviewers = @project_members.where(id: get_template_value('custom_docx_reviewer[]')).pluck(:full_name).join(', ')
+    report_author_role = get_template_value('custom_docx_author_role')
+    report_reviewer_role = get_template_value('custom_docx_reviewer_role')
+
+    @docx.header do |header|
+      header.table [[report_name, 'custom report']] do
+        border_size 1
+        cell_style cols[0], width: 8000
+        cell_style cols[1], width: 2800
+      end
+    end
+
+    @docx.footer do |footer|
+      pages = Caracal::Core::Models::TableCellModel.new do
+        p do
+          field :page
+          text ' of '
+          field :numpages
+        end
+      end
+      footer.table [['Confidential', pages]] do
+        border_top do
+          size 1
+        end
+        cell_style cols[0], width: 9500
+        cell_style cols[1], width: 1000
+      end
+    end
+
+    @docx.p
+
+    logo_data = File.read(Rails.root.join('app/assets/images/scinote_logo.png'))
+
+    c1 = Caracal::Core::Models::TableCellModel.new do
+      p report_name, bold: true
+      p ''
+    end
+
+    c2 = Caracal::Core::Models::TableCellModel.new do
+      img 'logo.png' do
+        data logo_data
+        height 20
+        width 100
+        align :left
+      end
+    end
+
+    c3 = Caracal::Core::Models::TableCellModel.new do
+      p "Author: #{report_authors}"
+      p "Role: #{report_author_role}"
+    end
+
+    c4 = Caracal::Core::Models::TableCellModel.new do
+      p "Reviewer: #{report_reviewers}"
+      p "Role: #{report_reviewer_role}"
+    end
+
+    c5 = Caracal::Core::Models::TableCellModel.new do
+      p "Report number:"
+      p report_number
+    end
+
+    @docx.table [[c1, c2], [c3, c4, c5]] do
+      border_size 2
+      cell_style rows[0], width: 3500
+      cell_style rows[1], width: 3500
+      cell_style rows[0][0], colspan: 2
+    end
+
+    @docx.p
+
+    @docx.table_of_contents do |toc|
+      toc.title 'Table of Contents'
+      toc.opts 'TOC \o "1-4" \h \z \u \t "Heading 5,1"'
+    end
+
+    @docx.page
+
+    my_modules_elements = []
+    @report.root_elements.each do |subject|
+      my_modules_elements += subject.children.active if subject.type_of == 'experiment'
+    end
+
+    @my_modules = MyModule.where(id: my_modules_elements.map { |element| element.my_module.id })
+
+    @docx.h1 'Chapter 1'
+    @docx.h2 'Sub chapter 1' if get_template_value('custom_docx_sub_chapter_1')
+    @docx.h2 'Sub chapter 2' if get_template_value('custom_docx_sub_chapter_2')
+    @docx.h1 'Chapter 2'
+    if get_template_value('custom_docx_sub_chapter_3')
+      @docx.h2 'Sub chapter 3 with inventory'
+      draw_repositories(get_template_value('custom_docx_sub_chapter_3_inventories[]'))
+    end
+    if get_template_value('custom_docx_sub_chapter_4')
+      @docx.h2 'Sub chapter 4 with inventory'
+      draw_repositories(get_template_value('custom_docx_sub_chapter_4_inventories[]'))
+    end
+    @docx.h2 'Sub chapter 5' if get_template_value('custom_docx_sub_chapter_5')
+    @docx.h2 'Sub chapter 6' if get_template_value('custom_docx_sub_chapter_6')
+    @docx.h2 'Sub chapter 7' if get_template_value('custom_docx_sub_chapter_7')
+    @docx.h1 'Chapter 3'
+    if get_template_value('custom_docx_sub_chapter_8')
+      @docx.h2 'Sub chapter 8 with task'
+      my_modules_elements.each do |element|
+        draw_my_module(element, without_results: true, without_repositories: true)
+      end
+    end
+    @docx.h2 'Sub chapter 9' if get_template_value('custom_docx_sub_chapter_9')
+    @docx.h2 'Sub chapter 10' if get_template_value('custom_docx_sub_chapter_10')
+    @docx.h2 'Sub chapter 11' if get_template_value('custom_docx_sub_chapter_11')
+    if get_template_value('custom_docx_sub_chapter_12')
+      @docx.h2 'Sub chapter 12'
+      @docx.h3 'Sub sub chapter 1' if get_template_value('custom_docx_sub_sub_chapter_1')
+      @docx.h3 'Sub sub chapter 2' if get_template_value('custom_docx_sub_sub_chapter_2')
+    end
+    @docx.h1 'Chapter 4'
+    if get_template_value('custom_docx_sub_chapter_13')
+      @docx.h2 'Sub chapter 13 with results'
+      my_modules_elements.each do |element|
+        draw_results(element.my_module)
+      end
+    end
+    @docx.h2 'Sub chapter 14' if get_template_value('custom_docx_sub_chapter_14')
+    @docx.h2 'Sub chapter 15' if get_template_value('custom_docx_sub_chapter_15')
+    @docx.h2 'Sub chapter 16' if get_template_value('custom_docx_sub_chapter_16')
+    @docx.h2 'Sub chapter 17' if get_template_value('custom_docx_sub_chapter_17')
+    @docx.h1 'Chapter 5'
+  end
+
+  def repository_docx_json(repository, rows)
+    headers = [
+      I18n.t('repositories.table.id'),
+      I18n.t('repositories.table.row_name'),
+      I18n.t('repositories.table.added_on'),
+      I18n.t('repositories.table.added_by')
+    ]
+    custom_columns = []
+    return false unless repository
+
+    repository.repository_columns.order(:id).each do |column|
+      headers.push(column.name)
+      custom_columns.push(column.id)
+    end
+
+    records = repository.repository_rows.where(id: rows)
+                        .select(:id, :name, :created_at, :created_by_id, :repository_id, :parent_id, :archived)
+    { headers: headers, rows: records, custom_columns: custom_columns }
+  end
+
+  def load_repositories(repositories_id)
+    live_repositories = Repository.accessible_by_teams(@report.team).where(id: repositories_id).sort_by { |r| r.name.downcase }
+    snapshots_of_deleted = RepositorySnapshot.left_outer_joins(:original_repository)
+                                             .where(team: @report.team)
+                                             .where(parent_id: repositories_id)
+                                             .where.not(original_repository: live_repositories)
+                                             .select('DISTINCT ON ("repositories"."parent_id") "repositories".*')
+                                             .sort_by { |r| r.name.downcase }
+    live_repositories + snapshots_of_deleted
+  end
+
+  def draw_repositories(repositories_id)
+    load_repositories(repositories_id).each do |repository|
+      rows = repository.repository_rows.where(id: @my_modules.joins(:my_module_repository_rows).select(:repository_row_id)).select(:id)
+      repository_data = repository_docx_json(repository, rows)
+
+      next unless repository_data[:rows].any? && can_read_repository?(@user, repository)
+
+      table = prepare_row_columns(repository_data, nil, repository)
+
+      @docx.p
+      @docx.p repository.name, bold: true, size: Constants::REPORT_DOCX_STEP_ELEMENTS_TITLE_SIZE
+      @docx.table table, border_size: Constants::REPORT_DOCX_TABLE_BORDER_SIZE
+
+      @docx.p
+      @docx.p
+    end
+  end
+end
diff --git a/app/views/reports/docx_templates/custom_template/edit.html.erb b/app/views/reports/docx_templates/custom_template/edit.html.erb
new file mode 100644
index 000000000..6bef2a79e
--- /dev/null
+++ b/app/views/reports/docx_templates/custom_template/edit.html.erb
@@ -0,0 +1,57 @@
+<% content_for :toc do %>
+  <h3 class="mb-4">Chapter 1</h3>
+  <div class="pl-6 flex flex-col gap-2">
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_1, label: 'Sub chapter 1') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_2, label: 'Sub chapter 2') %>
+  </div>
+  <h3 class="mb-4">Chapter 2</h3>
+  <div class="pl-6 flex flex-col gap-2">
+    <div>
+      <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_3, label: 'Sub chapter 3 with inventory') %>
+      <div class="pl-6 mb-4">
+        <%= render Reports::RepositoriesInputComponent.new(report: report, name: 'custom_docx_sub_chapter_3_inventories[]', label: 'Inventories') %>
+      </div>
+    </div>
+    <div>
+      <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_4, label: 'Sub chapter 4 with inventory') %>
+      <div class="pl-6 mb-4">
+        <%= render Reports::RepositoriesInputComponent.new(report: report, name: 'custom_docx_sub_chapter_4_inventories[]', label: 'Inventories') %>
+      </div>
+    </div>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_5, label: 'Sub chapter 5') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_6, label: 'Sub chapter 6') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_7, label: 'Sub chapter 7') %>
+  </div>
+  <h3 class="mb-4">Chapter 3</h3>
+  <div class="pl-6 flex flex-col gap-2">
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_8, label: 'Sub chapter 8 with task') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_9, label: 'Sub chapter 9') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_10, label: 'Sub chapter 10') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_11, label: 'Sub chapter 11') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_12, label: 'Sub chapter 12') %>
+    <div class="pl-6 flex flex-col gap-2">
+      <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_sub_chapter_1, label: 'Sub sub chapter 1') %>
+      <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_sub_chapter_2, label: 'Sub sub chapter 2') %>
+    </div>
+  </div>
+  <h3 class="mb-4">Chapter 4</h3>
+  <div class="pl-6 flex flex-col gap-2">
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_13, label: 'Sub chapter 13 with results') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_14, label: 'Sub chapter 14') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_15, label: 'Sub chapter 15') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_16, label: 'Sub chapter 16') %>
+    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_17, label: 'Sub chapter 17') %>
+  </div>
+  <h3 class="mb-4">Chapter 5</h3>
+<% end %>
+
+<% content_for :cover do %>
+  <%= render Reports::TextInputComponent.new(report: report, name: :custom_docx_report_name, label: 'Report name') %>
+  <%= render Reports::TextInputComponent.new(report: report, name: :custom_docx_report_number, label: 'Report number') %>
+
+  <%= render Reports::ProjectMembersInputComponent.new(report: report, name: 'custom_docx_author[]', label: 'Author') %>
+  <%= render Reports::TextInputComponent.new(report: report, name: :custom_docx_author_role, label: 'Author Role') %>
+
+  <%= render Reports::ProjectMembersInputComponent.new(report: report, name: 'custom_docx_reviewer[]', label: 'Reviewer') %>
+  <%= render Reports::TextInputComponent.new(report: report, name: :custom_docx_reviewer_role, label: 'Reviewer Role') %>
+<% end %>
diff --git a/app/views/reports/docx_templates/custom_template/name.txt b/app/views/reports/docx_templates/custom_template/name.txt
new file mode 100644
index 000000000..0ad39c916
--- /dev/null
+++ b/app/views/reports/docx_templates/custom_template/name.txt
@@ -0,0 +1 @@
+Custom Template
diff --git a/app/views/reports/docx_templates/scinote_template/docx.rb b/app/views/reports/docx_templates/scinote_template/docx.rb
new file mode 100644
index 000000000..5b5e05312
--- /dev/null
+++ b/app/views/reports/docx_templates/scinote_template/docx.rb
@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+module ScinoteTemplateDocx
+  def prepare_docx
+    @docx.page_numbers true, align: :right
+
+    insert_logo
+
+    @docx.p do
+      text I18n.t('projects.reports.new.generate_PDF.generated_on', timestamp: I18n.l(Time.zone.now, format: :full))
+    end
+
+    @docx.hr
+
+    @report.root_elements.each do |subject|
+      public_send("draw_#{subject.type_of}", subject)
+    end
+  end
+end
diff --git a/app/views/reports/docx_templates/scinote_template/name.txt b/app/views/reports/docx_templates/scinote_template/name.txt
new file mode 100644
index 000000000..9c7a580cc
--- /dev/null
+++ b/app/views/reports/docx_templates/scinote_template/name.txt
@@ -0,0 +1 @@
+SciNote Template
diff --git a/app/views/reports/wizard/_first_step.html.erb b/app/views/reports/wizard/_first_step.html.erb
index 5d9cda6fc..1fba29ada 100644
--- a/app/views/reports/wizard/_first_step.html.erb
+++ b/app/views/reports/wizard/_first_step.html.erb
@@ -1,5 +1,7 @@
 <div class="project-selector-container">
   <%= render partial: 'reports/wizard/project_template_selector', locals: {report: report} %>
 </div>
-<div class="report-template-values-container <%= 'hidden' if report.settings["template"].blank? %>">
+<div class="report-template-values-container pdf <%= 'hidden' if report.settings["template"].blank? %>">
+</div>
+<div class="report-template-values-container docx  <%= 'hidden' if report.settings["docx_template"].blank? %>">
 </div>
diff --git a/app/views/reports/wizard/_project_template_selector.html.erb b/app/views/reports/wizard/_project_template_selector.html.erb
index f29b6e7d6..3a7500e6a 100644
--- a/app/views/reports/wizard/_project_template_selector.html.erb
+++ b/app/views/reports/wizard/_project_template_selector.html.erb
@@ -23,6 +23,18 @@
                        values_editor_path: reports_new_template_values_path(report_id: report.id)
                      } %>
     </div>
+    <div class='template-selector'>
+      <%= label_tag :docxTemplateSelector, t('projects.reports.wizard.first_step.select_docx_template') %>
+      <%= select_tag :docxTemplateSelector,
+                     options_for_select(@docx_templates.invert, @active_docx_template),
+                     prompt: t('projects.reports.wizard.first_step.select_docx_template'),
+                     data: {
+                       disable_on_load: report.settings[:docx_template].blank? && report.new_record?,
+                       placeholder: t('projects.reports.wizard.first_step.select_docx_template'),
+                       selected_template: report.settings[:docx_template],
+                       values_editor_path: reports_new_docx_template_values_path(report_id: report.id)
+                     } %>
+    </div>
   </div>
   <div class="col-md-6">
     <div class="sci-input-container">
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index d7ae79061..0fab450eb 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -542,6 +542,7 @@ class Extends
   ]
 
   REPORT_TEMPLATES = {}
+  DOCX_REPORT_TEMPLATES = {}
 
   NOTIFIABLE_ACTIVITIES = %w(
     assign_user_to_project
diff --git a/config/initializers/report_templates.rb b/config/initializers/report_templates.rb
index e482295cd..0760dadda 100644
--- a/config/initializers/report_templates.rb
+++ b/config/initializers/report_templates.rb
@@ -13,3 +13,17 @@ Dir.chdir(Rails.root.join('app/views/reports/templates')) do
       end
   end
 end
+
+Dir.chdir(Rails.root.join('app/views/reports/docx_templates')) do
+  templates = Dir.glob('*').select { |entry| File.directory?(entry) }
+  templates.each do |template|
+    next if Extends::DOCX_REPORT_TEMPLATES[template.to_sym].present?
+
+    Extends::DOCX_REPORT_TEMPLATES[template.to_sym] =
+      if File.file?("#{template}/name.txt")
+        File.open("#{template}/name.txt").read.strip
+      else
+        template
+      end
+  end
+end
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 909bdfcfd..4e5d25a02 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -798,7 +798,8 @@ en:
           select_project_title: "Select project and report template"
           select_project_description: "You are about to create a new report. Please select a project for which you would like to create a report, and choose the report design template. Only projects with at least 1 task are displayed."
           select_project: "Select a project"
-          select_template: "Select your template"
+          select_template: "Select your PDF template"
+          select_docx_template: "Select your DOCX template"
           report_description: "Report description (optional)"
           report_description_placeholder: "In this report you can see..."
           values_editor:
@@ -807,6 +808,7 @@ en:
             header: "Header"
             cover: "Title page"
             footer: "Footer"
+            toc: "Table of contents"
             no_values_title: "No additional data required"
             no_values_description: "SciNote template doesn’t need any additional input for it to be successfully generated."
         second_step:
diff --git a/config/routes.rb b/config/routes.rb
index 49db07eb4..fdb9be508 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -266,6 +266,7 @@ Rails.application.routes.draw do
     end
     get 'reports/datatable', to: 'reports#datatable'
     get 'reports/new_template_values', to: 'reports#new_template_values', defaults: { format: 'json' }
+    get 'reports/new_docx_template_values', to: 'reports#new_docx_template_values', defaults: { format: 'json' }
     get 'reports/available_repositories', to: 'reports#available_repositories',
                                            defaults: { format: 'json' }
     get 'available_asset_type_columns',

From b4bcd69683cc4e9f9b50c2ca1ce7f980e95d1e45 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 13 Aug 2024 14:14:00 +0200
Subject: [PATCH 03/96] Add exclude metadata from reports [SCI-10978]

---
 app/assets/javascripts/reports/new.js         |  2 ++
 .../elements/_experiment_element.html.erb     |  8 +++--
 .../elements/_my_module_element.html.erb      | 32 +++++++++++--------
 .../_my_module_protocol_element.html.erb      |  8 +++--
 .../_my_module_result_asset_element.html.erb  |  4 ++-
 .../_my_module_result_table_element.html.erb  |  8 +++--
 .../_my_module_result_text_element.html.erb   |  8 +++--
 .../elements/_my_module_step_element.html.erb |  8 +++--
 .../elements/_project_header_element.html.erb |  8 +++--
 .../elements/_step_asset_element.html.erb     |  8 +++--
 .../elements/_step_checklist_element.html.erb |  8 +++--
 .../elements/_step_table_element.html.erb     |  8 +++--
 .../elements/_step_text_element.html.erb      |  8 +++--
 app/views/reports/wizard/_third_step.html.erb | 10 ++++++
 config/locales/en.yml                         |  1 +
 15 files changed, 84 insertions(+), 45 deletions(-)

diff --git a/app/assets/javascripts/reports/new.js b/app/assets/javascripts/reports/new.js
index ad280af9f..28e407826 100644
--- a/app/assets/javascripts/reports/new.js
+++ b/app/assets/javascripts/reports/new.js
@@ -1052,6 +1052,8 @@ function reportHandsonTableConverter() {
 
     reportData.report.settings.task.result_order = dropdownSelector.getValues('#taskResultsOrder');
 
+    reportData.report.settings.exclude_metada = $('.exclude-metadata-setting')[0].checked;
+
     return reportData;
   }
 
diff --git a/app/views/reports/elements/_experiment_element.html.erb b/app/views/reports/elements/_experiment_element.html.erb
index 86804dc9a..8ef08378e 100644
--- a/app/views/reports/elements/_experiment_element.html.erb
+++ b/app/views/reports/elements/_experiment_element.html.erb
@@ -9,9 +9,11 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h3>
-    <div class="user-time">
-      <%= t('projects.reports.elements.experiment.user_time', code: experiment.code, timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t('projects.reports.elements.experiment.user_time', code: experiment.code, timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
     <% if experiment.description.present? %>
       <%= custom_auto_link(experiment.description, team: current_team, base64_encoded_imgs: export_all) %>
     <% end %>
diff --git a/app/views/reports/elements/_my_module_element.html.erb b/app/views/reports/elements/_my_module_element.html.erb
index 43d9fd665..562495418 100644
--- a/app/views/reports/elements/_my_module_element.html.erb
+++ b/app/views/reports/elements/_my_module_element.html.erb
@@ -9,9 +9,11 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h4>
-    <div class="user-time">
-      <%= t('projects.reports.elements.module.user_time', code: my_module.code, timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t('projects.reports.elements.module.user_time', code: my_module.code, timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
     <p class="module-start-date">
       <% if my_module.started_on.present? %>
         <%= t('projects.reports.elements.module.started_on', started_on: l(my_module.started_on, format: :full)) %>
@@ -36,18 +38,20 @@
         </span>
       <% end %>
     </p>
-    <div class="row module-tags">
-      <div class="pull-left">
-        <%= t('projects.reports.elements.module.tags_header') %>
-      </div>
-      <% if (tags = my_module.tags.order(:id)).present? %>
-        <% tags.each do |tag| %>
-          <div class="pull-left module-tag" style="background-color: <%= tag.color %>;">
-            <%= tag.name %>
-          </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="row module-tags">
+        <div class="pull-left">
+          <%= t('projects.reports.elements.module.tags_header') %>
+        </div>
+        <% if (tags = my_module.tags.order(:id)).present? %>
+          <% tags.each do |tag| %>
+            <div class="pull-left module-tag" style="background-color: <%= tag.color %>;">
+              <%= tag.name %>
+            </div>
+          <% end %>
         <% end %>
-      <% end %>
-    </div>
+      </div>
+    <% end %>
     <div class="row">
       <div class="col-xs-12">
         <% if my_module.description.present? %>
diff --git a/app/views/reports/elements/_my_module_protocol_element.html.erb b/app/views/reports/elements/_my_module_protocol_element.html.erb
index 9fd76c321..88755ca91 100644
--- a/app/views/reports/elements/_my_module_protocol_element.html.erb
+++ b/app/views/reports/elements/_my_module_protocol_element.html.erb
@@ -9,9 +9,11 @@
         <%= t('projects.reports.elements.module.protocol.name') %>
       <% end %>
     </h4>
-    <div class="user-time">
-      <%= t('projects.reports.elements.module.protocol.user_time', code: protocol.original_code, timestamp: l(protocol.created_at, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t('projects.reports.elements.module.protocol.user_time', code: protocol.original_code, timestamp: l(protocol.created_at, format: :full)) %>
+      </div>
+    <% end %>
     <div class="row module-protocol-description">
       <% if @settings.dig('task', 'protocol', 'description') && protocol.description.present? %>
         <%= custom_auto_link(protocol.prepare_for_report(:description, export_all: export_all),
diff --git a/app/views/reports/elements/_my_module_result_asset_element.html.erb b/app/views/reports/elements/_my_module_result_asset_element.html.erb
index 65c9a3e43..71857134b 100644
--- a/app/views/reports/elements/_my_module_result_asset_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_asset_element.html.erb
@@ -26,7 +26,9 @@
         <% end %>
       </div>
       <div class="user-time">
-        <%= t("projects.reports.elements.result_asset.user_time", user: result.user.full_name, timestamp: l(timestamp, format: :full)) %>
+        <% unless @settings.dig('exclude_metadata') %>
+          <%= t("projects.reports.elements.result_asset.user_time", user: result.user.full_name, timestamp: l(timestamp, format: :full)) %>
+        <% end %>
         <% if report.settings.dig(:task, :file_results_previews) && ActiveStorageFileUtil.previewable_document?(asset&.file&.blob) %>
           <%= t('projects.reports.elements.result_asset.full_preview_attached') %>
         <% end %>
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 2464735b8..749b20985 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
@@ -21,9 +21,11 @@
       <% end %>
     <% end %>
    </div>
-    <div class="user-time">
-      <%= t('projects.reports.elements.result_table.user_time', timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t('projects.reports.elements.result_table.user_time', timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
   </div>
   <div class="report-element-body">
     <input type="hidden" class="hot-table-contents" value="<%= table.contents_utf_8.gsub(/\</, '&lt;').gsub(/\>/, '&gt;') %>" />
diff --git a/app/views/reports/elements/_my_module_result_text_element.html.erb b/app/views/reports/elements/_my_module_result_text_element.html.erb
index b3b96926f..d65b63a96 100644
--- a/app/views/reports/elements/_my_module_result_text_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_text_element.html.erb
@@ -11,9 +11,11 @@
         </em>
       <% end %>
     </div>
-    <div class="user-time">
-      <%= t("projects.reports.elements.result_text.user_time", timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t("projects.reports.elements.result_text.user_time", timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
   </div>
   <div class="report-element-body">
     <div class="row">
diff --git a/app/views/reports/elements/_my_module_step_element.html.erb b/app/views/reports/elements/_my_module_step_element.html.erb
index f0b636cd2..15f6d32ea 100644
--- a/app/views/reports/elements/_my_module_step_element.html.erb
+++ b/app/views/reports/elements/_my_module_step_element.html.erb
@@ -10,9 +10,11 @@
       <b><%= t('projects.reports.elements.step.step_pos', pos: (step.position_plus_one)) %></b>&nbsp;<%= step.name %>
       <%= step_status_label(step) %>
     </h5>
-    <div class="user-time">
-      <%= t("projects.reports.elements.step.#{step_type_str}.user_time", user: user.full_name , timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t("projects.reports.elements.step.#{step_type_str}.user_time", user: user.full_name , timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
   </div>
   <div class="report-element-children">
     <% step.step_orderable_elements.order(:position).each do |e| %>
diff --git a/app/views/reports/elements/_project_header_element.html.erb b/app/views/reports/elements/_project_header_element.html.erb
index 54ad6a629..735afe95e 100644
--- a/app/views/reports/elements/_project_header_element.html.erb
+++ b/app/views/reports/elements/_project_header_element.html.erb
@@ -7,9 +7,11 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h2>
-    <div class="user-time">
-      <%= t('projects.reports.elements.project_header.user_time', code: project.code, timestamp: l(project.created_at, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t('projects.reports.elements.project_header.user_time', code: project.code, timestamp: l(project.created_at, format: :full)) %>
+      </div>
+    <% end %>
   </div>
   <% if defined?(children) %>
     <div class="report-element-children">
diff --git a/app/views/reports/elements/_step_asset_element.html.erb b/app/views/reports/elements/_step_asset_element.html.erb
index 2842a7adf..75ea45762 100644
--- a/app/views/reports/elements/_step_asset_element.html.erb
+++ b/app/views/reports/elements/_step_asset_element.html.erb
@@ -18,9 +18,11 @@
         </em>
       <% end %>
     </span>
-    <div class="user-time">
-      &nbsp;<%= t('projects.reports.elements.step_asset.user_time', timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        &nbsp;<%= t('projects.reports.elements.step_asset.user_time', timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
   </div>
   <div class="report-element-body">
     <% if asset.previewable? && !asset.list? %>
diff --git a/app/views/reports/elements/_step_checklist_element.html.erb b/app/views/reports/elements/_step_checklist_element.html.erb
index f4d625d1a..9a7917aa3 100644
--- a/app/views/reports/elements/_step_checklist_element.html.erb
+++ b/app/views/reports/elements/_step_checklist_element.html.erb
@@ -9,9 +9,11 @@
                            team: current_team,
                            base64_encoded_imgs: export_all) %>
     </div>
-    <div class="user-time">
-      <%= t('projects.reports.elements.step_checklist.user_time', timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t('projects.reports.elements.step_checklist.user_time', timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
   </div>
   <div class="report-element-body">
     <% items.each do |item| %>
diff --git a/app/views/reports/elements/_step_table_element.html.erb b/app/views/reports/elements/_step_table_element.html.erb
index e3334f08c..1cc9c8b3c 100644
--- a/app/views/reports/elements/_step_table_element.html.erb
+++ b/app/views/reports/elements/_step_table_element.html.erb
@@ -18,9 +18,11 @@
         <% end %>
       <% end %>
     </div>
-    <div class="user-time">
-      <%= t("projects.reports.elements.#{table_type}.user_time", timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t("projects.reports.elements.#{table_type}.user_time", timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
   </div>
   <div class="report-element-body">
     <input type="hidden" class="hot-table-contents" value="<%= table.contents_utf_8.gsub(/\</, '&lt;').gsub(/\>/, '&gt;') %>" />
diff --git a/app/views/reports/elements/_step_text_element.html.erb b/app/views/reports/elements/_step_text_element.html.erb
index 01c274f89..9a62410c3 100644
--- a/app/views/reports/elements/_step_text_element.html.erb
+++ b/app/views/reports/elements/_step_text_element.html.erb
@@ -8,9 +8,11 @@
         </em>
       <% end %>
     </div>
-    <div class="user-time">
-      <%= t("projects.reports.elements.step_text.user_time", timestamp: l(timestamp, format: :full)) %>
-    </div>
+    <% unless @settings.dig('exclude_metadata') %>
+      <div class="user-time">
+        <%= t("projects.reports.elements.step_text.user_time", timestamp: l(timestamp, format: :full)) %>
+      </div>
+    <% end %>
   </div>
   <div class="report-element-body">
     <% if step_text.text.present? %>
diff --git a/app/views/reports/wizard/_third_step.html.erb b/app/views/reports/wizard/_third_step.html.erb
index 642eb9db5..d56af9b24 100644
--- a/app/views/reports/wizard/_third_step.html.erb
+++ b/app/views/reports/wizard/_third_step.html.erb
@@ -194,6 +194,16 @@
             <div class="divider"></div>
           </div>
         </li>
+        <li>
+          <div class="select-all-container">
+            <span class="sci-checkbox-container">
+              <input type="checkbox" class="sci-checkbox exclude-metadata-setting" value="exclude_metadata" <%= 'checked' if report.settings.dig(:exclude_metadata) %>/>
+              <span class="sci-checkbox-label"></span>
+            </span>
+            <%= t("projects.reports.wizard.third_step.exclude_metadata") %>
+            <div class="divider"></div>
+          </div>
+        </li>
       </ul>
   </ul>
 </div>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 4e5d25a02..55582e52c 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -851,6 +851,7 @@ en:
           results_comments: "Result comments"
           additional_content: "Additional content"
           task_activity: "Include task activity"
+          exclude_metadata: "Exclude metadata"
           archived: "[archived]"
           deleted: "[deleted]"
 

From 5105079f8123636f4fc06f609a1033249d569c9a Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Wed, 14 Aug 2024 10:52:16 +0200
Subject: [PATCH 04/96] Add exclude metadata settings [SCI-10978]

---
 app/assets/javascripts/reports/new.js         |  2 +-
 app/services/reports/docx/draw_experiment.rb  |  7 +++-
 app/services/reports/docx/draw_my_module.rb   | 39 +++++++++++--------
 .../reports/docx/draw_my_module_protocol.rb   |  6 ++-
 .../reports/docx/draw_project_header.rb       | 10 +++--
 .../reports/docx/draw_result_asset.rb         |  6 ++-
 .../reports/docx/draw_result_table.rb         |  7 +++-
 app/services/reports/docx/draw_result_text.rb |  7 +++-
 app/services/reports/docx/draw_results.rb     |  9 +++--
 app/services/reports/docx/draw_step.rb        | 13 ++++---
 app/services/reports/docx/draw_step_asset.rb  |  7 +++-
 .../reports/docx/draw_step_checklist.rb       |  7 +++-
 app/services/reports/docx/draw_step_table.rb  |  7 +++-
 app/services/reports/docx/draw_step_text.rb   |  7 +++-
 .../elements/_experiment_element.html.erb     |  2 +-
 .../elements/_my_module_element.html.erb      | 32 ++++++++-------
 .../_my_module_protocol_element.html.erb      |  2 +-
 .../_my_module_result_asset_element.html.erb  |  2 +-
 .../_my_module_result_table_element.html.erb  |  2 +-
 .../_my_module_result_text_element.html.erb   |  2 +-
 .../elements/_my_module_step_element.html.erb |  2 +-
 .../elements/_project_header_element.html.erb |  2 +-
 .../elements/_step_asset_element.html.erb     |  2 +-
 .../elements/_step_checklist_element.html.erb |  2 +-
 .../elements/_step_table_element.html.erb     |  2 +-
 .../elements/_step_text_element.html.erb      |  2 +-
 config/database.yml                           |  1 -
 27 files changed, 114 insertions(+), 75 deletions(-)

diff --git a/app/assets/javascripts/reports/new.js b/app/assets/javascripts/reports/new.js
index 28e407826..519bae098 100644
--- a/app/assets/javascripts/reports/new.js
+++ b/app/assets/javascripts/reports/new.js
@@ -1052,7 +1052,7 @@ function reportHandsonTableConverter() {
 
     reportData.report.settings.task.result_order = dropdownSelector.getValues('#taskResultsOrder');
 
-    reportData.report.settings.exclude_metada = $('.exclude-metadata-setting')[0].checked;
+    reportData.report.settings.exclude_metadata = $('.exclude-metadata-setting')[0].checked;
 
     return reportData;
   }
diff --git a/app/services/reports/docx/draw_experiment.rb b/app/services/reports/docx/draw_experiment.rb
index e02d018a7..d7355ab36 100644
--- a/app/services/reports/docx/draw_experiment.rb
+++ b/app/services/reports/docx/draw_experiment.rb
@@ -4,6 +4,7 @@ module Reports::Docx::DrawExperiment
   def draw_experiment(subject)
     color = @color
     link_style = @link_style
+    settings = @settings
     scinote_url = @scinote_url
     experiment = subject.experiment
     return unless can_read_experiment?(@user, experiment)
@@ -15,8 +16,10 @@ module Reports::Docx::DrawExperiment
     end
 
     @docx.p do
-      text I18n.t('projects.reports.elements.experiment.user_time',
-                  code: experiment.code, timestamp: I18n.l(experiment.created_at, format: :full)), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t('projects.reports.elements.experiment.user_time',
+                    code: experiment.code, timestamp: I18n.l(experiment.created_at, format: :full)), color: color[:gray]
+      end
       if experiment.archived?
         text ' | '
         text I18n.t('search.index.archived'), color: color[:gray]
diff --git a/app/services/reports/docx/draw_my_module.rb b/app/services/reports/docx/draw_my_module.rb
index e85ccf701..a174a6171 100644
--- a/app/services/reports/docx/draw_my_module.rb
+++ b/app/services/reports/docx/draw_my_module.rb
@@ -4,6 +4,7 @@ module Reports::Docx::DrawMyModule
   def draw_my_module(subject, without_results: false, without_repositories: false)
     color = @color
     link_style = @link_style
+    settings = @settings
     scinote_url = @scinote_url
     my_module = subject.my_module
     tags = my_module.tags.order(:id)
@@ -16,8 +17,10 @@ module Reports::Docx::DrawMyModule
     end
 
     @docx.p do
-      text I18n.t('projects.reports.elements.module.user_time', code: my_module.code,
-                  timestamp: I18n.l(my_module.created_at, format: :full)), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t('projects.reports.elements.module.user_time', code: my_module.code,
+                    timestamp: I18n.l(my_module.created_at, format: :full)), color: color[:gray]
+      end
       if my_module.archived?
         text ' | '
         text I18n.t('search.index.archived'), color: color[:gray]
@@ -38,22 +41,24 @@ module Reports::Docx::DrawMyModule
       end
     end
 
-    status = my_module.my_module_status
-    @docx.p do
-      text I18n.t('projects.reports.elements.module.status')
-      text ' '
-      text "[#{status.name}]", color: (status.light_color? ? '000000' : status.color.delete('#'))
-      if my_module.completed?
-        text " #{I18n.t('my_modules.states.completed')} #{I18n.l(my_module.completed_on, format: :full)}"
-      end
-    end
-
-    if tags.present?
+    unless settings['exclude_metadata']
+      status = my_module.my_module_status
       @docx.p do
-        text I18n.t('projects.reports.elements.module.tags_header')
-        tags.each do |tag|
-          text ' '
-          text "[#{tag.name}]", color: tag.color.delete('#')
+        text I18n.t('projects.reports.elements.module.status')
+        text ' '
+        text "[#{status.name}]", color: (status.light_color? ? '000000' : status.color.delete('#'))
+        if my_module.completed?
+          text " #{I18n.t('my_modules.states.completed')} #{I18n.l(my_module.completed_on, format: :full)}"
+        end
+      end
+
+      if tags.present?
+        @docx.p do
+          text I18n.t('projects.reports.elements.module.tags_header')
+          tags.each do |tag|
+            text ' '
+            text "[#{tag.name}]", color: tag.color.delete('#')
+          end
         end
       end
     end
diff --git a/app/services/reports/docx/draw_my_module_protocol.rb b/app/services/reports/docx/draw_my_module_protocol.rb
index 2096569ff..04d03800c 100644
--- a/app/services/reports/docx/draw_my_module_protocol.rb
+++ b/app/services/reports/docx/draw_my_module_protocol.rb
@@ -12,8 +12,10 @@ module Reports::Docx::DrawMyModuleProtocol
     end
 
     if @settings.dig('task', 'protocol', 'description') && protocol.description.present?
-      @docx.p I18n.t('projects.reports.elements.module.protocol.user_time', code: protocol.original_code,
-                     timestamp: I18n.l(protocol.created_at, format: :full)), color: @color[:gray]
+      unless @settings['exclude_metadata']
+        @docx.p I18n.t('projects.reports.elements.module.protocol.user_time', code: protocol.original_code,
+                      timestamp: I18n.l(protocol.created_at, format: :full)), color: @color[:gray]
+      end
       html = custom_auto_link(protocol.description, team: @report_team)
       Reports::HtmlToWordConverter.new(@docx, { scinote_url: @scinote_url,
                                                 link_style: @link_style }).html_to_word_converter(html)
diff --git a/app/services/reports/docx/draw_project_header.rb b/app/services/reports/docx/draw_project_header.rb
index defa8e36e..56e2b6569 100644
--- a/app/services/reports/docx/draw_project_header.rb
+++ b/app/services/reports/docx/draw_project_header.rb
@@ -15,10 +15,12 @@ module Reports::Docx::DrawProjectHeader
            link_style
     end
 
-    @docx.p do
-      text I18n.t('projects.reports.elements.project_header.user_time', code: project.code,
-                  timestamp: I18n.l(project.created_at, format: :full)), color: color[:gray]
-      br
+    unless @settings['exclude_metadata']
+      @docx.p do
+        text I18n.t('projects.reports.elements.project_header.user_time', code: project.code,
+                    timestamp: I18n.l(project.created_at, format: :full)), color: color[:gray]
+        br
+      end
     end
   end
 end
diff --git a/app/services/reports/docx/draw_result_asset.rb b/app/services/reports/docx/draw_result_asset.rb
index 030de2591..80520c4c7 100644
--- a/app/services/reports/docx/draw_result_asset.rb
+++ b/app/services/reports/docx/draw_result_asset.rb
@@ -25,8 +25,10 @@ module Reports::Docx::DrawResultAsset
         end
         text "  #{I18n.t('search.index.archived')} ", bold: true if result.archived?
         text ' ' + I18n.t('projects.reports.elements.result_asset.file_name', file: asset.file_name)
-        text ' ' + I18n.t('projects.reports.elements.result_asset.user_time',
-                          user: result.user.full_name, timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+        unless settings['exclude_metadata']
+          text ' ' + I18n.t('projects.reports.elements.result_asset.user_time',
+                            user: result.user.full_name, timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+        end
 
         if settings.dig(:task, :file_results_previews) && ActiveStorageFileUtil.previewable_document?(asset&.file&.blob)
           text " #{I18n.t('projects.reports.elements.result_asset.full_preview_attached')}", color: color[:gray]
diff --git a/app/services/reports/docx/draw_result_table.rb b/app/services/reports/docx/draw_result_table.rb
index 661d41a46..0d3923623 100644
--- a/app/services/reports/docx/draw_result_table.rb
+++ b/app/services/reports/docx/draw_result_table.rb
@@ -5,6 +5,7 @@ module Reports::Docx::DrawResultTable
     result = element.result
     table = element.orderable.table
     timestamp = table.created_at
+    settings = @settings
     color = @color
     obj = self
     table_data = JSON.parse(table.contents_utf_8)['data']
@@ -40,8 +41,10 @@ module Reports::Docx::DrawResultTable
     @docx.p do
       text I18n.t 'projects.reports.elements.result_table.table_name', name: table.name
       text ' '
-      text I18n.t('projects.reports.elements.result_table.user_time',
-                  timestamp: I18n.l(timestamp, format: :full), user: result.user.full_name), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t('projects.reports.elements.result_table.user_time',
+                    timestamp: I18n.l(timestamp, format: :full), user: result.user.full_name), color: color[:gray]
+      end
     end
   end
 end
diff --git a/app/services/reports/docx/draw_result_text.rb b/app/services/reports/docx/draw_result_text.rb
index 2ab606a7e..1dbfe17d5 100644
--- a/app/services/reports/docx/draw_result_text.rb
+++ b/app/services/reports/docx/draw_result_text.rb
@@ -4,12 +4,15 @@ module Reports::Docx::DrawResultText
   def draw_result_text(element)
     result_text = element.orderable
     timestamp = element.created_at
+    settings = @settings
     color = @color
     @docx.p do
       text result_text.name.presence || '', italic: true
       text ' '
-      text I18n.t('projects.reports.elements.result_text.user_time',
-                  timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t('projects.reports.elements.result_text.user_time',
+                    timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      end
     end
     html = custom_auto_link(result_text.text, team: @report_team)
     Reports::HtmlToWordConverter.new(@docx, { scinote_url: @scinote_url,
diff --git a/app/services/reports/docx/draw_results.rb b/app/services/reports/docx/draw_results.rb
index 0baedb9cf..c35942da8 100644
--- a/app/services/reports/docx/draw_results.rb
+++ b/app/services/reports/docx/draw_results.rb
@@ -3,6 +3,7 @@
 module Reports::Docx::DrawResults
   def draw_results(my_module)
     color = @color
+    settings = @settings
     return unless can_read_my_module?(@user, my_module)
 
     if my_module.results.any? && (%w(file_results table_results text_results).any? { |k| @settings.dig('task', k) })
@@ -11,9 +12,11 @@ module Reports::Docx::DrawResults
         @docx.p do
           text result.name.presence || I18n.t('projects.reports.unnamed'), italic: true
           text "  #{I18n.t('search.index.archived')} ", bold: true if result.archived?
-          text I18n.t('projects.reports.elements.result.user_time',
-                      timestamp: I18n.l(result.created_at, format: :full),
-                      user: result.user.full_name), color: color[:gray]
+          unless settings['exclude_metadata']
+            text I18n.t('projects.reports.elements.result.user_time',
+                        timestamp: I18n.l(result.created_at, format: :full),
+                        user: result.user.full_name), color: color[:gray]
+          end
         end
         draw_result_asset(result, @settings) if @settings.dig('task', 'file_results')
         result.result_orderable_elements.each do |element|
diff --git a/app/services/reports/docx/draw_step.rb b/app/services/reports/docx/draw_step.rb
index 6d4e27da6..b2892ba6a 100644
--- a/app/services/reports/docx/draw_step.rb
+++ b/app/services/reports/docx/draw_step.rb
@@ -6,6 +6,7 @@ module Reports::Docx::DrawStep
     step_type_str = step.completed ? 'completed' : 'uncompleted'
     user = (step.completed? && step.last_modified_by) || step.user
     timestamp = step.completed ? step.completed_on : step.created_at
+    settings = @settings
     @docx.p
     @docx.h4(
       "#{I18n.t('projects.reports.elements.step.step_pos', pos: step.position_plus_one)} #{step.name}"
@@ -17,11 +18,13 @@ module Reports::Docx::DrawStep
         text I18n.t('protocols.steps.uncompleted'), color: color[:gray], bold: true
       end
       text ' | '
-      text I18n.t(
-        "projects.reports.elements.step.#{step_type_str}.user_time",
-        user: user.full_name,
-        timestamp: I18n.l(timestamp, format: :full)
-      ), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t(
+          "projects.reports.elements.step.#{step_type_str}.user_time",
+          user: user.full_name,
+          timestamp: I18n.l(timestamp, format: :full)
+        ), color: color[:gray]
+      end
     end
 
     step.step_orderable_elements.order(:position).each do |element|
diff --git a/app/services/reports/docx/draw_step_asset.rb b/app/services/reports/docx/draw_step_asset.rb
index 8d83ca221..fab9c36f6 100644
--- a/app/services/reports/docx/draw_step_asset.rb
+++ b/app/services/reports/docx/draw_step_asset.rb
@@ -5,6 +5,7 @@ module Reports::Docx::DrawStepAsset
     timestamp = asset.created_at
     asset_url = Rails.application.routes.url_helpers.asset_download_url(asset)
     color = @color
+    settings = @settings
     @docx.p
 
     begin
@@ -23,8 +24,10 @@ module Reports::Docx::DrawStepAsset
         italic true
       end
       text ' '
-      text I18n.t('projects.reports.elements.step_asset.user_time',
-                  timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t('projects.reports.elements.step_asset.user_time',
+                    timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      end
     end
   end
 end
diff --git a/app/services/reports/docx/draw_step_checklist.rb b/app/services/reports/docx/draw_step_checklist.rb
index e2662e60e..c6e946e5b 100644
--- a/app/services/reports/docx/draw_step_checklist.rb
+++ b/app/services/reports/docx/draw_step_checklist.rb
@@ -4,6 +4,7 @@ module Reports::Docx::DrawStepChecklist
   def draw_step_checklist(checklist)
     team = @report_team
     user = @user
+    settings = @settings
 
     items = checklist.checklist_items
     timestamp = checklist.created_at
@@ -16,8 +17,10 @@ module Reports::Docx::DrawStepChecklist
         I18n.t('projects.reports.elements.step_checklist.checklist_name', name: checklist.name)
       ).text, italic: true
       text ' '
-      text I18n.t('projects.reports.elements.step_checklist.user_time',
-                  timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t('projects.reports.elements.step_checklist.user_time',
+                    timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      end
     end
     if items.any?
       @docx.ul do
diff --git a/app/services/reports/docx/draw_step_table.rb b/app/services/reports/docx/draw_step_table.rb
index a0826741a..8b3b4909b 100644
--- a/app/services/reports/docx/draw_step_table.rb
+++ b/app/services/reports/docx/draw_step_table.rb
@@ -4,6 +4,7 @@ module Reports::Docx::DrawStepTable
   def draw_step_table(table, table_type)
     color = @color
     timestamp = table.created_at
+    settings = @settings
     obj = self
     table_data = JSON.parse(table.contents_utf_8)['data']
     table_data = obj.add_headers_to_table(table_data, table_type == 'step_well_plates_table')
@@ -39,8 +40,10 @@ module Reports::Docx::DrawStepTable
     @docx.p do
       text I18n.t("projects.reports.elements.#{table_type}.table_name", name: table.name), italic: true
       text ' '
-      text I18n.t("projects.reports.elements.#{table_type}.user_time",
-                  timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t("projects.reports.elements.#{table_type}.user_time",
+                    timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      end
     end
   end
 end
diff --git a/app/services/reports/docx/draw_step_text.rb b/app/services/reports/docx/draw_step_text.rb
index 978386a94..6218595a0 100644
--- a/app/services/reports/docx/draw_step_text.rb
+++ b/app/services/reports/docx/draw_step_text.rb
@@ -5,11 +5,14 @@ module Reports::Docx::DrawStepText
     step_text = element.orderable
     timestamp = element.created_at
     color = @color
+    settings = @settings
     @docx.p do
       text step_text.name.presence || '', italic: true
       text ' '
-      text I18n.t('projects.reports.elements.result_text.user_time',
-                  timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      unless settings['exclude_metadata']
+        text I18n.t('projects.reports.elements.result_text.user_time',
+                    timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+      end
     end
     if step_text.text.present?
       html = custom_auto_link(step_text.text, team: @report_team)
diff --git a/app/views/reports/elements/_experiment_element.html.erb b/app/views/reports/elements/_experiment_element.html.erb
index 8ef08378e..475c96b7b 100644
--- a/app/views/reports/elements/_experiment_element.html.erb
+++ b/app/views/reports/elements/_experiment_element.html.erb
@@ -9,7 +9,7 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h3>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.experiment.user_time', code: experiment.code, timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_my_module_element.html.erb b/app/views/reports/elements/_my_module_element.html.erb
index 562495418..5ad3cee73 100644
--- a/app/views/reports/elements/_my_module_element.html.erb
+++ b/app/views/reports/elements/_my_module_element.html.erb
@@ -9,7 +9,7 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h4>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.module.user_time', code: my_module.code, timestamp: l(timestamp, format: :full)) %>
       </div>
@@ -24,21 +24,23 @@
         <%= t('projects.reports.elements.module.due_date', due_date: l(my_module.due_date, format: :full)) %>
       <% end %>
     </p>
-    <p class="module-status">
-      <% status = my_module.my_module_status %>
-      <%= t('projects.reports.elements.module.status') %>
-      <span class="status-block" style="background: <%= status.color %>;
-        <%= 'color: #000000; border: 1px solid #D0D5DD;' if status.light_color? %>">
-        <%= status.name %>
-      </span>
-      <% if my_module.completed? %>
-        <span style="margin-left: 10px;">
-          <%= t('my_modules.states.completed') %>
-          <%= l(my_module.completed_on, format: :full) %>
+    <% unless @settings['exclude_metadata'] %>
+      <p class="module-status">
+        <% status = my_module.my_module_status %>
+        <%= t('projects.reports.elements.module.status') %>
+        <span class="status-block" style="background: <%= status.color %>;
+          <%= 'color: #000000; border: 1px solid #D0D5DD;' if status.light_color? %>">
+          <%= status.name %>
         </span>
-      <% end %>
-    </p>
-    <% unless @settings.dig('exclude_metadata') %>
+        <% if my_module.completed? %>
+          <span style="margin-left: 10px;">
+            <%= t('my_modules.states.completed') %>
+            <%= l(my_module.completed_on, format: :full) %>
+          </span>
+        <% end %>
+      </p>
+    <% end %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="row module-tags">
         <div class="pull-left">
           <%= t('projects.reports.elements.module.tags_header') %>
diff --git a/app/views/reports/elements/_my_module_protocol_element.html.erb b/app/views/reports/elements/_my_module_protocol_element.html.erb
index 88755ca91..1aa86ecb1 100644
--- a/app/views/reports/elements/_my_module_protocol_element.html.erb
+++ b/app/views/reports/elements/_my_module_protocol_element.html.erb
@@ -9,7 +9,7 @@
         <%= t('projects.reports.elements.module.protocol.name') %>
       <% end %>
     </h4>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.module.protocol.user_time', code: protocol.original_code, timestamp: l(protocol.created_at, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_my_module_result_asset_element.html.erb b/app/views/reports/elements/_my_module_result_asset_element.html.erb
index 71857134b..5485a789d 100644
--- a/app/views/reports/elements/_my_module_result_asset_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_asset_element.html.erb
@@ -26,7 +26,7 @@
         <% end %>
       </div>
       <div class="user-time">
-        <% unless @settings.dig('exclude_metadata') %>
+        <% unless @settings['exclude_metadata'] %>
           <%= t("projects.reports.elements.result_asset.user_time", user: result.user.full_name, timestamp: l(timestamp, format: :full)) %>
         <% end %>
         <% if report.settings.dig(:task, :file_results_previews) && ActiveStorageFileUtil.previewable_document?(asset&.file&.blob) %>
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 749b20985..e5fd49f52 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
@@ -21,7 +21,7 @@
       <% end %>
     <% end %>
    </div>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.result_table.user_time', timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_my_module_result_text_element.html.erb b/app/views/reports/elements/_my_module_result_text_element.html.erb
index d65b63a96..94e02fa52 100644
--- a/app/views/reports/elements/_my_module_result_text_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_text_element.html.erb
@@ -11,7 +11,7 @@
         </em>
       <% end %>
     </div>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t("projects.reports.elements.result_text.user_time", timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_my_module_step_element.html.erb b/app/views/reports/elements/_my_module_step_element.html.erb
index 15f6d32ea..2be53b1a9 100644
--- a/app/views/reports/elements/_my_module_step_element.html.erb
+++ b/app/views/reports/elements/_my_module_step_element.html.erb
@@ -10,7 +10,7 @@
       <b><%= t('projects.reports.elements.step.step_pos', pos: (step.position_plus_one)) %></b>&nbsp;<%= step.name %>
       <%= step_status_label(step) %>
     </h5>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t("projects.reports.elements.step.#{step_type_str}.user_time", user: user.full_name , timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_project_header_element.html.erb b/app/views/reports/elements/_project_header_element.html.erb
index 735afe95e..9e355d6d9 100644
--- a/app/views/reports/elements/_project_header_element.html.erb
+++ b/app/views/reports/elements/_project_header_element.html.erb
@@ -7,7 +7,7 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h2>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.project_header.user_time', code: project.code, timestamp: l(project.created_at, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_step_asset_element.html.erb b/app/views/reports/elements/_step_asset_element.html.erb
index 75ea45762..880ab97ee 100644
--- a/app/views/reports/elements/_step_asset_element.html.erb
+++ b/app/views/reports/elements/_step_asset_element.html.erb
@@ -18,7 +18,7 @@
         </em>
       <% end %>
     </span>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         &nbsp;<%= t('projects.reports.elements.step_asset.user_time', timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_step_checklist_element.html.erb b/app/views/reports/elements/_step_checklist_element.html.erb
index 9a7917aa3..1951fde55 100644
--- a/app/views/reports/elements/_step_checklist_element.html.erb
+++ b/app/views/reports/elements/_step_checklist_element.html.erb
@@ -9,7 +9,7 @@
                            team: current_team,
                            base64_encoded_imgs: export_all) %>
     </div>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.step_checklist.user_time', timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_step_table_element.html.erb b/app/views/reports/elements/_step_table_element.html.erb
index 1cc9c8b3c..dfda2ac14 100644
--- a/app/views/reports/elements/_step_table_element.html.erb
+++ b/app/views/reports/elements/_step_table_element.html.erb
@@ -18,7 +18,7 @@
         <% end %>
       <% end %>
     </div>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t("projects.reports.elements.#{table_type}.user_time", timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_step_text_element.html.erb b/app/views/reports/elements/_step_text_element.html.erb
index 9a62410c3..8c8ff72eb 100644
--- a/app/views/reports/elements/_step_text_element.html.erb
+++ b/app/views/reports/elements/_step_text_element.html.erb
@@ -8,7 +8,7 @@
         </em>
       <% end %>
     </div>
-    <% unless @settings.dig('exclude_metadata') %>
+    <% unless @settings['exclude_metadata'] %>
       <div class="user-time">
         <%= t("projects.reports.elements.step_text.user_time", timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/config/database.yml b/config/database.yml
index a44a2ec67..c7f72cd5c 100644
--- a/config/database.yml
+++ b/config/database.yml
@@ -35,7 +35,6 @@ development:
 
   # The password associated with the postgres role (username).
   # password: mysecretpassword
-
   # Connect on a TCP socket. Omitted by default since the client uses a
   # domain socket that doesn't need configuration. Windows does not have
   # domain sockets, so uncomment these lines.

From dddf2be610e7a28790f0b79239a7b95605596b13 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 20 Aug 2024 15:01:42 +0200
Subject: [PATCH 05/96] Update caracal version [SCI-10985]

---
 Gemfile      |  3 +--
 Gemfile.lock | 16 +++++++++++-----
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/Gemfile b/Gemfile
index 453dea286..62c5bdb79 100644
--- a/Gemfile
+++ b/Gemfile
@@ -47,8 +47,7 @@ gem 'aspector' # Aspect-oriented programming for Rails
 gem 'auto_strip_attributes', '~> 2.1' # Removes unnecessary whitespaces AR
 gem 'bcrypt', '~> 3.1.10'
 # gem 'caracal'
-# gem 'caracal', git: 'https://github.com/scinote-eln/caracal.git', branch: 'rubyzip2' # Build docx report
-gem 'caracal_the_curve', '~> 1.4', '>= 1.4.6'
+gem 'caracal', git: 'https://github.com/scinote-eln/caracal.git', branch: 'custom-docx-reports' # Build docx report
 gem 'caxlsx' # Build XLSX files
 gem 'deface', '~> 1.9'
 gem 'down', '~> 5.0'
diff --git a/Gemfile.lock b/Gemfile.lock
index 5a29368f2..0baa4846f 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -22,6 +22,16 @@ GIT
       docile (>= 1.1.0)
       rails (>= 4)
 
+GIT
+  remote: https://github.com/scinote-eln/caracal.git
+  revision: f8e4c279adfee7801eb1024e1d6a18bb06c9c76a
+  branch: custom-docx-reports
+  specs:
+    caracal (1.4.1)
+      nokogiri (~> 1.6)
+      rubyzip (>= 2.3)
+      tilt (>= 1.4)
+
 GIT
   remote: https://github.com/scinote-eln/img2zpl
   revision: 23d61cfc3e90ac4caa62dd08546fa0d7590a5140
@@ -217,10 +227,6 @@ GEM
     capybara-email (3.0.2)
       capybara (>= 2.4, < 4.0)
       mail
-    caracal_the_curve (1.4.6)
-      nokogiri (~> 1.6)
-      rubyzip (>= 1.1.0, < 3.0)
-      tilt (>= 1.4)
     case_transform (0.2)
       activesupport
     caxlsx (4.0.0)
@@ -799,7 +805,7 @@ DEPENDENCIES
   canaid!
   capybara
   capybara-email
-  caracal_the_curve (~> 1.4, >= 1.4.6)
+  caracal!
   caxlsx
   cssbundling-rails
   cucumber-rails

From f912f6bc41502760b7659c47e7da33ce456f0017 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 27 Aug 2024 13:40:10 +0200
Subject: [PATCH 06/96] Fix docx templates [SCI-10988]

---
 .../reports/repositories_input_component.rb   |   5 +-
 app/services/reports/docx/draw_step.rb        |   2 +-
 .../docx_templates/custom_template/docx.rb    | 188 ------------------
 .../custom_template/edit.html.erb             |  57 ------
 .../docx_templates/custom_template/name.txt   |   1 -
 5 files changed, 3 insertions(+), 250 deletions(-)
 delete mode 100644 app/views/reports/docx_templates/custom_template/docx.rb
 delete mode 100644 app/views/reports/docx_templates/custom_template/edit.html.erb
 delete mode 100644 app/views/reports/docx_templates/custom_template/name.txt

diff --git a/app/components/reports/repositories_input_component.rb b/app/components/reports/repositories_input_component.rb
index c7909d8c7..f168cc396 100644
--- a/app/components/reports/repositories_input_component.rb
+++ b/app/components/reports/repositories_input_component.rb
@@ -2,10 +2,9 @@
 
 module Reports
   class RepositoriesInputComponent < TemplateValueComponent
-    def initialize(report:, name:, label:, placeholder: nil, editing: true, displayed_field: :name)
+    def initialize(report:, name:, label:, placeholder: nil, editing: true, displayed_field: :name, user: nil)
       super(report: report, name: name, label: label, placeholder: placeholder, editing: editing)
-
-      live_repositories = Repository.accessible_by_teams(report.team).sort_by { |r| r.name.downcase }
+      live_repositories = Repository.viewable_by_user(user, report.team).sort_by { |r| r.name.downcase }
       snapshots_of_deleted = RepositorySnapshot.left_outer_joins(:original_repository)
                                                .where(team: report.team)
                                                .where.not(original_repository: live_repositories)
diff --git a/app/services/reports/docx/draw_step.rb b/app/services/reports/docx/draw_step.rb
index b2892ba6a..ef762fcb9 100644
--- a/app/services/reports/docx/draw_step.rb
+++ b/app/services/reports/docx/draw_step.rb
@@ -17,8 +17,8 @@ module Reports::Docx::DrawStep
       else
         text I18n.t('protocols.steps.uncompleted'), color: color[:gray], bold: true
       end
-      text ' | '
       unless settings['exclude_metadata']
+        text ' | '
         text I18n.t(
           "projects.reports.elements.step.#{step_type_str}.user_time",
           user: user.full_name,
diff --git a/app/views/reports/docx_templates/custom_template/docx.rb b/app/views/reports/docx_templates/custom_template/docx.rb
deleted file mode 100644
index b2e16276a..000000000
--- a/app/views/reports/docx_templates/custom_template/docx.rb
+++ /dev/null
@@ -1,188 +0,0 @@
-# frozen_string_literal: true
-
-module CustomTemplateDocx
-  def prepare_docx
-    report_name = get_template_value('custom_docx_report_name')
-    report_number = get_template_value('custom_docx_report_number')
-
-    @project_members = @report.project&.users
-
-    report_authors = @project_members.where(id: get_template_value('custom_docx_author[]')).pluck(:full_name).join(', ')
-    report_reviewers = @project_members.where(id: get_template_value('custom_docx_reviewer[]')).pluck(:full_name).join(', ')
-    report_author_role = get_template_value('custom_docx_author_role')
-    report_reviewer_role = get_template_value('custom_docx_reviewer_role')
-
-    @docx.header do |header|
-      header.table [[report_name, 'custom report']] do
-        border_size 1
-        cell_style cols[0], width: 8000
-        cell_style cols[1], width: 2800
-      end
-    end
-
-    @docx.footer do |footer|
-      pages = Caracal::Core::Models::TableCellModel.new do
-        p do
-          field :page
-          text ' of '
-          field :numpages
-        end
-      end
-      footer.table [['Confidential', pages]] do
-        border_top do
-          size 1
-        end
-        cell_style cols[0], width: 9500
-        cell_style cols[1], width: 1000
-      end
-    end
-
-    @docx.p
-
-    logo_data = File.read(Rails.root.join('app/assets/images/scinote_logo.png'))
-
-    c1 = Caracal::Core::Models::TableCellModel.new do
-      p report_name, bold: true
-      p ''
-    end
-
-    c2 = Caracal::Core::Models::TableCellModel.new do
-      img 'logo.png' do
-        data logo_data
-        height 20
-        width 100
-        align :left
-      end
-    end
-
-    c3 = Caracal::Core::Models::TableCellModel.new do
-      p "Author: #{report_authors}"
-      p "Role: #{report_author_role}"
-    end
-
-    c4 = Caracal::Core::Models::TableCellModel.new do
-      p "Reviewer: #{report_reviewers}"
-      p "Role: #{report_reviewer_role}"
-    end
-
-    c5 = Caracal::Core::Models::TableCellModel.new do
-      p "Report number:"
-      p report_number
-    end
-
-    @docx.table [[c1, c2], [c3, c4, c5]] do
-      border_size 2
-      cell_style rows[0], width: 3500
-      cell_style rows[1], width: 3500
-      cell_style rows[0][0], colspan: 2
-    end
-
-    @docx.p
-
-    @docx.table_of_contents do |toc|
-      toc.title 'Table of Contents'
-      toc.opts 'TOC \o "1-4" \h \z \u \t "Heading 5,1"'
-    end
-
-    @docx.page
-
-    my_modules_elements = []
-    @report.root_elements.each do |subject|
-      my_modules_elements += subject.children.active if subject.type_of == 'experiment'
-    end
-
-    @my_modules = MyModule.where(id: my_modules_elements.map { |element| element.my_module.id })
-
-    @docx.h1 'Chapter 1'
-    @docx.h2 'Sub chapter 1' if get_template_value('custom_docx_sub_chapter_1')
-    @docx.h2 'Sub chapter 2' if get_template_value('custom_docx_sub_chapter_2')
-    @docx.h1 'Chapter 2'
-    if get_template_value('custom_docx_sub_chapter_3')
-      @docx.h2 'Sub chapter 3 with inventory'
-      draw_repositories(get_template_value('custom_docx_sub_chapter_3_inventories[]'))
-    end
-    if get_template_value('custom_docx_sub_chapter_4')
-      @docx.h2 'Sub chapter 4 with inventory'
-      draw_repositories(get_template_value('custom_docx_sub_chapter_4_inventories[]'))
-    end
-    @docx.h2 'Sub chapter 5' if get_template_value('custom_docx_sub_chapter_5')
-    @docx.h2 'Sub chapter 6' if get_template_value('custom_docx_sub_chapter_6')
-    @docx.h2 'Sub chapter 7' if get_template_value('custom_docx_sub_chapter_7')
-    @docx.h1 'Chapter 3'
-    if get_template_value('custom_docx_sub_chapter_8')
-      @docx.h2 'Sub chapter 8 with task'
-      my_modules_elements.each do |element|
-        draw_my_module(element, without_results: true, without_repositories: true)
-      end
-    end
-    @docx.h2 'Sub chapter 9' if get_template_value('custom_docx_sub_chapter_9')
-    @docx.h2 'Sub chapter 10' if get_template_value('custom_docx_sub_chapter_10')
-    @docx.h2 'Sub chapter 11' if get_template_value('custom_docx_sub_chapter_11')
-    if get_template_value('custom_docx_sub_chapter_12')
-      @docx.h2 'Sub chapter 12'
-      @docx.h3 'Sub sub chapter 1' if get_template_value('custom_docx_sub_sub_chapter_1')
-      @docx.h3 'Sub sub chapter 2' if get_template_value('custom_docx_sub_sub_chapter_2')
-    end
-    @docx.h1 'Chapter 4'
-    if get_template_value('custom_docx_sub_chapter_13')
-      @docx.h2 'Sub chapter 13 with results'
-      my_modules_elements.each do |element|
-        draw_results(element.my_module)
-      end
-    end
-    @docx.h2 'Sub chapter 14' if get_template_value('custom_docx_sub_chapter_14')
-    @docx.h2 'Sub chapter 15' if get_template_value('custom_docx_sub_chapter_15')
-    @docx.h2 'Sub chapter 16' if get_template_value('custom_docx_sub_chapter_16')
-    @docx.h2 'Sub chapter 17' if get_template_value('custom_docx_sub_chapter_17')
-    @docx.h1 'Chapter 5'
-  end
-
-  def repository_docx_json(repository, rows)
-    headers = [
-      I18n.t('repositories.table.id'),
-      I18n.t('repositories.table.row_name'),
-      I18n.t('repositories.table.added_on'),
-      I18n.t('repositories.table.added_by')
-    ]
-    custom_columns = []
-    return false unless repository
-
-    repository.repository_columns.order(:id).each do |column|
-      headers.push(column.name)
-      custom_columns.push(column.id)
-    end
-
-    records = repository.repository_rows.where(id: rows)
-                        .select(:id, :name, :created_at, :created_by_id, :repository_id, :parent_id, :archived)
-    { headers: headers, rows: records, custom_columns: custom_columns }
-  end
-
-  def load_repositories(repositories_id)
-    live_repositories = Repository.accessible_by_teams(@report.team).where(id: repositories_id).sort_by { |r| r.name.downcase }
-    snapshots_of_deleted = RepositorySnapshot.left_outer_joins(:original_repository)
-                                             .where(team: @report.team)
-                                             .where(parent_id: repositories_id)
-                                             .where.not(original_repository: live_repositories)
-                                             .select('DISTINCT ON ("repositories"."parent_id") "repositories".*')
-                                             .sort_by { |r| r.name.downcase }
-    live_repositories + snapshots_of_deleted
-  end
-
-  def draw_repositories(repositories_id)
-    load_repositories(repositories_id).each do |repository|
-      rows = repository.repository_rows.where(id: @my_modules.joins(:my_module_repository_rows).select(:repository_row_id)).select(:id)
-      repository_data = repository_docx_json(repository, rows)
-
-      next unless repository_data[:rows].any? && can_read_repository?(@user, repository)
-
-      table = prepare_row_columns(repository_data, nil, repository)
-
-      @docx.p
-      @docx.p repository.name, bold: true, size: Constants::REPORT_DOCX_STEP_ELEMENTS_TITLE_SIZE
-      @docx.table table, border_size: Constants::REPORT_DOCX_TABLE_BORDER_SIZE
-
-      @docx.p
-      @docx.p
-    end
-  end
-end
diff --git a/app/views/reports/docx_templates/custom_template/edit.html.erb b/app/views/reports/docx_templates/custom_template/edit.html.erb
deleted file mode 100644
index 6bef2a79e..000000000
--- a/app/views/reports/docx_templates/custom_template/edit.html.erb
+++ /dev/null
@@ -1,57 +0,0 @@
-<% content_for :toc do %>
-  <h3 class="mb-4">Chapter 1</h3>
-  <div class="pl-6 flex flex-col gap-2">
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_1, label: 'Sub chapter 1') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_2, label: 'Sub chapter 2') %>
-  </div>
-  <h3 class="mb-4">Chapter 2</h3>
-  <div class="pl-6 flex flex-col gap-2">
-    <div>
-      <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_3, label: 'Sub chapter 3 with inventory') %>
-      <div class="pl-6 mb-4">
-        <%= render Reports::RepositoriesInputComponent.new(report: report, name: 'custom_docx_sub_chapter_3_inventories[]', label: 'Inventories') %>
-      </div>
-    </div>
-    <div>
-      <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_4, label: 'Sub chapter 4 with inventory') %>
-      <div class="pl-6 mb-4">
-        <%= render Reports::RepositoriesInputComponent.new(report: report, name: 'custom_docx_sub_chapter_4_inventories[]', label: 'Inventories') %>
-      </div>
-    </div>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_5, label: 'Sub chapter 5') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_6, label: 'Sub chapter 6') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_7, label: 'Sub chapter 7') %>
-  </div>
-  <h3 class="mb-4">Chapter 3</h3>
-  <div class="pl-6 flex flex-col gap-2">
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_8, label: 'Sub chapter 8 with task') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_9, label: 'Sub chapter 9') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_10, label: 'Sub chapter 10') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_11, label: 'Sub chapter 11') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_12, label: 'Sub chapter 12') %>
-    <div class="pl-6 flex flex-col gap-2">
-      <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_sub_chapter_1, label: 'Sub sub chapter 1') %>
-      <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_sub_chapter_2, label: 'Sub sub chapter 2') %>
-    </div>
-  </div>
-  <h3 class="mb-4">Chapter 4</h3>
-  <div class="pl-6 flex flex-col gap-2">
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_13, label: 'Sub chapter 13 with results') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_14, label: 'Sub chapter 14') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_15, label: 'Sub chapter 15') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_16, label: 'Sub chapter 16') %>
-    <%= render Reports::CheckboxInputComponent.new(report: report, name: :custom_docx_sub_chapter_17, label: 'Sub chapter 17') %>
-  </div>
-  <h3 class="mb-4">Chapter 5</h3>
-<% end %>
-
-<% content_for :cover do %>
-  <%= render Reports::TextInputComponent.new(report: report, name: :custom_docx_report_name, label: 'Report name') %>
-  <%= render Reports::TextInputComponent.new(report: report, name: :custom_docx_report_number, label: 'Report number') %>
-
-  <%= render Reports::ProjectMembersInputComponent.new(report: report, name: 'custom_docx_author[]', label: 'Author') %>
-  <%= render Reports::TextInputComponent.new(report: report, name: :custom_docx_author_role, label: 'Author Role') %>
-
-  <%= render Reports::ProjectMembersInputComponent.new(report: report, name: 'custom_docx_reviewer[]', label: 'Reviewer') %>
-  <%= render Reports::TextInputComponent.new(report: report, name: :custom_docx_reviewer_role, label: 'Reviewer Role') %>
-<% end %>
diff --git a/app/views/reports/docx_templates/custom_template/name.txt b/app/views/reports/docx_templates/custom_template/name.txt
deleted file mode 100644
index 0ad39c916..000000000
--- a/app/views/reports/docx_templates/custom_template/name.txt
+++ /dev/null
@@ -1 +0,0 @@
-Custom Template

From dddffc11cd737df18669bf9da79a7140097b14ac Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Wed, 28 Aug 2024 11:57:41 +0200
Subject: [PATCH 07/96] Improve report wizards [SCI-10989]

---
 app/assets/javascripts/reports/new.js         | 13 ++++++--
 app/controllers/reports_controller.rb         | 32 ++++++++++++++++++-
 app/helpers/reports_helper.rb                 |  4 +++
 app/services/reports/docx.rb                  |  2 +-
 .../reports/template_values_editor.html.erb   |  6 +++-
 .../wizard/_no_template_values.html.erb       |  6 +++-
 .../_project_template_selector.html.erb       |  4 ++-
 config/locales/en.yml                         |  6 ++--
 8 files changed, 63 insertions(+), 10 deletions(-)

diff --git a/app/assets/javascripts/reports/new.js b/app/assets/javascripts/reports/new.js
index 519bae098..168aab5de 100644
--- a/app/assets/javascripts/reports/new.js
+++ b/app/assets/javascripts/reports/new.js
@@ -1258,7 +1258,8 @@ function reportHandsonTableConverter() {
   function reCheckContinueButton() {
     if (dropdownSelector.getValues('#projectSelector').length > 0
           && dropdownSelector.getValues('#templateSelector').length > 0
-          && dropdownSelector.getValues('#docxTemplateSelector').length > 0) {
+          && (dropdownSelector.getValues('#docxTemplateSelector').length > 0
+          || $('#docxTemplateSelector').closest('.hidden').length > 0)) {
       $('.continue-button').attr('disabled', false);
     } else {
       $('.continue-button').attr('disabled', true);
@@ -1281,6 +1282,12 @@ function reportHandsonTableConverter() {
         if (dropdownSelector.getValues('#projectSelector').length > 0) {
           dropdownSelector.enableSelector('#templateSelector');
           dropdownSelector.enableSelector('#docxTemplateSelector');
+          if ($('#templateSelector').data('defaultTemplate')) {
+            dropdownSelector.selectValues('#templateSelector', $('#templateSelector').data('defaultTemplate'));
+          }
+          if ($('#docxTemplateSelector').data('defaultTemplate')) {
+            dropdownSelector.selectValues('#docxTemplateSelector', $('#docxTemplateSelector').data('defaultTemplate'));
+          }
         } else {
           dropdownSelector.selectValues('#templateSelector', '');
           dropdownSelector.disableSelector('#templateSelector');
@@ -1354,7 +1361,7 @@ function reportHandsonTableConverter() {
   }
 
   function loadTemplate() {
-    let template = $('#templateSelector').val();
+    const template = dropdownSelector.getValues('#templateSelector');
     let params = {
       project_id: dropdownSelector.getValues('#projectSelector'),
       template: template
@@ -1384,7 +1391,7 @@ function reportHandsonTableConverter() {
   }
 
   function loadDocxTemplate() {
-    let template = $('#docxTemplateSelector').val();
+    const template = dropdownSelector.getValues('#docxTemplateSelector');
     let params = {
       project_id: dropdownSelector.getValues('#projectSelector'),
       template: template
diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index bb13046b4..7bb30bfe8 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -18,7 +18,8 @@ class ReportsController < ApplicationController
   before_action :check_create_permissions, only: %i(new create)
   before_action :check_manage_permissions, only: %i(edit update generate_pdf generate_docx)
   before_action :switch_team_with_param, only: :index
-  after_action :generate_pdf_report, only: %i(create update generate_pdf)
+  after_action :generate_pdf_report, only: %i(generate_pdf)
+  after_action :generate_report, only: %i(create update)
 
   # Index showing all reports of a single project
   def index
@@ -44,6 +45,8 @@ class ReportsController < ApplicationController
   def new_template_values
     if Extends::REPORT_TEMPLATES.key?(params[:template]&.to_sym)
       template = params[:template]
+      @type = :pdf
+      @template_name = Extends::REPORT_TEMPLATES[params[:template].to_sym]
     else
       return render_404
     end
@@ -69,6 +72,7 @@ class ReportsController < ApplicationController
     else
       render json: {
         html: render_to_string(partial: 'reports/wizard/no_template_values',
+                               locals: { type: @type, template: @template_name },
                                formats: :html)
       }
     end
@@ -77,6 +81,8 @@ class ReportsController < ApplicationController
   def new_docx_template_values
     if Extends::DOCX_REPORT_TEMPLATES.key?(params[:template]&.to_sym)
       template = params[:template]
+      @type = :docx
+      @template_name = Extends::DOCX_REPORT_TEMPLATES[params[:template].to_sym]
     else
       return render_404
     end
@@ -102,6 +108,7 @@ class ReportsController < ApplicationController
     else
       render json: {
         html: render_to_string(partial: 'reports/wizard/no_template_values',
+                               locals: { type: @type, template: @template_name },
                                formats: :html)
       }
     end
@@ -363,6 +370,9 @@ class ReportsController < ApplicationController
                                     .merge(MyModule.active)
                                     .group(:id)
                                     .select(:id, :name)
+    @default_template = Extends::REPORT_TEMPLATES.keys.first.to_s if Extends::REPORT_TEMPLATES.one?
+
+    @default_docx_template = Extends::DOCX_REPORT_TEMPLATES.keys.first.to_s if Extends::DOCX_REPORT_TEMPLATES.one? && custom_templates(Extends::DOCX_REPORT_TEMPLATES)
   end
 
   def check_project_read_permissions
@@ -430,6 +440,26 @@ class ReportsController < ApplicationController
     Rails.logger.error e.message
   end
 
+  def generate_docx_report
+    return unless @report.persisted?
+
+    @report.docx_processing!
+    log_activity(:generate_docx_report)
+
+    ensure_report_template!
+    Reports::DocxJob.perform_later(@report.id, user_id: current_user.id, root_url: root_url)
+  rescue ActiveRecord::ActiveRecordError => e
+    Rails.logger.error e.message
+  end
+
+  def generate_report
+    return unless @report.persisted?
+
+    generate_pdf_report
+
+    generate_docx_report if @report.settings['docx_template'].present? && custom_templates(Extends::DOCX_REPORT_TEMPLATES)
+  end
+
   def ensure_report_template!
     return if @report.settings['template'].present?
 
diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 7dcc85929..5a05d13e2 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -106,4 +106,8 @@ module ReportsHelper
       experiment_element.experiment.description
     end
   end
+
+  def custom_templates(templates)
+    templates.any? { |template, _| template != :scinote_template }
+  end
 end
diff --git a/app/services/reports/docx.rb b/app/services/reports/docx.rb
index 46445f338..72e6ce339 100644
--- a/app/services/reports/docx.rb
+++ b/app/services/reports/docx.rb
@@ -30,7 +30,7 @@ class Reports::Docx
     @link_style = {}
     @color = {}
     @scinote_url = options[:scinote_url][0..-2]
-    @template = @settings[:docx_template] || 'scinote_template'
+    @template = @settings[:docx_template].presence || 'scinote_template'
 
     extend "#{@template.camelize}Docx".constantize
   end
diff --git a/app/views/layouts/reports/template_values_editor.html.erb b/app/views/layouts/reports/template_values_editor.html.erb
index 225c32a4a..841b024ef 100644
--- a/app/views/layouts/reports/template_values_editor.html.erb
+++ b/app/views/layouts/reports/template_values_editor.html.erb
@@ -1,6 +1,10 @@
 <div class="template-editor-header">
   <h1 class="title">
-    <%= t('projects.reports.wizard.first_step.values_editor.title') %>
+    <% if @type == :pdf %>
+      <%= t('projects.reports.wizard.first_step.values_editor.title_pdf', template: @template_name) %>
+    <% else %>
+      <%= t('projects.reports.wizard.first_step.values_editor.title_docx', template: @template_name) %>
+    <% end %>
   </h1>
   <div class="collapse-buttons sci-btn-group pull-right">
      <button class="btn btn-light collapse-all">
diff --git a/app/views/reports/wizard/_no_template_values.html.erb b/app/views/reports/wizard/_no_template_values.html.erb
index bed919b36..4d3f958da 100644
--- a/app/views/reports/wizard/_no_template_values.html.erb
+++ b/app/views/reports/wizard/_no_template_values.html.erb
@@ -1,5 +1,9 @@
 <h1>
-  <%= t('projects.reports.wizard.first_step.values_editor.no_values_title') %>
+  <% if type == :pdf %>
+    <%= t('projects.reports.wizard.first_step.values_editor.no_values_title_pdf', template: ) %>
+  <% else %>
+    <%= t('projects.reports.wizard.first_step.values_editor.no_values_title_docx', template: ) %>
+  <% end %>
 </h1>
 <h3>
   <%= t('projects.reports.wizard.first_step.values_editor.no_values_description') %>
diff --git a/app/views/reports/wizard/_project_template_selector.html.erb b/app/views/reports/wizard/_project_template_selector.html.erb
index 3a7500e6a..ce8e5c6fc 100644
--- a/app/views/reports/wizard/_project_template_selector.html.erb
+++ b/app/views/reports/wizard/_project_template_selector.html.erb
@@ -20,10 +20,11 @@
                        disable_on_load: report.settings[:template].blank? && report.new_record?,
                        placeholder: t('projects.reports.wizard.first_step.select_template'),
                        selected_template: report.settings[:template],
+                       default_template: @default_template,
                        values_editor_path: reports_new_template_values_path(report_id: report.id)
                      } %>
     </div>
-    <div class='template-selector'>
+    <div class='template-selector <%= "hidden" unless custom_templates(Extends::DOCX_REPORT_TEMPLATES) %>'>
       <%= label_tag :docxTemplateSelector, t('projects.reports.wizard.first_step.select_docx_template') %>
       <%= select_tag :docxTemplateSelector,
                      options_for_select(@docx_templates.invert, @active_docx_template),
@@ -32,6 +33,7 @@
                        disable_on_load: report.settings[:docx_template].blank? && report.new_record?,
                        placeholder: t('projects.reports.wizard.first_step.select_docx_template'),
                        selected_template: report.settings[:docx_template],
+                       default_template: @default_docx_template,
                        values_editor_path: reports_new_docx_template_values_path(report_id: report.id)
                      } %>
     </div>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 55582e52c..3e481c9a8 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -803,13 +803,15 @@ en:
           report_description: "Report description (optional)"
           report_description_placeholder: "In this report you can see..."
           values_editor:
-            title: "Enter template data"
+            title_pdf: "PDF %{template}"
+            title_docx: "DOCX %{template}"
             description: "This template requires you to fill out additional information about this project. This is the only place you will be able to do so."
             header: "Header"
             cover: "Title page"
             footer: "Footer"
             toc: "Table of contents"
-            no_values_title: "No additional data required"
+            no_values_title_pdf: "PDF %{template}:  No additional data required"
+            no_values_title_docx: "DOCX %{template}: No additional data required"
             no_values_description: "SciNote template doesn’t need any additional input for it to be successfully generated."
         second_step:
           select_project_content: "Select and reorder experiments and tasks"

From 0e662d572125d1fde85cb954da4bfdd64b0df68a Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Fri, 30 Aug 2024 11:59:21 +0200
Subject: [PATCH 08/96] Fix caracal library version [SCI-10985]

---
 Gemfile.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 037850e82..09abcdc32 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -24,10 +24,10 @@ GIT
 
 GIT
   remote: https://github.com/scinote-eln/caracal.git
-  revision: f8e4c279adfee7801eb1024e1d6a18bb06c9c76a
+  revision: f30bd2d26229c8118cc392c3a18409cb9a12ae02
   branch: custom-docx-reports
   specs:
-    caracal (1.4.1)
+    caracal (1.4.2)
       nokogiri (~> 1.6)
       rubyzip (>= 2.3)
       tilt (>= 1.4)

From b2539d13667d467599c79218b8ce48c7a84905d0 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 3 Sep 2024 15:53:29 +0200
Subject: [PATCH 09/96] Fix repositories component for docx [SCI-10988]

---
 app/assets/javascripts/reports/new.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/assets/javascripts/reports/new.js b/app/assets/javascripts/reports/new.js
index 168aab5de..73abc4cfa 100644
--- a/app/assets/javascripts/reports/new.js
+++ b/app/assets/javascripts/reports/new.js
@@ -982,7 +982,7 @@ function reportHandsonTableConverter() {
 
     // Template values
     reportData.template_values = {};
-    $.each($('.report-template-values-container').find('.sci-input-field'), function(i, field) {
+    $.each($('.report-template-values-container').find('.sci-input-field').not('.report-template-value-dropdown'), (_, field) => {
       if (field.value.length === 0) return;
 
       reportData.template_values[field.name] = {

From cb4675c522ea28dca6c412761505e7fab98d1eb3 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Wed, 4 Sep 2024 11:56:07 +0200
Subject: [PATCH 10/96] Fix moving of dropdowns on report wizard [SCI-11016]

---
 app/assets/stylesheets/reports/new.scss | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/app/assets/stylesheets/reports/new.scss b/app/assets/stylesheets/reports/new.scss
index 0355c4064..b5258df6e 100644
--- a/app/assets/stylesheets/reports/new.scss
+++ b/app/assets/stylesheets/reports/new.scss
@@ -250,6 +250,16 @@
     }
   }
 
+  // scss-lint:disable ImportantRule
+  .dropdown-selector-container {
+    .dropdown-container {
+      left: auto !important;
+      margin: auto !important;
+      position: absolute !important;
+    }
+  }
+  // scss-lint:enable ImportantRule
+
   .project-selector-container {
     background: $color-white;
     box-shadow: $modal-shadow;

From 08bb1c9dc6b063083ce52fa8af7a10cb07198d2e Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 5 Sep 2024 12:54:21 +0200
Subject: [PATCH 11/96] Implement report template loader [SCI-10999]

---
 config/initializers/report_template_loader.rb | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 config/initializers/report_template_loader.rb

diff --git a/config/initializers/report_template_loader.rb b/config/initializers/report_template_loader.rb
new file mode 100644
index 000000000..1af443d04
--- /dev/null
+++ b/config/initializers/report_template_loader.rb
@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+require 'httparty'
+require 'active_storage/service/s3_service'
+
+template_zip_url_string = ENV.fetch('REPORT_TEMPLATES_ZIP_URL', nil)
+
+return unless template_zip_url_string
+
+template_zip_url = URI.parse(template_zip_url_string)
+contents = case template_zip_url.scheme
+           when 'https'
+             HTTParty.get(template_zip_url).body
+           when 's3'
+             ActiveStorage::Service::S3Service.new(
+               bucket: template_zip_url.host
+             ).download(template_zip_url.path[1..])
+           end
+
+root_folder = nil
+Zip::File.open_buffer(StringIO.new(contents)) do |zip|
+  zip.each do |entry|
+    # set root zip folder
+    root_folder = entry.name and next if entry.name.count('/') == 1
+
+    # create path while omitting root zip folder
+    path = Rails.root.join('app', 'views', 'reports', entry.name.sub(root_folder, ''))
+    path.dirname.mkpath
+
+    # don't try and write file if entry is a folder
+    next if entry.name.ends_with?('/')
+
+    path.open('wb') do |f|
+      f.write(entry.get_input_stream.read)
+    end
+  end
+end

From cce140d3872bba7523920e9fa648d4dd6bb2075e Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Thu, 5 Sep 2024 13:41:35 +0200
Subject: [PATCH 12/96] Update exclude metadata setting [SCI-11017]

---
 app/assets/javascripts/reports/new.js         |  3 ++-
 app/models/report.rb                          |  2 ++
 app/services/reports/docx/draw_experiment.rb  |  2 +-
 app/services/reports/docx/draw_my_module.rb   | 24 ++++++++---------
 .../reports/docx/draw_my_module_protocol.rb   |  2 +-
 .../reports/docx/draw_project_header.rb       |  2 +-
 .../reports/docx/draw_result_asset.rb         |  2 +-
 .../reports/docx/draw_result_table.rb         |  2 +-
 app/services/reports/docx/draw_result_text.rb |  2 +-
 app/services/reports/docx/draw_results.rb     |  2 +-
 app/services/reports/docx/draw_step.rb        | 14 +++++-----
 app/services/reports/docx/draw_step_asset.rb  |  2 +-
 .../reports/docx/draw_step_checklist.rb       |  2 +-
 app/services/reports/docx/draw_step_table.rb  |  2 +-
 app/services/reports/docx/draw_step_text.rb   |  2 +-
 .../elements/_experiment_element.html.erb     |  2 +-
 .../elements/_my_module_element.html.erb      | 26 +++++++++----------
 .../_my_module_protocol_element.html.erb      |  2 +-
 .../_my_module_result_asset_element.html.erb  |  2 +-
 .../_my_module_result_table_element.html.erb  |  2 +-
 .../_my_module_result_text_element.html.erb   |  2 +-
 .../elements/_my_module_step_element.html.erb |  6 +++--
 .../elements/_project_header_element.html.erb |  2 +-
 .../elements/_step_asset_element.html.erb     |  2 +-
 .../elements/_step_checklist_element.html.erb |  2 +-
 .../elements/_step_table_element.html.erb     |  2 +-
 .../elements/_step_text_element.html.erb      |  2 +-
 app/views/reports/wizard/_third_step.html.erb | 16 +++++++++---
 config/locales/en.yml                         |  3 ++-
 29 files changed, 76 insertions(+), 60 deletions(-)

diff --git a/app/assets/javascripts/reports/new.js b/app/assets/javascripts/reports/new.js
index 73abc4cfa..98023b3f0 100644
--- a/app/assets/javascripts/reports/new.js
+++ b/app/assets/javascripts/reports/new.js
@@ -1052,7 +1052,8 @@ function reportHandsonTableConverter() {
 
     reportData.report.settings.task.result_order = dropdownSelector.getValues('#taskResultsOrder');
 
-    reportData.report.settings.exclude_metadata = $('.exclude-metadata-setting')[0].checked;
+    reportData.report.settings.exclude_task_metadata = $('.exclude-task-metadata-setting')[0].checked;
+    reportData.report.settings.exclude_timestamps = $('.exclude-timestamps-setting')[0].checked;
 
     return reportData;
   }
diff --git a/app/models/report.rb b/app/models/report.rb
index 0d1fbc97d..2d9a85908 100644
--- a/app/models/report.rb
+++ b/app/models/report.rb
@@ -43,6 +43,8 @@ class Report < ApplicationRecord
 
   DEFAULT_SETTINGS = {
     all_tasks: true,
+    exclude_task_metadata: false,
+    exclude_timestamps: false,
     task: {
       protocol: {
         description: true,
diff --git a/app/services/reports/docx/draw_experiment.rb b/app/services/reports/docx/draw_experiment.rb
index d7355ab36..50b55e347 100644
--- a/app/services/reports/docx/draw_experiment.rb
+++ b/app/services/reports/docx/draw_experiment.rb
@@ -16,7 +16,7 @@ module Reports::Docx::DrawExperiment
     end
 
     @docx.p do
-      unless settings['exclude_metadata']
+      unless settings['exclude_timestamps']
         text I18n.t('projects.reports.elements.experiment.user_time',
                     code: experiment.code, timestamp: I18n.l(experiment.created_at, format: :full)), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_my_module.rb b/app/services/reports/docx/draw_my_module.rb
index a174a6171..3f48772bc 100644
--- a/app/services/reports/docx/draw_my_module.rb
+++ b/app/services/reports/docx/draw_my_module.rb
@@ -17,7 +17,7 @@ module Reports::Docx::DrawMyModule
     end
 
     @docx.p do
-      unless settings['exclude_metadata']
+      unless settings['exclude_timestamps']
         text I18n.t('projects.reports.elements.module.user_time', code: my_module.code,
                     timestamp: I18n.l(my_module.created_at, format: :full)), color: color[:gray]
       end
@@ -27,21 +27,21 @@ module Reports::Docx::DrawMyModule
       end
     end
 
-    if my_module.started_on.present?
-      @docx.p do
-        text I18n.t('projects.reports.elements.module.started_on',
-                    started_on: I18n.l(my_module.started_on, format: :full))
+    unless settings['exclude_task_metadata']
+      if my_module.started_on.present?
+        @docx.p do
+          text I18n.t('projects.reports.elements.module.started_on',
+                      started_on: I18n.l(my_module.started_on, format: :full))
+        end
       end
-    end
 
-    if my_module.due_date.present?
-      @docx.p do
-        text I18n.t('projects.reports.elements.module.due_date',
-                    due_date: I18n.l(my_module.due_date, format: :full))
+      if my_module.due_date.present?
+        @docx.p do
+          text I18n.t('projects.reports.elements.module.due_date',
+                      due_date: I18n.l(my_module.due_date, format: :full))
+        end
       end
-    end
 
-    unless settings['exclude_metadata']
       status = my_module.my_module_status
       @docx.p do
         text I18n.t('projects.reports.elements.module.status')
diff --git a/app/services/reports/docx/draw_my_module_protocol.rb b/app/services/reports/docx/draw_my_module_protocol.rb
index 04d03800c..9092b088d 100644
--- a/app/services/reports/docx/draw_my_module_protocol.rb
+++ b/app/services/reports/docx/draw_my_module_protocol.rb
@@ -12,7 +12,7 @@ module Reports::Docx::DrawMyModuleProtocol
     end
 
     if @settings.dig('task', 'protocol', 'description') && protocol.description.present?
-      unless @settings['exclude_metadata']
+      unless @settings['exclude_timestamps']
         @docx.p I18n.t('projects.reports.elements.module.protocol.user_time', code: protocol.original_code,
                       timestamp: I18n.l(protocol.created_at, format: :full)), color: @color[:gray]
       end
diff --git a/app/services/reports/docx/draw_project_header.rb b/app/services/reports/docx/draw_project_header.rb
index 56e2b6569..c0bbffeef 100644
--- a/app/services/reports/docx/draw_project_header.rb
+++ b/app/services/reports/docx/draw_project_header.rb
@@ -15,7 +15,7 @@ module Reports::Docx::DrawProjectHeader
            link_style
     end
 
-    unless @settings['exclude_metadata']
+    unless @settings['exclude_timestamps']
       @docx.p do
         text I18n.t('projects.reports.elements.project_header.user_time', code: project.code,
                     timestamp: I18n.l(project.created_at, format: :full)), color: color[:gray]
diff --git a/app/services/reports/docx/draw_result_asset.rb b/app/services/reports/docx/draw_result_asset.rb
index 80520c4c7..7eac0dff9 100644
--- a/app/services/reports/docx/draw_result_asset.rb
+++ b/app/services/reports/docx/draw_result_asset.rb
@@ -25,7 +25,7 @@ module Reports::Docx::DrawResultAsset
         end
         text "  #{I18n.t('search.index.archived')} ", bold: true if result.archived?
         text ' ' + I18n.t('projects.reports.elements.result_asset.file_name', file: asset.file_name)
-        unless settings['exclude_metadata']
+        unless settings['exclude_timestamps']
           text ' ' + I18n.t('projects.reports.elements.result_asset.user_time',
                             user: result.user.full_name, timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
         end
diff --git a/app/services/reports/docx/draw_result_table.rb b/app/services/reports/docx/draw_result_table.rb
index 0d3923623..bd73c48e9 100644
--- a/app/services/reports/docx/draw_result_table.rb
+++ b/app/services/reports/docx/draw_result_table.rb
@@ -41,7 +41,7 @@ module Reports::Docx::DrawResultTable
     @docx.p do
       text I18n.t 'projects.reports.elements.result_table.table_name', name: table.name
       text ' '
-      unless settings['exclude_metadata']
+      unless settings['exclude_timestamps']
         text I18n.t('projects.reports.elements.result_table.user_time',
                     timestamp: I18n.l(timestamp, format: :full), user: result.user.full_name), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_result_text.rb b/app/services/reports/docx/draw_result_text.rb
index 1dbfe17d5..252bf68d8 100644
--- a/app/services/reports/docx/draw_result_text.rb
+++ b/app/services/reports/docx/draw_result_text.rb
@@ -9,7 +9,7 @@ module Reports::Docx::DrawResultText
     @docx.p do
       text result_text.name.presence || '', italic: true
       text ' '
-      unless settings['exclude_metadata']
+      unless settings['exclude_timestamps']
         text I18n.t('projects.reports.elements.result_text.user_time',
                     timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_results.rb b/app/services/reports/docx/draw_results.rb
index c35942da8..ffa398081 100644
--- a/app/services/reports/docx/draw_results.rb
+++ b/app/services/reports/docx/draw_results.rb
@@ -12,7 +12,7 @@ module Reports::Docx::DrawResults
         @docx.p do
           text result.name.presence || I18n.t('projects.reports.unnamed'), italic: true
           text "  #{I18n.t('search.index.archived')} ", bold: true if result.archived?
-          unless settings['exclude_metadata']
+          unless settings['exclude_timestamps']
             text I18n.t('projects.reports.elements.result.user_time',
                         timestamp: I18n.l(result.created_at, format: :full),
                         user: result.user.full_name), color: color[:gray]
diff --git a/app/services/reports/docx/draw_step.rb b/app/services/reports/docx/draw_step.rb
index ef762fcb9..376911fc4 100644
--- a/app/services/reports/docx/draw_step.rb
+++ b/app/services/reports/docx/draw_step.rb
@@ -12,13 +12,15 @@ module Reports::Docx::DrawStep
       "#{I18n.t('projects.reports.elements.step.step_pos', pos: step.position_plus_one)} #{step.name}"
     )
     @docx.p do
-      if step.completed
-        text I18n.t('protocols.steps.completed'), color: color[:green], bold: true
-      else
-        text I18n.t('protocols.steps.uncompleted'), color: color[:gray], bold: true
+      unless settings['exclude_task_metadata']
+        if step.completed
+          text I18n.t('protocols.steps.completed'), color: color[:green], bold: true
+        else
+          text I18n.t('protocols.steps.uncompleted'), color: color[:gray], bold: true
+        end
       end
-      unless settings['exclude_metadata']
-        text ' | '
+      unless settings['exclude_timestamps']
+        text ' | ' unless settings['exclude_task_metadata']
         text I18n.t(
           "projects.reports.elements.step.#{step_type_str}.user_time",
           user: user.full_name,
diff --git a/app/services/reports/docx/draw_step_asset.rb b/app/services/reports/docx/draw_step_asset.rb
index fab9c36f6..14987e698 100644
--- a/app/services/reports/docx/draw_step_asset.rb
+++ b/app/services/reports/docx/draw_step_asset.rb
@@ -24,7 +24,7 @@ module Reports::Docx::DrawStepAsset
         italic true
       end
       text ' '
-      unless settings['exclude_metadata']
+      unless settings['exclude_timestamps']
         text I18n.t('projects.reports.elements.step_asset.user_time',
                     timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_step_checklist.rb b/app/services/reports/docx/draw_step_checklist.rb
index c6e946e5b..ffd2f8192 100644
--- a/app/services/reports/docx/draw_step_checklist.rb
+++ b/app/services/reports/docx/draw_step_checklist.rb
@@ -17,7 +17,7 @@ module Reports::Docx::DrawStepChecklist
         I18n.t('projects.reports.elements.step_checklist.checklist_name', name: checklist.name)
       ).text, italic: true
       text ' '
-      unless settings['exclude_metadata']
+      unless settings['exclude_timestamps']
         text I18n.t('projects.reports.elements.step_checklist.user_time',
                     timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_step_table.rb b/app/services/reports/docx/draw_step_table.rb
index 8b3b4909b..f7c115691 100644
--- a/app/services/reports/docx/draw_step_table.rb
+++ b/app/services/reports/docx/draw_step_table.rb
@@ -40,7 +40,7 @@ module Reports::Docx::DrawStepTable
     @docx.p do
       text I18n.t("projects.reports.elements.#{table_type}.table_name", name: table.name), italic: true
       text ' '
-      unless settings['exclude_metadata']
+      unless settings['exclude_timestamps']
         text I18n.t("projects.reports.elements.#{table_type}.user_time",
                     timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_step_text.rb b/app/services/reports/docx/draw_step_text.rb
index 6218595a0..66f0ed84c 100644
--- a/app/services/reports/docx/draw_step_text.rb
+++ b/app/services/reports/docx/draw_step_text.rb
@@ -9,7 +9,7 @@ module Reports::Docx::DrawStepText
     @docx.p do
       text step_text.name.presence || '', italic: true
       text ' '
-      unless settings['exclude_metadata']
+      unless settings['exclude_timestamps']
         text I18n.t('projects.reports.elements.result_text.user_time',
                     timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
       end
diff --git a/app/views/reports/elements/_experiment_element.html.erb b/app/views/reports/elements/_experiment_element.html.erb
index 475c96b7b..0020d7ec7 100644
--- a/app/views/reports/elements/_experiment_element.html.erb
+++ b/app/views/reports/elements/_experiment_element.html.erb
@@ -9,7 +9,7 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h3>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.experiment.user_time', code: experiment.code, timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_my_module_element.html.erb b/app/views/reports/elements/_my_module_element.html.erb
index 5ad3cee73..17bcaf304 100644
--- a/app/views/reports/elements/_my_module_element.html.erb
+++ b/app/views/reports/elements/_my_module_element.html.erb
@@ -9,22 +9,22 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h4>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.module.user_time', code: my_module.code, timestamp: l(timestamp, format: :full)) %>
       </div>
     <% end %>
-    <p class="module-start-date">
-      <% if my_module.started_on.present? %>
-        <%= t('projects.reports.elements.module.started_on', started_on: l(my_module.started_on, format: :full)) %>
-      <% end %>
-    </p>
-    <p class="module-due-date">
-      <% if my_module.due_date.present? %>
-        <%= t('projects.reports.elements.module.due_date', due_date: l(my_module.due_date, format: :full)) %>
-      <% end %>
-    </p>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_task_metadata'] %>
+      <p class="module-start-date">
+        <% if my_module.started_on.present? %>
+          <%= t('projects.reports.elements.module.started_on', started_on: l(my_module.started_on, format: :full)) %>
+        <% end %>
+      </p>
+      <p class="module-due-date">
+        <% if my_module.due_date.present? %>
+          <%= t('projects.reports.elements.module.due_date', due_date: l(my_module.due_date, format: :full)) %>
+        <% end %>
+      </p>
       <p class="module-status">
         <% status = my_module.my_module_status %>
         <%= t('projects.reports.elements.module.status') %>
@@ -39,8 +39,6 @@
           </span>
         <% end %>
       </p>
-    <% end %>
-    <% unless @settings['exclude_metadata'] %>
       <div class="row module-tags">
         <div class="pull-left">
           <%= t('projects.reports.elements.module.tags_header') %>
diff --git a/app/views/reports/elements/_my_module_protocol_element.html.erb b/app/views/reports/elements/_my_module_protocol_element.html.erb
index 1aa86ecb1..67f2c3adc 100644
--- a/app/views/reports/elements/_my_module_protocol_element.html.erb
+++ b/app/views/reports/elements/_my_module_protocol_element.html.erb
@@ -9,7 +9,7 @@
         <%= t('projects.reports.elements.module.protocol.name') %>
       <% end %>
     </h4>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.module.protocol.user_time', code: protocol.original_code, timestamp: l(protocol.created_at, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_my_module_result_asset_element.html.erb b/app/views/reports/elements/_my_module_result_asset_element.html.erb
index 5485a789d..de71933c6 100644
--- a/app/views/reports/elements/_my_module_result_asset_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_asset_element.html.erb
@@ -26,7 +26,7 @@
         <% end %>
       </div>
       <div class="user-time">
-        <% unless @settings['exclude_metadata'] %>
+        <% unless @settings['exclude_timestamps'] %>
           <%= t("projects.reports.elements.result_asset.user_time", user: result.user.full_name, timestamp: l(timestamp, format: :full)) %>
         <% end %>
         <% if report.settings.dig(:task, :file_results_previews) && ActiveStorageFileUtil.previewable_document?(asset&.file&.blob) %>
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 e5fd49f52..dbcced513 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
@@ -21,7 +21,7 @@
       <% end %>
     <% end %>
    </div>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.result_table.user_time', timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_my_module_result_text_element.html.erb b/app/views/reports/elements/_my_module_result_text_element.html.erb
index 94e02fa52..0dff3eb67 100644
--- a/app/views/reports/elements/_my_module_result_text_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_text_element.html.erb
@@ -11,7 +11,7 @@
         </em>
       <% end %>
     </div>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t("projects.reports.elements.result_text.user_time", timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_my_module_step_element.html.erb b/app/views/reports/elements/_my_module_step_element.html.erb
index 2be53b1a9..fa330886d 100644
--- a/app/views/reports/elements/_my_module_step_element.html.erb
+++ b/app/views/reports/elements/_my_module_step_element.html.erb
@@ -8,9 +8,11 @@
   <div class="report-element-body">
     <h5 class="step-name">
       <b><%= t('projects.reports.elements.step.step_pos', pos: (step.position_plus_one)) %></b>&nbsp;<%= step.name %>
-      <%= step_status_label(step) %>
+      <% unless @settings['exclude_task_metadata'] %>
+        <%= step_status_label(step) %>
+      <% end %>
     </h5>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t("projects.reports.elements.step.#{step_type_str}.user_time", user: user.full_name , timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_project_header_element.html.erb b/app/views/reports/elements/_project_header_element.html.erb
index 9e355d6d9..c6d3b9636 100644
--- a/app/views/reports/elements/_project_header_element.html.erb
+++ b/app/views/reports/elements/_project_header_element.html.erb
@@ -7,7 +7,7 @@
         <span class="label label-warning"><%= t('search.index.archived') %></span>
       <% end %>
     </h2>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.project_header.user_time', code: project.code, timestamp: l(project.created_at, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_step_asset_element.html.erb b/app/views/reports/elements/_step_asset_element.html.erb
index 880ab97ee..04d8313e4 100644
--- a/app/views/reports/elements/_step_asset_element.html.erb
+++ b/app/views/reports/elements/_step_asset_element.html.erb
@@ -18,7 +18,7 @@
         </em>
       <% end %>
     </span>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         &nbsp;<%= t('projects.reports.elements.step_asset.user_time', timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_step_checklist_element.html.erb b/app/views/reports/elements/_step_checklist_element.html.erb
index 1951fde55..02549a31b 100644
--- a/app/views/reports/elements/_step_checklist_element.html.erb
+++ b/app/views/reports/elements/_step_checklist_element.html.erb
@@ -9,7 +9,7 @@
                            team: current_team,
                            base64_encoded_imgs: export_all) %>
     </div>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t('projects.reports.elements.step_checklist.user_time', timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_step_table_element.html.erb b/app/views/reports/elements/_step_table_element.html.erb
index dfda2ac14..813c91766 100644
--- a/app/views/reports/elements/_step_table_element.html.erb
+++ b/app/views/reports/elements/_step_table_element.html.erb
@@ -18,7 +18,7 @@
         <% end %>
       <% end %>
     </div>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t("projects.reports.elements.#{table_type}.user_time", timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/elements/_step_text_element.html.erb b/app/views/reports/elements/_step_text_element.html.erb
index 8c8ff72eb..6e42a7487 100644
--- a/app/views/reports/elements/_step_text_element.html.erb
+++ b/app/views/reports/elements/_step_text_element.html.erb
@@ -8,7 +8,7 @@
         </em>
       <% end %>
     </div>
-    <% unless @settings['exclude_metadata'] %>
+    <% unless @settings['exclude_timestamps'] %>
       <div class="user-time">
         <%= t("projects.reports.elements.step_text.user_time", timestamp: l(timestamp, format: :full)) %>
       </div>
diff --git a/app/views/reports/wizard/_third_step.html.erb b/app/views/reports/wizard/_third_step.html.erb
index d56af9b24..327c1d857 100644
--- a/app/views/reports/wizard/_third_step.html.erb
+++ b/app/views/reports/wizard/_third_step.html.erb
@@ -184,7 +184,7 @@
         <%= t("projects.reports.wizard.third_step.additional_content") %>
       </span>
       <ul class="additional-contents collapse in" id="additionalContents">
-        <li>
+        <li class="additional-content-task-activity">
           <div class="select-all-container">
             <span class="sci-checkbox-container">
               <input type="checkbox" class="sci-checkbox task-setting" value="activities" <%= 'checked' if report.settings.dig(:task, :activities) %>/>
@@ -197,10 +197,20 @@
         <li>
           <div class="select-all-container">
             <span class="sci-checkbox-container">
-              <input type="checkbox" class="sci-checkbox exclude-metadata-setting" value="exclude_metadata" <%= 'checked' if report.settings.dig(:exclude_metadata) %>/>
+              <input type="checkbox" class="sci-checkbox exclude-task-metadata-setting" value="exclude_task_metadata" <%= 'checked' if report.settings.dig(:exclude_task_metadata) %>/>
               <span class="sci-checkbox-label"></span>
             </span>
-            <%= t("projects.reports.wizard.third_step.exclude_metadata") %>
+            <%= t("projects.reports.wizard.third_step.exclude_task_metadata") %>
+            <div class="divider"></div>
+          </div>
+        </li>
+        <li>
+          <div class="select-all-container">
+            <span class="sci-checkbox-container">
+              <input type="checkbox" class="sci-checkbox exclude-timestamps-setting" value="exclude_timestamps" <%= 'checked' if report.settings.dig(:exclude_timestamps) %>/>
+              <span class="sci-checkbox-label"></span>
+            </span>
+            <%= t("projects.reports.wizard.third_step.exclude_timestamps") %>
             <div class="divider"></div>
           </div>
         </li>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 3e481c9a8..f24bc62a7 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -853,7 +853,8 @@ en:
           results_comments: "Result comments"
           additional_content: "Additional content"
           task_activity: "Include task activity"
-          exclude_metadata: "Exclude metadata"
+          exclude_task_metadata: "Exclude task metadata"
+          exclude_timestamps: "Exclude timestamps"
           archived: "[archived]"
           deleted: "[deleted]"
 

From c128f2f0035dcd0dd4dfa32d0edc900402861503 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 5 Sep 2024 15:08:29 +0200
Subject: [PATCH 13/96] Check presence of template zip URL [SCI-10999]

---
 config/initializers/report_template_loader.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/initializers/report_template_loader.rb b/config/initializers/report_template_loader.rb
index 1af443d04..380651833 100644
--- a/config/initializers/report_template_loader.rb
+++ b/config/initializers/report_template_loader.rb
@@ -5,7 +5,7 @@ require 'active_storage/service/s3_service'
 
 template_zip_url_string = ENV.fetch('REPORT_TEMPLATES_ZIP_URL', nil)
 
-return unless template_zip_url_string
+return unless template_zip_url_string.present?
 
 template_zip_url = URI.parse(template_zip_url_string)
 contents = case template_zip_url.scheme

From 2ccf1abc91612793762770a6bc62e9c261d32c21 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Thu, 5 Sep 2024 16:21:39 +0200
Subject: [PATCH 14/96] Remove tag for attached files in docx [SCI-11027]

---
 app/services/reports/docx/draw_result_asset.rb | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/app/services/reports/docx/draw_result_asset.rb b/app/services/reports/docx/draw_result_asset.rb
index 7eac0dff9..fc690977f 100644
--- a/app/services/reports/docx/draw_result_asset.rb
+++ b/app/services/reports/docx/draw_result_asset.rb
@@ -29,10 +29,6 @@ module Reports::Docx::DrawResultAsset
           text ' ' + I18n.t('projects.reports.elements.result_asset.user_time',
                             user: result.user.full_name, timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
         end
-
-        if settings.dig(:task, :file_results_previews) && ActiveStorageFileUtil.previewable_document?(asset&.file&.blob)
-          text " #{I18n.t('projects.reports.elements.result_asset.full_preview_attached')}", color: color[:gray]
-        end
       end
 
       draw_result_comments(result) if @settings.dig('task', 'result_comments')

From a05c88569b5220477836c529458175972038ff33 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 5 Sep 2024 17:21:24 +0200
Subject: [PATCH 15/96] Require docx template files on initialization
 [SCI-10999]

---
 config/initializers/report_template_loader.rb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/config/initializers/report_template_loader.rb b/config/initializers/report_template_loader.rb
index 380651833..6461315f6 100644
--- a/config/initializers/report_template_loader.rb
+++ b/config/initializers/report_template_loader.rb
@@ -5,7 +5,7 @@ require 'active_storage/service/s3_service'
 
 template_zip_url_string = ENV.fetch('REPORT_TEMPLATES_ZIP_URL', nil)
 
-return unless template_zip_url_string.present?
+return if template_zip_url_string.blank?
 
 template_zip_url = URI.parse(template_zip_url_string)
 contents = case template_zip_url.scheme
@@ -33,5 +33,7 @@ Zip::File.open_buffer(StringIO.new(contents)) do |zip|
     path.open('wb') do |f|
       f.write(entry.get_input_stream.read)
     end
+
+    require path if entry.name.ends_with?('.rb')
   end
 end

From 8095b0731a3dca2ab272694ca79570d046f1b390 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 6 Sep 2024 11:15:34 +0200
Subject: [PATCH 16/96] Move template loading to a script [SCI-10999]

---
 .../load_report_templates                     | 21 +++++++++++--------
 1 file changed, 12 insertions(+), 9 deletions(-)
 rename config/initializers/report_template_loader.rb => bin/load_report_templates (54%)
 mode change 100644 => 100755

diff --git a/config/initializers/report_template_loader.rb b/bin/load_report_templates
old mode 100644
new mode 100755
similarity index 54%
rename from config/initializers/report_template_loader.rb
rename to bin/load_report_templates
index 6461315f6..8bb1c4f05
--- a/config/initializers/report_template_loader.rb
+++ b/bin/load_report_templates
@@ -1,39 +1,42 @@
-# frozen_string_literal: true
+#!/usr/bin/env ruby
 
 require 'httparty'
-require 'active_storage/service/s3_service'
+require 'zip'
 
 template_zip_url_string = ENV.fetch('REPORT_TEMPLATES_ZIP_URL', nil)
 
-return if template_zip_url_string.blank?
+return if template_zip_url_string.nil? || template_zip_url_string.empty?
 
 template_zip_url = URI.parse(template_zip_url_string)
 contents = case template_zip_url.scheme
            when 'https'
              HTTParty.get(template_zip_url).body
            when 's3'
-             ActiveStorage::Service::S3Service.new(
-               bucket: template_zip_url.host
-             ).download(template_zip_url.path[1..])
+             system("AWS_PAGER=\"\" aws s3api get-object --bucket #{template_zip_url.host} --key #{template_zip_url.path[1..]} ./report_templates.zip")
+             File.read('./report_templates.zip')
            end
 
+puts "Loaded report templates zip from #{template_zip_url_string}"
+
 root_folder = nil
 Zip::File.open_buffer(StringIO.new(contents)) do |zip|
+  puts 'Extracting report templates...'
+
   zip.each do |entry|
     # set root zip folder
     root_folder = entry.name and next if entry.name.count('/') == 1
 
     # create path while omitting root zip folder
-    path = Rails.root.join('app', 'views', 'reports', entry.name.sub(root_folder, ''))
+    path = Pathname.new("#{ENV.fetch('APP_HOME', '.')}/app/views/reports/#{entry.name.sub(root_folder, '')}")
     path.dirname.mkpath
 
     # don't try and write file if entry is a folder
-    next if entry.name.ends_with?('/')
+    next if entry.name.end_with?('/')
 
     path.open('wb') do |f|
       f.write(entry.get_input_stream.read)
     end
 
-    require path if entry.name.ends_with?('.rb')
+    puts "Extracted #{path}"
   end
 end

From 9d7a0c268de3efbfbcba485bbc388da999f594af Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Mon, 9 Sep 2024 11:37:37 +0200
Subject: [PATCH 17/96] Exclude timestamps for docx reports for task results
 [SCI-11017]

---
 app/views/reports/elements/_my_module_element.html.erb    | 8 +++++---
 .../elements/_my_module_result_asset_element.html.erb     | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/app/views/reports/elements/_my_module_element.html.erb b/app/views/reports/elements/_my_module_element.html.erb
index 17bcaf304..b8778e7a7 100644
--- a/app/views/reports/elements/_my_module_element.html.erb
+++ b/app/views/reports/elements/_my_module_element.html.erb
@@ -94,9 +94,11 @@
 
         <% if @settings.dig('task', 'file_results')  %>
           <%= render partial: 'reports/elements/my_module_result_asset_element', locals: { result: result, report: report, export_all: export_all } %>
-          <div class="user-time">
-            <%= t('projects.reports.elements.result.user_time', user: result.user.full_name, timestamp: l(result.created_at, format: :full)) %>
-          </div>
+          <% unless @settings['exclude_timestamps'] %>
+            <div class="user-time">
+              <%= t('projects.reports.elements.result.user_time', user: result.user.full_name, timestamp: l(result.created_at, format: :full)) %>
+            </div>
+          <% end %>
         <% end %>
 
         <div class="report-element-children">
diff --git a/app/views/reports/elements/_my_module_result_asset_element.html.erb b/app/views/reports/elements/_my_module_result_asset_element.html.erb
index de71933c6..f4cd9e072 100644
--- a/app/views/reports/elements/_my_module_result_asset_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_asset_element.html.erb
@@ -24,7 +24,7 @@
             <%= link_to t('projects.reports.elements.download'), asset_download_url(asset, disposition: 'attachment'), class: 'download-link', target: :_blank %>
           </em>
         <% end %>
-      </div>
+      </div>  
       <div class="user-time">
         <% unless @settings['exclude_timestamps'] %>
           <%= t("projects.reports.elements.result_asset.user_time", user: result.user.full_name, timestamp: l(timestamp, format: :full)) %>

From 388926e02126c0a2f7bd1e369c33af7daff671f8 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 29 Jul 2024 12:09:21 +0200
Subject: [PATCH 18/96] Add versioned file attachments to assets [SCI-10774]

---
 app/controllers/api/v1/results_controller.rb  |  2 +-
 app/controllers/asset_sync_controller.rb      |  4 ++--
 .../gene_sequence_assets_controller.rb        |  2 +-
 app/controllers/result_assets_controller.rb   |  2 +-
 app/controllers/results_controller.rb         |  2 +-
 app/controllers/steps_controller.rb           |  2 +-
 app/jobs/protocols/docx_import_job.rb         |  2 +-
 app/models/asset.rb                           |  5 +++--
 app/models/concerns/versioned_attachments.rb  | 19 +++++++++++++++++++
 app/models/repository_asset_value.rb          |  8 ++++----
 .../save_pdf_to_inventory_item.rb             |  2 +-
 app/services/team_importer.rb                 |  2 +-
 .../protocol_importers/attachments_builder.rb |  2 +-
 app/utilities/protocols_importer.rb           |  2 +-
 app/utilities/protocols_importer_v2.rb        |  2 +-
 15 files changed, 39 insertions(+), 19 deletions(-)
 create mode 100644 app/models/concerns/versioned_attachments.rb

diff --git a/app/controllers/api/v1/results_controller.rb b/app/controllers/api/v1/results_controller.rb
index c26c2ef02..4665f46a8 100644
--- a/app/controllers/api/v1/results_controller.rb
+++ b/app/controllers/api/v1/results_controller.rb
@@ -124,7 +124,7 @@ module Api
         Result.transaction do
           old_checksum = asset.file.blob.checksum
           if @form_multipart_upload
-            asset.file.attach(result_file_params[:file])
+            asset.attach_file_version(result_file_params[:file])
           else
             blob = create_blob_from_params
             asset.update!(file: blob)
diff --git a/app/controllers/asset_sync_controller.rb b/app/controllers/asset_sync_controller.rb
index 54c6e7440..ae8d0e126 100644
--- a/app/controllers/asset_sync_controller.rb
+++ b/app/controllers/asset_sync_controller.rb
@@ -45,7 +45,7 @@ class AssetSyncController < ApplicationController
       if wopi_file?(@asset)
         @asset.update_contents(request.body)
       else
-        @asset.file.attach(io: request.body, filename: @asset.file.filename)
+        @asset.attach_file_version(io: request.body, filename: @asset.file.filename)
         @asset.touch
       end
 
@@ -94,7 +94,7 @@ class AssetSyncController < ApplicationController
         metadata: @asset.blob.metadata
       )
 
-      new_asset.file.attach(blob)
+      new_asset.attach_file_version(blob)
 
       case @asset.parent
       when Step
diff --git a/app/controllers/gene_sequence_assets_controller.rb b/app/controllers/gene_sequence_assets_controller.rb
index a706a200f..d18cb72c7 100644
--- a/app/controllers/gene_sequence_assets_controller.rb
+++ b/app/controllers/gene_sequence_assets_controller.rb
@@ -75,7 +75,7 @@ class GeneSequenceAssetsController < ApplicationController
       @asset.file.purge
       @asset.preview_image.purge
 
-      @asset.file.attach(
+      @asset.attach_file_version(
         io: StringIO.new(params[:sequence_data].to_json),
         filename: "#{params[:sequence_name]}.json"
       )
diff --git a/app/controllers/result_assets_controller.rb b/app/controllers/result_assets_controller.rb
index e2c429260..400ae671e 100644
--- a/app/controllers/result_assets_controller.rb
+++ b/app/controllers/result_assets_controller.rb
@@ -125,7 +125,7 @@ class ResultAssetsController < ApplicationController
     ActiveRecord::Base.transaction do
       params[:results_files].each do |index, file|
         asset = Asset.create!(created_by: current_user, last_modified_by: current_user, team: current_team)
-        asset.file.attach(file[:signed_blob_id])
+        asset.attach_file_version(file[:signed_blob_id])
         result = Result.create!(user: current_user,
                                 my_module: @my_module,
                                 name: params[:results_names][index],
diff --git a/app/controllers/results_controller.rb b/app/controllers/results_controller.rb
index 075b2b669..3bc46e3d2 100644
--- a/app/controllers/results_controller.rb
+++ b/app/controllers/results_controller.rb
@@ -90,7 +90,7 @@ class ResultsController < ApplicationController
         team: @my_module.team,
         view_mode: @result.assets_view_mode
       )
-      @asset.file.attach(params[:signed_blob_id])
+      @asset.attach_file_version(params[:signed_blob_id])
       @asset.post_process_file
     end
 
diff --git a/app/controllers/steps_controller.rb b/app/controllers/steps_controller.rb
index 40f2845f5..ce97a4cc2 100644
--- a/app/controllers/steps_controller.rb
+++ b/app/controllers/steps_controller.rb
@@ -41,7 +41,7 @@ class StepsController < ApplicationController
         team: @protocol.team,
         view_mode: @step.assets_view_mode
       )
-      @asset.file.attach(params[:signed_blob_id])
+      @asset.attach_file_version(params[:signed_blob_id])
       @asset.post_process_file
 
       default_message_items = {
diff --git a/app/jobs/protocols/docx_import_job.rb b/app/jobs/protocols/docx_import_job.rb
index 49a34bbc5..dccd1a0dd 100644
--- a/app/jobs/protocols/docx_import_job.rb
+++ b/app/jobs/protocols/docx_import_job.rb
@@ -117,7 +117,7 @@ module Protocols
     def create_step_asset_element!(step, step_element_json)
       asset = @team.assets.new(created_by: @user, last_modified_by: @user)
       # Decode the file bytes
-      asset.file.attach(io: StringIO.new(Base64.decode64(step_element_json['contents'])), filename: 'file.blob')
+      asset.attach_file_version(io: StringIO.new(Base64.decode64(step_element_json['contents'])), filename: 'file.blob')
       asset.save!
       step.step_assets.create!(asset: asset)
       asset.post_process_file
diff --git a/app/models/asset.rb b/app/models/asset.rb
index 0c2601d82..9e0745642 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -8,6 +8,7 @@ class Asset < ApplicationRecord
   include ActiveStorageFileUtil
   include ActiveStorageConcerns
   include ActiveStorageHelper
+  include VersionedAttachments
 
   require 'tempfile'
   # Lock duration set to 30 minutes
@@ -17,7 +18,7 @@ class Asset < ApplicationRecord
   enum view_mode: { thumbnail: 0, list: 1, inline: 2 }
 
   # ActiveStorage configuration
-  has_one_attached :file
+  has_one_versioned_attached :file
   has_one_attached :file_pdf_preview
   has_one_attached :preview_image
 
@@ -166,7 +167,7 @@ class Asset < ApplicationRecord
         filename: blob.filename,
         metadata: blob.metadata
       )
-      to_asset.file.attach(to_blob)
+      to_asset.attach_file_version(to_blob)
     end
 
     if preview_image.attached?
diff --git a/app/models/concerns/versioned_attachments.rb b/app/models/concerns/versioned_attachments.rb
new file mode 100644
index 000000000..464ff1aff
--- /dev/null
+++ b/app/models/concerns/versioned_attachments.rb
@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+module VersionedAttachments
+  extend ActiveSupport::Concern
+
+  class_methods do
+    def has_one_versioned_attached(name)
+      has_one_attached name, dependent: :detach
+      has_many_attached "previous_#{name.to_s.pluralize}", dependent: :detach
+
+      define_method "attach_#{name}_version" do |*args, **options|
+        ActiveRecord::Base.transaction(requires_new: true) do
+          __send__("previous_#{name.to_s.pluralize}").attach(__send__(name).blob) if __send__(name).attached?
+          __send__(name).attach(*args, **options)
+        end
+      end
+    end
+  end
+end
diff --git a/app/models/repository_asset_value.rb b/app/models/repository_asset_value.rb
index 5e9ba015f..9e4685aa6 100644
--- a/app/models/repository_asset_value.rb
+++ b/app/models/repository_asset_value.rb
@@ -60,9 +60,9 @@ class RepositoryAssetValue < ApplicationRecord
 
   def update_data!(new_data, user)
     if new_data.is_a?(String) # assume it's a signed_id_token
-      asset.file.attach(new_data)
+      asset.attach_file_version(new_data)
     elsif new_data[:file_data]
-      asset.file.attach(io: StringIO.new(Base64.decode64(new_data[:file_data])), filename: new_data[:file_name])
+      asset.attach_file_version(io: StringIO.new(Base64.decode64(new_data[:file_data])), filename: new_data[:file_name])
     end
 
     asset.file_pdf_preview.purge if asset.file_pdf_preview.attached?
@@ -99,9 +99,9 @@ class RepositoryAssetValue < ApplicationRecord
     value.asset = Asset.create!(created_by: value.created_by, last_modified_by: value.created_by, team: team)
 
     if payload.is_a?(String) # assume it's a signed_id_token
-      value.asset.file.attach(payload)
+      value.asset.attach_file_version(payload)
     elsif payload[:file_data]
-      value.asset.file.attach(io: StringIO.new(Base64.decode64(payload[:file_data])), filename: payload[:file_name])
+      value.asset.attach_file_version(io: StringIO.new(Base64.decode64(payload[:file_data])), filename: payload[:file_name])
     end
 
     value.asset.post_process_file
diff --git a/app/services/report_actions/save_pdf_to_inventory_item.rb b/app/services/report_actions/save_pdf_to_inventory_item.rb
index 88b1e1a90..01866820f 100644
--- a/app/services/report_actions/save_pdf_to_inventory_item.rb
+++ b/app/services/report_actions/save_pdf_to_inventory_item.rb
@@ -44,7 +44,7 @@ module ReportActions
 
     def create_new_asset
       asset = Asset.create(created_by: @user, last_modified_by: @user, team: @team)
-      asset.file.attach(@report.pdf_file.blob)
+      asset.attach_file_version(@report.pdf_file.blob)
       asset
     end
 
diff --git a/app/services/team_importer.rb b/app/services/team_importer.rb
index e600b451e..e81c651c6 100644
--- a/app/services/team_importer.rb
+++ b/app/services/team_importer.rb
@@ -934,7 +934,7 @@ class TeamImporter
       user_id || find_user(asset.last_modified_by_id)
     asset.team = team
     asset.save!
-    asset.file.attach(io: file, filename: File.basename(file))
+    asset.attach_file_version(io: file, filename: File.basename(file))
     asset.post_process_file
     @asset_mappings[orig_asset_id] = asset.id
     @asset_counter += 1
diff --git a/app/utilities/protocol_importers/attachments_builder.rb b/app/utilities/protocol_importers/attachments_builder.rb
index df6788f1d..dd2bd4799 100644
--- a/app/utilities/protocol_importers/attachments_builder.rb
+++ b/app/utilities/protocol_importers/attachments_builder.rb
@@ -7,7 +7,7 @@ module ProtocolImporters
 
       step_json[:attachments].map do |f|
         asset = Asset.new(created_by: user, last_modified_by: user, team: team)
-        asset.file.attach(io: URI.open(f[:url]), filename: f[:name])
+        asset.attach_file_version(io: URI.open(f[:url]), filename: f[:name])
         asset
       end
     end
diff --git a/app/utilities/protocols_importer.rb b/app/utilities/protocols_importer.rb
index a66b8fe02..4738c8eb9 100644
--- a/app/utilities/protocols_importer.rb
+++ b/app/utilities/protocols_importer.rb
@@ -132,7 +132,7 @@ class ProtocolsImporter
         )
 
         # Decode the file bytes
-        asset.file.attach(io: StringIO.new(Base64.decode64(asset_json['bytes'])),
+        asset.attach_file_version(io: StringIO.new(Base64.decode64(asset_json['bytes'])),
                           filename: asset_json['fileName'],
                           content_type: asset_json['fileType'],
                           metadata: JSON.parse(asset_json['fileMetadata'] || '{}'))
diff --git a/app/utilities/protocols_importer_v2.rb b/app/utilities/protocols_importer_v2.rb
index ba6e3b813..9d91f438c 100644
--- a/app/utilities/protocols_importer_v2.rb
+++ b/app/utilities/protocols_importer_v2.rb
@@ -109,7 +109,7 @@ class ProtocolsImporterV2
       )
 
       # Decode the file bytes
-      asset.file.attach(io: StringIO.new(Base64.decode64(asset_json['bytes'])),
+      asset.attach_file_version(io: StringIO.new(Base64.decode64(asset_json['bytes'])),
                         filename: asset_json['fileName'],
                         content_type: asset_json['fileType'],
                         metadata: JSON.parse(asset_json['fileMetadata'] || '{}'))

From 157a23d025a36d9538e67c7da562218f6823f23e Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 16 Sep 2024 11:42:29 +0200
Subject: [PATCH 19/96] Fix viewable scope for sharable models [SCI-11057]

---
 app/models/concerns/shareable.rb | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/app/models/concerns/shareable.rb b/app/models/concerns/shareable.rb
index 6f157766e..3f94a0770 100644
--- a/app/models/concerns/shareable.rb
+++ b/app/models/concerns/shareable.rb
@@ -30,18 +30,17 @@ module Shareable
       readable = readable_by_user(user).left_outer_joins(:team_shared_objects)
       readable
         .where(team: teams)
-        .or(where(team_shared_objects: { team: teams }))
-        .or(where(if column_names.include?('permission_level')
-                    {
-                      permission_level: [
-                        Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_read],
-                        Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_write]
-                      ]
-                    }
-                  else
-                    {}
-                  end
-            ).where.not(team: teams))
+        .or(model.where(team_shared_objects: { team: teams }))
+        .or(model.where(if column_names.include?('permission_level')
+                          {
+                            permission_level: [
+                              Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_read],
+                              Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_write]
+                            ]
+                          }
+                        else
+                          {}
+                        end).where.not(team: teams))
         .distinct
     }
   rescue ActiveRecord::NoDatabaseError,

From 444b561060b8a71387c4221cc60bf305b259015d Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 17 Sep 2024 15:19:44 +0200
Subject: [PATCH 20/96] Implement file versions modal [SCI-11039]

---
 app/controllers/assets_controller.rb          | 16 +++--
 .../content/attachments/context_menu.vue      | 17 ++++-
 .../vue/shared/file_versions_modal.vue        | 66 +++++++++++++++++++
 app/models/concerns/versioned_attachments.rb  | 16 ++++-
 app/serializers/asset_serializer.rb           |  3 +-
 config/locales/en.yml                         |  7 ++
 config/routes.rb                              |  1 +
 7 files changed, 118 insertions(+), 8 deletions(-)
 create mode 100644 app/javascript/vue/shared/file_versions_modal.vue

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 383964890..314583de4 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -197,7 +197,7 @@ class AssetsController < ApplicationController
     return render_403 unless can_read_team?(@asset.team)
 
     @asset.last_modified_by = current_user
-    @asset.file.attach(io: params.require(:image), filename: orig_file_name)
+    @asset.attach_file_version(io: params.require(:image), filename: orig_file_name, current_user: current_user)
     @asset.save!
     create_edit_image_activity(@asset, current_user, :finish_editing)
     # release previous image space
@@ -242,9 +242,10 @@ class AssetsController < ApplicationController
 
     # Asset validation
     asset = Asset.new(created_by: current_user, team: current_team)
-    asset.file.attach(io: StringIO.new,
-                      filename: "#{params[:file_name]}.#{params[:file_type]}",
-                      content_type: wopi_content_type(params[:file_type]))
+    asset.attach_file_version(io: StringIO.new,
+                              filename: "#{params[:file_name]}.#{params[:file_type]}",
+                              content_type: wopi_content_type(params[:file_type]),
+                              current_user: current_user)
 
     unless asset.valid?(:wopi_file_creation)
       render json: {
@@ -397,6 +398,13 @@ class AssetsController < ApplicationController
     render json: { checksum: @asset.file.blob.checksum }
   end
 
+  def versions
+    render(
+      json: [@asset.file.blob] +
+            @asset.previous_files.map(&:blob).sort_by { |b| -1 * b.metadata['version'].to_i }
+    )
+  end
+
   private
 
   def load_vars
diff --git a/app/javascript/vue/shared/content/attachments/context_menu.vue b/app/javascript/vue/shared/content/attachments/context_menu.vue
index bb17af66c..5f9a6a7bb 100644
--- a/app/javascript/vue/shared/content/attachments/context_menu.vue
+++ b/app/javascript/vue/shared/content/attachments/context_menu.vue
@@ -34,6 +34,7 @@
       @duplicate="duplicate"
       @viewMode="changeViewMode"
       @move="showMoveModal"
+      @fileVersionsModal="fileVersionsModal = true"
       @menu-toggle="$emit('menu-toggle', $event)"
     ></MenuDropdown>
     <Teleport to="body">
@@ -55,6 +56,11 @@
         :targets_url="attachment.attributes.urls.move_targets"
         @confirm="moveAttachment($event)" @cancel="closeMoveModal"
       />
+      <FileVersionsModal
+        v-if="fileVersionsModal"
+        :url="attachment.attributes.urls.versions"
+        @close="fileVersionsModal = false"
+      />
     </Teleport>
   </div>
 </template>
@@ -65,6 +71,7 @@ import deleteAttachmentModal from './delete_modal.vue';
 import MoveAssetModal from '../modal/move.vue';
 import MoveMixin from './mixins/move.js';
 import MenuDropdown from '../../menu_dropdown.vue';
+import FileVersionsModal from '../../file_versions_modal.vue';
 import axios from '../../../../packs/custom_axios.js';
 
 export default {
@@ -73,6 +80,7 @@ export default {
     RenameAttachmentModal,
     deleteAttachmentModal,
     MoveAssetModal,
+    FileVersionsModal,
     MenuDropdown
   },
   mixins: [MoveMixin],
@@ -91,7 +99,8 @@ export default {
     return {
       viewModeOptions: ['inline', 'thumbnail', 'list'],
       deleteModal: false,
-      renameModal: false
+      renameModal: false,
+      fileVersionsModal: false
     };
   },
   computed: {
@@ -136,6 +145,12 @@ export default {
           });
         });
       }
+      if (this.attachment.attributes.urls.versions) {
+        menu.push({
+          text: this.i18n.t('assets.context_menu.versions'),
+          emit: 'fileVersionsModal'
+        });
+      }
       return menu;
     }
   },
diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
new file mode 100644
index 000000000..0aeb81b43
--- /dev/null
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -0,0 +1,66 @@
+<template>
+  <div ref="modal" @keydown.esc="close" class="modal" tabindex="-1" role="dialog">
+    <div class="modal-dialog" role="document">
+      <div class="modal-content">
+        <div class="modal-header">
+          <button @click="close" type="button" class="close" data-dismiss="modal" aria-label="Close"><i class="sn-icon sn-icon-close"></i></button>
+          <h4 class="modal-title">
+            {{ i18n.t("assets.file_versions_modal.title") }}
+          </h4>
+        </div>
+        <div class="modal-body">
+          <div v-if="fileVersions" v-for="fileVersion in fileVersions" :key="fileVersion.id">
+            <div class="flex w-full border border-sn-light-grey rounded mb-1.5 p-1.5 items-center">
+              <div class="basis-3/4">
+                <div class="mb-1.5">
+                  <span class="bg-sn-grey-300 me-2 px-2 py-0.5 rounded">v{{ fileVersion.attributes.version }}</span>
+                  <a :href="fileVersion.attributes.url" target="_blank">{{ fileVersion.attributes.filename }}</a>
+                  <small class="inline-block" v-if="fileVersion.attributes.restored_from_version">
+                    ({{ i18n.t("assets.file_versions_modal.restored_from_version", { version: fileVersion.attributes.restored_from_version }) }})
+                  </small>
+                </div>
+                <div class="flex text-xs text-sn-grey justify-start">
+                  <div class="mr-3">{{ fileVersion.attributes.created_at }}</div>
+                  <div class="mr-3">{{ fileVersion.attributes.created_by.full_name }}</div>
+                  <div>{{ (fileVersion.attributes.byte_size/1024).toFixed(1) }}KB</div>
+                </div>
+              </div>
+
+              <div class="basis-1/4 flex justify-end">
+                <a class="btn btn-icon p-0" :href="fileVersion.attributes.url" target="_blank"><i class="sn-icon sn-icon-export"></i></a>
+                <a class="btn btn-icon p-0 mx-3"><i class="sn-icon sn-icon-restore"></i></a>
+              </div>
+            </div>
+          </div>
+          <div v-else class="sci-loader"></div>
+        </div>
+      </div>
+    </div>
+  </div>
+</template>
+
+<script>
+import modalMixin from './modal_mixin';
+import axios from '../../packs/custom_axios';
+
+export default {
+  name: 'FileVersionsModal',
+  props: {
+    url: {
+      type: String,
+      required: true
+    }
+  },
+  mixins: [modalMixin],
+  data() {
+    return {
+      fileVersions: null
+    };
+  },
+  created() {
+    axios.get(this.url).then((response) => {
+      this.fileVersions = response.data.data;
+    });
+  }
+};
+</script>
diff --git a/app/models/concerns/versioned_attachments.rb b/app/models/concerns/versioned_attachments.rb
index 464ff1aff..6a32e6963 100644
--- a/app/models/concerns/versioned_attachments.rb
+++ b/app/models/concerns/versioned_attachments.rb
@@ -8,10 +8,22 @@ module VersionedAttachments
       has_one_attached name, dependent: :detach
       has_many_attached "previous_#{name.to_s.pluralize}", dependent: :detach
 
-      define_method "attach_#{name}_version" do |*args, **options|
+      define_method :"attach_#{name}_version" do |*args, **options|
         ActiveRecord::Base.transaction(requires_new: true) do
-          __send__("previous_#{name.to_s.pluralize}").attach(__send__(name).blob) if __send__(name).attached?
+          __send__(:"previous_#{name.to_s.pluralize}").attach(__send__(name).blob) if __send__(name).attached?
           __send__(name).attach(*args, **options)
+
+          new_blob = __send__(name).blob
+          new_blob.metadata['created_by_id'] = last_modified_by_id
+          new_blob.save!
+
+          # set version of current latest file if previous versions exist
+          next unless __send__(:"previous_#{name.to_s.pluralize}").any?
+
+          new_version =
+            (__send__(:"previous_#{name.to_s.pluralize}").last.blob.metadata['version'] || 1) + 1
+          new_blob.metadata['version'] = new_version
+          new_blob.save!
         end
       end
     end
diff --git a/app/serializers/asset_serializer.rb b/app/serializers/asset_serializer.rb
index 9817f448a..ba4fa56ef 100644
--- a/app/serializers/asset_serializer.rb
+++ b/app/serializers/asset_serializer.rb
@@ -138,7 +138,8 @@ class AssetSerializer < ActiveModel::Serializer
       load_asset: load_asset_path(object),
       asset_file: asset_file_url_path(object),
       marvin_js: marvin_js_asset_path(object),
-      marvin_js_icon: image_path('icon_small/marvinjs.svg')
+      marvin_js_icon: image_path('icon_small/marvinjs.svg'),
+      versions: (asset_versions_path(object) if attached)
     }
     user = scope[:user] || @instance_options[:user]
     if can_manage_asset?(user, object)
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 4b046bb51..78daf6634 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -4005,6 +4005,13 @@ en:
       inline_html: "Large"
       thumbnail_html: "Thumbnail"
       list_html: "List"
+      versions: "Versions"
+    file_versions_modal:
+      title: "Version history"
+      download: "Download"
+      restore: "Restore"
+      size: "Size"
+      restored_from_version: "restored from v%{version}"
     rename_modal:
       title: "Rename file"
       min_length_error: "File name must be at least 1 character long."
diff --git a/config/routes.rb b/config/routes.rb
index 3c2d9a9ae..3358bd239 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -861,6 +861,7 @@ Rails.application.routes.draw do
     get 'files/:id/edit', to: 'assets#edit', as: 'edit_asset'
     get 'files/:id/checksum', to: 'assets#checksum', as: 'asset_checksum'
     get 'files/:id/show', to: 'assets#show', as: 'asset_show'
+    get 'files/:id/versions', to: 'assets#versions', as: 'asset_versions'
     patch 'files/:id/toggle_view_mode', to: 'assets#toggle_view_mode', as: 'toggle_view_mode'
     get 'files/:id/load_asset', to: 'assets#load_asset', as: 'load_asset'
     post 'files/:id/update_image', to: 'assets#update_image',

From 48fb68c07ce6f147b259c545249e9a684084fcfe Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 17 Sep 2024 16:26:45 +0200
Subject: [PATCH 21/96] Implement restore functionality in file versions modal
 [SCI-11042]

---
 app/controllers/assets_controller.rb          |  7 +++++-
 .../attachments/attachment_actions.vue        |  1 +
 .../content/attachments/context_menu.vue      |  4 ++-
 .../vue/shared/content/attachments/inline.vue |  1 +
 .../vue/shared/content/attachments/list.vue   |  1 +
 .../shared/content/attachments/thumbnail.vue  |  1 +
 .../vue/shared/file_versions_modal.vue        | 25 +++++++++++++++----
 app/models/concerns/versioned_attachments.rb  | 18 +++++++++++++
 app/serializers/asset_serializer.rb           |  3 ++-
 config/routes.rb                              |  1 +
 10 files changed, 54 insertions(+), 8 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 314583de4..5fded7712 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -197,7 +197,7 @@ class AssetsController < ApplicationController
     return render_403 unless can_read_team?(@asset.team)
 
     @asset.last_modified_by = current_user
-    @asset.attach_file_version(io: params.require(:image), filename: orig_file_name, current_user: current_user)
+    @asset.attach_file_version(io: params.require(:image), filename: orig_file_name)
     @asset.save!
     create_edit_image_activity(@asset, current_user, :finish_editing)
     # release previous image space
@@ -405,6 +405,11 @@ class AssetsController < ApplicationController
     )
   end
 
+  def restore_version
+    @asset.restore_file_version(params[:version].to_i)
+    render json: @asset.file.blob
+  end
+
   private
 
   def load_vars
diff --git a/app/javascript/vue/shared/content/attachments/attachment_actions.vue b/app/javascript/vue/shared/content/attachments/attachment_actions.vue
index 71561f7c3..6147efa33 100644
--- a/app/javascript/vue/shared/content/attachments/attachment_actions.vue
+++ b/app/javascript/vue/shared/content/attachments/attachment_actions.vue
@@ -27,6 +27,7 @@
       @attachment:changed="$emit('attachment:changed', $event)"
       @attachment:update="$emit('attachment:update', $event)"
       @menu-toggle="$emit('attachment:toggle_menu', $event)"
+      @attachment:versionRestored="$emit('attachment:versionRestored', $event)"
       :withBorder="withBorder"
     />
   </div>
diff --git a/app/javascript/vue/shared/content/attachments/context_menu.vue b/app/javascript/vue/shared/content/attachments/context_menu.vue
index 5f9a6a7bb..8d7d67c6d 100644
--- a/app/javascript/vue/shared/content/attachments/context_menu.vue
+++ b/app/javascript/vue/shared/content/attachments/context_menu.vue
@@ -58,8 +58,10 @@
       />
       <FileVersionsModal
         v-if="fileVersionsModal"
-        :url="attachment.attributes.urls.versions"
+        :versionsUrl="attachment.attributes.urls.versions"
+        :restoreVersionUrl="attachment.attributes.urls.restore_version"
         @close="fileVersionsModal = false"
+        @fileVersionRestored="$emit('attachment:versionRestored', $event)"
       />
     </Teleport>
   </div>
diff --git a/app/javascript/vue/shared/content/attachments/inline.vue b/app/javascript/vue/shared/content/attachments/inline.vue
index 14788fc32..d1fec5fb7 100644
--- a/app/javascript/vue/shared/content/attachments/inline.vue
+++ b/app/javascript/vue/shared/content/attachments/inline.vue
@@ -38,6 +38,7 @@
           @attachment:delete="deleteAttachment"
           @attachment:moved="attachmentMoved"
           @attachment:uploaded="reloadAttachments"
+          @attachment:versionRestored="reloadAttachments"
           @attachment:changed="$emit('attachment:changed', $event)"
           @attachment:update="$emit('attachment:update', $event)"
           @attachment:toggle_menu="toggleMenuDropdown"
diff --git a/app/javascript/vue/shared/content/attachments/list.vue b/app/javascript/vue/shared/content/attachments/list.vue
index d8cdc5ad6..2a2aeb03b 100644
--- a/app/javascript/vue/shared/content/attachments/list.vue
+++ b/app/javascript/vue/shared/content/attachments/list.vue
@@ -37,6 +37,7 @@
           @attachment:delete="deleteAttachment"
           @attachment:moved="attachmentMoved"
           @attachment:uploaded="reloadAttachments"
+          @attachment:versionRestored="reloadAttachments"
           @attachment:changed="$emit('attachment:changed', $event)"
           @attachment:update="$emit('attachment:update', $event)"
           @attachment:toggle_menu="toggleMenuDropdown"
diff --git a/app/javascript/vue/shared/content/attachments/thumbnail.vue b/app/javascript/vue/shared/content/attachments/thumbnail.vue
index ebdc25442..bc7ac5684 100644
--- a/app/javascript/vue/shared/content/attachments/thumbnail.vue
+++ b/app/javascript/vue/shared/content/attachments/thumbnail.vue
@@ -54,6 +54,7 @@
           @attachment:delete="deleteAttachment"
           @attachment:moved="attachmentMoved"
           @attachment:uploaded="reloadAttachments"
+          @attachment:versionRestored="reloadAttachments"
           @attachment:changed="$emit('attachment:changed', $event)"
           @attachment:update="$emit('attachment:update', $event)"
           @attachment:toggle_menu="toggleMenu"
diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
index 0aeb81b43..47c8ffd7a 100644
--- a/app/javascript/vue/shared/file_versions_modal.vue
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -28,7 +28,7 @@
 
               <div class="basis-1/4 flex justify-end">
                 <a class="btn btn-icon p-0" :href="fileVersion.attributes.url" target="_blank"><i class="sn-icon sn-icon-export"></i></a>
-                <a class="btn btn-icon p-0 mx-3"><i class="sn-icon sn-icon-restore"></i></a>
+                <a v-if="restoreVersionUrl" @click="restoreVersion(fileVersion.attributes.version)" class="btn btn-icon p-0 mx-3"><i class="sn-icon sn-icon-restore"></i></a>
               </div>
             </div>
           </div>
@@ -46,7 +46,11 @@ import axios from '../../packs/custom_axios';
 export default {
   name: 'FileVersionsModal',
   props: {
-    url: {
+    versionsUrl: {
+      type: String,
+      required: true
+    },
+    restoreVersionUrl: {
       type: String,
       required: true
     }
@@ -58,9 +62,20 @@ export default {
     };
   },
   created() {
-    axios.get(this.url).then((response) => {
-      this.fileVersions = response.data.data;
-    });
+    this.loadVersions();
+  },
+  methods: {
+    loadVersions() {
+      axios.get(this.versionsUrl).then((response) => {
+        this.fileVersions = response.data.data;
+      });
+    },
+    restoreVersion(version) {
+      axios.post(this.restoreVersionUrl, { version: version }).then(() => {
+        this.loadVersions();
+        this.$emit('fileVersionRestored');
+      });
+    }
   }
 };
 </script>
diff --git a/app/models/concerns/versioned_attachments.rb b/app/models/concerns/versioned_attachments.rb
index 6a32e6963..77159a023 100644
--- a/app/models/concerns/versioned_attachments.rb
+++ b/app/models/concerns/versioned_attachments.rb
@@ -26,6 +26,24 @@ module VersionedAttachments
           new_blob.save!
         end
       end
+
+      define_method :"restore_#{name}_version" do |version|
+        ActiveRecord::Base.transaction(requires_new: true) do
+          blob = __send__(:"previous_#{name.to_s.pluralize}").map(&:blob).find do |b|
+            (b.metadata['version'] || 1) == version
+          end
+
+          blob.open do |tmp_file|
+            new_blob = ActiveStorage::Blob.create_and_upload!(
+              io: tmp_file,
+              filename: blob.filename,
+              metadata: blob.metadata.merge({ 'restored_from_version' => version })
+            )
+
+            __send__(:"attach_#{name}_version", new_blob)
+          end
+        end
+      end
     end
   end
 end
diff --git a/app/serializers/asset_serializer.rb b/app/serializers/asset_serializer.rb
index ba4fa56ef..51abd6204 100644
--- a/app/serializers/asset_serializer.rb
+++ b/app/serializers/asset_serializer.rb
@@ -152,7 +152,8 @@ class AssetSerializer < ActiveModel::Serializer
         duplicate: asset_duplicate_path(object),
         move_targets: asset_move_tagets_path(object),
         move: asset_move_path(object),
-        rename: asset_rename_path(object)
+        rename: asset_rename_path(object),
+        restore_version: asset_restore_version_path(object)
       )
     end
 
diff --git a/config/routes.rb b/config/routes.rb
index 3358bd239..bdd085d7e 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -862,6 +862,7 @@ Rails.application.routes.draw do
     get 'files/:id/checksum', to: 'assets#checksum', as: 'asset_checksum'
     get 'files/:id/show', to: 'assets#show', as: 'asset_show'
     get 'files/:id/versions', to: 'assets#versions', as: 'asset_versions'
+    post 'files/:id/restore_version', to: 'assets#restore_version', as: 'asset_restore_version'
     patch 'files/:id/toggle_view_mode', to: 'assets#toggle_view_mode', as: 'toggle_view_mode'
     get 'files/:id/load_asset', to: 'assets#load_asset', as: 'load_asset'
     post 'files/:id/update_image', to: 'assets#update_image',

From 9aa43f4c36a800b0e4e714a19e3ce02f0d1f2500 Mon Sep 17 00:00:00 2001
From: Martin Artnik <85488244+artoscinote@users.noreply.github.com>
Date: Wed, 18 Sep 2024 13:36:49 +0200
Subject: [PATCH 22/96] Add restore file permission check [SCI-11042]

---
 app/controllers/assets_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 5fded7712..c4a93ef29 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -18,7 +18,7 @@ class AssetsController < ApplicationController
 
   before_action :load_vars, except: :create_wopi_file
   before_action :check_read_permission, except: %i(edit destroy duplicate create_wopi_file toggle_view_mode)
-  before_action :check_manage_permission, only: %i(edit destroy duplicate rename toggle_view_mode)
+  before_action :check_manage_permission, only: %i(edit destroy duplicate rename toggle_view_mode restore_version)
 
   def file_preview
     editable = can_manage_asset?(@asset) && (@asset.repository_asset_value.blank? ||

From 6c2c416bbffebb51d38af3452c2ed5329ae7b075 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 18 Sep 2024 13:51:03 +0200
Subject: [PATCH 23/96] Implement disabled file versioning state [SCI-11040]

---
 app/assets/stylesheets/themes/scinote.scss    |  4 +
 app/controllers/assets_controller.rb          | 14 ++-
 .../vue/shared/file_versions_modal.vue        | 90 +++++++++++++++----
 app/models/concerns/versioned_attachments.rb  |  6 ++
 app/serializers/asset_serializer.rb           |  4 +-
 config/locales/en.yml                         |  5 +-
 6 files changed, 99 insertions(+), 24 deletions(-)

diff --git a/app/assets/stylesheets/themes/scinote.scss b/app/assets/stylesheets/themes/scinote.scss
index 711677980..fd7f60180 100644
--- a/app/assets/stylesheets/themes/scinote.scss
+++ b/app/assets/stylesheets/themes/scinote.scss
@@ -1362,6 +1362,10 @@ th.custom-field .modal-tooltiptext {
   cursor: pointer;
 }
 
+.tooltip {
+  z-index: 9999;
+}
+
 .tooltip-open {
   background-color: $color-concrete;
   color: $color-black;
diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index c4a93ef29..dfa46e7fe 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -399,13 +399,23 @@ class AssetsController < ApplicationController
   end
 
   def versions
+    blobs =
+      [@asset.file.blob] +
+      @asset.previous_files.map(&:blob).sort_by { |b| -1 * b.metadata['version'].to_i }[0..(VersionedAttachments.enabled? ? -1 : 1)]
     render(
-      json: [@asset.file.blob] +
-            @asset.previous_files.map(&:blob).sort_by { |b| -1 * b.metadata['version'].to_i }
+      json: ActiveModel::SerializableResource.new(
+        blobs,
+        each_serializer: ActiveStorage::BlobSerializer
+      ).as_json.merge(
+        enabled: VersionedAttachments.enabled?,
+        enable_url: ENV.fetch('SCINOTE_FILE_VERSIONING_ENABLE_URL', nil)
+      )
     )
   end
 
   def restore_version
+    render_403 unless VersionedAttachments.enabled?
+
     @asset.restore_file_version(params[:version].to_i)
     render json: @asset.file.blob
   end
diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
index 47c8ffd7a..63d12c456 100644
--- a/app/javascript/vue/shared/file_versions_modal.vue
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -9,30 +9,68 @@
           </h4>
         </div>
         <div class="modal-body">
-          <div v-if="fileVersions" v-for="fileVersion in fileVersions" :key="fileVersion.id">
-            <div class="flex w-full border border-sn-light-grey rounded mb-1.5 p-1.5 items-center">
-              <div class="basis-3/4">
-                <div class="mb-1.5">
-                  <span class="bg-sn-grey-300 me-2 px-2 py-0.5 rounded">v{{ fileVersion.attributes.version }}</span>
-                  <a :href="fileVersion.attributes.url" target="_blank">{{ fileVersion.attributes.filename }}</a>
-                  <small class="inline-block" v-if="fileVersion.attributes.restored_from_version">
-                    ({{ i18n.t("assets.file_versions_modal.restored_from_version", { version: fileVersion.attributes.restored_from_version }) }})
-                  </small>
+          <div class="relative" v-if="fileVersions">
+            <div v-for="(fileVersion, index) in fileVersions" :key="fileVersion.id">
+              <div class="flex w-full border border-sn-light-grey rounded mb-1.5 p-1.5 items-center">
+                <div class="basis-3/4">
+                  <div class="mb-1.5">
+                    <span v-if="fileVersion.attributes.version === 1" class="bg-sn-science-blue text-sn-white me-2 px-2 py-0.5 rounded">
+                      {{ i18n.t("assets.file_versions_modal.original_file") }}
+                    </span>
+                    <span v-else class="bg-sn-grey-300 me-2 px-2 py-0.5 rounded">v{{ fileVersion.attributes.version }}</span>
+                    <a :href="fileVersion.attributes.url" target="_blank">{{ fileVersion.attributes.filename }}</a>
+                    <small class="inline-block ml-1" v-if="fileVersion.attributes.restored_from_version">
+                      ({{ i18n.t("assets.file_versions_modal.restored_from_version", { version: fileVersion.attributes.restored_from_version }) }})
+                    </small>
+                  </div>
+                  <div class="flex text-xs text-sn-grey justify-start">
+                    <div class="mr-3">{{ fileVersion.attributes.created_at }}</div>
+                    <div class="mr-3">{{ fileVersion.attributes.created_by.full_name }}</div>
+                    <div>{{ Math.round(fileVersion.attributes.byte_size/1024) }}KB</div>
+                  </div>
                 </div>
-                <div class="flex text-xs text-sn-grey justify-start">
-                  <div class="mr-3">{{ fileVersion.attributes.created_at }}</div>
-                  <div class="mr-3">{{ fileVersion.attributes.created_by.full_name }}</div>
-                  <div>{{ (fileVersion.attributes.byte_size/1024).toFixed(1) }}KB</div>
-                </div>
-              </div>
 
-              <div class="basis-1/4 flex justify-end">
-                <a class="btn btn-icon p-0" :href="fileVersion.attributes.url" target="_blank"><i class="sn-icon sn-icon-export"></i></a>
-                <a v-if="restoreVersionUrl" @click="restoreVersion(fileVersion.attributes.version)" class="btn btn-icon p-0 mx-3"><i class="sn-icon sn-icon-restore"></i></a>
+                <div class="basis-1/4 flex justify-end">
+                  <a class="btn btn-icon p-0 mr-3"đ
+                    v-if="enabled || index === 0"
+                    :href="fileVersion.attributes.url"
+                    target="_blank"
+                    data-render-tooltip="true"
+                    :title="i18n.t('assets.file_versions_modal.download')"
+                  >
+                    <i class="sn-icon sn-icon-export"></i>
+                  </a>
+                  <a v-if="restoreVersionUrl && index !== 0"
+                    @click="restoreVersion(fileVersion.attributes.version)"
+                    data-render-tooltip="true"
+                    :title="i18n.t('assets.file_versions_modal.restore')"
+                    class="btn btn-icon p-0 mr-3"
+                  >
+                    <i class="sn-icon sn-icon-restore"></i>
+                  </a>
+                </div>
               </div>
             </div>
+            <div v-if="!enabled" class="absolute bottom-0 w-full h-[150px] bg-gradient-to-t from-white to-transparent"></div>
           </div>
           <div v-else class="sci-loader"></div>
+          <div v-if="!enabled" class="bg-sn-super-light-blue p-4 rounded flex items-start">
+            <div class="mr-2">
+              <i class="sn-icon sn-icon-upgrade"></i>
+            </div>
+            <div>
+              <h3 class="mt-1 mb-2">{{ i18n.t('assets.file_versions_modal.title') }}</h3>
+              {{ i18n.t('assets.file_versions_modal.disabled_disclaimer') }}
+            </div>
+          </div>
+        </div>
+        <div class="modal-footer">
+          <button type='button' class='btn btn-secondary' @click="close">
+            {{ i18n.t('general.cancel') }}
+          </button>
+          <a v-if="!enabled" :href="enableUrl" class='btn btn-primary' target="_blank">
+            {{ i18n.t('assets.file_versions_modal.enable_button') }}
+          </a>
         </div>
       </div>
     </div>
@@ -58,16 +96,30 @@ export default {
   mixins: [modalMixin],
   data() {
     return {
-      fileVersions: null
+      fileVersions: null,
+      enabled: null,
+      enableUrl: null
     };
   },
   created() {
     this.loadVersions();
   },
+  beforeUnmount() {
+    document.querySelectorAll('[data-render-tooltip]').forEach((e) => {
+      window.destroyTooltip(e);
+    });
+  },
   methods: {
     loadVersions() {
       axios.get(this.versionsUrl).then((response) => {
         this.fileVersions = response.data.data;
+        this.enabled = response.data.enabled;
+        this.enableUrl = response.data.enable_url;
+        this.$nextTick(() => {
+          document.querySelectorAll('[data-render-tooltip]').forEach((e) => {
+            window.initTooltip(e);
+          });
+        });
       });
     },
     restoreVersion(version) {
diff --git a/app/models/concerns/versioned_attachments.rb b/app/models/concerns/versioned_attachments.rb
index 77159a023..6adc4d809 100644
--- a/app/models/concerns/versioned_attachments.rb
+++ b/app/models/concerns/versioned_attachments.rb
@@ -46,4 +46,10 @@ module VersionedAttachments
       end
     end
   end
+
+  module_function
+
+  def enabled?
+    ApplicationSettings.instance.values['storage_locations_enabled']
+  end
 end
diff --git a/app/serializers/asset_serializer.rb b/app/serializers/asset_serializer.rb
index 51abd6204..53c31236d 100644
--- a/app/serializers/asset_serializer.rb
+++ b/app/serializers/asset_serializer.rb
@@ -152,11 +152,11 @@ class AssetSerializer < ActiveModel::Serializer
         duplicate: asset_duplicate_path(object),
         move_targets: asset_move_tagets_path(object),
         move: asset_move_path(object),
-        rename: asset_rename_path(object),
-        restore_version: asset_restore_version_path(object)
+        rename: asset_rename_path(object)
       )
     end
 
+    urls[:restore_version] = asset_restore_version_path(object) if VersionedAttachments.enabled?
     urls[:open_vector_editor_edit] = edit_gene_sequence_asset_path(object.id) if can_manage_asset?(user, object)
 
     if can_manage_asset?(user, object) && can_open_asset_locally?(user, object)
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 78daf6634..a1e5ddc46 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -4009,9 +4009,12 @@ en:
     file_versions_modal:
       title: "Version history"
       download: "Download"
-      restore: "Restore"
+      restore: "Restore this version"
       size: "Size"
       restored_from_version: "restored from v%{version}"
+      original_file: "Original file"
+      enable_button: "Enable"
+      disabled_disclaimer: "This feature is currently disabled"
     rename_modal:
       title: "Rename file"
       min_length_error: "File name must be at least 1 character long."

From 294eef13a2cae68bd99bb28c7776c7bac99cc775 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 18 Sep 2024 14:12:42 +0200
Subject: [PATCH 24/96] Fix file versioning disclamer load [SCI-11040]

---
 app/javascript/vue/shared/file_versions_modal.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
index 63d12c456..d1c893c4b 100644
--- a/app/javascript/vue/shared/file_versions_modal.vue
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -54,7 +54,7 @@
             <div v-if="!enabled" class="absolute bottom-0 w-full h-[150px] bg-gradient-to-t from-white to-transparent"></div>
           </div>
           <div v-else class="sci-loader"></div>
-          <div v-if="!enabled" class="bg-sn-super-light-blue p-4 rounded flex items-start">
+          <div v-if="fileVersions && !enabled" class="bg-sn-super-light-blue p-4 rounded flex items-start">
             <div class="mr-2">
               <i class="sn-icon sn-icon-upgrade"></i>
             </div>
@@ -68,7 +68,7 @@
           <button type='button' class='btn btn-secondary' @click="close">
             {{ i18n.t('general.cancel') }}
           </button>
-          <a v-if="!enabled" :href="enableUrl" class='btn btn-primary' target="_blank">
+          <a v-if="fileVersions && !enabled" :href="enableUrl" class='btn btn-primary' target="_blank">
             {{ i18n.t('assets.file_versions_modal.enable_button') }}
           </a>
         </div>

From 8bc8ccb2f7ccc3f903b1e26545ee3d68385488c1 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Wed, 18 Sep 2024 15:43:17 +0200
Subject: [PATCH 25/96] Improve rendering of docx tables [SCI-11056]

---
 app/helpers/input_sanitize_helper.rb          |  3 ++-
 app/services/reports/docx_renderer.rb         |  7 +++++
 .../reports/html_to_word_converter.rb         | 27 ++++++++++++++++++-
 3 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/app/helpers/input_sanitize_helper.rb b/app/helpers/input_sanitize_helper.rb
index e30a23666..7b479bbbd 100644
--- a/app/helpers/input_sanitize_helper.rb
+++ b/app/helpers/input_sanitize_helper.rb
@@ -40,11 +40,12 @@ module InputSanitizeHelper
     preview_repository = options.fetch(:preview_repository, false)
     format_opt = wrapper_tag.merge(sanitize: false)
     base64_encoded_imgs = options.fetch(:base64_encoded_imgs, false)
-    text = simple_format(text, {}, format_opt) if simple_f
 
     # allow base64 images when sanitizing if base64_encoded_imgs is true
     sanitizer_config = Constants::INPUT_SANITIZE_CONFIG.deep_dup
+
     text = sanitize_input(text, tags, sanitizer_config: sanitizer_config)
+    text = simple_format(text, {}, format_opt) if simple_f
 
     if text =~ SmartAnnotations::TagToHtml::USER_REGEX || text =~ SmartAnnotations::TagToHtml::REGEX
       text = smart_annotation_parser(text, team, base64_encoded_imgs, preview_repository)
diff --git a/app/services/reports/docx_renderer.rb b/app/services/reports/docx_renderer.rb
index 91872dc46..dd027bc4b 100644
--- a/app/services/reports/docx_renderer.rb
+++ b/app/services/reports/docx_renderer.rb
@@ -130,6 +130,13 @@ module Reports
         row[:data].each do |cell|
           docx_cell = Caracal::Core::Models::TableCellModel.new do |c|
             cell.each do |content|
+              c.background content[:style][:background] if content.dig(:style, :background).present?
+              if content.dig(:style, :vertical_align).present? && content[:style][:vertical_align] != :middle
+                c.vertical_align content[:style][:vertical_align]
+              else
+                c.vertical_align :center
+              end
+
               if content[:type] == 'p'
                 Reports::DocxRenderer.render_p_element(c, content, options.merge({ skip_br: true }))
               elsif content[:type] == 'table'
diff --git a/app/services/reports/html_to_word_converter.rb b/app/services/reports/html_to_word_converter.rb
index f4e312f8e..07a0c0919 100644
--- a/app/services/reports/html_to_word_converter.rb
+++ b/app/services/reports/html_to_word_converter.rb
@@ -208,7 +208,7 @@ module Reports
 
       if style
         style_keys.each do |key|
-          style_el = style.value.split(';').select { |i| (i.include? key) }[0]
+          style_el = style.value.split(';').find { |i| i.strip.start_with?(key) }
           next unless style_el
 
           value = style_el.split(':')[1].strip if style_el
@@ -259,6 +259,29 @@ module Reports
       }
     end
 
+    def table_cell_styling(elem)
+      style = elem.attributes['style']
+      result = {}
+      style_keys = %w(background-color vertical-align)
+
+      if style
+        style_keys.each do |key|
+          style_el = style.value.split(';').find { |i| (i.include? key) }
+          next unless style_el
+
+          value = style_el.split(':')[1].strip if style_el
+
+          case key
+          when 'background-color'
+            result[:background] = normalized_hex_color(value)
+          when 'vertical-align'
+            result[:vertical_align] = value.to_sym
+          end
+        end
+      end
+      result
+    end
+
     def tiny_mce_table_element(table_element)
       # array of elements
       rows = table_element.css('tbody').first.children.map do |row|
@@ -267,11 +290,13 @@ module Reports
         cells = row.children.map do |cell|
           next unless cell.name == 'td'
 
+          style = table_cell_styling(cell)
           # Parse cell content
           formated_cell = recursive_children(cell.children, [], true)
 
           # Combine text elements to single paragraph
           formated_cell = combine_docx_elements(formated_cell)
+          formated_cell.each { |element| element[:style] = style } if style.present?
           formated_cell
         end.reject(&:blank?)
         { type: 'tr', data: cells }

From e53ea89f1409aa8fd591c7cb4f65af43537bff08 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Fri, 27 Sep 2024 16:03:05 +0200
Subject: [PATCH 26/96] Fix carcal version [SCI-11024]

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 4f4b947cf..bd0d3f156 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -24,7 +24,7 @@ GIT
 
 GIT
   remote: https://github.com/scinote-eln/caracal.git
-  revision: f30bd2d26229c8118cc392c3a18409cb9a12ae02
+  revision: 7f5a653b23af51f38c9ecaf855fdffa6bc5427b2
   branch: custom-docx-reports
   specs:
     caracal (1.4.2)

From a3d549495b2c73d73c808512ca5c33f8bcef9ef7 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 1 Oct 2024 07:52:54 +0200
Subject: [PATCH 27/96] Fix adding backgroung color to docx tables [SCI-11119]

---
 app/services/reports/html_to_word_converter.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/services/reports/html_to_word_converter.rb b/app/services/reports/html_to_word_converter.rb
index 07a0c0919..6d589a020 100644
--- a/app/services/reports/html_to_word_converter.rb
+++ b/app/services/reports/html_to_word_converter.rb
@@ -262,7 +262,7 @@ module Reports
     def table_cell_styling(elem)
       style = elem.attributes['style']
       result = {}
-      style_keys = %w(background-color vertical-align)
+      style_keys = %w(background-color vertical-align background)
 
       if style
         style_keys.each do |key|
@@ -272,7 +272,7 @@ module Reports
           value = style_el.split(':')[1].strip if style_el
 
           case key
-          when 'background-color'
+          when 'background-color', 'background'
             result[:background] = normalized_hex_color(value)
           when 'vertical-align'
             result[:vertical_align] = value.to_sym

From 1a04e249ba00e956ab3d023fcbebcd7d1b72039b Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 1 Oct 2024 11:07:12 +0200
Subject: [PATCH 28/96] Add support for inventory columns selection for docx
 report [SCI-11095]

---
 app/assets/javascripts/reports/new.js         | 37 ++++++++++-
 app/assets/stylesheets/reports/new.scss       |  9 +++
 app/models/my_module.rb                       | 16 ++---
 app/models/report.rb                          | 12 +++-
 .../reports/docx/draw_my_module_repository.rb |  3 +-
 .../reports/docx/repository_helper.rb         | 14 ++--
 app/views/reports/wizard/_third_step.html.erb | 66 +++++++++++++------
 config/locales/en.yml                         |  5 ++
 8 files changed, 127 insertions(+), 35 deletions(-)

diff --git a/app/assets/javascripts/reports/new.js b/app/assets/javascripts/reports/new.js
index 98023b3f0..bcc8ad5d3 100644
--- a/app/assets/javascripts/reports/new.js
+++ b/app/assets/javascripts/reports/new.js
@@ -968,6 +968,16 @@ function reportHandsonTableConverter() {
 }
 
 (function() {
+  function getSelectedRepositoryColumnValues(element, selectedAll = false) {
+    const values = [];
+    $(element).find('option').each((_, option) => {
+      if ($(option).attr('selected-value') || selectedAll) {
+        values.push(option.value);
+      }
+    });
+    return values;
+  }
+
   function getReportData() {
     var reportData = {};
 
@@ -1046,8 +1056,17 @@ function reportHandsonTableConverter() {
       reportData.report.settings.task[e.value] = e.checked;
     });
     reportData.report.settings.task.repositories = [];
-    $.each($('.task-contents-container .repositories-contents .repositories-setting:checked'), function(i, e) {
-      reportData.report.settings.task.repositories.push(parseInt(e.value, 10));
+    reportData.report.settings.task.excluded_repository_columns = {};
+
+    $.each($('.task-contents-container .repositories-contents .repositories-setting:checked'), (_, e) => {
+      const value = parseInt(e.value, 10);
+      const $repositoryColumn = $(e).parent().siblings('.repository-columns')[0];
+      const selectedValues = dropdownSelector.getValues($repositoryColumn);
+      const excludedValues = getSelectedRepositoryColumnValues($repositoryColumn, true)
+        .filter((item) => !selectedValues.includes(item))
+        .map((el) => parseInt(el, 10));
+      reportData.report.settings.task.repositories.push(value);
+      reportData.report.settings.task.excluded_repository_columns[value] = excludedValues;
     });
 
     reportData.report.settings.task.result_order = dropdownSelector.getValues('#taskResultsOrder');
@@ -1359,6 +1378,20 @@ function reportHandsonTableConverter() {
     if (dropdownSelector.getValues('#docxTemplateSelector').length > 0) {
       loadDocxTemplate();
     }
+
+    $('.repository-columns').each((_, element) => {
+      const elementId = `#${$(element).attr('id')}`;
+      const elements = getSelectedRepositoryColumnValues(elementId);
+
+      dropdownSelector.init(elementId, {
+        selectAppearance: 'simple',
+        optionClass: 'checkbox-icon'
+      });
+
+      if (elements.length) {
+        dropdownSelector.selectValues(elementId, elements);
+      }
+    });
   }
 
   function loadTemplate() {
diff --git a/app/assets/stylesheets/reports/new.scss b/app/assets/stylesheets/reports/new.scss
index b5258df6e..8b50742d8 100644
--- a/app/assets/stylesheets/reports/new.scss
+++ b/app/assets/stylesheets/reports/new.scss
@@ -260,6 +260,15 @@
   }
   // scss-lint:enable ImportantRule
 
+  .repositories-contents {
+    .dropdown-selector-container {
+      display: inline-flex;
+      flex-shrink: 0;
+      margin-left: auto;
+      width: 200px;
+    }
+  }
+
   .project-selector-container {
     background: $color-white;
     box-shadow: $modal-shadow;
diff --git a/app/models/my_module.rb b/app/models/my_module.rb
index 36b7578ff..bca3c406e 100644
--- a/app/models/my_module.rb
+++ b/app/models/my_module.rb
@@ -391,17 +391,17 @@ class MyModule < ApplicationRecord
     { data: data, headers: headers }
   end
 
-  def repository_docx_json(repository)
-    headers = [
-      I18n.t('repositories.table.id'),
-      I18n.t('repositories.table.row_name'),
-      I18n.t('repositories.table.added_on'),
-      I18n.t('repositories.table.added_by')
-    ]
+  def repository_docx_json(repository, excluded_columns)
+    headers = Report.default_repository_columns.filter_map do |key, value|
+      value unless excluded_columns.include?(key.to_s.to_i)
+    end
+
     custom_columns = []
     return false unless repository
 
     repository.repository_columns.order(:id).each do |column|
+      next if excluded_columns.include?(column.id)
+
       if column.data_type == 'RepositoryStockValue'
         if repository.has_stock_consumption?
           headers.push(I18n.t('repositories.table.row_consumption'))
@@ -416,7 +416,7 @@ class MyModule < ApplicationRecord
 
     records = repository.assigned_rows(self)
                         .select(:id, :name, :created_at, :created_by_id, :repository_id, :parent_id, :archived)
-    { headers: headers, rows: records, custom_columns: custom_columns }
+    { headers: headers, rows: records, custom_columns: custom_columns, excluded_columns: excluded_columns }
   end
 
   def deep_clone(current_user)
diff --git a/app/models/report.rb b/app/models/report.rb
index 2d9a85908..61f092e33 100644
--- a/app/models/report.rb
+++ b/app/models/report.rb
@@ -64,7 +64,8 @@ class Report < ApplicationRecord
       result_comments: true,
       result_order: 'new',
       activities: true,
-      repositories: []
+      repositories: [],
+      excluded_repository_columns: {}
     }
   }.freeze
 
@@ -126,4 +127,13 @@ class Report < ApplicationRecord
     ReportActions::ReportContent.new(report, content, {}, current_user).save_with_content
     report
   end
+
+  def self.default_repository_columns
+    {
+      '-1': I18n.t('repositories.table.id'),
+      '-2': I18n.t('repositories.table.row_name'),
+      '-3': I18n.t('repositories.table.added_on'),
+      '-4': I18n.t('repositories.table.added_by')
+    }
+  end
 end
diff --git a/app/services/reports/docx/draw_my_module_repository.rb b/app/services/reports/docx/draw_my_module_repository.rb
index e6560c46e..a82b44b40 100644
--- a/app/services/reports/docx/draw_my_module_repository.rb
+++ b/app/services/reports/docx/draw_my_module_repository.rb
@@ -5,11 +5,12 @@ module Reports::Docx::DrawMyModuleRepository
     my_module = subject.my_module
     repository = subject.repository
     repository = assigned_repository_or_snapshot(my_module, repository)
+    excluded_repository_columns = @settings.dig(:task, :excluded_repository_columns, repository.id.to_s) || {}
 
     return unless repository && can_read_experiment?(@user, my_module.experiment) &&
                   (repository.is_a?(RepositorySnapshot) || can_read_repository?(@user, repository))
 
-    repository_data = my_module.repository_docx_json(repository)
+    repository_data = my_module.repository_docx_json(repository, excluded_repository_columns)
 
     return false unless repository_data[:rows].any? && can_read_repository?(@user, repository)
 
diff --git a/app/services/reports/docx/repository_helper.rb b/app/services/reports/docx/repository_helper.rb
index 50b693891..d962fd97d 100644
--- a/app/services/reports/docx/repository_helper.rb
+++ b/app/services/reports/docx/repository_helper.rb
@@ -6,12 +6,16 @@ module Reports::Docx::RepositoryHelper
 
   def prepare_row_columns(repository_data, my_module = nil, repository = nil)
     result = [repository_data[:headers]]
+    excluded_columns = repository_data[:excluded_columns]
+
     repository_data[:rows].each do |record|
       row = []
-      row.push(record.code)
-      row.push(escape_input(record.archived ? "#{record.name} [#{I18n.t('general.archived')}]" : record.name))
-      row.push(I18n.l(record.created_at, format: :full))
-      row.push(escape_input(record.created_by.full_name))
+      row.push(record.code) unless excluded_columns.include?(-1)
+      unless excluded_columns.include?(-2)
+        row.push(escape_input(record.archived ? "#{record.name} [#{I18n.t('general.archived')}]" : record.name))
+      end
+      row.push(I18n.l(record.created_at, format: :full)) unless excluded_columns.include?(-3)
+      row.push(escape_input(record.created_by.full_name)) unless excluded_columns.include?(-4)
 
       cell_values = {}
       custom_cells = record.repository_cells
@@ -38,6 +42,8 @@ module Reports::Docx::RepositoryHelper
       end
 
       repository_data[:custom_columns].each do |column_id|
+        next if excluded_columns.include?(column_id)
+
         value = cell_values[column_id]
         row.push(value)
       end
diff --git a/app/views/reports/wizard/_third_step.html.erb b/app/views/reports/wizard/_third_step.html.erb
index 327c1d857..2cbf865db 100644
--- a/app/views/reports/wizard/_third_step.html.erb
+++ b/app/views/reports/wizard/_third_step.html.erb
@@ -55,7 +55,10 @@
       </span><br>
       <span class="repositories-items-description">
         <i class="sn-icon sn-icon-info"></i>
-        <span><%= t("projects.reports.wizard.third_step.assigned_items_description") %></span>
+        <div class="flex-col font-normal">
+          <p><%= t("projects.reports.wizard.third_step.assigned_items_description") %></p>
+          <p><%= t("projects.reports.wizard.third_step.assigned_items_repository_items_description_html") %></p>
+        </div>
       </span>
       <ul class="collapse in" id="repositoriesContents">
         <li>
@@ -68,25 +71,50 @@
           <ul class="repositories-contents">
             <% @repositories.each do |repository| %>
               <li>
-                <span class="sci-checkbox-container">
-                  <input type="checkbox"
-                         class="sci-checkbox repositories-setting"
-                         value="<%= repository.is_a?(RepositorySnapshot) ? repository.parent_id : repository.id %>"
-                         <%= 'checked' if report.new_record? ||
-                                          @project_contents[:repositories].include?(repository.id) ||
-                                          (repository.is_a?(Repository) && repository.repository_snapshots.exists?(id: @project_contents[:repositories])) %> />
-                  <span class="sci-checkbox-label"></span>
-                </span>
-                <%= repository.name %>
-                <% if repository.archived? %>
-                  <span class="archived">
-                    <%= t("projects.reports.wizard.third_step.archived") %>
+                 <div class="flex items-center">
+                  <span class="sci-checkbox-container">
+                    <input type="checkbox"
+                          class="sci-checkbox repositories-setting"
+                          value="<%= repository.is_a?(RepositorySnapshot) ? repository.parent_id : repository.id %>"
+                          <%= 'checked' if report.new_record? ||
+                                            @project_contents[:repositories].include?(repository.id) ||
+                                            (repository.is_a?(Repository) && repository.repository_snapshots.exists?(id: @project_contents[:repositories])) %> />
+                    <span class="sci-checkbox-label"></span>
                   </span>
-                <% elsif repository.is_a?(RepositorySnapshot) %>
-                  <span class="deleted">
-                    <%= t("projects.reports.wizard.third_step.deleted") %>
-                  </span>
-                <% end %>
+                  <%= repository.name %>
+                  <% if repository.archived? %>
+                    <span class="archived">
+                      <%= t("projects.reports.wizard.third_step.archived") %>
+                    </span>
+                  <% elsif repository.is_a?(RepositorySnapshot) %>
+                    <span class="deleted">
+                      <%= t("projects.reports.wizard.third_step.deleted") %>
+                    </span>
+                  <% end %>
+                  <select class="repository-columns"
+                          id=<%= "repository-#{repository.id}" %>
+                          data-combine-tags="true"
+                          data-placeholder="<%= t("projects.reports.wizard.third_step.repository_column.placeholder") %>"
+                          data-select-multiple-all-selected="<%= t("projects.reports.wizard.third_step.repository_column.all_selected") %>"
+                          data-select-multiple-name="<%= t("projects.reports.wizard.third_step.repository_column.selected") %>"
+                          multiple
+                  >
+                   <% Report.default_repository_columns.each do |key, value| %>
+                      <option value="<%= key %>"
+                              selected-value="<%= report.settings.dig(:task, :excluded_repository_columns, repository.id.to_s)&.include?(key.to_s.to_i) ? '' : 'selected' %>"
+                      >
+                        <%= value %>
+                      </option>
+                    <% end %>
+                    <% repository.repository_columns.find_each do |repository_column| %>
+                      <option value="<%= repository_column.id %>"
+                              selected-value="<%= report.settings.dig(:task, :excluded_repository_columns, repository.id.to_s)&.include?(repository_column.id.to_i) ? '' : 'selected' %>"
+                      >
+                        <%= repository_column.name %>
+                      </option>
+                    <% end %>
+                  </select>
+                </div>
                 <div class="divider"></div>
               </li>
             <% end %>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index e3d65629d..371aa7200 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -844,6 +844,7 @@ en:
           step_comments: "Step comments"
           assigned_items: "Assigned items"
           assigned_items_description: "Inventories selected below will only contain the items that you assigned to the tasks directly."
+          assigned_items_repository_items_description_html: "You can customize inventory columns <strong>only for the docx report.</strong> The stock management column by default reflects item consumption."
           include_all_assigned_iitems: "Include all assigned items from the following inventories"
           results: "Results"
           all_results: "Include all results elements"
@@ -866,6 +867,10 @@ en:
           exclude_timestamps: "Exclude timestamps"
           archived: "[archived]"
           deleted: "[deleted]"
+          repository_column:
+            placeholder: 'Select columns'
+            all_selected: 'All columns selected'
+            selected: 'columns selected'
 
       new:
         report_name_placeholder: "Name your report"

From 104825af7980cf3f8f38856db523ca0ad8a4c837 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 2 Oct 2024 11:05:45 +0200
Subject: [PATCH 29/96] Change how asset sync conflict resolution works with
 file versioning [SCI-11043]

---
 app/controllers/asset_sync_controller.rb | 27 ++++++++++++------------
 config/locales/en.yml                    |  2 +-
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/app/controllers/asset_sync_controller.rb b/app/controllers/asset_sync_controller.rb
index ae8d0e126..968503cd7 100644
--- a/app/controllers/asset_sync_controller.rb
+++ b/app/controllers/asset_sync_controller.rb
@@ -16,7 +16,8 @@ class AssetSyncController < ApplicationController
     asset_sync_token = current_user.asset_sync_tokens.find_or_create_by(asset_id: params[:asset_id])
 
     unless asset_sync_token.token_valid?
-      asset_sync_token = current_user.asset_sync_tokens.create(asset_id: params[:asset_id])
+      asset_sync_token =
+        current_user.asset_sync_tokens.create(asset_id: params[:asset_id])
     end
 
     render json: AssetSyncTokenSerializer.new(asset_sync_token).as_json
@@ -27,18 +28,7 @@ class AssetSyncController < ApplicationController
   end
 
   def update
-    if @asset_sync_token.conflicts?(request.headers['VersionToken'])
-      ActiveRecord::Base.transaction do
-        conflict_response = AssetSyncTokenSerializer.new(conflicting_asset_copy_token).as_json
-        error_message = { message: I18n.t('assets.conflict_error', filename: @asset.file.filename) }
-        log_activity(:create)
-        render json: conflict_response.merge(error_message), status: :conflict
-      end
-
-      return
-    end
-
-    orig_file_size = @asset.file_size
+    asset_conflicts = @asset_sync_token.conflicts?(request.headers['VersionToken'])
 
     ActiveRecord::Base.transaction do
       @asset.update(last_modified_by: current_user)
@@ -49,12 +39,21 @@ class AssetSyncController < ApplicationController
         @asset.touch
       end
 
-      @asset.team.release_space(orig_file_size)
       @asset.post_process_file
 
       log_activity(:edit)
     end
 
+    if asset_conflicts
+      ActiveRecord::Base.transaction do
+        conflict_response = AssetSyncTokenSerializer.new(@asset_sync_token).as_json
+        error_message = { message: I18n.t('assets.conflict_error', filename: @asset.file.filename) }
+        render json: conflict_response.merge(error_message), status: :conflict
+      end
+
+      return
+    end
+
     render json: AssetSyncTokenSerializer.new(@asset_sync_token).as_json
   end
 
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 397eb5886..570263530 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -4049,7 +4049,7 @@ en:
     edit_launching_application_modal:
       title: "Launching application"
       description: "%{file_name} will now open in %{application}. Saved changes in %{application} will automatically be synced in SciNote."
-    conflict_error: "A newer version of the file was already present in the SciNote web app and your file was saved as “%{filename}”. Close this window and re-open file to get the latest changes."
+    conflict_error: "The file got updated in the SciNote web app while you were editing. Your version will be stored as the latest version, and the previous one is kept in version history."
     default_error: "An error occurred while saving to SciNote. Please save changes to your open document using “Save As…” to avoid losing any working changes."
     default_error_with_filename: "An error occurred while saving “%{filename}” to SciNote. Please save changes to your open document using “Save As…” to avoid losing any working changes."
 

From 74f3ea2108bba187c03e78299d13fca2aa0927c5 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 2 Oct 2024 14:22:51 +0200
Subject: [PATCH 30/96] Add file editing & versioning to inventories
 [SCI-11043]

---
 .../content/attachments/open_locally_menu.vue | 34 +++++++++++++++----
 .../shared/file_preview/_content.html.erb     |  4 +--
 config/locales/en.yml                         |  2 +-
 3 files changed, 30 insertions(+), 10 deletions(-)

diff --git a/app/javascript/vue/shared/content/attachments/open_locally_menu.vue b/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
index 8ea7048cc..9d40e11cf 100644
--- a/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
+++ b/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
@@ -1,8 +1,8 @@
 <template>
-  <div class="sn-open-locally-menu" @mouseenter="fetchLocalAppInfo">
-    <div v-if="(!canOpenLocally || disableLocalOpen) && (attachment.attributes.wopi && attachment.attributes.urls.edit_asset)">
+  <div class="sn-open-locally-menu flex" @mouseenter="fetchLocalAppInfo">
+    <div v-if="(!canOpenLocally) && (attachment.attributes.wopi && attachment.attributes.urls.edit_asset)">
       <a :href="editWopiSupported ? attachment.attributes.urls.edit_asset : null" target="_blank"
-         class="block whitespace-nowrap rounded px-3 py-2.5 hover:!text-sn-blue hover:no-underline cursor-pointer hover:bg-sn-super-light-grey"
+         class="btn btn-light"
          :class="{ 'disabled': !editWopiSupported }"
          :title="editWopiSupported ? null : attachment.attributes.wopi_context.title"
          style="pointer-events: all"
@@ -26,6 +26,7 @@
           {{ menu[0].text }}
         </a>
     </div>
+    <a @click="fileVersionsModal = true" class="btn btn-light"><i class="sn-icon sn-icon-history-search"></i>{{ i18n.t('assets.context_menu.versions') }}</a>
 
     <Teleport to="body">
       <NoPredefinedAppModal
@@ -47,6 +48,13 @@
         v-if="showUpdateVersionModal"
         @close="showUpdateVersionModal = false"
       />
+       <FileVersionsModal
+        v-if="fileVersionsModal"
+        :versionsUrl="attachment.attributes.urls.versions"
+        :restoreVersionUrl="attachment.attributes.urls.restore_version"
+        @close="fileVersionsModal = false"
+        @fileVersionRestored="refreshPreview"
+      />
     </Teleport>
   </div>
 </template>
@@ -55,14 +63,19 @@
 import OpenLocallyMixin from './mixins/open_locally.js';
 import MenuDropdown from '../../menu_dropdown.vue';
 import UpdateVersionModal from '../modal/update_version_modal.vue';
+import FileVersionsModal from '../../file_versions_modal.vue';
 
 export default {
   name: 'OpenLocallyMenu',
   mixins: [OpenLocallyMixin],
-  components: { MenuDropdown, UpdateVersionModal },
+  components: { MenuDropdown, UpdateVersionModal, FileVersionsModal },
   props: {
-    attachment: { type: Object, required: true },
-    disableLocalOpen: { type: Boolean, default: false }
+    attachment: { type: Object, required: true }
+  },
+  data() {
+    return {
+      fileVersionsModal: false
+    };
   },
   created() {
     this.fetchLocalAppInfo();
@@ -92,7 +105,7 @@ export default {
         });
       }
 
-      if (this.canOpenLocally && !this.disableLocalOpen) {
+      if (this.canOpenLocally) {
         const text = this.localAppName
           ? this.i18n.t('attachments.open_locally_in', { application: this.localAppName })
           : this.i18n.t('attachments.open_locally');
@@ -116,6 +129,13 @@ export default {
   methods: {
     openImageEditor() {
       document.getElementById('editImageButton').click();
+    },
+    refreshPreview() {
+      const imageElement = document.querySelector('.file-preview-container .asset-image');
+
+      if (!imageElement) return;
+
+      window.ActiveStoragePreviews.reCheckPreview({ target: imageElement });
     }
   }
 };
diff --git a/app/views/shared/file_preview/_content.html.erb b/app/views/shared/file_preview/_content.html.erb
index b99944c80..00d259dee 100644
--- a/app/views/shared/file_preview/_content.html.erb
+++ b/app/views/shared/file_preview/_content.html.erb
@@ -4,7 +4,7 @@
     <% if can_edit && !preview %>
       <% if wopi_enabled? && wopi_file?(asset) %>
         <div id="openLocallyMenu" data-behaviour="vue">
-          <open-locally-menu :disable-local-open="<%= asset.repository_asset_value.present? %>" :attachment="<%= { attributes: AssetSerializer.new(asset, scope: { user: current_user }).as_json }.to_json %>" />
+          <open-locally-menu :attachment="<%= { attributes: AssetSerializer.new(asset, scope: { user: current_user }).as_json }.to_json %>" />
         </div>
       <% elsif asset.file.metadata[:asset_type] == 'marvinjs' %>
         <button class="btn btn-light marvinjs-edit-button"
@@ -40,7 +40,7 @@
         </button>
       <% end %>
       <div id="openLocallyMenu" data-behaviour="vue">
-        <open-locally-menu :disable-local-open="<%= asset.repository_asset_value.present? %>" :attachment="<%= { attributes: AssetSerializer.new(asset, scope: { user: current_user }).as_json }.to_json %>" />
+        <open-locally-menu :attachment="<%= { attributes: AssetSerializer.new(asset, scope: { user: current_user }).as_json }.to_json %>" />
       </div>
     <% end %>
     <a class="btn btn-light file-download-link" href="<%= rails_blob_path(asset.file, disposition: 'attachment') %>" data-turbolinks="false">
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 570263530..1d5fc4813 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -4013,7 +4013,7 @@ en:
       inline_html: "Large"
       thumbnail_html: "Thumbnail"
       list_html: "List"
-      versions: "Versions"
+      versions: "Version history"
     file_versions_modal:
       title: "Version history"
       download: "Download"

From 6fc694abf36817bcc22b0e385d855b4ed8dc9d05 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 2 Oct 2024 15:38:37 +0200
Subject: [PATCH 31/96] Add missing serializer

---
 .../active_storage/blob_serializer.rb         | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 app/serializers/active_storage/blob_serializer.rb

diff --git a/app/serializers/active_storage/blob_serializer.rb b/app/serializers/active_storage/blob_serializer.rb
new file mode 100644
index 000000000..c667bdced
--- /dev/null
+++ b/app/serializers/active_storage/blob_serializer.rb
@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+module ActiveStorage
+  class BlobSerializer < ActiveModel::Serializer
+    include Rails.application.routes.url_helpers
+
+    attributes :filename, :url, :created_at, :byte_size, :version, :restored_from_version, :created_by
+
+    def version
+      object.metadata['version'] || 1
+    end
+
+    def restored_from_version
+      object.metadata['restored_from_version']
+    end
+
+    def created_at
+      object.created_at.strftime('%B %d, %Y at %H:%M')
+    end
+
+    def created_by
+      User.select(:id, :full_name, :email).find_by(
+        id: object.metadata['created_by_id'] || object.attachments.first&.record&.created_by_id
+      )
+    end
+  end
+end

From 680502558f790a058b4a9cf34cfebcc61713c93d Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Thu, 3 Oct 2024 09:46:44 +0200
Subject: [PATCH 32/96] Fix caracal version [SCI-11124]

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index bd0d3f156..abcf53353 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -24,7 +24,7 @@ GIT
 
 GIT
   remote: https://github.com/scinote-eln/caracal.git
-  revision: 7f5a653b23af51f38c9ecaf855fdffa6bc5427b2
+  revision: 9b5613c12092c4988d8394054fe966ed3f4f093c
   branch: custom-docx-reports
   specs:
     caracal (1.4.2)

From 2f0303b2dca5bddfc008d15b59526bfd87584c21 Mon Sep 17 00:00:00 2001
From: Martin Artnik <85488244+artoscinote@users.noreply.github.com>
Date: Fri, 4 Oct 2024 12:30:18 +0200
Subject: [PATCH 33/96] Revert "Revert "Timeout slow libreoffice preview
 generation [SCI-10809]""

---
 app/jobs/pdf_preview_job.rb                   | 36 ++-----------
 app/jobs/reports/docx_preview_job.rb          | 34 +-----------
 app/services/pdf_preview_service.rb           | 52 +++++++++++++++++++
 config/initializers/constants.rb              |  3 ++
 .../previewer/libreoffice_previewer.rb        |  7 ++-
 5 files changed, 65 insertions(+), 67 deletions(-)
 create mode 100644 app/services/pdf_preview_service.rb

diff --git a/app/jobs/pdf_preview_job.rb b/app/jobs/pdf_preview_job.rb
index 8f161d226..1a9a22cb8 100644
--- a/app/jobs/pdf_preview_job.rb
+++ b/app/jobs/pdf_preview_job.rb
@@ -16,39 +16,9 @@ class PdfPreviewJob < ApplicationJob
 
   def perform(asset_id)
     asset = Asset.find(asset_id)
-    blob = asset.file.blob
-    blob.open(tmpdir: tempdir) do |input|
-      work_dir = File.dirname(input.path)
-      preview_filename = "#{File.basename(input.path, '.*')}.pdf"
-      preview_file = File.join(work_dir, preview_filename)
-      Rails.logger.info "Starting preparing document preview for file #{blob.filename.sanitized}..."
 
-      ActiveRecord::Base.transaction do
-        success = system(
-          libreoffice_path, '--headless', '--invisible', '--convert-to', 'pdf', '--outdir', work_dir, input.path
-        )
-        unless success && File.file?(preview_file)
-          raise StandardError, "There was an error generating PDF preview, blob id: #{blob.id}"
-        end
-
-        ActiveRecord::Base.no_touching do
-          asset.file_pdf_preview.attach(io: File.open(preview_file), filename: "#{blob.filename.base}.pdf")
-          asset.update(pdf_preview_processing: false)
-        end
-        Rails.logger.info("Finished preparing PDF preview for file #{blob.filename.sanitized}.")
-      end
-    ensure
-      File.delete(preview_file) if File.file?(preview_file)
-    end
-  end
-
-  private
-
-  def tempdir
-    Rails.root.join('tmp')
-  end
-
-  def libreoffice_path
-    ENV['LIBREOFFICE_PATH'] || 'soffice'
+    PdfPreviewService.new(asset.file.blob, asset.file_pdf_preview).generate!
+  ensure
+    asset.update(pdf_preview_processing: false)
   end
 end
diff --git a/app/jobs/reports/docx_preview_job.rb b/app/jobs/reports/docx_preview_job.rb
index 5134bc529..9c35c6160 100644
--- a/app/jobs/reports/docx_preview_job.rb
+++ b/app/jobs/reports/docx_preview_job.rb
@@ -15,39 +15,7 @@ module Reports
 
     def perform(report_id)
       report = Report.find(report_id)
-      blob = report.docx_file.blob
-      blob.open(tmpdir: tempdir) do |input|
-        work_dir = File.dirname(input.path)
-        preview_filename = "#{File.basename(input.path, '.*')}.pdf"
-        preview_file = File.join(work_dir, preview_filename)
-        Rails.logger.info "Starting preparing document preview for file #{blob.filename.sanitized}..."
-
-        ActiveRecord::Base.transaction do
-          success = system(
-            libreoffice_path, '--headless', '--invisible', '--convert-to', 'pdf', '--outdir', work_dir, input.path
-          )
-          unless success && File.file?(preview_file)
-            raise StandardError, "There was an error generating PDF preview, blob id: #{blob.id}"
-          end
-
-          ActiveRecord::Base.no_touching do
-            report.docx_preview_file.attach(io: File.open(preview_file), filename: "#{blob.filename.base}.pdf")
-          end
-          Rails.logger.info("Finished preparing PDF preview for file #{blob.filename.sanitized}.")
-        end
-      ensure
-        File.delete(preview_file) if File.file?(preview_file)
-      end
-    end
-
-    private
-
-    def tempdir
-      Rails.root.join('tmp')
-    end
-
-    def libreoffice_path
-      ENV['LIBREOFFICE_PATH'] || 'soffice'
+      PdfPreviewService.new(report.docx_file.blob, report.docx_preview_file).generate!
     end
   end
 end
diff --git a/app/services/pdf_preview_service.rb b/app/services/pdf_preview_service.rb
new file mode 100644
index 000000000..dce368ea2
--- /dev/null
+++ b/app/services/pdf_preview_service.rb
@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+class PdfPreviewService
+  def initialize(blob, attached)
+    @blob = blob
+    @attached = attached
+  end
+
+  def generate!
+    preview_file = nil
+
+    @blob.open(tmpdir: tempdir) do |input|
+      work_dir = File.dirname(input.path)
+      preview_filename = "#{File.basename(input.path, '.*')}.pdf"
+      preview_file = File.join(work_dir, preview_filename)
+      Rails.logger.info "Starting preparing document preview for file #{@blob.filename.sanitized}..."
+
+      ActiveRecord::Base.transaction do
+        success = system(
+          'timeout',
+          Constants::PREVIEW_TIMEOUT_SECONDS.to_s,
+          libreoffice_path,
+          '--headless',
+          '--invisible',
+          '--convert-to',
+          'pdf', '--outdir',
+          work_dir, input.path
+        )
+        unless success && File.file?(preview_file)
+          raise StandardError, "There was an error generating PDF preview, blob id: #{@blob.id}"
+        end
+
+        ActiveRecord::Base.no_touching do
+          attached.attach(io: File.open(preview_file), filename: "#{@blob.filename.base}.pdf")
+        end
+        Rails.logger.info("Finished preparing PDF preview for file #{@blob.filename.sanitized}.")
+      end
+    end
+  ensure
+    File.delete(preview_file) if File.file?(preview_file)
+  end
+
+  private
+
+  def tempdir
+    Rails.root.join('tmp')
+  end
+
+  def libreoffice_path
+    ENV['LIBREOFFICE_PATH'] || 'soffice'
+  end
+end
diff --git a/config/initializers/constants.rb b/config/initializers/constants.rb
index bceb558de..4ebb75ae5 100644
--- a/config/initializers/constants.rb
+++ b/config/initializers/constants.rb
@@ -328,6 +328,9 @@ class Constants
 
   PREVIEWABLE_FILE_TYPES = TEXT_EXTRACT_FILE_TYPES
 
+  # default preview timeout to 15 minutes
+  PREVIEW_TIMEOUT_SECONDS = ENV['PREVIEW_TIMEOUT_SECONDS'] ? ENV['PREVIEW_TIMEOUT_SECONDS'].to_i : 900
+
   WHITELISTED_IMAGE_TYPES = [
     'gif', 'jpeg', 'pjpeg', 'png', 'x-png', 'svg+xml', 'bmp', 'tiff', 'jpg'
   ].freeze
diff --git a/lib/active_storage/previewer/libreoffice_previewer.rb b/lib/active_storage/previewer/libreoffice_previewer.rb
index 31752df28..334e7a765 100644
--- a/lib/active_storage/previewer/libreoffice_previewer.rb
+++ b/lib/active_storage/previewer/libreoffice_previewer.rb
@@ -22,7 +22,12 @@ module ActiveStorage
 
           begin
             success = system(
-              libreoffice_path, '--headless', '--invisible', '--convert-to', 'png', '--outdir', work_dir, input.path
+              'timeout',
+              Constants::PREVIEW_TIMEOUT_SECONDS.to_s,
+              libreoffice_path,
+              '--headless', '--invisible', '--convert-to', 'png', '--outdir',
+              work_dir,
+              input.path
             )
 
             unless success && File.file?(preview_file)

From e2c49c7e619378cb384c9b8306df823cf57ffac4 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Mon, 7 Oct 2024 14:45:04 +0200
Subject: [PATCH 34/96] Remove some empty in docx reports [SCI-11056]

---
 app/services/reports/docx/draw_experiment.rb  | 17 +++++-----
 app/services/reports/docx/draw_my_module.rb   | 26 ++++++++------
 .../reports/docx/draw_my_module_protocol.rb   |  1 -
 .../reports/docx/draw_result_comments.rb      |  5 +--
 .../reports/docx/draw_result_table.rb         |  2 +-
 app/services/reports/docx/draw_result_text.rb | 15 ++++----
 app/services/reports/docx/draw_step.rb        | 34 +++++++++----------
 app/services/reports/docx/draw_step_asset.rb  |  2 +-
 .../reports/docx/draw_step_checklist.rb       |  2 +-
 .../reports/docx/draw_step_comments.rb        |  5 +--
 app/services/reports/docx/draw_step_table.rb  |  2 +-
 app/services/reports/docx/draw_step_text.rb   | 16 +++++----
 12 files changed, 70 insertions(+), 57 deletions(-)

diff --git a/app/services/reports/docx/draw_experiment.rb b/app/services/reports/docx/draw_experiment.rb
index 50b55e347..ebe3ae7ca 100644
--- a/app/services/reports/docx/draw_experiment.rb
+++ b/app/services/reports/docx/draw_experiment.rb
@@ -15,14 +15,15 @@ module Reports::Docx::DrawExperiment
             link_style
     end
 
-    @docx.p do
-      unless settings['exclude_timestamps']
-        text I18n.t('projects.reports.elements.experiment.user_time',
-                    code: experiment.code, timestamp: I18n.l(experiment.created_at, format: :full)), color: color[:gray]
-      end
-      if experiment.archived?
-        text ' | '
-        text I18n.t('search.index.archived'), color: color[:gray]
+    if !settings['exclude_timestamps'] || experiment.archived?
+      @docx.p do
+        unless settings['exclude_timestamps']
+          text I18n.t('projects.reports.elements.experiment.user_time',
+                      code: experiment.code,
+                      timestamp: I18n.l(experiment.created_at, format: :full)), color: color[:gray]
+          text ' | ' if experiment.archived?
+        end
+        text I18n.t('search.index.archived'), color: color[:gray] if experiment.archived?
       end
     end
     html = custom_auto_link(experiment.description, team: @report_team)
diff --git a/app/services/reports/docx/draw_my_module.rb b/app/services/reports/docx/draw_my_module.rb
index 3f48772bc..bd859baab 100644
--- a/app/services/reports/docx/draw_my_module.rb
+++ b/app/services/reports/docx/draw_my_module.rb
@@ -16,14 +16,15 @@ module Reports::Docx::DrawMyModule
             link_style
     end
 
-    @docx.p do
-      unless settings['exclude_timestamps']
-        text I18n.t('projects.reports.elements.module.user_time', code: my_module.code,
-                    timestamp: I18n.l(my_module.created_at, format: :full)), color: color[:gray]
-      end
-      if my_module.archived?
-        text ' | '
-        text I18n.t('search.index.archived'), color: color[:gray]
+    if my_module.archived? || !settings['exclude_timestamps']
+      @docx.p do
+        unless settings['exclude_timestamps']
+          text I18n.t('projects.reports.elements.module.user_time', code: my_module.code,
+                      timestamp: I18n.l(my_module.created_at, format: :full)), color: color[:gray]
+          text ' | ' if my_module.archived?
+        end
+
+        text I18n.t('search.index.archived'), color: color[:gray] if my_module.archived?
       end
     end
 
@@ -74,10 +75,13 @@ module Reports::Docx::DrawMyModule
     filter_steps_for_report(my_module.protocol.steps, @settings).order(:position).each do |step|
       draw_step(step)
     end
-
-    draw_results(my_module) unless without_results
-
     @docx.p
+
+    unless without_results
+      draw_results(my_module)
+      @docx.p
+    end
+
     subject.children.active.each do |child|
       next if without_repositories && child.type_of == 'my_module_repository'
 
diff --git a/app/services/reports/docx/draw_my_module_protocol.rb b/app/services/reports/docx/draw_my_module_protocol.rb
index 9092b088d..0f3b56dbe 100644
--- a/app/services/reports/docx/draw_my_module_protocol.rb
+++ b/app/services/reports/docx/draw_my_module_protocol.rb
@@ -20,7 +20,6 @@ module Reports::Docx::DrawMyModuleProtocol
       Reports::HtmlToWordConverter.new(@docx, { scinote_url: @scinote_url,
                                                 link_style: @link_style }).html_to_word_converter(html)
       @docx.p
-      @docx.p
     end
   end
 end
diff --git a/app/services/reports/docx/draw_result_comments.rb b/app/services/reports/docx/draw_result_comments.rb
index 3fc68ef1f..ebec9ad13 100644
--- a/app/services/reports/docx/draw_result_comments.rb
+++ b/app/services/reports/docx/draw_result_comments.rb
@@ -8,8 +8,10 @@ module Reports::Docx::DrawResultComments
     @docx.p
     @docx.p I18n.t('projects.reports.elements.result_comments.name', result: result.name),
             bold: true, size: Constants::REPORT_DOCX_STEP_ELEMENTS_TITLE_SIZE
-    comments.each do |comment|
+    comments.find_each.with_index do |comment, index|
       comment_ts = comment.created_at
+
+      @docx.p unless index.zero?
       @docx.p I18n.t('projects.reports.elements.result_comments.comment_prefix',
                      user: comment.user.full_name,
                      date: I18n.l(comment_ts, format: :full_date),
@@ -17,7 +19,6 @@ module Reports::Docx::DrawResultComments
       html = custom_auto_link(comment.message, team: @report_team)
       Reports::HtmlToWordConverter.new(@docx, { scinote_url: @scinote_url,
                                                 link_style: @link_style }).html_to_word_converter(html)
-      @docx.p
     end
   end
 end
diff --git a/app/services/reports/docx/draw_result_table.rb b/app/services/reports/docx/draw_result_table.rb
index bd73c48e9..f919cc8a4 100644
--- a/app/services/reports/docx/draw_result_table.rb
+++ b/app/services/reports/docx/draw_result_table.rb
@@ -40,8 +40,8 @@ module Reports::Docx::DrawResultTable
     end
     @docx.p do
       text I18n.t 'projects.reports.elements.result_table.table_name', name: table.name
-      text ' '
       unless settings['exclude_timestamps']
+        text ' '
         text I18n.t('projects.reports.elements.result_table.user_time',
                     timestamp: I18n.l(timestamp, format: :full), user: result.user.full_name), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_result_text.rb b/app/services/reports/docx/draw_result_text.rb
index 252bf68d8..baf9bc9f3 100644
--- a/app/services/reports/docx/draw_result_text.rb
+++ b/app/services/reports/docx/draw_result_text.rb
@@ -6,12 +6,15 @@ module Reports::Docx::DrawResultText
     timestamp = element.created_at
     settings = @settings
     color = @color
-    @docx.p do
-      text result_text.name.presence || '', italic: true
-      text ' '
-      unless settings['exclude_timestamps']
-        text I18n.t('projects.reports.elements.result_text.user_time',
-                    timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+    if result_text.name.present? || !settings['exclude_timestamps']
+      @docx.p do
+        text result_text.name.to_s, italic: true
+        text ' ' if result_text.name.present?
+
+        unless settings['exclude_timestamps']
+          text I18n.t('projects.reports.elements.result_text.user_time',
+                      timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+        end
       end
     end
     html = custom_auto_link(result_text.text, team: @report_team)
diff --git a/app/services/reports/docx/draw_step.rb b/app/services/reports/docx/draw_step.rb
index 376911fc4..579a24c4e 100644
--- a/app/services/reports/docx/draw_step.rb
+++ b/app/services/reports/docx/draw_step.rb
@@ -11,21 +11,24 @@ module Reports::Docx::DrawStep
     @docx.h4(
       "#{I18n.t('projects.reports.elements.step.step_pos', pos: step.position_plus_one)} #{step.name}"
     )
-    @docx.p do
-      unless settings['exclude_task_metadata']
-        if step.completed
-          text I18n.t('protocols.steps.completed'), color: color[:green], bold: true
-        else
-          text I18n.t('protocols.steps.uncompleted'), color: color[:gray], bold: true
+
+    unless settings['exclude_task_metadata'] || settings['exclude_timestamps']
+      @docx.p do
+        unless settings['exclude_task_metadata']
+          if step.completed
+            text I18n.t('protocols.steps.completed'), color: color[:green], bold: true
+          else
+            text I18n.t('protocols.steps.uncompleted'), color: color[:gray], bold: true
+          end
+        end
+        unless settings['exclude_timestamps']
+          text ' | ' unless settings['exclude_task_metadata']
+          text I18n.t(
+            "projects.reports.elements.step.#{step_type_str}.user_time",
+            user: user.full_name,
+            timestamp: I18n.l(timestamp, format: :full)
+          ), color: color[:gray]
         end
-      end
-      unless settings['exclude_timestamps']
-        text ' | ' unless settings['exclude_task_metadata']
-        text I18n.t(
-          "projects.reports.elements.step.#{step_type_str}.user_time",
-          user: user.full_name,
-          timestamp: I18n.l(timestamp, format: :full)
-        ), color: color[:gray]
       end
     end
 
@@ -46,9 +49,6 @@ module Reports::Docx::DrawStep
     end
 
     draw_step_comments(step) if @settings.dig('task', 'protocol', 'step_comments')
-
-    @docx.p
-    @docx.p
   end
 
   def handle_step_table(table)
diff --git a/app/services/reports/docx/draw_step_asset.rb b/app/services/reports/docx/draw_step_asset.rb
index 14987e698..5b6569919 100644
--- a/app/services/reports/docx/draw_step_asset.rb
+++ b/app/services/reports/docx/draw_step_asset.rb
@@ -23,8 +23,8 @@ module Reports::Docx::DrawStepAsset
       link I18n.t('projects.reports.elements.download'), asset_url do
         italic true
       end
-      text ' '
       unless settings['exclude_timestamps']
+        text ' '
         text I18n.t('projects.reports.elements.step_asset.user_time',
                     timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_step_checklist.rb b/app/services/reports/docx/draw_step_checklist.rb
index ffd2f8192..5c510c9f9 100644
--- a/app/services/reports/docx/draw_step_checklist.rb
+++ b/app/services/reports/docx/draw_step_checklist.rb
@@ -16,8 +16,8 @@ module Reports::Docx::DrawStepChecklist
         team,
         I18n.t('projects.reports.elements.step_checklist.checklist_name', name: checklist.name)
       ).text, italic: true
-      text ' '
       unless settings['exclude_timestamps']
+        text ' '
         text I18n.t('projects.reports.elements.step_checklist.user_time',
                     timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_step_comments.rb b/app/services/reports/docx/draw_step_comments.rb
index 87d0abc5f..f9733eaeb 100644
--- a/app/services/reports/docx/draw_step_comments.rb
+++ b/app/services/reports/docx/draw_step_comments.rb
@@ -8,8 +8,10 @@ module Reports::Docx::DrawStepComments
     @docx.p
     @docx.p I18n.t('projects.reports.elements.step_comments.name', step: step.name),
             bold: true, size: Constants::REPORT_DOCX_STEP_ELEMENTS_TITLE_SIZE
-    comments.each do |comment|
+    comments.find_each.with_index do |comment, index|
       comment_ts = comment.created_at
+
+      @docx.p unless index.zero?
       @docx.p I18n.t('projects.reports.elements.step_comments.comment_prefix',
                      user: comment.user.full_name,
                      date: I18n.l(comment_ts, format: :full_date),
@@ -17,7 +19,6 @@ module Reports::Docx::DrawStepComments
       html = custom_auto_link(comment.message, team: @report_team)
       Reports::HtmlToWordConverter.new(@docx, { scinote_url: @scinote_url,
                                                 link_style: @link_style }).html_to_word_converter(html)
-      @docx.p
     end
   end
 end
diff --git a/app/services/reports/docx/draw_step_table.rb b/app/services/reports/docx/draw_step_table.rb
index f7c115691..3565c200e 100644
--- a/app/services/reports/docx/draw_step_table.rb
+++ b/app/services/reports/docx/draw_step_table.rb
@@ -39,8 +39,8 @@ module Reports::Docx::DrawStepTable
     end
     @docx.p do
       text I18n.t("projects.reports.elements.#{table_type}.table_name", name: table.name), italic: true
-      text ' '
       unless settings['exclude_timestamps']
+        text ' '
         text I18n.t("projects.reports.elements.#{table_type}.user_time",
                     timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
       end
diff --git a/app/services/reports/docx/draw_step_text.rb b/app/services/reports/docx/draw_step_text.rb
index 66f0ed84c..5fc364639 100644
--- a/app/services/reports/docx/draw_step_text.rb
+++ b/app/services/reports/docx/draw_step_text.rb
@@ -6,12 +6,16 @@ module Reports::Docx::DrawStepText
     timestamp = element.created_at
     color = @color
     settings = @settings
-    @docx.p do
-      text step_text.name.presence || '', italic: true
-      text ' '
-      unless settings['exclude_timestamps']
-        text I18n.t('projects.reports.elements.result_text.user_time',
-                    timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+
+    if step_text.name.present? || !settings['exclude_timestamps']
+      @docx.p do
+        text step_text.name.to_s, italic: true
+        text ' ' if step_text.name.present?
+
+        unless settings['exclude_timestamps']
+          text I18n.t('projects.reports.elements.result_text.user_time',
+                      timestamp: I18n.l(timestamp, format: :full)), color: color[:gray]
+        end
       end
     end
     if step_text.text.present?

From c902c22e41a5c60e2d3cec183a1e182c9c35c63e Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 8 Oct 2024 11:50:52 +0200
Subject: [PATCH 35/96] Enable file versioning for WOPI [SCI-11049]

---
 app/controllers/wopi_controller.rb | 2 --
 app/models/asset.rb                | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/app/controllers/wopi_controller.rb b/app/controllers/wopi_controller.rb
index 6dbe4051e..a34b01d27 100644
--- a/app/controllers/wopi_controller.rb
+++ b/app/controllers/wopi_controller.rb
@@ -200,7 +200,6 @@ class WopiController < ActionController::Base
         if @asset.lock == lock
           logger.warn 'WOPI: replacing file'
 
-          @team.release_space(@asset.estimated_size)
           @asset.last_modified_by = @user
           @asset.update_contents(request.body)
           @asset.save
@@ -220,7 +219,6 @@ class WopiController < ActionController::Base
       elsif !@asset.file_size.nil? && @asset.file_size.zero?
         logger.warn 'WOPI: initializing empty file'
 
-        @team.release_space(@asset.estimated_size)
         @asset.update_contents(request.body)
         @asset.last_modified_by = @user
         @asset.save
diff --git a/app/models/asset.rb b/app/models/asset.rb
index 9e0745642..157593fac 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -342,7 +342,7 @@ class Asset < ApplicationRecord
   end
 
   def update_contents(new_file)
-    file.attach(io: new_file, filename: file_name)
+    file.attach_file_version(io: new_file, filename: file_name)
     self.version = version.nil? ? 1 : version + 1
     save
   end

From fb94790743f7db502a4a0232d97df9898f520c89 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 8 Oct 2024 12:50:07 +0200
Subject: [PATCH 36/96] Fix file versioning for WOPI [SCI-11049]

---
 app/models/asset.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/asset.rb b/app/models/asset.rb
index 157593fac..5a9085cda 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -342,7 +342,7 @@ class Asset < ApplicationRecord
   end
 
   def update_contents(new_file)
-    file.attach_file_version(io: new_file, filename: file_name)
+    attach_file_version(io: new_file, filename: file_name)
     self.version = version.nil? ? 1 : version + 1
     save
   end

From 100c84732d26b9e1821a2e60e5d8f4ae4c01aeb0 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 8 Oct 2024 13:27:17 +0200
Subject: [PATCH 37/96] Fix WOPI file creation [SCI-11049]

---
 app/controllers/assets_controller.rb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index dfa46e7fe..52a5292a0 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -244,8 +244,7 @@ class AssetsController < ApplicationController
     asset = Asset.new(created_by: current_user, team: current_team)
     asset.attach_file_version(io: StringIO.new,
                               filename: "#{params[:file_name]}.#{params[:file_type]}",
-                              content_type: wopi_content_type(params[:file_type]),
-                              current_user: current_user)
+                              content_type: wopi_content_type(params[:file_type]))
 
     unless asset.valid?(:wopi_file_creation)
       render json: {

From c71366acc57dd86371135d831903e4b3881c7d52 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Mon, 14 Oct 2024 10:20:43 +0200
Subject: [PATCH 38/96] Update notifications flyout [SCI-10735]

---
 .../stylesheets/navigation/notifications.scss |  2 +-
 .../user_notifications_controller.rb          | 25 ++++++--
 .../notifications/notification_item.vue       | 50 +++++++++++-----
 .../notifications/notifications_flyout.vue    | 59 ++++++++++++++++++-
 app/javascript/vue/navigation/top_menu.vue    | 12 ++--
 app/serializers/notification_serializer.rb    |  5 +-
 app/views/shared/navigation/_top.html.erb     |  1 +
 config/locales/en.yml                         |  3 +
 config/routes.rb                              |  4 ++
 9 files changed, 132 insertions(+), 29 deletions(-)

diff --git a/app/assets/stylesheets/navigation/notifications.scss b/app/assets/stylesheets/navigation/notifications.scss
index 688a94995..c7049d6ef 100644
--- a/app/assets/stylesheets/navigation/notifications.scss
+++ b/app/assets/stylesheets/navigation/notifications.scss
@@ -30,7 +30,7 @@
     flex-direction: column;
     height: calc(100vh - 8rem);
     padding: 1.5rem;
-    width: 400px;
+    width: 600px;
 
   .sci--navigation--notificaitons-flyout-title {
     @include font-h2;
diff --git a/app/controllers/user_notifications_controller.rb b/app/controllers/user_notifications_controller.rb
index ca05c3bbc..0f1ffa0eb 100644
--- a/app/controllers/user_notifications_controller.rb
+++ b/app/controllers/user_notifications_controller.rb
@@ -5,11 +5,18 @@ class UserNotificationsController < ApplicationController
 
   def index
     page = (params.dig(:page, :number) || 1).to_i
-    notifications = load_notifications.page(page).per(Constants::INFINITE_SCROLL_LIMIT)
+    notifications = load_notifications
+
+    case params[:tab]
+    when 'all'
+      notifications = notifications.where.not(read_at: nil)
+    when 'unread'
+      notifications = notifications.where(read_at: nil)
+    end
+
+    notifications = notifications.page(page).per(Constants::INFINITE_SCROLL_LIMIT)
 
     render json: notifications, each_serializer: NotificationSerializer
-
-    notifications.mark_as_read!
   end
 
   def unseen_counter
@@ -18,6 +25,17 @@ class UserNotificationsController < ApplicationController
     }
   end
 
+  def mark_all_read
+    load_notifications.mark_as_read!
+    render json: { success: true }
+  end
+
+  def toggle_read
+    notification = current_user.notifications.find(params[:id])
+    notification.update(read_at: (params[:mark_as_read] ? DateTime.now : nil))
+    render json: notification, serializer: NotificationSerializer
+  end
+
   private
 
   def load_notifications
@@ -25,5 +43,4 @@ class UserNotificationsController < ApplicationController
                 .in_app
                 .order(created_at: :desc)
   end
-
 end
diff --git a/app/javascript/vue/navigation/notifications/notification_item.vue b/app/javascript/vue/navigation/notifications/notification_item.vue
index b187636f1..1b33f05d8 100644
--- a/app/javascript/vue/navigation/notifications/notification_item.vue
+++ b/app/javascript/vue/navigation/notifications/notification_item.vue
@@ -1,12 +1,20 @@
 <template>
   <div class="sci-navigation--notificaitons-flyout-notification">
-    <div class="sci-navigation--notificaitons-flyout-notification-date">
-      {{ notification.attributes.created_at }}
+    <div class="flex item-center">
+      <div class="sci-navigation--notificaitons-flyout-notification-date">
+        {{ notification.attributes.created_at }}
+      </div>
+      <div class="ml-auto cursor-pointer" @click="toggleRead()">
+        <div v-if="!notification.attributes.checked" class="w-2.5 h-2.5 bg-sn-coral rounded-full cursor-pointer"></div>
+        <div v-else class="w-2.5 h-2.5 border-2 border-sn-grey rounded-full border-solid cursor-pointer"></div>
+      </div>
     </div>
-    <div class="sci-navigation--notificaitons-flyout-notification-title"
-         v-html="notification.attributes.title"
-         :data-seen="notification.attributes.checked"></div>
-    <div v-html="notification.attributes.message" class="sci-navigation--notificaitons-flyout-notification-message"></div>
+    <a :href="lastBreadcrumbUrl" @click="toggleRead(true)" class="hover:no-underline text-black hover:text-black">
+      <div class="sci-navigation--notificaitons-flyout-notification-title"
+          v-html="notification.attributes.title"
+          :data-seen="notification.attributes.checked"></div>
+      <div v-html="notification.attributes.message" class="sci-navigation--notificaitons-flyout-notification-message"></div>
+    </a>
     <div v-if="notification.attributes.breadcrumbs" class="flex items-center flex-wrap gap-0.5">
       <template v-for="(breadcrumb, index) in notification.attributes.breadcrumbs" :key="index">
         <div class="flex items-center gap-0.5">
@@ -19,23 +27,33 @@
 </template>
 
 <script>
+import axios from '../../../packs/custom_axios.js';
+
 export default {
   name: 'NotificationItem',
   props: {
     notification: Object
   },
   computed: {
-    icon() {
-      switch (this.notification.attributes.type_of) {
-        case 'deliver':
-          return 'fas fa-truck';
-        case 'assignment':
-          return 'fas fa-list-alt';
-        case 'recent_changes':
-          return 'fas fa-list-alt';
-        case 'deliver_error':
-          return 'sn-icon sn-icon-alert-warning';
+    lastBreadcrumbUrl() {
+      if (!this.notification.attributes.breadcrumbs) {
+        return null;
       }
+      return this.notification.attributes.breadcrumbs[this.notification.attributes.breadcrumbs.length - 1]?.url;
+    }
+  },
+  methods: {
+    toggleRead(check = false) {
+      const params = {};
+      if (!this.notification.attributes.checked || check) {
+        params.mark_as_read = true;
+      }
+
+      axios.post(this.notification.attributes.toggle_read_url, params)
+        .then((response) => {
+          const notification = response.data.data;
+          this.$emit('updateNotification', notification);
+        });
     }
   }
 };
diff --git a/app/javascript/vue/navigation/notifications/notifications_flyout.vue b/app/javascript/vue/navigation/notifications/notifications_flyout.vue
index 7b8a4e40f..8f21e3c0d 100644
--- a/app/javascript/vue/navigation/notifications/notifications_flyout.vue
+++ b/app/javascript/vue/navigation/notifications/notifications_flyout.vue
@@ -6,17 +6,45 @@
         {{ i18n.t('nav.settings') }}
       </a>
     </div>
-    <hr>
+    <div class="flex items-center">
+      <div
+        @click="changeTab('all')"
+        class="px-4 py-2 text-sn-grey cursor-pointer border-solid border-0 border-b-4 border-transparent"
+        :class="{'!text-sn-black border-sn-blue': activeTab === 'all'}"
+      >
+        {{ i18n.t('nav.notifications.all') }}
+      </div>
+      <div
+        @click="changeTab('unread')"
+        class="px-4 py-2 text-sn-grey cursor-pointer border-solid border-0 border-b-4 border-transparent"
+        :class="{'!text-sn-black border-sn-blue': activeTab === 'unread'}"
+      >
+        {{ i18n.t('nav.notifications.unread') }}
+      </div>
+      <div
+        @click="changeTab('read')"
+        class="px-4 py-2 text-sn-grey cursor-pointer border-solid border-0 border-b-4 border-transparent"
+        :class="{'!text-sn-black  border-sn-blue': activeTab === 'read'}"
+      >
+      {{ i18n.t('nav.notifications.read') }}
+      </div>
+      <div class="py-4 ml-auto cursor-pointer" @click="markAllNotificationsAsRead">
+        {{ i18n.t('nav.notifications.read_all') }}
+      </div>
+    </div>
+    <hr class="!mt-0.5">
     <perfect-scrollbar @wheel="preventPropagation" ref="scrollContainer" class="sci--navigation--notificaitons-flyout-notifications">
       <div class="sci-navigation--notificaitons-flyout-subtitle" v-if="todayNotifications.length">
         {{ i18n.t('nav.notifications.today') }}
       </div>
       <NotificationItem v-for="notification in todayNotifications" :key="notification.type_of + '-' + notification.id"
+        @updateNotification="updateNotification"
         :notification="notification" />
       <div class="sci-navigation--notificaitons-flyout-subtitle" v-if="olderNotifications.length">
         {{ i18n.t('nav.notifications.older') }}
       </div>
       <NotificationItem v-for="notification in olderNotifications" :key="notification.type_of + '-' + notification.id"
+        @updateNotification="updateNotification"
         :notification="notification" />
       <div class="next-page-loader">
         <img src="/images/medium/loading.svg" v-if="loadingPage" />
@@ -37,6 +65,7 @@ export default {
   },
   props: {
     notificationsUrl: String,
+    markAllNotificationsUrl: String,
     unseenNotificationsCount: Number,
     preferencesUrl: String
   },
@@ -45,11 +74,14 @@ export default {
       notifications: [],
       nextPageUrl: null,
       scrollBar: null,
-      loadingPage: false
+      activeTab: 'all',
+      loadingPage: false,
+      firstPageUrl: null
     };
   },
   created() {
     this.nextPageUrl = this.notificationsUrl;
+    this.firstPageUrl = this.notificationsUrl;
     this.loadNotifications();
   },
   mounted() {
@@ -76,6 +108,27 @@ export default {
     }
   },
   methods: {
+    changeTab(tab) {
+      this.activeTab = tab;
+      this.notifications = [];
+      this.nextPageUrl = this.firstPageUrl;
+      this.loadNotifications();
+    },
+    markAllNotificationsAsRead() {
+      axios.post(this.markAllNotificationsUrl)
+        .then(() => {
+          this.notifications = this.notifications.map((n) => {
+            n.attributes.checked = true;
+            return n;
+          });
+          this.$emit('update:unseenNotificationsCount');
+        });
+    },
+    updateNotification(notification) {
+      const index = this.notifications.findIndex((n) => n.id === notification.id);
+      this.notifications.splice(index, 1, notification);
+      this.$emit('update:unseenNotificationsCount');
+    },
     preventPropagation(e) {
       e.stopPropagation();
       e.preventDefault();
@@ -85,7 +138,7 @@ export default {
 
       this.loadingPage = true;
 
-      axios.get(this.nextPageUrl)
+      axios.get(this.nextPageUrl, { params: { tab: this.activeTab } })
         .then((response) => {
           this.notifications = this.notifications.concat(response.data.data);
           this.nextPageUrl = response.data.links.next;
diff --git a/app/javascript/vue/navigation/top_menu.vue b/app/javascript/vue/navigation/top_menu.vue
index 77d92fcde..516794eb8 100644
--- a/app/javascript/vue/navigation/top_menu.vue
+++ b/app/javascript/vue/navigation/top_menu.vue
@@ -45,8 +45,9 @@
         <NotificationsFlyout
           :preferencesUrl="user.preferences_url"
           :notificationsUrl="notificationsUrl"
+          :markAllNotificationsUrl="markAllNotificationsUrl"
           :unseenNotificationsCount="unseenNotificationsCount"
-          @update:unseenNotificationsCount="checkUnseenNotifications()"
+          @update:unseenNotificationsCount="checkUnseenNotifications(false)"
           @close="$refs.notificationDropdown.$refs.field.click();"/>
       </template>
     </GeneralDropdown>
@@ -92,6 +93,7 @@ export default {
   props: {
     url: String,
     notificationsUrl: String,
+    markAllNotificationsUrl: String,
     unseenNotificationsUrl: String,
     quickSearchUrl: String,
     teamsUrl: String,
@@ -119,7 +121,7 @@ export default {
 
     $(document).on('turbolinks:load', () => {
       this.notificationsOpened = false;
-      this.checkUnseenNotifications();
+      this.checkUnseenNotifications(false);
       this.refreshCurrentTeam();
       this.hideSearch = !!document.getElementById('GlobalSearch');
       this.globalSearchKey += 1;
@@ -177,11 +179,13 @@ export default {
     searchValue(e) {
       window.open(`${this.searchUrl}?q=${e.target.value}`, '_self');
     },
-    checkUnseenNotifications() {
+    checkUnseenNotifications(repeat = true) {
       clearTimeout(this.unseenNotificationsTimeout);
       $.get(this.unseenNotificationsUrl, (result) => {
         this.unseenNotificationsCount = result.unseen;
-        this.unseenNotificationsTimeout = setTimeout(this.checkUnseenNotifications, 30000);
+        if (repeat) {
+          this.unseenNotificationsTimeout = setTimeout(this.checkUnseenNotifications, 30000);
+        }
       });
     },
     refreshCurrentTeam() {
diff --git a/app/serializers/notification_serializer.rb b/app/serializers/notification_serializer.rb
index ebb8ef838..75244c379 100644
--- a/app/serializers/notification_serializer.rb
+++ b/app/serializers/notification_serializer.rb
@@ -4,7 +4,7 @@ class NotificationSerializer < ActiveModel::Serializer
   include Rails.application.routes.url_helpers
   include BreadcrumbsHelper
 
-  attributes :id, :title, :message, :created_at, :read_at, :type, :breadcrumbs, :checked, :today
+  attributes :id, :title, :message, :created_at, :read_at, :type, :breadcrumbs, :checked, :today, :toggle_read_url
 
   def title
     object.to_notification.title
@@ -31,4 +31,7 @@ class NotificationSerializer < ActiveModel::Serializer
     object.read_at.present?
   end
 
+  def toggle_read_url
+    toggle_read_user_notification_path(object)
+  end
 end
diff --git a/app/views/shared/navigation/_top.html.erb b/app/views/shared/navigation/_top.html.erb
index 382300e8d..2a670e52f 100644
--- a/app/views/shared/navigation/_top.html.erb
+++ b/app/views/shared/navigation/_top.html.erb
@@ -3,6 +3,7 @@
     <top-menu-container
       url="<%= top_menu_navigations_path %>"
       notifications-url="<%= user_notifications_path %>"
+      mark-all-notifications-url="<%= mark_all_read_user_notifications_path %>"
       quick-search-url="<%= quick_search_path %>"
       unseen-notifications-url="<%= unseen_counter_user_notifications_path %>"
       teams-url="<%= visible_teams_teams_path %>"
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 33393ab12..362b1e56f 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -310,6 +310,9 @@ en:
     academy_tooltip: "SciNote Academy"
     notifications:
       title: "Notifications"
+      read: "Read"
+      unread: "Unread"
+      read_all: "Read all"
       all: "All"
       message: "Messages"
       system: "System"
diff --git a/config/routes.rb b/config/routes.rb
index fdadab610..0fdc7fe93 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -168,6 +168,10 @@ Rails.application.routes.draw do
       collection do
         get :filter_groups
         get :unseen_counter
+        post :mark_all_read
+      end
+      member do
+        post :toggle_read
       end
     end
 

From 262ae9c2c07b3d89d58c1fa9212acd07f2981b80 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Mon, 14 Oct 2024 13:45:39 +0200
Subject: [PATCH 39/96] Add activities for asset restore [SCI-11157]

---
 app/controllers/assets_controller.rb    | 37 +++++++++++++++++++++++++
 config/initializers/extends.rb          | 14 ++++++----
 config/locales/global_activities/en.yml |  8 ++++++
 3 files changed, 54 insertions(+), 5 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 52a5292a0..4fe1988dc 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -416,6 +416,33 @@ class AssetsController < ApplicationController
     render_403 unless VersionedAttachments.enabled?
 
     @asset.restore_file_version(params[:version].to_i)
+
+    message_items = {
+      version: params[:version].to_i,
+      file: @asset.file_name
+    }
+
+    case @asset.parent
+    when Step
+      if @asset.parent.protocol.in_module?
+        message_items.merge!({ my_module: @assoc.protocol.my_module.id, step: @asset.parent.id })
+        log_restore_activity(:task_step_restore_asset_version, @assoc.protocol,
+                             @assoc.protocol.team, @assoc.my_module&.project, message_items)
+      else
+        message_items.merge!({ protocol: @assoc.protocol.id, step: @asset.parent.id })
+        log_restore_activity(:protocol_step_restore_asset_version, @assoc.protocol,
+                             @assoc.protocol.team, nil, message_items)
+      end
+    when Result
+      message_items.merge!({ result: @assoc.id, my_module: @assoc.my_module.id })
+      log_restore_activity(:task_result_restore_asset_version, @assoc,
+                           @assoc.my_module.team, @assoc.my_module.project, message_items)
+    when RepositoryCell
+      message_items.merge!({ repository_column: @assoc.repository_column.id, repository: @repository.id })
+      log_restore_activity(:repository_column_restore_asset_version, @repository,
+                           @repository.team, nil, message_items)
+    end
+
     render json: @asset.file.blob
   end
 
@@ -494,4 +521,14 @@ class AssetsController < ApplicationController
               result: result.id
             }.merge(message_items))
   end
+
+  def log_restore_activity(type_of, subject, team, project = nil, message_items = {})
+    Activities::CreateActivityService
+      .call(activity_type: type_of,
+            owner: current_user,
+            subject: subject,
+            team: team,
+            project: project,
+            message_items: message_items)
+  end
 end
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index 8a4a4b76c..e891e9749 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -516,25 +516,29 @@ class Extends
     storage_location_repository_row_created: 323,
     storage_location_repository_row_deleted: 324,
     storage_location_repository_row_moved: 325,
-    container_storage_location_imported: 326
+    container_storage_location_imported: 326,
+    task_step_restore_asset_version: 327,
+    task_result_restore_asset_version: 328,
+    repository_column_restore_asset_version: 329,
+    protocol_step_restore_asset_version: 330
   }
 
   ACTIVITY_GROUPS = {
     projects: [*0..7, 32, 33, 34, 95, 108, 65, 109, *158..162, 241, 242, 243],
-    task_results: [23, 26, 25, 42, 24, 40, 41, 99, 110, 122, 116, 128, *246..248, *257..273, *284..291, 301, 303, 306],
+    task_results: [23, 26, 25, 42, 24, 40, 41, 99, 110, 122, 116, 128, *246..248, *257..273, *284..291, 301, 303, 306, 328],
     task: [8, 58, 9, 59, *10..14, 35, 36, 37, 53, 54, *60..63, 138, 139, 140, 64, 66, 106, 126, 120, 132,
            148, 166],
     task_protocol: [15, 22, 16, 18, 19, 20, 21, 17, 38, 39, 100, 111, 45, 46, 47, 121, 124, 115, 118, 127, 130, 137,
-                    184, 185, 188, 189, *192..203, 221, 222, 224, 225, 226, 236, *249..252, *274..278, 299, 302, 305],
+                    184, 185, 188, 189, *192..203, 221, 222, 224, 225, 226, 236, *249..252, *274..278, 299, 302, 305, 327],
     task_inventory: [55, 56, 146, 147, 183],
     experiment: [*27..31, 57, 141, 165],
     reports: [48, 50, 49, 163, 164],
     inventories: [70, 71, 105, 144, 145, 72, 73, 74, 102, 142, 143, 75, 76, 77,
-                  78, 96, 107, 113, 114, *133..136, 180, 181, 182, *292..298, 308],
+                  78, 96, 107, 113, 114, *133..136, 180, 181, 182, *292..298, 308, 329],
     protocol_repository: [80, 103, 89, 87, 79, 90, 91, 88, 85, 86, 84, 81, 82,
                           83, 101, 112, 123, 125, 117, 119, 129, 131, 187, 186,
                           190, 191, *204..215, 220, 223, 227, 228, 229, *230..235,
-                          *237..240, *253..256, *279..283, 300, 304, 307],
+                          *237..240, *253..256, *279..283, 300, 304, 307, 330],
     team: [92, 94, 93, 97, 104, 244, 245],
     label_templates: [*216..219],
     storage_locations: [*309..315],
diff --git a/config/locales/global_activities/en.yml b/config/locales/global_activities/en.yml
index 6d1a470a1..02b98c683 100644
--- a/config/locales/global_activities/en.yml
+++ b/config/locales/global_activities/en.yml
@@ -340,6 +340,10 @@ en:
       storage_location_repository_row_deleted_html: "%{user} unassigned %{repository_row} from box %{storage_location} %{position}."
       storage_location_repository_row_moved_html: "%{user} moved item %{repository_row} from box %{storage_location_original} %{positions} to box %{storage_location_destination} %{positions}."
       container_storage_location_imported_html: "%{user} assigned %{assigned_count} item(s) and unassigned %{unassigned_count} item(s) by import to %{storage_location}."
+      task_step_restore_asset_version_html: "%{user} restored version <strong>%{version}</strong> of the file <strong>%{file}</strong> on protocol's step <strong>%{step}</strong> on task %{my_module}."
+      task_result_restore_asset_version_html: "%{user} restored version <strong>%{version}</strong> of the file <strong>%{file}</strong> on result %{result} on task %{my_module}."
+      repository_column_restore_asset_version_html: "%{user} restored version <strong>%{version}</strong> of the file <strong>%{file}</strong> in inventory column %{repository_column} in inventory %{repository}."
+      protocol_step_restore_asset_version_html: "%{user} restored version <strong>%{version}</strong> of the file <strong>%{file}</strong> on Protocol's Template %{protocol} step <strong>%{step}</strong> in Protocol repository."
     activity_name:
       create_project: "Project created"
       rename_project: "Project renamed"
@@ -637,6 +641,10 @@ en:
       storage_location_repository_row_deleted: "Inventory item location unassigned"
       storage_location_repository_row_moved: "Inventory item location moved"
       container_storage_location_imported: "Box import"
+      task_step_restore_asset_version: "Task step file version restored"
+      task_result_restore_asset_version: "Result file version restored"
+      repository_column_restore_asset_version: "Inventroy item file version restored"
+      protocol_step_restore_asset_version: "Protocol step file version restored"
     activity_group:
       projects: "Projects"
       task_results: "Task results"

From 50d2bf53dc61b9f5d8e13f07d51d323a13684ff1 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Mon, 14 Oct 2024 13:56:55 +0200
Subject: [PATCH 40/96] Add restore asset permission [SCI-11169]

---
 app/controllers/assets_controller.rb | 7 ++++++-
 app/permissions/asset.rb             | 4 ++++
 app/serializers/asset_serializer.rb  | 2 +-
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 4fe1988dc..47d92e5f7 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -18,7 +18,8 @@ class AssetsController < ApplicationController
 
   before_action :load_vars, except: :create_wopi_file
   before_action :check_read_permission, except: %i(edit destroy duplicate create_wopi_file toggle_view_mode)
-  before_action :check_manage_permission, only: %i(edit destroy duplicate rename toggle_view_mode restore_version)
+  before_action :check_manage_permission, only: %i(edit destroy duplicate rename toggle_view_mode)
+  before_action :check_restore_permission, only: :restore_version
 
   def file_preview
     editable = can_manage_asset?(@asset) && (@asset.repository_asset_value.blank? ||
@@ -475,6 +476,10 @@ class AssetsController < ApplicationController
     render_403 and return unless can_manage_asset?(@asset)
   end
 
+  def check_restore_permission
+    render_403 and return unless can_restore_asset?(@asset)
+  end
+
   def append_wd_params(url)
     exclude_params = %w(wdPreviousSession wdPreviousCorrelation)
     wd_params = params.as_json.select { |key, _value| key[/^wd.*/] && !(exclude_params.include? key) }.to_query
diff --git a/app/permissions/asset.rb b/app/permissions/asset.rb
index bd6acb444..4349fdfe5 100644
--- a/app/permissions/asset.rb
+++ b/app/permissions/asset.rb
@@ -32,6 +32,10 @@ Canaid::Permissions.register_for(Asset) do
     end
   end
 
+  can :restore_asset do |user, asset|
+    VersionedAttachments.enabled? && can_manage_asset?(user, asset)
+  end
+
   can :open_asset_locally do |_user, asset|
     ENV['ASSET_SYNC_URL'].present?
   end
diff --git a/app/serializers/asset_serializer.rb b/app/serializers/asset_serializer.rb
index 53c31236d..d3408bf93 100644
--- a/app/serializers/asset_serializer.rb
+++ b/app/serializers/asset_serializer.rb
@@ -156,7 +156,7 @@ class AssetSerializer < ActiveModel::Serializer
       )
     end
 
-    urls[:restore_version] = asset_restore_version_path(object) if VersionedAttachments.enabled?
+    urls[:restore_version] = asset_restore_version_path(object) if can_restore_asset?(user, object)
     urls[:open_vector_editor_edit] = edit_gene_sequence_asset_path(object.id) if can_manage_asset?(user, object)
 
     if can_manage_asset?(user, object) && can_open_asset_locally?(user, object)

From adcc401a79f5d8fc29f2cc348f9a5a0cf61d76e4 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Mon, 14 Oct 2024 14:38:50 +0200
Subject: [PATCH 41/96] Add collapsable breadcrumbs component [SCI-11184]

---
 .../user_notifications_controller.rb          |  2 +-
 .../packs/vue/design_system/breadcrumbs.js    | 22 +++++
 .../notifications/notification_item.vue       | 11 +--
 app/javascript/vue/shared/breadcrumbs.vue     | 93 +++++++++++++++++++
 .../design_elements/_breadcrumbs.html.erb     |  8 ++
 app/views/design_elements/index.html.erb      |  2 +
 config/webpack/webpack.config.js              |  1 +
 7 files changed, 132 insertions(+), 7 deletions(-)
 create mode 100644 app/javascript/packs/vue/design_system/breadcrumbs.js
 create mode 100644 app/javascript/vue/shared/breadcrumbs.vue
 create mode 100644 app/views/design_elements/_breadcrumbs.html.erb

diff --git a/app/controllers/user_notifications_controller.rb b/app/controllers/user_notifications_controller.rb
index 0f1ffa0eb..127d35289 100644
--- a/app/controllers/user_notifications_controller.rb
+++ b/app/controllers/user_notifications_controller.rb
@@ -8,7 +8,7 @@ class UserNotificationsController < ApplicationController
     notifications = load_notifications
 
     case params[:tab]
-    when 'all'
+    when 'read'
       notifications = notifications.where.not(read_at: nil)
     when 'unread'
       notifications = notifications.where(read_at: nil)
diff --git a/app/javascript/packs/vue/design_system/breadcrumbs.js b/app/javascript/packs/vue/design_system/breadcrumbs.js
new file mode 100644
index 000000000..207ba469a
--- /dev/null
+++ b/app/javascript/packs/vue/design_system/breadcrumbs.js
@@ -0,0 +1,22 @@
+import { createApp } from 'vue/dist/vue.esm-bundler.js';
+import Breadcrumbs from '../../../vue/shared/breadcrumbs.vue';
+import { mountWithTurbolinks } from '../helpers/turbolinks.js';
+
+const app = createApp({
+  computed: {
+    breadcrumbs() {
+      return [
+        { name: 'Home', url: '/' },
+        { name: 'Very very very long name ', url: '' },
+        { name: 'Data', url: '' },
+        { name: 'Very very very very very very very very very very long name ', url: '' },
+        { name: 'Very very very very very very very  long name ', url: '' },
+        { name: 'Very very very very very long name ', url: '' },
+        { name: 'Very very very very long name ', url: '' }
+      ];
+    }
+  }
+});
+app.component('Breadcrumbs', Breadcrumbs);
+app.config.globalProperties.i18n = window.I18n;
+mountWithTurbolinks(app, '#breadcrumbs');
diff --git a/app/javascript/vue/navigation/notifications/notification_item.vue b/app/javascript/vue/navigation/notifications/notification_item.vue
index 1b33f05d8..9ab899648 100644
--- a/app/javascript/vue/navigation/notifications/notification_item.vue
+++ b/app/javascript/vue/navigation/notifications/notification_item.vue
@@ -16,24 +16,23 @@
       <div v-html="notification.attributes.message" class="sci-navigation--notificaitons-flyout-notification-message"></div>
     </a>
     <div v-if="notification.attributes.breadcrumbs" class="flex items-center flex-wrap gap-0.5">
-      <template v-for="(breadcrumb, index) in notification.attributes.breadcrumbs" :key="index">
-        <div class="flex items-center gap-0.5">
-          <i v-if="index > 0" class="sn-icon sn-icon-right"></i>
-          <a :href="breadcrumb.url" :title="breadcrumb.name" class="truncate max-w-[20ch] inline-block">{{ breadcrumb.name }}</a>
-        </div>
-      </template>
+      <Breadcrumbs :breadcrumbs="notification.attributes.breadcrumbs" />
     </div>
   </div>
 </template>
 
 <script>
 import axios from '../../../packs/custom_axios.js';
+import Breadcrumbs from '../../shared/breadcrumbs.vue';
 
 export default {
   name: 'NotificationItem',
   props: {
     notification: Object
   },
+  components: {
+    Breadcrumbs
+  },
   computed: {
     lastBreadcrumbUrl() {
       if (!this.notification.attributes.breadcrumbs) {
diff --git a/app/javascript/vue/shared/breadcrumbs.vue b/app/javascript/vue/shared/breadcrumbs.vue
new file mode 100644
index 000000000..ff58fd6bd
--- /dev/null
+++ b/app/javascript/vue/shared/breadcrumbs.vue
@@ -0,0 +1,93 @@
+<template>
+  <div ref="container" class="w-full flex items-center flex-wrap gap-0.5">
+    <template v-if="!allVisible">
+      <div class="flex items-center gap-0.5">
+        <a :href="breadcrumbs[0].url" :title="breadcrumbs[0].name" class="max-w-[200px]">
+          <StringWithEllipsis class="w-full" :text="breadcrumbs[0].name"></StringWithEllipsis>
+        </a>
+      </div>
+      <div class="flex items-center gap-0.5">
+        <i class="sn-icon sn-icon-right text-sn-grey"></i>
+        <GeneralDropdown>
+          <template v-slot:field>
+            <a>...</a>
+          </template>
+          <template v-slot:flyout>
+            <div class="max-w-[600px]">
+              <div v-for="(breadcrumb, index) in hiddenBreadcrumbs" :key="index" class="p-2 hover:bg-sn-super-light-grey cursor-pointer">
+                <a :href="breadcrumb.url" :title="breadcrumb.name" class="max-w-[200px] hover:no-underline">
+                  <StringWithEllipsis class="w-full" :text="breadcrumb.name"></StringWithEllipsis>
+                </a>
+              </div>
+            </div>
+          </template>
+        </GeneralDropdown>
+        <i class="sn-icon sn-icon-right text-sn-grey"></i>
+      </div>
+    </template>
+    <div v-for="(breadcrumb, index) in visibleBreadcrumbs" :key="index" class="flex items-center gap-0.5">
+      <i v-if="index > 0" class="sn-icon sn-icon-right text-sn-grey"></i>
+      <a :href="breadcrumb.url" :title="breadcrumb.name" class="max-w-[200px]">
+        <StringWithEllipsis class="w-full" :text="breadcrumb.name"></StringWithEllipsis>
+      </a>
+    </div>
+  </div>
+</template>
+
+<script>
+import StringWithEllipsis from './string_with_ellipsis.vue';
+import GeneralDropdown from './general_dropdown.vue';
+
+export default {
+  name: 'Breadcrumbs',
+  props: {
+    breadcrumbs: {
+      type: Array,
+      required: true
+    }
+  },
+  components: {
+    StringWithEllipsis,
+    GeneralDropdown
+  },
+  data() {
+    return {
+      containerSize: 0,
+      breadcrumbSize: 200
+    };
+  },
+  computed: {
+    breadcrumbsVisibleCount() {
+      const size = Math.floor(this.containerSize / this.breadcrumbSize);
+      if (size < 2) {
+        return 2;
+      }
+      return size;
+    },
+    allVisible() {
+      return this.breadcrumbs.length <= this.breadcrumbsVisibleCount;
+    },
+    hiddenBreadcrumbs() {
+      return this.breadcrumbs.slice(1, this.breadcrumbs.length - this.breadcrumbsVisibleCount + 1);
+    },
+    visibleBreadcrumbs() {
+      if (this.allVisible) {
+        return this.breadcrumbs;
+      }
+      return this.breadcrumbs.slice(this.breadcrumbs.length - this.breadcrumbsVisibleCount + 1);
+    }
+  },
+  mounted() {
+    this.setContainerSize();
+    window.addEventListener('resize', this.setContainerSize);
+  },
+  beforeDestroy() {
+    window.removeEventListener('resize', this.setContainerSize);
+  },
+  methods: {
+    setContainerSize() {
+      this.containerSize = this.$refs.container.offsetWidth;
+    }
+  }
+};
+</script>;
diff --git a/app/views/design_elements/_breadcrumbs.html.erb b/app/views/design_elements/_breadcrumbs.html.erb
new file mode 100644
index 000000000..dc24c31d1
--- /dev/null
+++ b/app/views/design_elements/_breadcrumbs.html.erb
@@ -0,0 +1,8 @@
+<div>
+  <h1>breadcrumbs</h1>
+  <div id="breadcrumbs" class="flex items-center gap-4">
+    <Breadcrumbs :breadcrumbs="breadcrumbs">
+  </div>
+</div>
+
+<%= javascript_include_tag 'vue_design_system_breadcrumbs' %>
diff --git a/app/views/design_elements/index.html.erb b/app/views/design_elements/index.html.erb
index 523cfe07e..5f9585a19 100644
--- a/app/views/design_elements/index.html.erb
+++ b/app/views/design_elements/index.html.erb
@@ -14,6 +14,8 @@
 
 <%= render partial: 'select' %>
 
+<%= render partial: 'breadcrumbs' %>
+
 <%= render partial: 'modals' %>
 
 <%= render partial: 'icons', locals: {icons_list: icons_list} %>
diff --git a/config/webpack/webpack.config.js b/config/webpack/webpack.config.js
index 6cdd886b8..07ac593cd 100644
--- a/config/webpack/webpack.config.js
+++ b/config/webpack/webpack.config.js
@@ -54,6 +54,7 @@ const entryList = {
   vue_experiments_list: './app/javascript/packs/vue/experiments_list.js',
   vue_my_modules_list: './app/javascript/packs/vue/my_modules_list.js',
   vue_design_system_select: './app/javascript/packs/vue/design_system/select.js',
+  vue_design_system_breadcrumbs: './app/javascript/packs/vue/design_system/breadcrumbs.js',
   vue_protocols_list: './app/javascript/packs/vue/protocols_list.js',
   vue_repositories_table: './app/javascript/packs/vue/repositories_table.js',
   vue_import_repository_modal: './app/javascript/packs/vue/import_repository_modal.js',

From 2c5624620411a122242cdd0ee6a21a6d66e15994 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Mon, 14 Oct 2024 15:12:48 +0200
Subject: [PATCH 42/96] Add file versioning to ove and marvinjs files
 [SCI-11170]

---
 .../gene_sequence_assets_controller.rb        |  1 -
 app/services/marvin_js_service.rb             | 32 +++++++++++--------
 2 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/app/controllers/gene_sequence_assets_controller.rb b/app/controllers/gene_sequence_assets_controller.rb
index d18cb72c7..a8f01908c 100644
--- a/app/controllers/gene_sequence_assets_controller.rb
+++ b/app/controllers/gene_sequence_assets_controller.rb
@@ -72,7 +72,6 @@ class GeneSequenceAssetsController < ApplicationController
 
       ensure_asset!
 
-      @asset.file.purge
       @asset.preview_image.purge
 
       @asset.attach_file_version(
diff --git a/app/services/marvin_js_service.rb b/app/services/marvin_js_service.rb
index 8713763ef..8541ed490 100644
--- a/app/services/marvin_js_service.rb
+++ b/app/services/marvin_js_service.rb
@@ -22,7 +22,7 @@ class MarvinJsService
       asset = Asset.new(created_by: current_user,
                           last_modified_by: current_user,
                           team_id: current_team.id)
-      attach_file(asset.file, file, params)
+      attach_file_version(asset, file, params)
       asset.save!
       asset.post_process_file
       connect_asset(asset, params, current_user)
@@ -40,21 +40,14 @@ class MarvinJsService
 
       file = generate_image(params)
       asset.update(last_modified_by: current_user) if asset.is_a?(Asset)
-      attach_file(attachment, file, params)
-      asset.post_process_file if asset.instance_of?(Asset)
-      asset
-    end
 
-    def update_file_name(new_name, asset_id, current_user, current_team)
-      asset = current_team.assets.find(asset_id)
-      prepared_name = prepare_name(new_name)
-
-      ActiveRecord::Base.transaction do
-        asset.last_modified_by = current_user
-        asset.rename_file(prepared_name)
-        asset.save!
+      if params[:object_type] == 'TinyMceAsset'
+        attach_file(attachment, file, params)
+      else
+        attach_file_version(asset, file, params)
       end
 
+      asset.post_process_file if asset.instance_of?(Asset)
       asset
     end
 
@@ -90,6 +83,19 @@ class MarvinJsService
       )
     end
 
+    def attach_file_version(asset, file, params)
+      asset.attach_file_version(
+        io: file,
+        filename: "#{prepare_name(params[:name])}.jpg",
+        content_type: 'image/jpeg',
+        metadata: {
+          name: prepare_name(params[:name]),
+          description: params[:description],
+          asset_type: 'marvinjs'
+        }
+      )
+    end
+
     def prepare_name(sketch_name)
       if !sketch_name.blank?
         sketch_name

From f99c701ab67912cf3aa79884bd72d0fe909d7fa0 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Mon, 14 Oct 2024 16:49:41 +0200
Subject: [PATCH 43/96] Fix report wizard for selecting of deleted inventories
 [SCI-11173]

---
 app/views/reports/wizard/_third_step.html.erb | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/app/views/reports/wizard/_third_step.html.erb b/app/views/reports/wizard/_third_step.html.erb
index 2cbf865db..9d66ed661 100644
--- a/app/views/reports/wizard/_third_step.html.erb
+++ b/app/views/reports/wizard/_third_step.html.erb
@@ -78,7 +78,8 @@
                           value="<%= repository.is_a?(RepositorySnapshot) ? repository.parent_id : repository.id %>"
                           <%= 'checked' if report.new_record? ||
                                             @project_contents[:repositories].include?(repository.id) ||
-                                            (repository.is_a?(Repository) && repository.repository_snapshots.exists?(id: @project_contents[:repositories])) %> />
+                                            (repository.is_a?(Repository) && repository.repository_snapshots.exists?(id: @project_contents[:repositories])) ||
+                                            (repository.is_a?(RepositorySnapshot) && @project_contents[:repositories].include?(repository.parent_id)) %> />
                     <span class="sci-checkbox-label"></span>
                   </span>
                   <%= repository.name %>
@@ -101,14 +102,20 @@
                   >
                    <% Report.default_repository_columns.each do |key, value| %>
                       <option value="<%= key %>"
-                              selected-value="<%= report.settings.dig(:task, :excluded_repository_columns, repository.id.to_s)&.include?(key.to_s.to_i) ? '' : 'selected' %>"
+                              selected-value="<%= report.settings.dig(:task, 
+                                                                      :excluded_repository_columns,
+                                                                      (repository.is_a?(RepositorySnapshot) ? repository.parent_id : repository.id).to_s)
+                                                                 &.include?(key.to_s.to_i) ? '' : 'selected' %>"
                       >
                         <%= value %>
                       </option>
                     <% end %>
                     <% repository.repository_columns.find_each do |repository_column| %>
                       <option value="<%= repository_column.id %>"
-                              selected-value="<%= report.settings.dig(:task, :excluded_repository_columns, repository.id.to_s)&.include?(repository_column.id.to_i) ? '' : 'selected' %>"
+                              selected-value="<%= report.settings.dig(:task,
+                                                                      :excluded_repository_columns,
+                                                                      (repository.is_a?(RepositorySnapshot) ? repository.parent_id : repository.id).to_s)
+                                                                 &.include?(repository_column.id.to_i) ? '' : 'selected' %>"
                       >
                         <%= repository_column.name %>
                       </option>

From 76d4e7ca7676c713b21da74700181a3a71cce092 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 15 Oct 2024 15:51:55 +0200
Subject: [PATCH 44/96] Update caracal version [SCI-11144]

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index abcf53353..05c8ada65 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -24,7 +24,7 @@ GIT
 
 GIT
   remote: https://github.com/scinote-eln/caracal.git
-  revision: 9b5613c12092c4988d8394054fe966ed3f4f093c
+  revision: 54c21353798569476a1eaa73b5fd3e275ac85419
   branch: custom-docx-reports
   specs:
     caracal (1.4.2)

From 8d6c0b4380f4c8fb708c3bb9c86b9ef9e8f5c514 Mon Sep 17 00:00:00 2001
From: Martin Artnik <85488244+artoscinote@users.noreply.github.com>
Date: Fri, 18 Oct 2024 14:38:35 +0200
Subject: [PATCH 45/96] Change download path for report templates

---
 bin/load_report_templates | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/load_report_templates b/bin/load_report_templates
index 8bb1c4f05..e0190f306 100755
--- a/bin/load_report_templates
+++ b/bin/load_report_templates
@@ -12,8 +12,8 @@ contents = case template_zip_url.scheme
            when 'https'
              HTTParty.get(template_zip_url).body
            when 's3'
-             system("AWS_PAGER=\"\" aws s3api get-object --bucket #{template_zip_url.host} --key #{template_zip_url.path[1..]} ./report_templates.zip")
-             File.read('./report_templates.zip')
+             system("AWS_PAGER=\"\" aws s3api get-object --bucket #{template_zip_url.host} --key #{template_zip_url.path[1..]} #{ENV.fetch('APP_HOME', '.')}/app/views/reports/report_templates.zip")
+             File.read("#{ENV.fetch('APP_HOME', '.')}/app/views/reports/report_templates.zip")
            end
 
 puts "Loaded report templates zip from #{template_zip_url_string}"

From bed20b29131132b0f77192c92708b244a213806f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 18 Oct 2024 14:58:08 +0200
Subject: [PATCH 46/96] Bump actionmailer from 7.0.8.4 to 7.0.8.5 (#7976)

Bumps [actionmailer](https://github.com/rails/rails) from 7.0.8.4 to 7.0.8.5.
- [Release notes](https://github.com/rails/rails/releases)
- [Changelog](https://github.com/rails/rails/blob/v7.2.1.1/actionmailer/CHANGELOG.md)
- [Commits](https://github.com/rails/rails/compare/v7.0.8.4...v7.0.8.5)

---
updated-dependencies:
- dependency-name: actionmailer
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 Gemfile.lock | 119 ++++++++++++++++++++++++---------------------------
 1 file changed, 56 insertions(+), 63 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 82d0e20e7..f5256be2b 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -52,47 +52,47 @@ GIT
 GEM
   remote: http://rubygems.org/
   specs:
-    actioncable (7.0.8.4)
-      actionpack (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    actioncable (7.0.8.5)
+      actionpack (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (7.0.8.4)
-      actionpack (= 7.0.8.4)
-      activejob (= 7.0.8.4)
-      activerecord (= 7.0.8.4)
-      activestorage (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    actionmailbox (7.0.8.5)
+      actionpack (= 7.0.8.5)
+      activejob (= 7.0.8.5)
+      activerecord (= 7.0.8.5)
+      activestorage (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.0.8.4)
-      actionpack (= 7.0.8.4)
-      actionview (= 7.0.8.4)
-      activejob (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    actionmailer (7.0.8.5)
+      actionpack (= 7.0.8.5)
+      actionview (= 7.0.8.5)
+      activejob (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.0)
-    actionpack (7.0.8.4)
-      actionview (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    actionpack (7.0.8.5)
+      actionview (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
       rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (7.0.8.4)
-      actionpack (= 7.0.8.4)
-      activerecord (= 7.0.8.4)
-      activestorage (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    actiontext (7.0.8.5)
+      actionpack (= 7.0.8.5)
+      activerecord (= 7.0.8.5)
+      activestorage (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.0.8.4)
-      activesupport (= 7.0.8.4)
+    actionview (7.0.8.5)
+      activesupport (= 7.0.8.5)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
@@ -102,14 +102,14 @@ GEM
       activemodel (>= 4.1)
       case_transform (>= 0.2)
       jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
-    activejob (7.0.8.4)
-      activesupport (= 7.0.8.4)
+    activejob (7.0.8.5)
+      activesupport (= 7.0.8.5)
       globalid (>= 0.3.6)
-    activemodel (7.0.8.4)
-      activesupport (= 7.0.8.4)
-    activerecord (7.0.8.4)
-      activemodel (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    activemodel (7.0.8.5)
+      activesupport (= 7.0.8.5)
+    activerecord (7.0.8.5)
+      activemodel (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
     activerecord-import (1.4.1)
       activerecord (>= 4.2)
     activerecord-session_store (2.1.0)
@@ -119,14 +119,14 @@ GEM
       multi_json (~> 1.11, >= 1.11.2)
       rack (>= 2.0.8, < 4)
       railties (>= 6.1)
-    activestorage (7.0.8.4)
-      actionpack (= 7.0.8.4)
-      activejob (= 7.0.8.4)
-      activerecord (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    activestorage (7.0.8.5)
+      actionpack (= 7.0.8.5)
+      activejob (= 7.0.8.5)
+      activerecord (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (7.0.8.4)
+    activesupport (7.0.8.5)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -447,20 +447,17 @@ GEM
       rails (>= 3.2.0)
     net-http (0.4.1)
       uri
-    net-imap (0.4.10)
+    net-imap (0.4.17)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
     net-protocol (0.2.2)
       timeout
-    net-smtp (0.4.0.1)
+    net-smtp (0.5.0)
       net-protocol
     newrelic_rpm (9.2.2)
     nio4r (2.7.3)
-    nokogiri (1.16.7)
-      mini_portile2 (~> 2.8.2)
-      racc (~> 1.4)
     nokogiri (1.16.7-arm64-darwin)
       racc (~> 1.4)
     nokogiri (1.16.7-x86_64-linux)
@@ -547,7 +544,7 @@ GEM
       nio4r (~> 2.0)
     raabro (1.4.0)
     racc (1.8.1)
-    rack (2.2.9)
+    rack (2.2.10)
     rack-attack (6.6.1)
       rack (>= 1.0, < 3)
     rack-cors (2.0.2)
@@ -564,20 +561,20 @@ GEM
       rack (~> 2.2, >= 2.2.4)
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails (7.0.8.4)
-      actioncable (= 7.0.8.4)
-      actionmailbox (= 7.0.8.4)
-      actionmailer (= 7.0.8.4)
-      actionpack (= 7.0.8.4)
-      actiontext (= 7.0.8.4)
-      actionview (= 7.0.8.4)
-      activejob (= 7.0.8.4)
-      activemodel (= 7.0.8.4)
-      activerecord (= 7.0.8.4)
-      activestorage (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    rails (7.0.8.5)
+      actioncable (= 7.0.8.5)
+      actionmailbox (= 7.0.8.5)
+      actionmailer (= 7.0.8.5)
+      actionpack (= 7.0.8.5)
+      actiontext (= 7.0.8.5)
+      actionview (= 7.0.8.5)
+      activejob (= 7.0.8.5)
+      activemodel (= 7.0.8.5)
+      activerecord (= 7.0.8.5)
+      activestorage (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
       bundler (>= 1.15.0)
-      railties (= 7.0.8.4)
+      railties (= 7.0.8.5)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -598,9 +595,9 @@ GEM
       railties (> 3.1)
     rails_serve_static_assets (0.0.5)
     rails_stdout_logging (0.0.5)
-    railties (7.0.8.4)
-      actionpack (= 7.0.8.4)
-      activesupport (= 7.0.8.4)
+    railties (7.0.8.5)
+      actionpack (= 7.0.8.5)
+      activesupport (= 7.0.8.5)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -715,8 +712,6 @@ GEM
       faraday-follow_redirects
     sys-uname (1.2.3)
       ffi (~> 1.1)
-    tailwindcss-rails (2.4.0)
-      railties (>= 6.0.0)
     tailwindcss-rails (2.4.0-arm64-darwin)
       railties (>= 6.0.0)
     tailwindcss-rails (2.4.0-x86_64-linux)
@@ -776,7 +771,6 @@ GEM
 
 PLATFORMS
   arm64-darwin
-  ruby
   x86_64-linux
 
 DEPENDENCIES
@@ -810,7 +804,6 @@ DEPENDENCIES
   deface (~> 1.9)
   delayed_job_active_record
   devise (~> 4.8.1)
-  devise-async!
   devise_invitable
   discard
   doorkeeper (>= 4.6)

From 1267293d50ffff19a814e275218e9b57de4432ee Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 18 Oct 2024 14:58:34 +0200
Subject: [PATCH 47/96] Bump actiontext from 7.0.8.4 to 7.0.8.5 (#7975)

Bumps [actiontext](https://github.com/rails/rails) from 7.0.8.4 to 7.0.8.5.
- [Release notes](https://github.com/rails/rails/releases)
- [Changelog](https://github.com/rails/rails/blob/v7.2.1.1/actiontext/CHANGELOG.md)
- [Commits](https://github.com/rails/rails/compare/v7.0.8.4...v7.0.8.5)

---
updated-dependencies:
- dependency-name: actiontext
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index f5256be2b..878d8ba33 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -428,7 +428,7 @@ GEM
       net-imap
       net-pop
       net-smtp
-    marcel (1.0.2)
+    marcel (1.0.4)
     matrix (0.4.2)
     method_source (1.0.0)
     mime-types (3.4.1)

From 3961b21c001f2624220990e1e89cdc8e0d7e51c9 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 21 Oct 2024 17:23:13 +0200
Subject: [PATCH 48/96] Add confirmation modal for repository file delete
 [SCI-11198]

---
 .../repositories/repository_datatable.js      | 35 +++++++++++++++++++
 .../javascripts/repositories/row_editor.js    | 18 +++-------
 .../_delete_asset_value_modal.html.erb        | 19 ++++++++++
 app/views/repositories/show.html.erb          |  1 +
 config/locales/en.yml                         |  4 +++
 5 files changed, 64 insertions(+), 13 deletions(-)
 create mode 100644 app/views/repositories/_delete_asset_value_modal.html.erb

diff --git a/app/assets/javascripts/repositories/repository_datatable.js b/app/assets/javascripts/repositories/repository_datatable.js
index 933bed39a..d030666ce 100644
--- a/app/assets/javascripts/repositories/repository_datatable.js
+++ b/app/assets/javascripts/repositories/repository_datatable.js
@@ -328,6 +328,40 @@ var RepositoryDatatable = (function(global) {
     });
   }
 
+  function initDeleteAssetValueConfirmModal() {
+    $('#deleteRepositoryAssetValueModal').on('shown.bs.modal', function() {
+      let $fileBtn = $(this).data('cellFileBtn');
+      let $input = $(this).data('cellInput');
+      let $label = $(this).data('cellLabel');
+
+      $('#confirmAssetValueDelete').one('click', function() {
+        $fileBtn.addClass('new-file');
+        $label.text('');
+        $input.val('');
+        $fileBtn.removeClass('error');
+
+        if (!$input.data('is-empty')) { // set hidden field for deletion only if original value has been set on rendering
+          $input
+            .prev('.file-hidden-field-container')
+            .html(`<input type="hidden"
+                       form="${$input.attr('form')}"
+                       name="repository_cells[${$input.data('col-id')}]"
+                       value=""/>`);
+        }
+
+        $('#deleteRepositoryAssetValueModal').modal('hide');
+      });
+    });
+
+    $('#deleteRepositoryAssetValueModal').on('hidden.bs.modal', function() {
+      const $deleteRepositoryAssetValueModal = $('#deleteRepositoryAssetValueModal');
+
+      $deleteRepositoryAssetValueModal.data('cellFileBtn', null);
+      $deleteRepositoryAssetValueModal.data('cellInput', null);
+      $deleteRepositoryAssetValueModal.data('cellLabel', null);
+    });
+  }
+
   function initActiveRemindersFilter() {
     $(TABLE_WRAPPER_ID).find('#only_reminders').on('change', function() {
       var $activeRemindersFilter = $(this).closest('.active-reminders-filter');
@@ -804,6 +838,7 @@ var RepositoryDatatable = (function(global) {
         initSaveButton();
         initCancelButton();
         initBSTooltips();
+        initDeleteAssetValueConfirmModal();
         window.initRepositoryStateMenu();
         DataTableHelpers.initLengthAppearance($(TABLE_ID).closest('.dataTables_wrapper'));
 
diff --git a/app/assets/javascripts/repositories/row_editor.js b/app/assets/javascripts/repositories/row_editor.js
index 490b6f63d..422b01acf 100644
--- a/app/assets/javascripts/repositories/row_editor.js
+++ b/app/assets/javascripts/repositories/row_editor.js
@@ -80,25 +80,17 @@ var RepositoryDatatableRowEditor = (function() {
       $fileBtn.removeClass('error');
     });
 
-
     deleteButtons.on('click', function() {
+      const $deleteRepositoryAssetValueModal = $('#deleteRepositoryAssetValueModal');
       let $fileBtn = $(this).parent();
       let $input = $fileBtn.prev('input[type=file]');
       let $label = $fileBtn.find('label');
 
-      $fileBtn.addClass('new-file');
-      $label.text('');
-      $input.val('');
-      $fileBtn.removeClass('error');
+      $deleteRepositoryAssetValueModal.data('cellFileBtn', $fileBtn);
+      $deleteRepositoryAssetValueModal.data('cellInput', $input);
+      $deleteRepositoryAssetValueModal.data('cellLabel', $label);
 
-      if (!$input.data('is-empty')) { // set hidden field for deletion only if original value has been set on rendering
-        $input
-          .prev('.file-hidden-field-container')
-          .html(`<input type="hidden"
-                     form="${$input.attr('form')}"
-                     name="repository_cells[${$input.data('col-id')}]"
-                     value=""/>`);
-      }
+      $('#deleteRepositoryAssetValueModal').modal('show');
     });
   }
 
diff --git a/app/views/repositories/_delete_asset_value_modal.html.erb b/app/views/repositories/_delete_asset_value_modal.html.erb
new file mode 100644
index 000000000..81ccb9356
--- /dev/null
+++ b/app/views/repositories/_delete_asset_value_modal.html.erb
@@ -0,0 +1,19 @@
+<div class="modal fade" id="deleteRepositoryAssetValueModal" tabindex="-1" role="dialog" aria-labelledby="deleteRepositoryAssetValueModalLabel">
+  <div class="modal-dialog" role="document" data-e2e="e2e-MD-invInventoryDeleteAssetAT">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" data-e2e="e2e-BT-invInventoryDeleteAssetMD-close" class="close" data-dismiss="modal" aria-label="Close"><i class="sn-icon sn-icon-close"></i></button>
+        <h4 class="modal-title"><%= t("repositories.modal_delete_asset_value.title") %></h4>
+      </div>
+      <div class="modal-body">
+        <%= t("repositories.modal_delete_asset_value.notice_html") %>
+      </div>
+      <div class="modal-footer">
+        <button type="button" data-e2e="e2e-BT-invInventoryDeleteAssetMD-cancel" class="btn btn-secondary" data-dismiss="modal"><%= t("general.cancel")%></button>
+        <button id="confirmAssetValueDelete" type="button" data-e2e="e2e-BT-invInventoryDeleteAssetMD-delete" class="btn btn-danger delete-asset-value-modal-button" data-dismiss="modal">
+          <%= t("repositories.modal_delete_asset_value.delete") %>
+        </button>
+      </div>
+    </div>
+  </div>
+</div>
diff --git a/app/views/repositories/show.html.erb b/app/views/repositories/show.html.erb
index 6e4ff35b1..8948c2a85 100644
--- a/app/views/repositories/show.html.erb
+++ b/app/views/repositories/show.html.erb
@@ -78,6 +78,7 @@
 
 
 <%= render partial: "repositories/delete_record_modal" %>
+<%= render partial: "repositories/delete_asset_value_modal" %>
 <%= render partial: 'repositories/export_repository_rows_modal',
            locals: { repository: @repository } %>
 
diff --git a/config/locales/en.yml b/config/locales/en.yml
index c8c99ec10..62f4a64ee 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -2425,6 +2425,10 @@ en:
       title: "Delete items"
       notice: "Are you sure you want to delete the selected item(s)?"
       delete: "Delete"
+    modal_delete_asset_value:
+      title: "Confirm file deletion?"
+      notice_html: "<p>Deleting this file will remove the entire column history.<br><br></p><p>This action is irreversible.<br><br></p><p>To retain version history, replace the file with a new one instead.</p>"
+      delete: "Delete"
     modal_delete_column:
       title: "Delete a column"
       message: "Are you sure you wish to permanently delete selected column %{column}? This action is irreversible."

From 21fb93110acffbc04619cbfb5f1a897a8961f096 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Mon, 21 Oct 2024 17:26:39 +0200
Subject: [PATCH 49/96] Add option for enabling Aws::Rails::SesMailer for
 sending emails with AWS SDK [SCI-11207] (#7981)

---
 config/environments/production.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/environments/production.rb b/config/environments/production.rb
index 84d6ba993..5480eee37 100644
--- a/config/environments/production.rb
+++ b/config/environments/production.rb
@@ -30,7 +30,7 @@ Rails.application.configure do
   }
   config.action_mailer.perform_deliveries = true
   config.action_mailer.raise_delivery_errors = true
-  config.action_mailer.delivery_method = :smtp
+  config.action_mailer.delivery_method = ENV['SMTP_USE_AWS_SES'] == 'true' ? :ses : :smtp
 
   config.action_mailer.smtp_settings = {
     address: Rails.application.secrets.mailer_address,

From 9c524d8e0e91dce870fad274bde8daa6fea252e3 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Wed, 23 Oct 2024 16:58:03 +0200
Subject: [PATCH 50/96] Exclude API status and health endpoints, scheduled jobs
 from NewRelic monitoring, update APM agent [SCI-11212] (#7987)

---
 Gemfile.lock                                       | 2 +-
 app/controllers/api/api_controller.rb              | 2 ++
 app/jobs/my_modules/due_date_reminder_job.rb       | 2 ++
 app/jobs/notification_cleanup_job.rb               | 2 ++
 app/jobs/repository_item_date_reminder_job.rb      | 2 ++
 app/services/label_printers/fluics/sync_service.rb | 1 +
 app/services/templates_service.rb                  | 1 +
 config/environments/production.rb                  | 2 +-
 config/initializers/silencer.rb                    | 3 ++-
 config/routes.rb                                   | 6 ++++--
 10 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 878d8ba33..e26778e55 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -456,7 +456,7 @@ GEM
       timeout
     net-smtp (0.5.0)
       net-protocol
-    newrelic_rpm (9.2.2)
+    newrelic_rpm (9.14.0)
     nio4r (2.7.3)
     nokogiri (1.16.7-arm64-darwin)
       racc (~> 1.4)
diff --git a/app/controllers/api/api_controller.rb b/app/controllers/api/api_controller.rb
index 27141eded..3eb460f18 100644
--- a/app/controllers/api/api_controller.rb
+++ b/app/controllers/api/api_controller.rb
@@ -8,6 +8,8 @@ module Api
 
     before_action :authenticate_request!, except: %i(status health)
 
+    newrelic_ignore only: %i(health status)
+
     rescue_from StandardError do |e|
       logger.error e.message
       logger.error e.backtrace.join("\n")
diff --git a/app/jobs/my_modules/due_date_reminder_job.rb b/app/jobs/my_modules/due_date_reminder_job.rb
index 839f4d07f..8db0409cc 100644
--- a/app/jobs/my_modules/due_date_reminder_job.rb
+++ b/app/jobs/my_modules/due_date_reminder_job.rb
@@ -2,6 +2,8 @@
 
 module MyModules
   class DueDateReminderJob < ApplicationJob
+    newrelic_ignore
+
     def perform
       my_modules = MyModule.uncomplete.approaching_due_dates
 
diff --git a/app/jobs/notification_cleanup_job.rb b/app/jobs/notification_cleanup_job.rb
index cea9fa32f..61a939cb9 100644
--- a/app/jobs/notification_cleanup_job.rb
+++ b/app/jobs/notification_cleanup_job.rb
@@ -1,6 +1,8 @@
 # frozen_string_literal: true
 
 class NotificationCleanupJob < ApplicationJob
+  newrelic_ignore
+
   def perform
     Notification.where('created_at < ?', 3.months.ago).delete_all
   end
diff --git a/app/jobs/repository_item_date_reminder_job.rb b/app/jobs/repository_item_date_reminder_job.rb
index 0ed56f118..fe35ea0a8 100644
--- a/app/jobs/repository_item_date_reminder_job.rb
+++ b/app/jobs/repository_item_date_reminder_job.rb
@@ -1,6 +1,8 @@
 # frozen_string_literal: true
 
 class RepositoryItemDateReminderJob < ApplicationJob
+  newrelic_ignore
+
   queue_as :default
 
   def perform
diff --git a/app/services/label_printers/fluics/sync_service.rb b/app/services/label_printers/fluics/sync_service.rb
index 987a42c33..3510d3c48 100644
--- a/app/services/label_printers/fluics/sync_service.rb
+++ b/app/services/label_printers/fluics/sync_service.rb
@@ -9,6 +9,7 @@ module LabelPrinters
       end
 
       def sync_templates!
+        NewRelic::Agent.ignore_transaction
         LabelPrinter.fluics.each do |printer|
           api_client = ApiClient.new(printer.fluics_api_key)
           templates = api_client.list_templates
diff --git a/app/services/templates_service.rb b/app/services/templates_service.rb
index 8bdb18caf..5b2f5ba37 100644
--- a/app/services/templates_service.rb
+++ b/app/services/templates_service.rb
@@ -49,6 +49,7 @@ class TemplatesService
   end
 
   def update_all_templates
+    NewRelic::Agent.ignore_transaction
     processed_counter = 0
     updated_counter = 0
     Team.find_each do |team|
diff --git a/config/environments/production.rb b/config/environments/production.rb
index 5480eee37..bc4505cb3 100644
--- a/config/environments/production.rb
+++ b/config/environments/production.rb
@@ -73,7 +73,7 @@ Rails.application.configure do
   # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
   config.force_ssl = ENV['RAILS_FORCE_SSL'].present?
 
-  config.ssl_options = { redirect: { exclude: ->(request) { request.path =~ %r{api\/health} } } }
+  config.ssl_options = { redirect: { exclude: ->(request) { request.path =~ %r{api/health|status} } } }
 
   # Use the lowest log level to ensure availability of diagnostic information
   # when problems arise.
diff --git a/config/initializers/silencer.rb b/config/initializers/silencer.rb
index cccc5657b..2b442e781 100644
--- a/config/initializers/silencer.rb
+++ b/config/initializers/silencer.rb
@@ -8,7 +8,8 @@ Rails.application.configure do
     silence: [
       # Silence WickedPDF rendering in logs
       %r{/projects/[0-9]*/reports/generate.pdf},
-      '/api/health'
+      '/api/health',
+      '/api/status'
     ]
   )
 end
diff --git a/config/routes.rb b/config/routes.rb
index 0fdc7fe93..7a08d12f2 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -3,6 +3,10 @@ Rails.application.routes.draw do
     skip_controllers :applications, :authorized_applications, :token_info
   end
 
+  # Global healthcheck endpoints
+  get 'api/health', to: 'api/api#health', as: 'api_health'
+  get 'api/status', to: 'api/api#status', as: 'api_status'
+
   post 'access_tokens/revoke', to: 'doorkeeper/access_tokens#revoke'
 
   # Addons
@@ -901,8 +905,6 @@ Rails.application.routes.draw do
     end
 
     namespace :api, defaults: { format: 'json' } do
-      get 'health', to: 'api#health'
-      get 'status', to: 'api#status'
       namespace :service do
         post 'projects_json_export', to: 'projects_json_export#projects_json_export'
         resources :teams, only: [] do

From 1939902eb1633e608ace5159d2e2959266d936d7 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Thu, 24 Oct 2024 13:22:21 +0200
Subject: [PATCH 51/96] Fix NewRelic ignore calls for ActiveJobs [SCI-11212]
 (#7988)

---
 app/jobs/my_modules/due_date_reminder_job.rb  | 3 +--
 app/jobs/notification_cleanup_job.rb          | 3 +--
 app/jobs/repository_item_date_reminder_job.rb | 3 +--
 app/services/templates_service.rb             | 2 ++
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/app/jobs/my_modules/due_date_reminder_job.rb b/app/jobs/my_modules/due_date_reminder_job.rb
index 8db0409cc..9975a5436 100644
--- a/app/jobs/my_modules/due_date_reminder_job.rb
+++ b/app/jobs/my_modules/due_date_reminder_job.rb
@@ -2,9 +2,8 @@
 
 module MyModules
   class DueDateReminderJob < ApplicationJob
-    newrelic_ignore
-
     def perform
+      NewRelic::Agent.ignore_transaction
       my_modules = MyModule.uncomplete.approaching_due_dates
 
       my_modules.each do |task|
diff --git a/app/jobs/notification_cleanup_job.rb b/app/jobs/notification_cleanup_job.rb
index 61a939cb9..31c2380d4 100644
--- a/app/jobs/notification_cleanup_job.rb
+++ b/app/jobs/notification_cleanup_job.rb
@@ -1,9 +1,8 @@
 # frozen_string_literal: true
 
 class NotificationCleanupJob < ApplicationJob
-  newrelic_ignore
-
   def perform
+    NewRelic::Agent.ignore_transaction
     Notification.where('created_at < ?', 3.months.ago).delete_all
   end
 end
diff --git a/app/jobs/repository_item_date_reminder_job.rb b/app/jobs/repository_item_date_reminder_job.rb
index fe35ea0a8..555ca1e74 100644
--- a/app/jobs/repository_item_date_reminder_job.rb
+++ b/app/jobs/repository_item_date_reminder_job.rb
@@ -1,11 +1,10 @@
 # frozen_string_literal: true
 
 class RepositoryItemDateReminderJob < ApplicationJob
-  newrelic_ignore
-
   queue_as :default
 
   def perform
+    NewRelic::Agent.ignore_transaction
     process_repository_values(RepositoryDateTimeValue, DateTime.current)
     process_repository_values(RepositoryDateValue, Date.current)
   end
diff --git a/app/services/templates_service.rb b/app/services/templates_service.rb
index 5b2f5ba37..75a6d0c12 100644
--- a/app/services/templates_service.rb
+++ b/app/services/templates_service.rb
@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require 'newrelic_rpm'
+
 class TemplatesService
   def initialize(base_dir = nil)
     @base_dir = base_dir ? base_dir : "#{Rails.root}/app/assets/templates"

From 2e2308e866b20f757d3d58b5a680d84ba2200b08 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Fri, 25 Oct 2024 10:30:33 +0200
Subject: [PATCH 52/96] Add option to add task name into results [SCI-11220]

---
 app/services/reports/docx/draw_results.rb | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/app/services/reports/docx/draw_results.rb b/app/services/reports/docx/draw_results.rb
index ffa398081..a708c262e 100644
--- a/app/services/reports/docx/draw_results.rb
+++ b/app/services/reports/docx/draw_results.rb
@@ -1,12 +1,21 @@
 # frozen_string_literal: true
 
 module Reports::Docx::DrawResults
-  def draw_results(my_module)
+  def draw_results(my_module, with_my_module_name: false)
     color = @color
     settings = @settings
+    scinote_url = @scinote_url
+    link_style = @link_style
     return unless can_read_my_module?(@user, my_module)
 
     if my_module.results.any? && (%w(file_results table_results text_results).any? { |k| @settings.dig('task', k) })
+      if with_my_module_name
+        @docx.h3 do
+          link  my_module.name,
+                scinote_url + Rails.application.routes.url_helpers.protocols_my_module_path(my_module),
+                link_style
+        end
+      end
       @docx.h4 I18n.t('Results')
       order_results_for_report(my_module.results, @settings.dig('task', 'result_order')).each do |result|
         @docx.p do

From 749c1cd494adfb9579d418eb2c04cc99ce9cbb41 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 25 Oct 2024 10:53:42 +0200
Subject: [PATCH 53/96] Fix names for duplicated OVE or MarvinJS files
 [SCI-11183]

---
 app/models/asset.rb | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/app/models/asset.rb b/app/models/asset.rb
index 5a9085cda..80c08166d 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -152,20 +152,28 @@ class Asset < ApplicationRecord
 
     return unless new_asset.save
 
-    duplicate_file(new_asset)
+    duplicate_file(new_asset, new_name: new_name)
     new_asset
   end
 
-  def duplicate_file(to_asset)
+  def duplicate_file(to_asset, new_name: nil)
     return unless file.attached?
 
     raise ArgumentError, 'Destination asset should be persisted first!' unless to_asset.persisted?
 
     file.blob.open do |tmp_file|
+      metadata = blob.metadata.dup
+
+      # set new name in metadata for OVE and MarvinJS files
+      if new_name && file.blob.metadata['asset_type'].in?(%w(gene_sequence marvinjs))
+        new_metadata_name = File.basename(new_name, File.extname(new_name))
+        metadata['name'] = new_metadata_name
+      end
+
       to_blob = ActiveStorage::Blob.create_and_upload!(
         io: tmp_file,
         filename: blob.filename,
-        metadata: blob.metadata
+        metadata: metadata
       )
       to_asset.attach_file_version(to_blob)
     end

From 3815e5e78dfb1f0719b3c95e5525c3002c1e8995 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Fri, 25 Oct 2024 11:36:27 +0200
Subject: [PATCH 54/96] Add select/deselect button for repository column
 selection on report wizard [SCI-11219]

---
 app/views/reports/wizard/_third_step.html.erb | 1 +
 config/locales/en.yml                         | 1 +
 2 files changed, 2 insertions(+)

diff --git a/app/views/reports/wizard/_third_step.html.erb b/app/views/reports/wizard/_third_step.html.erb
index 9d66ed661..a1f8216f7 100644
--- a/app/views/reports/wizard/_third_step.html.erb
+++ b/app/views/reports/wizard/_third_step.html.erb
@@ -98,6 +98,7 @@
                           data-placeholder="<%= t("projects.reports.wizard.third_step.repository_column.placeholder") %>"
                           data-select-multiple-all-selected="<%= t("projects.reports.wizard.third_step.repository_column.all_selected") %>"
                           data-select-multiple-name="<%= t("projects.reports.wizard.third_step.repository_column.selected") %>"
+                          data-select-all-button="<%= t("projects.reports.wizard.third_step.repository_column.select_deselect_all") %>"
                           multiple
                   >
                    <% Report.default_repository_columns.each do |key, value| %>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index d8a9904cf..880b00f85 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -872,6 +872,7 @@ en:
           archived: "[archived]"
           deleted: "[deleted]"
           repository_column:
+            select_deselect_all: 'Select/deselect all'
             placeholder: 'Select columns'
             all_selected: 'All columns selected'
             selected: 'columns selected'

From c2b7c12497dbd2a9ff4271e8bc3120e7a8342cd2 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Fri, 25 Oct 2024 12:46:58 +0200
Subject: [PATCH 55/96] Add default text if not repository columns are selected
 for reports [SCI-11211]

---
 app/services/reports/docx/draw_my_module_repository.rb | 7 ++++++-
 app/services/reports/docx/repository_helper.rb         | 2 ++
 config/locales/en.yml                                  | 1 +
 3 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/app/services/reports/docx/draw_my_module_repository.rb b/app/services/reports/docx/draw_my_module_repository.rb
index b5102a25a..11f1ed0c8 100644
--- a/app/services/reports/docx/draw_my_module_repository.rb
+++ b/app/services/reports/docx/draw_my_module_repository.rb
@@ -20,7 +20,12 @@ module Reports::Docx::DrawMyModuleRepository
     @docx.p I18n.t('projects.reports.elements.module_repository.name',
                    repository: repository.name,
                    my_module: my_module.name), bold: true, size: Constants::REPORT_DOCX_STEP_ELEMENTS_TITLE_SIZE
-    @docx.table table, border_size: Constants::REPORT_DOCX_TABLE_BORDER_SIZE
+
+    if table.present?
+      @docx.table table, border_size: Constants::REPORT_DOCX_TABLE_BORDER_SIZE
+    else
+      @docx.p I18n.t('projects.reports.elements.module_repository.no_columns'), italic: true
+    end
 
     @docx.p
     @docx.p
diff --git a/app/services/reports/docx/repository_helper.rb b/app/services/reports/docx/repository_helper.rb
index 26d2a43b6..d8166ca9b 100644
--- a/app/services/reports/docx/repository_helper.rb
+++ b/app/services/reports/docx/repository_helper.rb
@@ -5,6 +5,8 @@ module Reports::Docx::RepositoryHelper
   include ActionView::Helpers::NumberHelper
 
   def prepare_row_columns_for_docx(repository_data, my_module = nil, repository = nil)
+    return if repository_data[:headers].blank?
+
     result = [repository_data[:headers]]
     excluded_columns = repository_data[:excluded_columns]
 
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 880b00f85..5e1c931a8 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -978,6 +978,7 @@ en:
           name: "%{repository} of task %{my_module}"
           table_name: "%{name}"
           no_items: "No items"
+          no_columns: "No columns selected"
         result:
           user_time: "Added on %{timestamp} by %{user}."
         result_asset:

From cbe0e9f2f2ef74ec04965ff02d64e7283ed1cf00 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 25 Oct 2024 15:22:18 +0200
Subject: [PATCH 56/96] When restoring files, also restore preview image
 [SCI-11216]

---
 app/controllers/assets_controller.rb               | 1 +
 app/controllers/gene_sequence_assets_controller.rb | 4 +---
 app/models/asset.rb                                | 4 ++--
 app/models/concerns/versioned_attachments.rb       | 5 ++---
 4 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 47d92e5f7..92ae7c6d7 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -417,6 +417,7 @@ class AssetsController < ApplicationController
     render_403 unless VersionedAttachments.enabled?
 
     @asset.restore_file_version(params[:version].to_i)
+    @asset.restore_preview_image_version(params[:version].to_i) if @asset.preview_image.attached?
 
     message_items = {
       version: params[:version].to_i,
diff --git a/app/controllers/gene_sequence_assets_controller.rb b/app/controllers/gene_sequence_assets_controller.rb
index a8f01908c..69526e9a6 100644
--- a/app/controllers/gene_sequence_assets_controller.rb
+++ b/app/controllers/gene_sequence_assets_controller.rb
@@ -72,14 +72,12 @@ class GeneSequenceAssetsController < ApplicationController
 
       ensure_asset!
 
-      @asset.preview_image.purge
-
       @asset.attach_file_version(
         io: StringIO.new(params[:sequence_data].to_json),
         filename: "#{params[:sequence_name]}.json"
       )
 
-      @asset.preview_image.attach(
+      @asset.attach_preview_image_version(
         io: StringIO.new(Base64.decode64(params[:base64_image].split(',').last)),
         filename: "#{params[:sequence_name]}.png"
       )
diff --git a/app/models/asset.rb b/app/models/asset.rb
index 80c08166d..e9ed753cd 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -19,8 +19,8 @@ class Asset < ApplicationRecord
 
   # ActiveStorage configuration
   has_one_versioned_attached :file
+  has_one_versioned_attached :preview_image
   has_one_attached :file_pdf_preview
-  has_one_attached :preview_image
 
   # Asset validation
   # This could cause some problems if you create empty asset and want to
@@ -185,7 +185,7 @@ class Asset < ApplicationRecord
           filename: blob.filename,
           metadata: blob.metadata
         )
-        to_asset.preview_image.attach(to_blob)
+        to_asset.attach_preview_image_version(to_blob)
       end
     end
 
diff --git a/app/models/concerns/versioned_attachments.rb b/app/models/concerns/versioned_attachments.rb
index 6adc4d809..a286c9022 100644
--- a/app/models/concerns/versioned_attachments.rb
+++ b/app/models/concerns/versioned_attachments.rb
@@ -15,10 +15,9 @@ module VersionedAttachments
 
           new_blob = __send__(name).blob
           new_blob.metadata['created_by_id'] = last_modified_by_id
-          new_blob.save!
 
           # set version of current latest file if previous versions exist
-          next unless __send__(:"previous_#{name.to_s.pluralize}").any?
+          new_blob.save! and next unless __send__(:"previous_#{name.to_s.pluralize}").any?
 
           new_version =
             (__send__(:"previous_#{name.to_s.pluralize}").last.blob.metadata['version'] || 1) + 1
@@ -50,6 +49,6 @@ module VersionedAttachments
   module_function
 
   def enabled?
-    ApplicationSettings.instance.values['storage_locations_enabled']
+    ApplicationSettings.instance.values['versioned_attachments_enabled']
   end
 end

From ddba2500861575608df6c7313899388369e27f28 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 28 Oct 2024 10:19:33 +0100
Subject: [PATCH 57/96] Fix user-based sorting of repository items [SCI-11215]

---
 app/models/linked_repository.rb | 4 ++--
 app/models/repository.rb        | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/models/linked_repository.rb b/app/models/linked_repository.rb
index a6874ad91..5e1872924 100644
--- a/app/models/linked_repository.rb
+++ b/app/models/linked_repository.rb
@@ -24,9 +24,9 @@ class LinkedRepository < Repository
       'repository_rows.created_at',
       'users.full_name',
       'repository_rows.updated_at',
-      'last_modified_bies_repository_rows.full_name',
+      'last_modified_by.full_name',
       'repository_rows.archived_on',
-      'archived_bies_repository_rows.full_name',
+      'archived_by.full_name',
       'repository_rows.external_id'
     ]
   end
diff --git a/app/models/repository.rb b/app/models/repository.rb
index 166dd6f89..d60d072c3 100644
--- a/app/models/repository.rb
+++ b/app/models/repository.rb
@@ -83,9 +83,9 @@ class Repository < RepositoryBase
       'repository_rows.created_at',
       'users.full_name',
       'repository_rows.updated_at',
-      'last_modified_bies_repository_rows.full_name',
+      'last_modified_by.full_name',
       'repository_rows.archived_on',
-      'archived_bies_repository_rows.full_name'
+      'archived_by.full_name'
     ]
   end
 

From ab658cfeb1a8dbb9b5231b8660191ef4275b80a9 Mon Sep 17 00:00:00 2001
From: Martin Artnik <85488244+artoscinote@users.noreply.github.com>
Date: Mon, 28 Oct 2024 10:50:24 +0100
Subject: [PATCH 58/96] Refactor SoftLockedRepository logic [SCI-11148] (#7985)

---
 app/controllers/api/v1/base_controller.rb              |  3 +++
 app/controllers/assets_controller.rb                   |  3 +--
 app/controllers/repositories_controller.rb             |  2 +-
 app/helpers/repository_datatable_helper.rb             |  5 ++---
 app/models/soft_locked_repository.rb                   |  8 ++++++++
 app/permissions/repository.rb                          |  3 ++-
 app/services/toolbars/repositories_service.rb          |  8 ++++----
 app/services/toolbars/repository_rows_service.rb       | 10 +++++-----
 app/views/repositories/_repository_table.html.erb      |  2 +-
 app/views/repositories/_toolbar_buttons.html.erb       |  2 +-
 .../_manage_column_modal_index.html.erb                |  2 +-
 11 files changed, 29 insertions(+), 19 deletions(-)

diff --git a/app/controllers/api/v1/base_controller.rb b/app/controllers/api/v1/base_controller.rb
index 72eb1780e..213e4bc56 100644
--- a/app/controllers/api/v1/base_controller.rb
+++ b/app/controllers/api/v1/base_controller.rb
@@ -180,6 +180,9 @@ module Api
 
       def load_inventory(key = :inventory_id)
         @inventory = @team.repositories.find(params.require(key))
+
+        @inventory.unlock! if @inventory.is_a?(SoftLockedRepository)
+
         raise PermissionError.new(Repository, :read) unless can_read_repository?(@inventory)
       end
 
diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 92ae7c6d7..3497dfbfa 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -22,8 +22,7 @@ class AssetsController < ApplicationController
   before_action :check_restore_permission, only: :restore_version
 
   def file_preview
-    editable = can_manage_asset?(@asset) && (@asset.repository_asset_value.blank? ||
-                !@asset.repository_cell.repository_row.repository.is_a?(SoftLockedRepository))
+    editable = can_manage_asset?(@asset) && @asset.repository_asset_value.blank?
     render json: { html: render_to_string(
       partial: 'shared/file_preview/content',
       locals: {
diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index bddd1c863..e17486afc 100644
--- a/app/controllers/repositories_controller.rb
+++ b/app/controllers/repositories_controller.rb
@@ -495,7 +495,7 @@ class RepositoriesController < ApplicationController
   end
 
   def set_inline_name_editing
-    return unless can_manage_repository?(@repository) && !@repository.is_a?(SoftLockedRepository)
+    return unless can_manage_repository?(@repository)
 
     @inline_editable_title_config = {
       name: 'title',
diff --git a/app/helpers/repository_datatable_helper.rb b/app/helpers/repository_datatable_helper.rb
index 2f64004d0..a1f4364d2 100644
--- a/app/helpers/repository_datatable_helper.rb
+++ b/app/helpers/repository_datatable_helper.rb
@@ -12,8 +12,7 @@ module RepositoryDatatableHelper
     repository_row_connections_enabled = Repository.repository_row_connections_enabled?
     reminders_enabled = Repository.reminders_enabled?
     stock_managable = has_stock_management && !options[:disable_stock_management] &&
-                      can_manage_repository_stock?(repository) &&
-                      !repository.is_a?(SoftLockedRepository)
+                      can_manage_repository_stock?(repository)
     stock_consumption_permitted = has_stock_management && options[:include_stock_consumption] && options[:my_module] &&
                                   stock_consumption_permitted?(repository, options[:my_module])
     default_columns_method_name = "#{repository.class.name.underscore}_default_columns"
@@ -31,7 +30,7 @@ module RepositoryDatatableHelper
       row['relationships_enabled'] = repository_row_connections_enabled
       row['hasActiveReminders'] = record.has_active_reminders if reminders_enabled
 
-      unless options[:view_mode] || repository.is_a?(SoftLockedRepository)
+      unless options[:view_mode]
         row['recordUpdateUrl'] =
           Rails.application.routes.url_helpers.repository_repository_row_path(repository, record)
 
diff --git a/app/models/soft_locked_repository.rb b/app/models/soft_locked_repository.rb
index 93a51178d..43e44c73d 100644
--- a/app/models/soft_locked_repository.rb
+++ b/app/models/soft_locked_repository.rb
@@ -8,4 +8,12 @@ class SoftLockedRepository < Repository
   def shareable_write?
     false
   end
+
+  def unlocked?
+    @unlocked == true
+  end
+
+  def unlock!
+    @unlocked = true
+  end
 end
diff --git a/app/permissions/repository.rb b/app/permissions/repository.rb
index 3a7283793..8466b745f 100644
--- a/app/permissions/repository.rb
+++ b/app/permissions/repository.rb
@@ -28,7 +28,8 @@ Canaid::Permissions.register_for(Repository) do
      create_repository_columns)
     .each do |perm|
     can perm do |_, repository|
-      repository.active? && repository.repository_snapshots.provisioning.none?
+      repository.active? && repository.repository_snapshots.provisioning.none? &&
+        (!repository.is_a?(SoftLockedRepository) || repository.unlocked?)
     end
   end
 
diff --git a/app/services/toolbars/repositories_service.rb b/app/services/toolbars/repositories_service.rb
index 34ac15a30..c66059b23 100644
--- a/app/services/toolbars/repositories_service.rb
+++ b/app/services/toolbars/repositories_service.rb
@@ -31,7 +31,7 @@ module Toolbars
     private
 
     def rename_action
-      return unless @single && can_manage_repository?(@repository) && !@repository.is_a?(SoftLockedRepository)
+      return unless @single && can_manage_repository?(@repository)
 
       {
         name: :update,
@@ -67,7 +67,7 @@ module Toolbars
 
     def archive_action
       return unless @repositories.all? do |repository|
-        can_archive_repository?(repository) && !@repository.is_a?(SoftLockedRepository)
+        can_archive_repository?(repository)
       end
 
       {
@@ -92,7 +92,7 @@ module Toolbars
 
     def restore_action
       return unless @repositories.all? do |repository|
-        can_archive_repository?(repository) && !repository.is_a?(SoftLockedRepository)
+        can_archive_repository?(repository)
       end
 
       {
@@ -105,7 +105,7 @@ module Toolbars
     end
 
     def delete_action
-      return unless @single && can_delete_repository?(@repository) && !@repository.is_a?(SoftLockedRepository)
+      return unless @single && can_delete_repository?(@repository)
 
       {
         name: :delete,
diff --git a/app/services/toolbars/repository_rows_service.rb b/app/services/toolbars/repository_rows_service.rb
index cfbbdf84e..ad0924727 100644
--- a/app/services/toolbars/repository_rows_service.rb
+++ b/app/services/toolbars/repository_rows_service.rb
@@ -42,7 +42,7 @@ module Toolbars
     private
 
     def restore_action
-      return unless can_manage_repository_rows?(@repository) && !@repository.is_a?(SoftLockedRepository)
+      return unless can_manage_repository_rows?(@repository)
 
       return unless @repository_rows.all?(&:archived?)
 
@@ -57,7 +57,7 @@ module Toolbars
     end
 
     def edit_action
-      return unless can_manage_repository_rows?(@repository) && !@repository.is_a?(SoftLockedRepository)
+      return unless can_manage_repository_rows?(@repository)
 
       return unless @repository_rows.all?(&:active?)
 
@@ -87,7 +87,7 @@ module Toolbars
     end
 
     def duplicate_action
-      return unless can_create_repository_rows?(@repository) && !@repository.is_a?(SoftLockedRepository)
+      return unless can_create_repository_rows?(@repository)
 
       return unless @repository_rows.all?(&:active?)
 
@@ -151,7 +151,7 @@ module Toolbars
     end
 
     def archive_action
-      return unless can_manage_repository_rows?(@repository) && !@repository.is_a?(SoftLockedRepository)
+      return unless can_manage_repository_rows?(@repository)
 
       return unless @repository_rows.all?(&:active?)
 
@@ -166,7 +166,7 @@ module Toolbars
     end
 
     def delete_action
-      return unless can_delete_repository_rows?(@repository) && !@repository.is_a?(SoftLockedRepository)
+      return unless can_delete_repository_rows?(@repository)
 
       return unless @repository_rows.all?(&:archived?)
 
diff --git a/app/views/repositories/_repository_table.html.erb b/app/views/repositories/_repository_table.html.erb
index 1dfd4fd57..4f542613c 100644
--- a/app/views/repositories/_repository_table.html.erb
+++ b/app/views/repositories/_repository_table.html.erb
@@ -48,7 +48,7 @@
         <% if @repository.is_a?(LinkedRepository) %>
           <th id="row-external-id"><%= t('repositories.table.external_id') %></th>
         <% end %>
-        <% columns_editable = can_manage_repository_columns?(@repository) && !repository.is_a?(SoftLockedRepository) %>
+        <% columns_editable = can_manage_repository_columns?(@repository) %>
         <% repository.repository_columns.order(:id).each do |column| %>
           <th
             class="repository-column <%= 'row-stock item-stock' if column.data_type == 'RepositoryStockValue' %>"
diff --git a/app/views/repositories/_toolbar_buttons.html.erb b/app/views/repositories/_toolbar_buttons.html.erb
index 2a2655d4a..04565d5a1 100644
--- a/app/views/repositories/_toolbar_buttons.html.erb
+++ b/app/views/repositories/_toolbar_buttons.html.erb
@@ -11,7 +11,7 @@
           <span class="button-text"><%= t('repositories.index.snapshot_provisioning_in_progress') %></span>
         </div>
       <% end %>
-      <% if can_create_repository_rows?(@repository) && !@repository.is_a?(SoftLockedRepository) %>
+      <% if can_create_repository_rows?(@repository) %>
         <button type="button" data-toggle="tooltip" data-placement="bottom" title="<%= t('repositories.show.button_tooltip.new') %>"
                 class="btn btn-primary editAdd auto-shrink-button"
                 id="addRepositoryRecord" data-view-mode="active">
diff --git a/app/views/repository_columns/_manage_column_modal_index.html.erb b/app/views/repository_columns/_manage_column_modal_index.html.erb
index a4d8e4131..63ab8b353 100644
--- a/app/views/repository_columns/_manage_column_modal_index.html.erb
+++ b/app/views/repository_columns/_manage_column_modal_index.html.erb
@@ -12,7 +12,7 @@
 </div>
 
 <div class="modal-footer">
-  <% if can_create_repository_columns?(@repository) && !@repository.is_a?(SoftLockedRepository) %>
+  <% if can_create_repository_columns?(@repository) %>
     <button id="new-repo-column-modal"
             data-view-mode="active"
             class="btn btn-secondary manage-repo-column"

From 9b0521a1681fb9d79d6f58c6d602cfd5acf4e4da Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Mon, 28 Oct 2024 13:55:07 +0100
Subject: [PATCH 59/96] Create snapshot provisioning immediatelly when task is
 locked [SCI-11185]

---
 app/models/my_module.rb                                  | 6 ++++++
 app/models/my_module_status_consequence.rb               | 2 ++
 .../my_module_status_consequences/repository_snapshot.rb | 9 +++++++--
 3 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/app/models/my_module.rb b/app/models/my_module.rb
index 36b7578ff..690427c26 100644
--- a/app/models/my_module.rb
+++ b/app/models/my_module.rb
@@ -565,6 +565,12 @@ class MyModule < ApplicationRecord
 
     yield
 
+    if status_changing_direction == :forward
+      my_module_status.my_module_status_consequences.each do |consequence|
+        consequence.before_forward_call(self)
+      end
+    end
+
     if my_module_status.my_module_status_consequences.any?(&:runs_in_background?)
       MyModuleStatusConsequencesJob
         .perform_later(self, my_module_status.my_module_status_consequences.to_a, status_changing_direction)
diff --git a/app/models/my_module_status_consequence.rb b/app/models/my_module_status_consequence.rb
index b9b7b2f71..6abce4dc8 100644
--- a/app/models/my_module_status_consequence.rb
+++ b/app/models/my_module_status_consequence.rb
@@ -7,6 +7,8 @@ class MyModuleStatusConsequence < ApplicationRecord
 
   def backward(my_module); end
 
+  def before_forward_call(my_module); end
+
   def runs_in_background?
     false
   end
diff --git a/app/models/my_module_status_consequences/repository_snapshot.rb b/app/models/my_module_status_consequences/repository_snapshot.rb
index 30d47ce73..e39f8efeb 100644
--- a/app/models/my_module_status_consequences/repository_snapshot.rb
+++ b/app/models/my_module_status_consequences/repository_snapshot.rb
@@ -6,9 +6,14 @@ module MyModuleStatusConsequences
       true
     end
 
-    def forward(my_module)
+    def before_forward_call(my_module)
       my_module.assigned_repositories.each do |repository|
-        repository_snapshot = ::RepositorySnapshot.create_preliminary!(repository, my_module)
+        ::RepositorySnapshot.create_preliminary!(repository, my_module)
+      end
+    end
+
+    def forward(my_module)
+      my_module.repository_snapshots.where(status: :provisioning).find_each do |repository_snapshot|
         service = Repositories::SnapshotProvisioningService.call(repository_snapshot: repository_snapshot)
 
         unless service.succeed?

From aae0abcd67d3c4c59e8392034e6adce62ff61d70 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 28 Oct 2024 15:03:05 +0100
Subject: [PATCH 60/96] UI fixes for File versions modal [SCI-11218]

---
 .../shared/content/attachments/context_menu.vue | 12 ++++++------
 .../vue/shared/file_versions_modal.vue          | 17 ++++++++++++-----
 .../active_storage/blob_serializer.rb           | 10 +++++++++-
 3 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/app/javascript/vue/shared/content/attachments/context_menu.vue b/app/javascript/vue/shared/content/attachments/context_menu.vue
index 8d7d67c6d..49135586b 100644
--- a/app/javascript/vue/shared/content/attachments/context_menu.vue
+++ b/app/javascript/vue/shared/content/attachments/context_menu.vue
@@ -135,6 +135,12 @@ export default {
           data_e2e: 'e2e-BT-attachmentOptions-delete'
         });
       }
+      if (this.attachment.attributes.urls.versions) {
+        menu.push({
+          text: this.i18n.t('assets.context_menu.versions'),
+          emit: 'fileVersionsModal'
+        });
+      }
       if (this.attachment.attributes.urls.toggle_view_mode) {
         this.viewModeOptions.forEach((viewMode, i) => {
           menu.push({
@@ -147,12 +153,6 @@ export default {
           });
         });
       }
-      if (this.attachment.attributes.urls.versions) {
-        menu.push({
-          text: this.i18n.t('assets.context_menu.versions'),
-          emit: 'fileVersionsModal'
-        });
-      }
       return menu;
     }
   },
diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
index d1c893c4b..f56c7f7a0 100644
--- a/app/javascript/vue/shared/file_versions_modal.vue
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -12,26 +12,33 @@
           <div class="relative" v-if="fileVersions">
             <div v-for="(fileVersion, index) in fileVersions" :key="fileVersion.id">
               <div class="flex w-full border border-sn-light-grey rounded mb-1.5 p-1.5 items-center">
-                <div class="basis-3/4">
+                <div class="basis-full">
                   <div class="mb-1.5">
                     <span v-if="fileVersion.attributes.version === 1" class="bg-sn-science-blue text-sn-white me-2 px-2 py-0.5 rounded">
                       {{ i18n.t("assets.file_versions_modal.original_file") }}
                     </span>
                     <span v-else class="bg-sn-grey-300 me-2 px-2 py-0.5 rounded">v{{ fileVersion.attributes.version }}</span>
-                    <a :href="fileVersion.attributes.url" target="_blank">{{ fileVersion.attributes.filename }}</a>
+                    <a :href="fileVersion.attributes.url" target="_blank" class="align-text-bottom">
+                      <span :class="{
+                          'max-w-80': !fileVersion.attributes.restored_from_version && fileVersion.attributes.version !== 1,
+                          'max-w-64': !!fileVersion.attributes.restored_from_version || fileVersion.attributes.version === 1
+                        }"
+                        class="text-ellipsis overflow-hidden text-nowrap inline-block align-middle"
+                      >{{ fileVersion.attributes.basename }}.</span><span class="inline-block align-middle">{{ fileVersion.attributes.extension }}</span>
+                    </a>
                     <small class="inline-block ml-1" v-if="fileVersion.attributes.restored_from_version">
                       ({{ i18n.t("assets.file_versions_modal.restored_from_version", { version: fileVersion.attributes.restored_from_version }) }})
                     </small>
                   </div>
                   <div class="flex text-xs text-sn-grey justify-start">
                     <div class="mr-3">{{ fileVersion.attributes.created_at }}</div>
-                    <div class="mr-3">{{ fileVersion.attributes.created_by.full_name }}</div>
+                    <div class="mr-3 text-nowrap text-ellipsis overflow-hidden max-w-52">{{ fileVersion.attributes.created_by.full_name }}</div>
                     <div>{{ Math.round(fileVersion.attributes.byte_size/1024) }}KB</div>
                   </div>
                 </div>
 
                 <div class="basis-1/4 flex justify-end">
-                  <a class="btn btn-icon p-0 mr-3"đ
+                  <a class="btn btn-icon p-0 px-2 hover:bg-sn-light-grey"
                     v-if="enabled || index === 0"
                     :href="fileVersion.attributes.url"
                     target="_blank"
@@ -44,7 +51,7 @@
                     @click="restoreVersion(fileVersion.attributes.version)"
                     data-render-tooltip="true"
                     :title="i18n.t('assets.file_versions_modal.restore')"
-                    class="btn btn-icon p-0 mr-3"
+                    class="btn btn-icon p-0 px-2 hover:bg-sn-light-grey"
                   >
                     <i class="sn-icon sn-icon-restore"></i>
                   </a>
diff --git a/app/serializers/active_storage/blob_serializer.rb b/app/serializers/active_storage/blob_serializer.rb
index c667bdced..155c40555 100644
--- a/app/serializers/active_storage/blob_serializer.rb
+++ b/app/serializers/active_storage/blob_serializer.rb
@@ -4,7 +4,15 @@ module ActiveStorage
   class BlobSerializer < ActiveModel::Serializer
     include Rails.application.routes.url_helpers
 
-    attributes :filename, :url, :created_at, :byte_size, :version, :restored_from_version, :created_by
+    attributes :filename, :extension, :basename, :url, :created_at, :byte_size, :version, :restored_from_version, :created_by
+
+    def basename
+      object.filename.base
+    end
+
+    def extension
+      object.filename.extension_without_delimiter
+    end
 
     def version
       object.metadata['version'] || 1

From 0b7705f95f1608c80fa1c5ebcdfa1c3ce142fd90 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 09:38:46 +0100
Subject: [PATCH 61/96] Bump rexml from 3.3.7 to 3.3.9 (#7998)

Bumps [rexml](https://github.com/ruby/rexml) from 3.3.7 to 3.3.9.
- [Release notes](https://github.com/ruby/rexml/releases)
- [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md)
- [Commits](https://github.com/ruby/rexml/compare/v3.3.7...v3.3.9)

---
updated-dependencies:
- dependency-name: rexml
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index e26778e55..f5fbeaf45 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -613,7 +613,7 @@ GEM
     responders (3.1.1)
       actionpack (>= 5.2)
       railties (>= 5.2)
-    rexml (3.3.7)
+    rexml (3.3.9)
     rgl (0.6.3)
       pairing_heap (>= 0.3.0)
       rexml (~> 3.2, >= 3.2.4)

From 480754d3d4c9acc5d491a8b36a4c54651553b99e Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 29 Oct 2024 09:43:11 +0100
Subject: [PATCH 62/96] Fix date format in file versions modal [SCI-11223]

---
 app/controllers/assets_controller.rb              | 3 ++-
 app/javascript/vue/shared/file_versions_modal.vue | 2 +-
 app/serializers/active_storage/blob_serializer.rb | 4 +++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 92ae7c6d7..86d59579e 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -405,7 +405,8 @@ class AssetsController < ApplicationController
     render(
       json: ActiveModel::SerializableResource.new(
         blobs,
-        each_serializer: ActiveStorage::BlobSerializer
+        each_serializer: ActiveStorage::BlobSerializer,
+        user: current_user
       ).as_json.merge(
         enabled: VersionedAttachments.enabled?,
         enable_url: ENV.fetch('SCINOTE_FILE_VERSIONING_ENABLE_URL', nil)
diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
index f56c7f7a0..767592321 100644
--- a/app/javascript/vue/shared/file_versions_modal.vue
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -33,7 +33,7 @@
                   <div class="flex text-xs text-sn-grey justify-start">
                     <div class="mr-3">{{ fileVersion.attributes.created_at }}</div>
                     <div class="mr-3 text-nowrap text-ellipsis overflow-hidden max-w-52">{{ fileVersion.attributes.created_by.full_name }}</div>
-                    <div>{{ Math.round(fileVersion.attributes.byte_size/1024) }}KB</div>
+                    <div>{{ i18n.t("assets.file_versions_modal.size") }}: {{ Math.round(fileVersion.attributes.byte_size/1024) }}KB</div>
                   </div>
                 </div>
 
diff --git a/app/serializers/active_storage/blob_serializer.rb b/app/serializers/active_storage/blob_serializer.rb
index 155c40555..a758badd7 100644
--- a/app/serializers/active_storage/blob_serializer.rb
+++ b/app/serializers/active_storage/blob_serializer.rb
@@ -23,7 +23,9 @@ module ActiveStorage
     end
 
     def created_at
-      object.created_at.strftime('%B %d, %Y at %H:%M')
+      return object.created_at unless @instance_options[:user]
+
+      object.created_at.strftime("#{@instance_options[:user].date_format}, %H:%M")
     end
 
     def created_by

From c6a4e71d69dd8c2482c00e73f0a64c760f1775a5 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 29 Oct 2024 09:56:03 +0100
Subject: [PATCH 63/96] Enable file editing for inventory files [SCI-11041]

---
 app/controllers/assets_controller.rb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 3497dfbfa..8a9e2ad0c 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -22,12 +22,11 @@ class AssetsController < ApplicationController
   before_action :check_restore_permission, only: :restore_version
 
   def file_preview
-    editable = can_manage_asset?(@asset) && @asset.repository_asset_value.blank?
     render json: { html: render_to_string(
       partial: 'shared/file_preview/content',
       locals: {
         asset: @asset,
-        can_edit: editable,
+        can_edit: can_manage_asset?(@asset),
         gallery: params[:gallery],
         preview: params[:preview]
       },

From 1283632e338069e995deb83f82247274ab4ed921 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 13:25:13 +0100
Subject: [PATCH 64/96] Bump elliptic from 6.5.7 to 6.6.0 (#8001)

Bumps [elliptic](https://github.com/indutny/elliptic) from 6.5.7 to 6.6.0.
- [Commits](https://github.com/indutny/elliptic/compare/v6.5.7...v6.6.0)

---
updated-dependencies:
- dependency-name: elliptic
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 yarn.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/yarn.lock b/yarn.lock
index 5ae46aae5..d0d4c1fb0 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -3548,9 +3548,9 @@ element-resize-detector@^1.2.1:
     batch-processor "1.0.0"
 
 elliptic@^6.5.3, elliptic@^6.5.4:
-  version "6.5.7"
-  resolved "https://registry.yarnpkg.com/elliptic/-/elliptic-6.5.7.tgz#8ec4da2cb2939926a1b9a73619d768207e647c8b"
-  integrity sha512-ESVCtTwiA+XhY3wyh24QqRGBoP3rEdDUl3EDUUo9tft074fi19IrdpH7hLCMMP3CIj7jb3W96rn8lt/BqIlt5Q==
+  version "6.6.0"
+  resolved "https://registry.yarnpkg.com/elliptic/-/elliptic-6.6.0.tgz#5919ec723286c1edf28685aa89261d4761afa210"
+  integrity sha512-dpwoQcLc/2WLQvJvLRHKZ+f9FgOdjnq11rurqwekGQygGPsYSK29OMMD2WalatiqQ+XGFDglTNixpPfI+lpaAA==
   dependencies:
     bn.js "^4.11.9"
     brorand "^1.1.0"

From d707f9121c71a96bbd8853d719f473d14b913e64 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Tue, 29 Oct 2024 15:12:27 +0100
Subject: [PATCH 65/96] Remove constraint for the protocol template name
 [SCI-10851]

---
 app/models/protocol.rb | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 1c961de68..6a5a61e2a 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -75,21 +75,6 @@ class Protocol < ApplicationRecord
     # Only one draft can exist for each protocol
     validate :ensure_single_draft
   end
-  with_options if: -> { in_repository? && !parent && !archived_changed?(from: false) } do |protocol|
-    # Active protocol must have unique name inside its team
-    protocol
-      .validates_uniqueness_of :name, case_sensitive: false,
-                               scope: :team,
-                               conditions: lambda {
-                                 where(
-                                   protocol_type: [
-                                     Protocol.protocol_types[:in_repository_published_original],
-                                     Protocol.protocol_types[:in_repository_draft]
-                                   ],
-                                   parent_id: nil
-                                 )
-                               }
-  end
   with_options if: -> { in_repository? && archived? && !previous_version } do |protocol|
     protocol.validates :archived_by, presence: true
     protocol.validates :archived_on, presence: true

From ba450688070011af09531a2b4f86def9a5c909f9 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 29 Oct 2024 16:41:31 +0100
Subject: [PATCH 66/96] Add file delete confirmation modal to item sidebar
 [SCI-11198]

---
 .../RepositoryAssetValue.vue                  | 29 +++++++++++++------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/app/javascript/vue/repository_item_sidebar/repository_values/RepositoryAssetValue.vue b/app/javascript/vue/repository_item_sidebar/repository_values/RepositoryAssetValue.vue
index 4cc769ba7..ea8d5bfe9 100644
--- a/app/javascript/vue/repository_item_sidebar/repository_values/RepositoryAssetValue.vue
+++ b/app/javascript/vue/repository_item_sidebar/repository_values/RepositoryAssetValue.vue
@@ -26,9 +26,9 @@
               data-id="true" data-status="asset-present" :data-preview-url=this?.preview_url :href=this?.url>
               {{ file_name }}
             </a>
-            <tooltip-preview v-if="tooltipShowing && medium_preview_url" :id="id" :url="url" :file_name="file_name"
+            <TooltipPreview v-if="tooltipShowing && medium_preview_url" :id="id" :url="url" :file_name="file_name"
               :preview_url="preview_url" :icon_html="icon_html" :medium_preview_url="medium_preview_url">
-            </tooltip-preview>
+            </TooltipPreview>
           </div>
         </div>
       </div>
@@ -44,17 +44,26 @@
       {{ error }}
     </div>
     <input type="file" ref="fileInput" @change="handleFileChange" style="display: none" />
+
+    <Teleport to="body">
+      <ConfirmationModal
+        :title="i18n.t('repositories.modal_delete_asset_value.title')"
+        :description="i18n.t('repositories.modal_delete_asset_value.notice_html')"
+        confirmClass="btn btn-danger"
+        :confirmText="i18n.t('repositories.modal_delete_asset_value.delete')"
+        ref="deleteRepositoryAssetValueModal"
+      ></ConfirmationModal>
+    </Teleport>
   </div>
 </template>
 
 <script>
 import TooltipPreview from './TooltipPreview.vue';
+import ConfirmationModal from '../../shared/confirmation_modal.vue';
 
 export default {
   name: 'RepositoryAssetvalue',
-  components: {
-    'tooltip-preview': TooltipPreview
-  },
+  components: { TooltipPreview, ConfirmationModal },
   data() {
     return {
       tooltipShowing: false,
@@ -103,10 +112,12 @@ export default {
         this.uploadFiles(event.target.files[0]);
       }
     },
-    clearFile() {
-      this.$refs.fileInput.value = '';
-      this.error = '';
-      this.updateCell(null);
+    async clearFile() {
+      if (await this.$refs.deleteRepositoryAssetValueModal.show()) {
+        this.$refs.fileInput.value = '';
+        this.error = '';
+        this.updateCell(null);
+      }
     },
     uploadFiles(file) {
       this.uploading = true;

From 2d6d47bf692c73c086eacbeefcf1a1879b5087c7 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Wed, 30 Oct 2024 11:12:55 +0100
Subject: [PATCH 67/96] Fix look of the select all button [SCI-11219]

---
 app/assets/javascripts/sitewide/dropdown_selector.js | 2 +-
 app/assets/stylesheets/shared/dropdown_selector.scss | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/app/assets/javascripts/sitewide/dropdown_selector.js b/app/assets/javascripts/sitewide/dropdown_selector.js
index b78704270..41902a504 100644
--- a/app/assets/javascripts/sitewide/dropdown_selector.js
+++ b/app/assets/javascripts/sitewide/dropdown_selector.js
@@ -353,7 +353,7 @@ var dropdownSelector = (function() {
 
     // If we setup Select All we draw it and add correspond logic
     if (selectElement.data('select-all-button')) {
-      $(`<div class="dropdown-select-all btn">${selectElement.data('select-all-button')}</div>`)
+      $(`<div class="dropdown-select-all">${selectElement.data('select-all-button')}</div>`)
         .appendTo(dropdownContainer.find('.dropdown-container'))
         .click(() => {
           // For AJAX dropdown we will use only "Deselect All"
diff --git a/app/assets/stylesheets/shared/dropdown_selector.scss b/app/assets/stylesheets/shared/dropdown_selector.scss
index ef119838a..21c9ff9e8 100644
--- a/app/assets/stylesheets/shared/dropdown_selector.scss
+++ b/app/assets/stylesheets/shared/dropdown_selector.scss
@@ -175,6 +175,10 @@
       top: 0;
       width: 100%;
       z-index: 5;
+
+      &:hover {
+        background: $color-concrete;
+      }
     }
 
     .dropdown-blank {

From 19c8c7c504245a68cf7d216f8974c02e3f1cd2ae Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Wed, 30 Oct 2024 11:41:19 +0100
Subject: [PATCH 68/96] Fix adding of well plates from step toolbar [SCI-11228]

---
 app/javascript/vue/results/result.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/javascript/vue/results/result.vue b/app/javascript/vue/results/result.vue
index 3dac62e7f..b2e449cb7 100644
--- a/app/javascript/vue/results/result.vue
+++ b/app/javascript/vue/results/result.vue
@@ -134,7 +134,7 @@
         <ContentToolbar
           v-if="orderedElements.length > 2 && insertMenu.length > 0"
           :insertMenu="insertMenu"
-          @create:table="(...args) => this.createElement('table', ...args)"
+          @create:table="(args) => args ? this.createElement('table', ...args) : this.createElement('table')"
           @create:text="createElement('text')"
           @create:file="openLoadFromComputer"
           @create:wopi_file="openWopiFileModal"

From 649a8abe66ac9ad6ea0f3acc6223f513f95b6cea Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Wed, 30 Oct 2024 11:44:30 +0100
Subject: [PATCH 69/96] Fixes for notifications improvment [SCI-11235]

---
 .../notifications/notification_item.vue         | 17 +++++++++++------
 .../notifications/notifications_flyout.vue      |  4 +++-
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/app/javascript/vue/navigation/notifications/notification_item.vue b/app/javascript/vue/navigation/notifications/notification_item.vue
index 9ab899648..15aea8d55 100644
--- a/app/javascript/vue/navigation/notifications/notification_item.vue
+++ b/app/javascript/vue/navigation/notifications/notification_item.vue
@@ -1,15 +1,17 @@
 <template>
-  <div class="sci-navigation--notificaitons-flyout-notification">
+  <div class="sci-navigation--notificaitons-flyout-notification hover:bg-sn-super-light-grey !px-2 !-mx-2">
     <div class="flex item-center">
-      <div class="sci-navigation--notificaitons-flyout-notification-date">
-        {{ notification.attributes.created_at }}
-      </div>
+      <a :href="lastBreadcrumbUrl" @click="toggleRead(true); closeFlyout()" class="hover:no-underline text-black hover:text-black grow">
+        <div class="sci-navigation--notificaitons-flyout-notification-date">
+          {{ notification.attributes.created_at }}
+        </div>
+      </a>
       <div class="ml-auto cursor-pointer" @click="toggleRead()">
         <div v-if="!notification.attributes.checked" class="w-2.5 h-2.5 bg-sn-coral rounded-full cursor-pointer"></div>
-        <div v-else class="w-2.5 h-2.5 border-2 border-sn-grey rounded-full border-solid cursor-pointer"></div>
+        <div v-else class="w-2.5 h-2.5 border-2 border-sn-grey rounded-full border-solid cursor-pointer hover:border-sn-coral"></div>
       </div>
     </div>
-    <a :href="lastBreadcrumbUrl" @click="toggleRead(true)" class="hover:no-underline text-black hover:text-black">
+    <a :href="lastBreadcrumbUrl" @click="toggleRead(true); closeFlyout()" class="hover:no-underline text-black hover:text-black">
       <div class="sci-navigation--notificaitons-flyout-notification-title"
           v-html="notification.attributes.title"
           :data-seen="notification.attributes.checked"></div>
@@ -42,6 +44,9 @@ export default {
     }
   },
   methods: {
+    closeFlyout() {
+      this.$emit('close');
+    },
     toggleRead(check = false) {
       const params = {};
       if (!this.notification.attributes.checked || check) {
diff --git a/app/javascript/vue/navigation/notifications/notifications_flyout.vue b/app/javascript/vue/navigation/notifications/notifications_flyout.vue
index 8f21e3c0d..880aa6133 100644
--- a/app/javascript/vue/navigation/notifications/notifications_flyout.vue
+++ b/app/javascript/vue/navigation/notifications/notifications_flyout.vue
@@ -28,7 +28,7 @@
       >
       {{ i18n.t('nav.notifications.read') }}
       </div>
-      <div class="py-4 ml-auto cursor-pointer" @click="markAllNotificationsAsRead">
+      <div v-if="activeTab !== 'read'" class="py-2 ml-auto cursor-pointer" @click="markAllNotificationsAsRead">
         {{ i18n.t('nav.notifications.read_all') }}
       </div>
     </div>
@@ -39,12 +39,14 @@
       </div>
       <NotificationItem v-for="notification in todayNotifications" :key="notification.type_of + '-' + notification.id"
         @updateNotification="updateNotification"
+        @close="$emit('close')"
         :notification="notification" />
       <div class="sci-navigation--notificaitons-flyout-subtitle" v-if="olderNotifications.length">
         {{ i18n.t('nav.notifications.older') }}
       </div>
       <NotificationItem v-for="notification in olderNotifications" :key="notification.type_of + '-' + notification.id"
         @updateNotification="updateNotification"
+        @close="$emit('close')"
         :notification="notification" />
       <div class="next-page-loader">
         <img src="/images/medium/loading.svg" v-if="loadingPage" />

From d3292f6c4a5bf39c36b025b29eab5c5abaa6ce82 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 30 Oct 2024 15:23:48 +0100
Subject: [PATCH 70/96] Clone file version history when making new protocol
 draft [SCI-11230]

---
 app/models/asset.rb    | 64 +++++++++++++++++++++++++-----------------
 app/models/protocol.rb | 16 ++++++-----
 app/models/step.rb     |  4 +--
 3 files changed, 49 insertions(+), 35 deletions(-)

diff --git a/app/models/asset.rb b/app/models/asset.rb
index e9ed753cd..74b839d11 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -146,49 +146,61 @@ class Asset < ApplicationRecord
     file&.blob&.content_type
   end
 
-  def duplicate(new_name: nil)
+  def duplicate(new_name: nil, include_file_versions: false)
     new_asset = dup
     file.filename = new_name if new_name
 
     return unless new_asset.save
 
-    duplicate_file(new_asset, new_name: new_name)
+    duplicate_file(new_asset, new_name: new_name, include_file_versions: include_file_versions)
+
     new_asset
   end
 
-  def duplicate_file(to_asset, new_name: nil)
+  def duplicate_blob(blob, attach_method, metadata: nil)
+    new_blob = nil
+
+    blob.open do |tmp_file|
+      new_blob = ActiveStorage::Blob.create_and_upload!(
+        io: tmp_file,
+        filename: blob.filename,
+        metadata: metadata || blob.metadata
+      )
+
+      attach_method.call(new_blob)
+    end
+
+    new_blob
+  end
+
+  def duplicate_file_versions(to_asset)
+    previous_files.map(&:blob).sort_by(&:created_at).each do |blob|
+      duplicate_blob(blob, to_asset.previous_files.method(:attach)) # .update_column(:created_at, blob.created_at)
+    end
+  end
+
+  def duplicate_file(to_asset, new_name: nil, include_file_versions: false)
     return unless file.attached?
 
     raise ArgumentError, 'Destination asset should be persisted first!' unless to_asset.persisted?
 
-    file.blob.open do |tmp_file|
-      metadata = blob.metadata.dup
+    metadata = file.blob.metadata.dup
 
-      # set new name in metadata for OVE and MarvinJS files
-      if new_name && file.blob.metadata['asset_type'].in?(%w(gene_sequence marvinjs))
-        new_metadata_name = File.basename(new_name, File.extname(new_name))
-        metadata['name'] = new_metadata_name
-      end
-
-      to_blob = ActiveStorage::Blob.create_and_upload!(
-        io: tmp_file,
-        filename: blob.filename,
-        metadata: metadata
-      )
-      to_asset.attach_file_version(to_blob)
+    # set new name in metadata for OVE and MarvinJS files
+    if new_name && file.blob.metadata['asset_type'].in?(%w(gene_sequence marvinjs))
+      new_metadata_name = File.basename(new_name, File.extname(new_name))
+      metadata['name'] = new_metadata_name
     end
 
-    if preview_image.attached?
-      preview_image.blob.open do |tmp_preview_image|
-        to_blob = ActiveStorage::Blob.create_and_upload!(
-          io: tmp_preview_image,
-          filename: blob.filename,
-          metadata: blob.metadata
-        )
-        to_asset.attach_preview_image_version(to_blob)
-      end
+    unless include_file_versions
+      metadata.delete('version')
+      metadata.delete('restored_from_version')
     end
 
+    duplicate_file_versions(to_asset) if include_file_versions
+    duplicate_blob(blob, to_asset.method(:attach_file_version), metadata: metadata)
+    duplicate_blob(preview_image.blob, to_asset.method(:attach_preview_image_version)) if preview_image.attached?
+
     to_asset.post_process_file
   end
 
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 46156dc67..061801c69 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -351,7 +351,9 @@ class Protocol < ApplicationRecord
   end
 
   # Deep-clone given array of assets
-  def self.deep_clone_assets(assets_to_clone)
+  # There is an issue with Delayed Job delayed methods, ruby 3, and keyword arguments (https://github.com/collectiveidea/delayed_job/issues/1134)
+  # so we're forced to use a normal argument with default value.
+  def self.deep_clone_assets(assets_to_clone, include_file_versions = false)
     ActiveRecord::Base.no_touching do
       assets_to_clone.each do |src_id, dest_id|
         src = Asset.find_by(id: src_id)
@@ -360,12 +362,12 @@ class Protocol < ApplicationRecord
         next unless src.present? && dest.present?
 
         # Clone file
-        src.duplicate_file(dest)
+        src.duplicate_file(dest, include_file_versions: include_file_versions)
       end
     end
   end
 
-  def self.clone_contents(src, dest, current_user, clone_keywords, only_contents = false)
+  def self.clone_contents(src, dest, current_user, clone_keywords, only_contents: false, include_file_versions: false)
     dest.update(description: src.description, name: src.name) unless only_contents
 
     src.clone_tinymce_assets(dest, dest.team)
@@ -382,7 +384,7 @@ class Protocol < ApplicationRecord
 
     # Copy steps
     src.steps.each do |step|
-      step.duplicate(dest, current_user, step_position: step.position)
+      step.duplicate(dest, current_user, step_position: step.position, include_file_versions: include_file_versions)
     end
   end
 
@@ -615,7 +617,7 @@ class Protocol < ApplicationRecord
     return draft if draft.invalid?
 
     ActiveRecord::Base.no_touching do
-      draft = deep_clone(draft, current_user)
+      draft = deep_clone(draft, current_user, include_file_versions: true)
     end
 
     parent_protocol.user_assignments.each do |parent_user_assignment|
@@ -760,7 +762,7 @@ class Protocol < ApplicationRecord
     end
   end
 
-  def deep_clone(clone, current_user)
+  def deep_clone(clone, current_user, include_file_versions: false)
     # Save cloned protocol first
     success = clone.save
 
@@ -772,7 +774,7 @@ class Protocol < ApplicationRecord
 
     raise ActiveRecord::RecordNotSaved unless success
 
-    Protocol.clone_contents(self, clone, current_user, true, true)
+    Protocol.clone_contents(self, clone, current_user, true, only_contents: true, include_file_versions: include_file_versions)
 
     clone.reload
     clone
diff --git a/app/models/step.rb b/app/models/step.rb
index 4652e0c47..b777c7694 100644
--- a/app/models/step.rb
+++ b/app/models/step.rb
@@ -117,7 +117,7 @@ class Step < ApplicationRecord
     step_texts.order(created_at: :asc).first
   end
 
-  def duplicate(protocol, user, step_position: nil, step_name: nil)
+  def duplicate(protocol, user, step_position: nil, step_name: nil, include_file_versions: false)
     ActiveRecord::Base.transaction do
       assets_to_clone = []
 
@@ -153,7 +153,7 @@ class Step < ApplicationRecord
       end
 
       # Call clone helper
-      Protocol.delay(queue: :assets).deep_clone_assets(assets_to_clone)
+      Protocol.delay(queue: :assets).deep_clone_assets(assets_to_clone, include_file_versions)
 
       new_step
     end

From 96d5176bf10c73f0ecccbc8774ae5bf253dd87f3 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Mon, 4 Nov 2024 10:57:14 +0100
Subject: [PATCH 71/96] Fix image preview if image is delete immediately
 [SCI-11236]

---
 app/assets/javascripts/sitewide/active_storage_previews.js | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/assets/javascripts/sitewide/active_storage_previews.js b/app/assets/javascripts/sitewide/active_storage_previews.js
index fe0ab846e..d1085dd33 100644
--- a/app/assets/javascripts/sitewide/active_storage_previews.js
+++ b/app/assets/javascripts/sitewide/active_storage_previews.js
@@ -22,8 +22,10 @@ var ActiveStoragePreviews = (function() {
       if (!$(img).parent().hasClass('processing')) $(img).parent().addClass('processing');
 
       setTimeout(() => {
-        img.src = src;
-        img.retryCount += 1;
+        if (document.body.contains(img)) {
+          img.src = src;
+          img.retryCount += 1;
+        }
       }, RETRY_DELAY);
     },
     showPreview: function(ev) {

From 53b60a6b1eb5ddb24015bf7c5b737b794ee75ca9 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 4 Nov 2024 13:54:18 +0100
Subject: [PATCH 72/96] Fix generation of docx report preview [SCI-11227]

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

diff --git a/app/services/pdf_preview_service.rb b/app/services/pdf_preview_service.rb
index dce368ea2..cb12e2159 100644
--- a/app/services/pdf_preview_service.rb
+++ b/app/services/pdf_preview_service.rb
@@ -31,7 +31,7 @@ class PdfPreviewService
         end
 
         ActiveRecord::Base.no_touching do
-          attached.attach(io: File.open(preview_file), filename: "#{@blob.filename.base}.pdf")
+          @attached.attach(io: File.open(preview_file), filename: "#{@blob.filename.base}.pdf")
         end
         Rails.logger.info("Finished preparing PDF preview for file #{@blob.filename.sanitized}.")
       end

From 0a4ddb8038bda10ada39557995cef714aa1a929c Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 4 Nov 2024 15:10:28 +0100
Subject: [PATCH 73/96] Fix repository asset permission checks [SCI-11238]

---
 app/controllers/assets_controller.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 813298a3f..8c5c7ca2f 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -453,7 +453,8 @@ class AssetsController < ApplicationController
     @asset = Asset.find_by(id: params[:id])
     return render_404 unless @asset
 
-    current_user.permission_team = @asset.team
+    # don't overwrite permission team if asset is in a repositoy, since then sharing rules may apply and depend on user's current team
+    current_user.permission_team = @asset.team unless @asset.repository_cell
 
     @assoc ||= @asset.step
     @assoc ||= @asset.result

From d0877c7d1591164922e2a59f17fb766c35c028f7 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 5 Nov 2024 10:56:08 +0100
Subject: [PATCH 74/96] Change link in activities for protocols [SCI-11240]

---
 app/helpers/global_activities_helper.rb                   | 2 +-
 app/views/global_activities/references/_protocol.html.erb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/helpers/global_activities_helper.rb b/app/helpers/global_activities_helper.rb
index af945712a..4d09aaee1 100644
--- a/app/helpers/global_activities_helper.rb
+++ b/app/helpers/global_activities_helper.rb
@@ -91,7 +91,7 @@ module GlobalActivitiesHelper
              end
     when Protocol
       if obj.my_module.nil?
-        path = protocols_path(team: obj.team.id)
+        path = protocol_path(obj)
       elsif obj.my_module.navigable?
         path = protocols_my_module_path(obj.my_module)
       else
diff --git a/app/views/global_activities/references/_protocol.html.erb b/app/views/global_activities/references/_protocol.html.erb
index 1ff72f58b..930a249cf 100644
--- a/app/views/global_activities/references/_protocol.html.erb
+++ b/app/views/global_activities/references/_protocol.html.erb
@@ -9,7 +9,7 @@
   <% if subject.in_repository? %>
     <div class="ga-breadcrumb">
       <span class="sn-icon sn-icon-protocols-templates"></span>
-        <%= route_to_other_team protocols_path(team: subject.team),
+        <%= route_to_other_team protocol_path(subject),
                                 team,
                                 subject.name&.truncate(Constants::NAME_TRUNCATION_LENGTH),
                                 title: subject.name %>

From 83150f59c066a1a61d3afd215320f1bca29afa09 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Tue, 5 Nov 2024 16:21:53 +0100
Subject: [PATCH 75/96] Optimize date time reminders query for inventories
 [SCI-11156] (#8018)

---
 app/models/repository_cell.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/models/repository_cell.rb b/app/models/repository_cell.rb
index 9afda532d..73a9f3bd8 100644
--- a/app/models/repository_cell.rb
+++ b/app/models/repository_cell.rb
@@ -77,9 +77,9 @@ class RepositoryCell < ApplicationRecord
       '"repository_date_time_values"."id" = "repository_cells"."value_id" AND ' \
       '"repository_cells"."value_type" = \'RepositoryDateTimeValueBase\' ' \
       'AND repository_reminder_columns.metadata ->> \'reminder_value\' <> \'\' AND ' \
-      '(repository_date_time_values.data - NOW()) <= ' \
-      '(repository_reminder_columns.metadata ->> \'reminder_value\')::int * ' \
-      '(repository_reminder_columns.metadata ->> \'reminder_unit\')::int * interval \'1 sec\''
+      'repository_date_time_values.data <= ' \
+      '(NOW() AT TIME ZONE \'UTC\') + (repository_reminder_columns.metadata ->> \'reminder_value\')::int * ' \
+      '(repository_reminder_columns.metadata ->> \'reminder_unit\')::int * \'1 SECOND\'::interval'
     ).joins(
       'LEFT OUTER JOIN "hidden_repository_cell_reminders" ON ' \
       '"repository_cells"."id" = "hidden_repository_cell_reminders"."repository_cell_id" AND ' \

From 02174196033df5b104dc3b90771eba12d1ab0d1c Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Thu, 7 Nov 2024 11:53:27 +0100
Subject: [PATCH 76/96] Fix error during non-grid box creation [SCI-11246]

---
 app/javascript/vue/storage_locations/modals/new_edit.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/storage_locations/modals/new_edit.vue b/app/javascript/vue/storage_locations/modals/new_edit.vue
index b0a97df6f..16057a0ac 100644
--- a/app/javascript/vue/storage_locations/modals/new_edit.vue
+++ b/app/javascript/vue/storage_locations/modals/new_edit.vue
@@ -44,11 +44,11 @@
                   <span class="sci-radio-label"></span>
                 </div>
                 <span>{{ i18n.t('storage_locations.index.edit_modal.grid') }}</span>
-                <div class="sci-input-container-v2 !w-28">
+                <div class="sci-input-container-v2 !w-28" v-if="object.metadata.dimensions">
                   <input type="number" :disabled="!canChangeGrid"  v-model="object.metadata.dimensions[0]" min="1" max="24">
                 </div>
                 <i class="sn-icon sn-icon-close-small"></i>
-                <div class="sci-input-container-v2 !w-28">
+                <div class="sci-input-container-v2 !w-28" v-if="object.metadata.dimensions">
                   <input type="number" :disabled="!canChangeGrid"  v-model="object.metadata.dimensions[1]" min="1" max="24">
                 </div>
               </div>

From 1a5530efdec50e6f668c701869657960688968bf Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 7 Nov 2024 11:59:36 +0100
Subject: [PATCH 77/96] Add 203dpi label templates [SCI-10901]

---
 app/models/team.rb                            |  1 +
 app/models/zebra_label_template.rb            | 11 ++++++++
 config/initializers/extends.rb                | 18 +++++++++++++
 config/locales/en.yml                         |  3 ++-
 ...0240718073215_add203_dpi_label_template.rb | 26 +++++++++++++++++++
 5 files changed, 58 insertions(+), 1 deletion(-)
 create mode 100644 db/migrate/20240718073215_add203_dpi_label_template.rb

diff --git a/app/models/team.rb b/app/models/team.rb
index 311fc27bb..ac4da78fc 100644
--- a/app/models/team.rb
+++ b/app/models/team.rb
@@ -221,6 +221,7 @@ class Team < ApplicationRecord
 
   def create_default_label_templates
     ZebraLabelTemplate.default.update(team: self, default: true)
+    ZebraLabelTemplate.default_203dpi.update(team: self, default: false)
     FluicsLabelTemplate.default.update(team: self, default: true)
   end
 end
diff --git a/app/models/zebra_label_template.rb b/app/models/zebra_label_template.rb
index a3174b05a..619271a2a 100644
--- a/app/models/zebra_label_template.rb
+++ b/app/models/zebra_label_template.rb
@@ -11,4 +11,15 @@ class ZebraLabelTemplate < LabelTemplate
       density: 12
     )
   end
+
+  def self.default_203dpi
+    ZebraLabelTemplate.new(
+      name: I18n.t('label_templates.default_zebra_name_203dpi'),
+      width_mm: 25.4,
+      height_mm: 12.7,
+      content: Extends::DEFAULT_LABEL_TEMPLATE_203DPI[:zpl],
+      unit: 0,
+      density: 12
+    )
+  end
 end
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index e891e9749..1bae5cbbd 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -619,6 +619,24 @@ class Extends
       HEREDOC
   }
 
+  DEFAULT_LABEL_TEMPLATE_203DPI = {
+    zpl:
+      <<~HEREDOC
+        ^XA
+        ^MTT
+        ^MUD,200,200
+        ^PR2
+        ^MD30
+        ^LH0,8
+        ^PW180
+        ^CF0,15
+        ^FO0,5^FD{{ITEM_ID}}^FS
+        ^FO0,13^BQN,2,3^FDMA,{{ITEM_ID}}^FS
+        ^FO70,27^FB100,2,0,L^FD{{NAME}}^FS^FS
+        ^XZ
+      HEREDOC
+  }
+
   LABEL_TEMPLATE_FORMAT_MAP = {
     'ZebraLabelTemplate' => 'ZPL',
     'FluicsLabelTemplate' => 'Fluics'
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 17ecd6671..496297c9f 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1045,7 +1045,8 @@ en:
     types:
       fluics_label_template: 'Fluics'
       zebra_label_template: 'ZPL'
-    default_zebra_name: 'SciNote Item (ZPL)'
+    default_zebra_name: 'SciNote Item (ZPL, 300dpi)'
+    default_zebra_name_203dpi: 'SciNote Item (ZPL, 203dpi)'
     default_fluics_name: 'SciNote Item (Fluics)'
     new_label_template: 'New label'
     fluics:
diff --git a/db/migrate/20240718073215_add203_dpi_label_template.rb b/db/migrate/20240718073215_add203_dpi_label_template.rb
new file mode 100644
index 000000000..7e9adc45f
--- /dev/null
+++ b/db/migrate/20240718073215_add203_dpi_label_template.rb
@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+class Add203DpiLabelTemplate < ActiveRecord::Migration[7.0]
+  def up
+    Team.find_each do |team|
+      team.label_templates.find_by(type: 'ZebraLabelTemplate', name: 'SciNote Item (ZPL)')&.update(name: I18n.t('label_templates.default_zebra_name'))
+      team.label_templates.create!(
+        type: 'ZebraLabelTemplate',
+        name: I18n.t('label_templates.default_zebra_name_203dpi'),
+        default: false,
+        content: Extends::DEFAULT_LABEL_TEMPLATE_203DPI,
+        width_mm: 25.4,
+        height_mm: 12.7,
+        unit: 'in',
+        density: 12
+      )
+    end
+  end
+
+  def down
+    Team.find_each do |team|
+      team.label_templates.find_by(type: 'ZebraLabelTemplate', name: I18n.t('label_templates.default_zebra_name'))&.update(name: 'SciNote Item (ZPL)')
+      team.label_templates.find_by(type: 'ZebraLabelTemplate', name: I18n.t('label_templates.default_zebra_name_203dpi'))&.destroy
+    end
+  end
+end

From 7231224d84122b140d028faaa345791e9958cc2a Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 7 Nov 2024 15:47:51 +0100
Subject: [PATCH 78/96] Fix displaying of long tinymce tables [SCI-11241]

---
 .../javascripts/my_modules/protocols.js       | 14 ++--------
 .../shareable_links/handson_table_wraping.js  | 21 ++++++---------
 app/assets/javascripts/sitewide/utils.js      | 27 +++++++------------
 app/javascript/packs/tiny_mce.js              |  9 +++----
 4 files changed, 23 insertions(+), 48 deletions(-)

diff --git a/app/assets/javascripts/my_modules/protocols.js b/app/assets/javascripts/my_modules/protocols.js
index 7d74d1e41..70dbc5593 100644
--- a/app/assets/javascripts/my_modules/protocols.js
+++ b/app/assets/javascripts/my_modules/protocols.js
@@ -29,7 +29,8 @@ function initEditMyModuleDescription() {
   });
 
   setTimeout(function() {
-    TinyMCE.wrapTables(viewObject);
+    const notesContainerEl = document.getElementById('notes-container');
+    window.wrapTables(notesContainerEl);
   }, 100);
 }
 
@@ -327,16 +328,6 @@ function initAccessModal() {
   });
 }
 
-function initWrapTables() {
-  const viewMode = new URLSearchParams(window.location.search).get('view_mode');
-  if (['archived', 'locked'].includes(viewMode)) {
-    setTimeout(() => {
-      const notesContainerEl = document.getElementById('notes-container');
-      window.wrapTables(notesContainerEl);
-    }, 100);
-  }
-}
-
 /**
  * Initializes page
  */
@@ -348,7 +339,6 @@ function init() {
   initProtocolSectionOpenEvent();
   initDetailsDropdown();
   initAccessModal();
-  initWrapTables();
 }
 
 init();
diff --git a/app/assets/javascripts/shareable_links/handson_table_wraping.js b/app/assets/javascripts/shareable_links/handson_table_wraping.js
index 084c6d1ae..68c91b104 100644
--- a/app/assets/javascripts/shareable_links/handson_table_wraping.js
+++ b/app/assets/javascripts/shareable_links/handson_table_wraping.js
@@ -1,17 +1,12 @@
 /* global */
 
 (function () {
-  const rtf = $('.rtf-view').toArray();
-  for (let i = 0; i < rtf.length; i += 1) {
-    const container = $(rtf[i]).find('table').toArray();
-
-    for (let j = 0; j < container.length; j += 1) {
-      const table = $(container[j]);
-      if ($(table).parent().hasClass('table-wrapper')) return;
-
-      $(table).wrap(`
-        <div class="table-wrapper w-full" style="overflow: auto;"></div>
-      `);
-    }
-  }
+  $('.rtf-view').toArray().forEach((rtf) => {
+    $(rtf).find('table').toArray().forEach((table) => {
+      if ($(table).parents('table').length === 0) {
+        $(table).css('float', 'none')
+          .wrapAll('<div class="table-wrapper w-full" style="overflow: auto"></div>');
+      }
+    });
+  });
 }());
diff --git a/app/assets/javascripts/sitewide/utils.js b/app/assets/javascripts/sitewide/utils.js
index d4ae79462..bfd02c99f 100644
--- a/app/assets/javascripts/sitewide/utils.js
+++ b/app/assets/javascripts/sitewide/utils.js
@@ -142,23 +142,14 @@ $.fn.initSubmitModal = function(modalID, modelName) {
  * @returns {string} - HTML with tables wrapped.
  */
 function wrapTables(htmlStringOrDomEl) {
-  if (typeof htmlStringOrDomEl === 'string') {
-    const container = $(`<span class="text-base">${htmlStringOrDomEl}</span>`);
-    container.find('table').toArray().forEach((table) => {
-      if ($(table).parent().hasClass('table-wrapper')) return;
-      $(table).css('float', 'none').wrapAll(`
-          <div class="table-wrapper" style="overflow: auto; width: 100%"></div>
-        `);
-    });
-    return container.prop('outerHTML');
-  }
-  // Check if the value is a DOM element
-  if (htmlStringOrDomEl instanceof Element) {
-    const tableElement = $(htmlStringOrDomEl).find('table');
-    if (tableElement.length > 0) {
-      tableElement.wrap('<div class="table-wrapper" style="overflow: auto; width: 100%"></div>');
-      const updatedHtml = $(htmlStringOrDomEl).html();
-      $(htmlStringOrDomEl).replaceWith(updatedHtml);
+  const htmlContent = `<span class="text-base">${htmlStringOrDomEl}</span>`;
+  const container = typeof htmlStringOrDomEl === 'string' ? $(htmlContent) : $(htmlStringOrDomEl);
+
+  container.find('table').toArray().forEach((table) => {
+    if ($(table).parents('table').length === 0) {
+      $(table).css('float', 'none')
+        .wrapAll('<div class="table-wrapper w-full" style="overflow: auto"></div>');
     }
-  }
+  });
+  return container.prop('outerHTML');
 }
diff --git a/app/javascript/packs/tiny_mce.js b/app/javascript/packs/tiny_mce.js
index 723d3ab0a..cc041eb4c 100644
--- a/app/javascript/packs/tiny_mce.js
+++ b/app/javascript/packs/tiny_mce.js
@@ -489,11 +489,10 @@ window.TinyMCE = (() => {
     },
     wrapTables: (container) => {
       container.find('table').toArray().forEach((table) => {
-        if ($(table).parent().hasClass('table-wrapper')) return;
-
-        $(table).css('float', 'none').wrapAll(`
-          <div class="table-wrapper" style="overflow: auto; width: ${container.width()}px"></div>
-        `);
+        if ($(table).parents('table').length === 0) {
+          $(table).css('float', 'none')
+            .wrapAll('<div class="table-wrapper w-full" style="overflow: auto"></div>');
+        }
       });
     }
   };

From 778552e80918e8a2ab59be148349aa969e9f587b Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 8 Nov 2024 10:27:05 +0100
Subject: [PATCH 79/96] Remove duplicate openLocallyMenu element [SCI-11249]

---
 app/views/shared/file_preview/_content.html.erb | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/app/views/shared/file_preview/_content.html.erb b/app/views/shared/file_preview/_content.html.erb
index 00d259dee..33d89125f 100644
--- a/app/views/shared/file_preview/_content.html.erb
+++ b/app/views/shared/file_preview/_content.html.erb
@@ -2,11 +2,7 @@
   <span class="file-name"><%= asset.file.metadata[:name] || asset.file_name %></span>
   <div class="sci-btn-group">
     <% if can_edit && !preview %>
-      <% if wopi_enabled? && wopi_file?(asset) %>
-        <div id="openLocallyMenu" data-behaviour="vue">
-          <open-locally-menu :attachment="<%= { attributes: AssetSerializer.new(asset, scope: { user: current_user }).as_json }.to_json %>" />
-        </div>
-      <% elsif asset.file.metadata[:asset_type] == 'marvinjs' %>
+      <% if asset.file.metadata[:asset_type] == 'marvinjs' %>
         <button class="btn btn-light marvinjs-edit-button"
           data-sketch-id="<%= asset.id %>"
           data-update-url="<%= marvin_js_asset_path(asset) %>"

From fcfb3dc8f78be05bfed73ed12764794c9f906668 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 8 Nov 2024 13:49:29 +0100
Subject: [PATCH 80/96] Fix 203dpi label migtation [SCI-10901]

---
 db/migrate/20240718073215_add203_dpi_label_template.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/db/migrate/20240718073215_add203_dpi_label_template.rb b/db/migrate/20240718073215_add203_dpi_label_template.rb
index 7e9adc45f..46c8e9cde 100644
--- a/db/migrate/20240718073215_add203_dpi_label_template.rb
+++ b/db/migrate/20240718073215_add203_dpi_label_template.rb
@@ -8,7 +8,7 @@ class Add203DpiLabelTemplate < ActiveRecord::Migration[7.0]
         type: 'ZebraLabelTemplate',
         name: I18n.t('label_templates.default_zebra_name_203dpi'),
         default: false,
-        content: Extends::DEFAULT_LABEL_TEMPLATE_203DPI,
+        content: Extends::DEFAULT_LABEL_TEMPLATE_203DPI[:zpl],
         width_mm: 25.4,
         height_mm: 12.7,
         unit: 'in',

From 1a99350611dd067536b851bc8a73dda15cb86ba5 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 8 Nov 2024 14:30:09 +0100
Subject: [PATCH 81/96] Make file versioning disclaimer overridable [SCI-11040]

---
 app/controllers/assets_controller.rb              |  3 ++-
 app/javascript/vue/shared/file_versions_modal.vue | 11 ++++++-----
 app/models/concerns/versioned_attachments.rb      |  7 +++++++
 3 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 8c5c7ca2f..5f4914759 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -407,7 +407,8 @@ class AssetsController < ApplicationController
         user: current_user
       ).as_json.merge(
         enabled: VersionedAttachments.enabled?,
-        enable_url: ENV.fetch('SCINOTE_FILE_VERSIONING_ENABLE_URL', nil)
+        enable_url: ENV.fetch('SCINOTE_FILE_VERSIONING_ENABLE_URL', nil),
+        disabled_disclaimer: VersionedAttachments.disabled_disclaimer
       )
     )
   end
diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
index 767592321..1cf084138 100644
--- a/app/javascript/vue/shared/file_versions_modal.vue
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -67,7 +67,7 @@
             </div>
             <div>
               <h3 class="mt-1 mb-2">{{ i18n.t('assets.file_versions_modal.title') }}</h3>
-              {{ i18n.t('assets.file_versions_modal.disabled_disclaimer') }}
+              {{ disabledDisclaimer.text }}
             </div>
           </div>
         </div>
@@ -76,7 +76,7 @@
             {{ i18n.t('general.cancel') }}
           </button>
           <a v-if="fileVersions && !enabled" :href="enableUrl" class='btn btn-primary' target="_blank">
-            {{ i18n.t('assets.file_versions_modal.enable_button') }}
+            {{ disabledDisclaimer.button }}
           </a>
         </div>
       </div>
@@ -96,8 +96,7 @@ export default {
       required: true
     },
     restoreVersionUrl: {
-      type: String,
-      required: true
+      type: String
     }
   },
   mixins: [modalMixin],
@@ -105,7 +104,8 @@ export default {
     return {
       fileVersions: null,
       enabled: null,
-      enableUrl: null
+      enableUrl: null,
+      disabledDisclaimer: null
     };
   },
   created() {
@@ -122,6 +122,7 @@ export default {
         this.fileVersions = response.data.data;
         this.enabled = response.data.enabled;
         this.enableUrl = response.data.enable_url;
+        this.disabledDisclaimer = response.data.disabled_disclaimer;
         this.$nextTick(() => {
           document.querySelectorAll('[data-render-tooltip]').forEach((e) => {
             window.initTooltip(e);
diff --git a/app/models/concerns/versioned_attachments.rb b/app/models/concerns/versioned_attachments.rb
index a286c9022..b999fc501 100644
--- a/app/models/concerns/versioned_attachments.rb
+++ b/app/models/concerns/versioned_attachments.rb
@@ -51,4 +51,11 @@ module VersionedAttachments
   def enabled?
     ApplicationSettings.instance.values['versioned_attachments_enabled']
   end
+
+  def disabled_disclaimer
+    {
+      text: I18n.t('assets.file_versions_modal.disabled_disclaimer'),
+      button: I18n.t('assets.file_versions_modal.enable_button')
+    }
+  end
 end

From bfeea3ca431780225eefd3e5196bca7c27b252ee Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 8 Nov 2024 14:52:49 +0100
Subject: [PATCH 82/96] Don't export protocol asset version metadata
 [SCI-11237]

---
 app/utilities/protocols_exporter_v2.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/utilities/protocols_exporter_v2.rb b/app/utilities/protocols_exporter_v2.rb
index a4e2ba3ea..e7ff623fa 100644
--- a/app/utilities/protocols_exporter_v2.rb
+++ b/app/utilities/protocols_exporter_v2.rb
@@ -132,7 +132,7 @@ module ProtocolsExporterV2
       "<asset id=\"#{asset.id}\" guid=\"#{asset_guid}\" fileRef=\"#{asset_file_name}\">\n" \
       "<fileName>#{asset.file_name}</fileName>\n" \
       "<fileType>#{asset.content_type}</fileType>\n" \
-      "<fileMetadata><!--[CDATA[  #{asset.file.metadata.to_json}  ]]--></fileMetadata>\n" \
+      "<fileMetadata><!--[CDATA[  #{asset.file.metadata.except('version', 'restored_from_version').to_json}  ]]--></fileMetadata>\n" \
       "</asset>\n"
   end
 end

From f2c9a7c0a5c0482d2e1b3503c4239d6165064203 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Mon, 11 Nov 2024 15:39:36 +0100
Subject: [PATCH 83/96] Fix dangerous use of uri open, remove unused obsolete
 file encryptor module [SCI-11259] (#8030)

---
 Gemfile                                       |  2 +-
 .../users/omniauth_callbacks_controller.rb    |  5 +----
 app/models/asset.rb                           |  1 -
 app/utilities/encryptor.rb                    | 19 -------------------
 .../protocol_importers/attachments_builder.rb |  2 +-
 5 files changed, 3 insertions(+), 26 deletions(-)
 delete mode 100644 app/utilities/encryptor.rb

diff --git a/Gemfile b/Gemfile
index e28a8437a..3bddf41df 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-source 'http://rubygems.org'
+source 'https://rubygems.org'
 
 ruby '~> 3.2.2'
 
diff --git a/app/controllers/users/omniauth_callbacks_controller.rb b/app/controllers/users/omniauth_callbacks_controller.rb
index 74d7fc180..ad62346c3 100644
--- a/app/controllers/users/omniauth_callbacks_controller.rb
+++ b/app/controllers/users/omniauth_callbacks_controller.rb
@@ -114,10 +114,7 @@ module Users
           email: auth_hash['info']['email'],
           password: generate_user_password
         )
-        if auth_hash['info']['picture_url']
-          avatar = URI.open(auth_hash['info']['picture_url'])
-          @user.avatar.attach(io: avatar, filename: 'linkedin_avatar.jpg')
-        end
+        @user.avatar.attach(io: URI(auth_hash['info']['picture_url']).open, filename: 'linkedin_avatar.jpg') if auth_hash['info']['picture_url']
         user_identity = UserIdentity.new(user: @user,
                                          provider: auth_hash['provider'],
                                          uid: auth_hash['uid'])
diff --git a/app/models/asset.rb b/app/models/asset.rb
index 74b839d11..6f0f2632f 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -3,7 +3,6 @@
 class Asset < ApplicationRecord
   include SearchableModel
   include DatabaseHelper
-  include Encryptor
   include WopiUtil
   include ActiveStorageFileUtil
   include ActiveStorageConcerns
diff --git a/app/utilities/encryptor.rb b/app/utilities/encryptor.rb
deleted file mode 100644
index b18637391..000000000
--- a/app/utilities/encryptor.rb
+++ /dev/null
@@ -1,19 +0,0 @@
-module Encryptor
-  def decrypt(data)
-    return '' unless data.present?
-    cipher = build_cipher(:decrypt, 'f5awRubeTUd2E*8duxum')
-    cipher.update(Base64.urlsafe_decode64(data).unpack('m')[0]) + cipher.final
-  end
-
-  def encrypt(data)
-    return '' unless data.present?
-    cipher = build_cipher(:encrypt, 'f5awRubeTUd2E*8duxum')
-    Base64.urlsafe_encode64([cipher.update(data) + cipher.final].pack('m'))
-  end
-
-  def build_cipher(type, password)
-    cipher = OpenSSL::Cipher::Cipher.new('DES-EDE3-CBC').send(type)
-    cipher.pkcs5_keyivgen(password)
-    cipher
-  end
-end
\ No newline at end of file
diff --git a/app/utilities/protocol_importers/attachments_builder.rb b/app/utilities/protocol_importers/attachments_builder.rb
index dd2bd4799..f0c50b5ea 100644
--- a/app/utilities/protocol_importers/attachments_builder.rb
+++ b/app/utilities/protocol_importers/attachments_builder.rb
@@ -7,7 +7,7 @@ module ProtocolImporters
 
       step_json[:attachments].map do |f|
         asset = Asset.new(created_by: user, last_modified_by: user, team: team)
-        asset.attach_file_version(io: URI.open(f[:url]), filename: f[:name])
+        asset.attach_file_version(io: URI(f[:url]).open, filename: f[:name])
         asset
       end
     end

From 0be982e25fe5c845e5e662bb5e7f43c0560da9f1 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Mon, 11 Nov 2024 16:44:45 +0100
Subject: [PATCH 84/96] Fix restore action for file preview file reload
 [SCI-11253]

---
 .../vue/shared/content/attachments/open_locally_menu.vue        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/javascript/vue/shared/content/attachments/open_locally_menu.vue b/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
index 9d40e11cf..0db3edd45 100644
--- a/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
+++ b/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
@@ -135,7 +135,7 @@ export default {
 
       if (!imageElement) return;
 
-      window.ActiveStoragePreviews.reCheckPreview({ target: imageElement });
+      $('#filePreviewModal').modal('hide');
     }
   }
 };

From 2d70773cda2ad3947eb5567a8e4d15f70954603a Mon Sep 17 00:00:00 2001
From: andrej-scinote <andrej@scinote.net>
Date: Tue, 12 Nov 2024 16:37:42 +0100
Subject: [PATCH 85/96] Limit quick search possible classes and improve params
 check for reports and activities [SCI-11260] (#8034)

---
 .../global_activities_controller.rb           | 20 ++++++++++++++++++-
 app/controllers/reports_controller.rb         |  2 +-
 app/controllers/search_controller.rb          |  5 ++++-
 app/helpers/reports_helper.rb                 | 13 ++++++++++++
 config/locales/en.yml                         |  1 +
 5 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/app/controllers/global_activities_controller.rb b/app/controllers/global_activities_controller.rb
index b531c5ac1..b84085994 100644
--- a/app/controllers/global_activities_controller.rb
+++ b/app/controllers/global_activities_controller.rb
@@ -151,7 +151,25 @@ class GlobalActivitiesController < ApplicationController
   end
 
   def activity_filter_params
-    params.permit(:name, filter: {})
+    params.permit(
+      :name,
+      filter: [
+        :to_date,
+        :from_date,
+        { types: [] },
+        { subjects: {
+          'Report' => [],
+          'Project' => [],
+          'MyModule' => [],
+          'Protocol' => [],
+          'Experiment' => [],
+          'RepositoryRow' => [],
+          'RepositoryBase' => []
+        } },
+        { users: [] },
+        { teams: [] }
+      ]
+    )
   end
 
   def activity_filters
diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index 8e779bb0c..fd262a6dc 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -361,7 +361,7 @@ class ReportsController < ApplicationController
 
   def report_params
     params.require(:report)
-          .permit(:name, :description, :grouped_by, :report_contents, settings: {})
+          .permit(:name, :description, :grouped_by, :report_contents, settings: permit_report_settings_structure(Report::DEFAULT_SETTINGS))
   end
 
   def search_params
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index a86d04a82..afa8fd4e4 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -145,7 +145,10 @@ class SearchController < ApplicationController
 
   def quick
     results = if params[:filter].present?
-                object_quick_search(params[:filter].singularize)
+                class_name = params[:filter].singularize
+                return render_422(t('general.invalid_params')) unless Constants::QUICK_SEARCH_SEARCHABLE_OBJECTS.include?(class_name)
+
+                object_quick_search(class_name)
               else
                 Constants::QUICK_SEARCH_SEARCHABLE_OBJECTS.filter_map do |object|
                   next if object == 'label_template' && !LabelTemplate.enabled?
diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 7dcc85929..2abd4fdc2 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -106,4 +106,17 @@ module ReportsHelper
       experiment_element.experiment.description
     end
   end
+
+  def permit_report_settings_structure(settings_definition)
+    settings_definition.each_with_object([]) do |(key, value), permitted|
+      permitted << case value
+                   when Hash
+                     { key => permit_report_settings_structure(value) }
+                   when Array
+                     { key => [] }
+                   else
+                     key
+                   end
+    end
+  end
 end
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 496297c9f..49a57d68d 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -4305,6 +4305,7 @@ en:
     comment_placeholder: "Your Message"
     comment_placeholder_new: "Add new comment…"
     archived: "Archived"
+    invalid_params: "Invalid params"
     sort:
       title: "Sorting"
       new_html: "Started last"

From feface91419aaf3cee41a9b64db5e321e5bf781d Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Wed, 13 Nov 2024 12:15:55 +0100
Subject: [PATCH 86/96] Fix restore version in file preview [SCI-11253]

---
 .../vue/shared/content/attachments/open_locally_menu.vue    | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/javascript/vue/shared/content/attachments/open_locally_menu.vue b/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
index 0db3edd45..e67a39111 100644
--- a/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
+++ b/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
@@ -131,11 +131,11 @@ export default {
       document.getElementById('editImageButton').click();
     },
     refreshPreview() {
-      const imageElement = document.querySelector('.file-preview-container .asset-image');
+      const filePreview = document.querySelector('.file-preview-container');
 
-      if (!imageElement) return;
+      if (!filePreview) return;
 
-      $('#filePreviewModal').modal('hide');
+      window.location.reload();
     }
   }
 };

From dfba7adf989452d3c9c5896ed748e817c7c764df Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Thu, 14 Nov 2024 15:33:03 +0100
Subject: [PATCH 87/96] Fix pemrisison for acrived rows and download link
 [SCI-11284][SCI-11285]

---
 app/javascript/vue/shared/file_versions_modal.vue | 2 +-
 app/permissions/asset.rb                          | 1 +
 app/serializers/active_storage/blob_serializer.rb | 6 +++++-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
index 1cf084138..1a0553e97 100644
--- a/app/javascript/vue/shared/file_versions_modal.vue
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -40,7 +40,7 @@
                 <div class="basis-1/4 flex justify-end">
                   <a class="btn btn-icon p-0 px-2 hover:bg-sn-light-grey"
                     v-if="enabled || index === 0"
-                    :href="fileVersion.attributes.url"
+                    :href="fileVersion.attributes.download_url"
                     target="_blank"
                     data-render-tooltip="true"
                     :title="i18n.t('assets.file_versions_modal.download')"
diff --git a/app/permissions/asset.rb b/app/permissions/asset.rb
index 4349fdfe5..8f576ca09 100644
--- a/app/permissions/asset.rb
+++ b/app/permissions/asset.rb
@@ -27,6 +27,7 @@ Canaid::Permissions.register_for(Asset) do
       if object.repository_column.repository.is_a?(RepositorySnapshot)
         false
       else
+        object.repository_row.active? &&
         can_manage_repository_assets?(user, object.repository_column.repository)
       end
     end
diff --git a/app/serializers/active_storage/blob_serializer.rb b/app/serializers/active_storage/blob_serializer.rb
index a758badd7..ff3a1ed8d 100644
--- a/app/serializers/active_storage/blob_serializer.rb
+++ b/app/serializers/active_storage/blob_serializer.rb
@@ -4,7 +4,7 @@ module ActiveStorage
   class BlobSerializer < ActiveModel::Serializer
     include Rails.application.routes.url_helpers
 
-    attributes :filename, :extension, :basename, :url, :created_at, :byte_size, :version, :restored_from_version, :created_by
+    attributes :filename, :extension, :basename, :url, :created_at, :byte_size, :version, :restored_from_version, :created_by, :download_url
 
     def basename
       object.filename.base
@@ -14,6 +14,10 @@ module ActiveStorage
       object.filename.extension_without_delimiter
     end
 
+    def download_url
+      rails_blob_url(object, disposition: 'attachment')
+    end
+
     def version
       object.metadata['version'] || 1
     end

From c600fda71cd74a2873cff0f86043979c7e9c5809 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Thu, 14 Nov 2024 16:18:00 +0100
Subject: [PATCH 88/96] Remove test docx template

---
 .../docx_templates/custom_template/docx.rb    | 188 ------------------
 1 file changed, 188 deletions(-)
 delete mode 100644 app/views/reports/docx_templates/custom_template/docx.rb

diff --git a/app/views/reports/docx_templates/custom_template/docx.rb b/app/views/reports/docx_templates/custom_template/docx.rb
deleted file mode 100644
index 3e554a794..000000000
--- a/app/views/reports/docx_templates/custom_template/docx.rb
+++ /dev/null
@@ -1,188 +0,0 @@
-# frozen_string_literal: true
-
-module CustomTemplateDocx
-  def prepare_docx
-    report_name = get_template_value('custom_docx_report_name')
-    report_number = get_template_value('custom_docx_report_number')
-
-    @project_members = @report.project&.users
-
-    report_authors = @project_members.where(id: get_template_value('custom_docx_author[]')).pluck(:full_name).join(', ')
-    report_reviewers = @project_members.where(id: get_template_value('custom_docx_reviewer[]')).pluck(:full_name).join(', ')
-    report_author_role = get_template_value('custom_docx_author_role')
-    report_reviewer_role = get_template_value('custom_docx_reviewer_role')
-
-    @docx.header do |header|
-      header.table [[report_name, 'custom report']] do
-        border_size 1
-        cell_style cols[0], width: 8000
-        cell_style cols[1], width: 2800
-      end
-    end
-
-    @docx.footer do |footer|
-      pages = Caracal::Core::Models::TableCellModel.new do
-        p do
-          field :page
-          text ' of '
-          field :numpages
-        end
-      end
-      footer.table [['Confidential', pages]] do
-        border_top do
-          size 1
-        end
-        cell_style cols[0], width: 9500
-        cell_style cols[1], width: 1000
-      end
-    end
-
-    @docx.p
-
-    logo_data = File.read(Rails.root.join('app/assets/images/scinote_logo.png'))
-
-    c1 = Caracal::Core::Models::TableCellModel.new do
-      p report_name, bold: true
-      p ''
-    end
-
-    c2 = Caracal::Core::Models::TableCellModel.new do
-      img 'logo.png' do
-        data logo_data
-        height 20
-        width 100
-        align :left
-      end
-    end
-
-    c3 = Caracal::Core::Models::TableCellModel.new do
-      p "Author: #{report_authors}"
-      p "Role: #{report_author_role}"
-    end
-
-    c4 = Caracal::Core::Models::TableCellModel.new do
-      p "Reviewer: #{report_reviewers}"
-      p "Role: #{report_reviewer_role}"
-    end
-
-    c5 = Caracal::Core::Models::TableCellModel.new do
-      p "Report number:"
-      p report_number
-    end
-
-    @docx.table [[c1, c2], [c3, c4, c5]] do
-      border_size 2
-      cell_style rows[0], width: 3500
-      cell_style rows[1], width: 3500
-      cell_style rows[0][0], colspan: 2
-    end
-
-    @docx.p
-
-    @docx.table_of_contents do |toc|
-      toc.title 'Table of Contents'
-      toc.opts 'TOC \o "1-4" \h \z \u \t "Heading 5,1"'
-    end
-
-    @docx.page
-
-    my_modules_elements = []
-    @report.root_elements.each do |subject|
-      my_modules_elements += subject.children.active if subject.type_of == 'experiment'
-    end
-
-    @my_modules = MyModule.where(id: my_modules_elements.map { |element| element.my_module.id })
-
-    @docx.h1 'Chapter 1'
-    @docx.h2 'Sub chapter 1' if get_template_value('custom_docx_sub_chapter_1')
-    @docx.h2 'Sub chapter 2' if get_template_value('custom_docx_sub_chapter_2')
-    @docx.h1 'Chapter 2'
-    if get_template_value('custom_docx_sub_chapter_3')
-      @docx.h2 'Sub chapter 3 with inventory'
-      draw_repositories(get_template_value('custom_docx_sub_chapter_3_inventories[]'))
-    end
-    if get_template_value('custom_docx_sub_chapter_4')
-      @docx.h2 'Sub chapter 4 with inventory'
-      draw_repositories(get_template_value('custom_docx_sub_chapter_4_inventories[]'))
-    end
-    @docx.h2 'Sub chapter 5' if get_template_value('custom_docx_sub_chapter_5')
-    @docx.h2 'Sub chapter 6' if get_template_value('custom_docx_sub_chapter_6')
-    @docx.h2 'Sub chapter 7' if get_template_value('custom_docx_sub_chapter_7')
-    @docx.h1 'Chapter 3'
-    if get_template_value('custom_docx_sub_chapter_8')
-      @docx.h2 'Sub chapter 8 with task'
-      my_modules_elements.each do |element|
-        draw_my_module(element, without_results: true, without_repositories: true)
-      end
-    end
-    @docx.h2 'Sub chapter 9' if get_template_value('custom_docx_sub_chapter_9')
-    @docx.h2 'Sub chapter 10' if get_template_value('custom_docx_sub_chapter_10')
-    @docx.h2 'Sub chapter 11' if get_template_value('custom_docx_sub_chapter_11')
-    if get_template_value('custom_docx_sub_chapter_12')
-      @docx.h2 'Sub chapter 12'
-      @docx.h3 'Sub sub chapter 1' if get_template_value('custom_docx_sub_sub_chapter_1')
-      @docx.h3 'Sub sub chapter 2' if get_template_value('custom_docx_sub_sub_chapter_2')
-    end
-    @docx.h1 'Chapter 4'
-    if get_template_value('custom_docx_sub_chapter_13')
-      @docx.h2 'Sub chapter 13 with results'
-      my_modules_elements.each do |element|
-        draw_results(element.my_module)
-      end
-    end
-    @docx.h2 'Sub chapter 14' if get_template_value('custom_docx_sub_chapter_14')
-    @docx.h2 'Sub chapter 15' if get_template_value('custom_docx_sub_chapter_15')
-    @docx.h2 'Sub chapter 16' if get_template_value('custom_docx_sub_chapter_16')
-    @docx.h2 'Sub chapter 17' if get_template_value('custom_docx_sub_chapter_17')
-    @docx.h1 'Chapter 5'
-  end
-
-  def repository_docx_json(repository, rows)
-    headers = [
-      I18n.t('repositories.table.id'),
-      I18n.t('repositories.table.row_name'),
-      I18n.t('repositories.table.added_on'),
-      I18n.t('repositories.table.added_by')
-    ]
-    custom_columns = []
-    return false unless repository
-
-    repository.repository_columns.order(:id).each do |column|
-      headers.push(column.name)
-      custom_columns.push(column.id)
-    end
-
-    records = repository.repository_rows.where(id: rows)
-                        .select(:id, :name, :created_at, :created_by_id, :repository_id, :parent_id, :archived)
-    { headers: headers, rows: records, custom_columns: custom_columns }
-  end
-
-  def load_repositories(repositories_id)
-    live_repositories = Repository.accessible_by_teams(@report.team).where(id: repositories_id).sort_by { |r| r.name.downcase }
-    snapshots_of_deleted = RepositorySnapshot.left_outer_joins(:original_repository)
-                                             .where(team: @report.team)
-                                             .where(parent_id: repositories_id)
-                                             .where.not(original_repository: live_repositories)
-                                             .select('DISTINCT ON ("repositories"."parent_id") "repositories".*')
-                                             .sort_by { |r| r.name.downcase }
-    live_repositories + snapshots_of_deleted
-  end
-
-  def draw_repositories(repositories_id)
-    load_repositories(repositories_id).each do |repository|
-      rows = repository.repository_rows.where(id: @my_modules.joins(:my_module_repository_rows).select(:repository_row_id)).select(:id)
-      repository_data = repository_docx_json(repository, rows)
-
-      next unless repository_data[:rows].any? && can_read_repository?(@user, repository)
-
-      table = prepare_row_columns_for_docx(repository_data, nil, repository)
-
-      @docx.p
-      @docx.p repository.name, bold: true, size: Constants::REPORT_DOCX_STEP_ELEMENTS_TITLE_SIZE
-      @docx.table table, border_size: Constants::REPORT_DOCX_TABLE_BORDER_SIZE
-
-      @docx.p
-      @docx.p
-    end
-  end
-end

From 23002e047802e007df5f3cd3626198c772f88aeb Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Fri, 15 Nov 2024 09:56:22 +0100
Subject: [PATCH 89/96] Add missing permissions for repository columns
 [SCI-11147] (#7995)

---
 .../api/v1/inventory_columns_controller.rb    |  7 +++++-
 .../repository_columns_controller.rb          |  7 +++++-
 app/permissions/repository.rb                 | 11 ++++++---
 .../extends/permission_extends.rb             |  2 ++
 ...5317_add_missing_repository_permissions.rb | 24 +++++++++++++++++++
 db/schema.rb                                  |  3 ++-
 6 files changed, 48 insertions(+), 6 deletions(-)
 create mode 100644 db/migrate/20241028105317_add_missing_repository_permissions.rb

diff --git a/app/controllers/api/v1/inventory_columns_controller.rb b/app/controllers/api/v1/inventory_columns_controller.rb
index 320c2b82c..393e62736 100644
--- a/app/controllers/api/v1/inventory_columns_controller.rb
+++ b/app/controllers/api/v1/inventory_columns_controller.rb
@@ -8,8 +8,9 @@ module Api
       before_action only: %i(show update destroy) do
         load_inventory_column(:id)
       end
-      before_action :check_manage_permissions, only: %i(update destroy)
       before_action :check_create_permissions, only: %i(create)
+      before_action :check_manage_permissions, only: %i(update)
+      before_action :check_delete_permissions, only: %i(destroy)
 
       def index
         columns = timestamps_filter(@inventory.repository_columns).includes(:repository_list_items)
@@ -61,6 +62,10 @@ module Api
         raise PermissionError.new(RepositoryColumn, :manage) unless can_manage_repository_column?(@inventory_column)
       end
 
+      def check_delete_permissions
+        raise PermissionError.new(RepositoryColumn, :delete) unless can_delete_repository_column?(@inventory_column)
+      end
+
       def check_create_permissions
         raise PermissionError.new(RepositoryColumn, :create) unless can_create_repository_columns?(@inventory)
       end
diff --git a/app/controllers/repository_columns_controller.rb b/app/controllers/repository_columns_controller.rb
index 707a6beb8..73cefa87b 100644
--- a/app/controllers/repository_columns_controller.rb
+++ b/app/controllers/repository_columns_controller.rb
@@ -5,7 +5,8 @@ class RepositoryColumnsController < ApplicationController
   before_action :load_repository
   before_action :load_column, only: %i(edit update destroy_html destroy items)
   before_action :check_create_permissions, only: %i(new create)
-  before_action :check_manage_permissions, only: %i(edit update destroy_html destroy)
+  before_action :check_manage_permissions, only: %i(edit update)
+  before_action :check_delete_permissions, only: %i(destroy_html destroy)
   before_action :load_asset_type_columns, only: :available_asset_type_columns
 
   def index
@@ -130,6 +131,10 @@ class RepositoryColumnsController < ApplicationController
     render_403 unless can_manage_repository_column?(@repository_column)
   end
 
+  def check_delete_permissions
+    render_403 unless can_delete_repository_column?(@repository_column)
+  end
+
   def search_params
     params.permit(:q, :repository_id)
   end
diff --git a/app/permissions/repository.rb b/app/permissions/repository.rb
index 8466b745f..738358423 100644
--- a/app/permissions/repository.rb
+++ b/app/permissions/repository.rb
@@ -25,7 +25,8 @@ Canaid::Permissions.register_for(Repository) do
      create_repository_rows
      manage_repository_rows
      delete_repository_rows
-     create_repository_columns)
+     create_repository_columns
+     manage_repository_columns)
     .each do |perm|
     can perm do |_, repository|
       repository.active? && repository.repository_snapshots.provisioning.none? &&
@@ -106,7 +107,7 @@ Canaid::Permissions.register_for(Repository) do
   end
 
   can :manage_repository_columns do |user, repository|
-    repository.repository_snapshots.provisioning.none? && can_create_repository_columns?(user, repository)
+    repository.permission_granted?(user, RepositoryPermissions::COLUMNS_UPDATE)
   end
 
   # repository: create/update/delete filters
@@ -123,6 +124,10 @@ Canaid::Permissions.register_for(RepositoryColumn) do
   # repository: update/delete field
   # Tested in scope of RepositoryPermissions spec
   can :manage_repository_column do |user, repository_column|
-    repository_column.repository.repository_snapshots.provisioning.none? && can_create_repository_columns?(user, repository_column.repository)
+    repository_column.repository.repository_snapshots.provisioning.none? && repository_column.repository.permission_granted?(user, RepositoryPermissions::COLUMNS_UPDATE)
+  end
+
+  can :delete_repository_column do |user, repository_column|
+    repository_column.repository.repository_snapshots.provisioning.none? && repository_column.repository.permission_granted?(user, RepositoryPermissions::COLUMNS_DELETE)
   end
 end
diff --git a/config/initializers/extends/permission_extends.rb b/config/initializers/extends/permission_extends.rb
index b7b2843a1..177a38dbb 100644
--- a/config/initializers/extends/permission_extends.rb
+++ b/config/initializers/extends/permission_extends.rb
@@ -210,6 +210,8 @@ module PermissionExtends
       RepositoryPermissions::READ,
       RepositoryPermissions::READ_ARCHIVED,
       RepositoryPermissions::COLUMNS_CREATE,
+      RepositoryPermissions::COLUMNS_UPDATE,
+      RepositoryPermissions::COLUMNS_DELETE,
       RepositoryPermissions::ROWS_CREATE,
       RepositoryPermissions::ROWS_UPDATE,
       RepositoryPermissions::ROWS_DELETE,
diff --git a/db/migrate/20241028105317_add_missing_repository_permissions.rb b/db/migrate/20241028105317_add_missing_repository_permissions.rb
new file mode 100644
index 000000000..f42fb2585
--- /dev/null
+++ b/db/migrate/20241028105317_add_missing_repository_permissions.rb
@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+class AddMissingRepositoryPermissions < ActiveRecord::Migration[6.1]
+  NORMAL_USER_PERMISSIONS = [
+    RepositoryPermissions::COLUMNS_UPDATE,
+    RepositoryPermissions::COLUMNS_DELETE
+  ].freeze
+
+  def change
+    reversible do |dir|
+      dir.up do
+        @normal_user_role = UserRole.find_predefined_normal_user_role
+        @normal_user_role.permissions = @normal_user_role.permissions | NORMAL_USER_PERMISSIONS
+        @normal_user_role.save(validate: false)
+      end
+
+      dir.down do
+        @normal_user_role = UserRole.find_predefined_normal_user_role
+        @normal_user_role.permissions = @normal_user_role.permissions - NORMAL_USER_PERMISSIONS
+        @normal_user_role.save(validate: false)
+      end
+    end
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index 6bbdd86ef..3b8768536 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_10_02_122340) do
+ActiveRecord::Schema[7.0].define(version: 2024_10_28_105317) do
   # These are extensions that must be enabled in order to support this database
   enable_extension "btree_gist"
   enable_extension "pg_trgm"
@@ -635,6 +635,7 @@ ActiveRecord::Schema[7.0].define(version: 2024_10_02_122340) do
     t.bigint "archived_by_id"
     t.bigint "restored_by_id"
     t.string "external_id"
+    t.integer "repository_rows_count", default: 0, null: false
     t.index ["archived"], name: "index_repositories_on_archived"
     t.index ["archived_by_id"], name: "index_repositories_on_archived_by_id"
     t.index ["discarded_at"], name: "index_repositories_on_discarded_at"

From aceeaae49c88751047bc47dabe81ab72dbc78f9c Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 12 Nov 2024 13:16:17 +0100
Subject: [PATCH 90/96] Fix view permission for protocol template [SCI-11256]

---
 app/controllers/protocols_controller.rb | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index 63a782d59..29d7368a6 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -18,11 +18,13 @@ class ProtocolsController < ApplicationController
     print
     versions_modal
     protocol_status_bar
-    linked_children
-    linked_children_datatable
     versions_list
     permissions
   )
+  before_action :check_linked_protocol_view_permissions, only: %i(
+    linked_children
+    linked_children_datatable
+  )
   before_action :switch_team_with_param, only: %i(index protocolsio_index)
   before_action :check_view_all_permissions, only: %i(
     index
@@ -933,6 +935,16 @@ class ProtocolsController < ApplicationController
   end
 
   def check_view_permissions
+    @protocol = Protocol.find_by(id: params[:id])
+    current_team_switch(@protocol.team) if current_team != @protocol.team
+    unless @protocol.present? &&
+           (can_read_protocol_in_module?(@protocol) ||
+           can_read_protocol_in_repository?(@protocol))
+      render_403
+    end
+  end
+
+  def check_linked_protocol_view_permissions
     @protocol = Protocol.find_by(id: params[:id])
     current_team_switch(@protocol.team) if current_team != @protocol.team
     unless @protocol.present? &&

From 60a06627c120142f267bb2f8fc9948f91abffacf Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Fri, 15 Nov 2024 10:16:54 +0100
Subject: [PATCH 91/96] Update Recaptcha config, stricken CSP config for
 external services [SCI-11281] (#8043)

---
 Gemfile                        |  2 +-
 Gemfile.lock                   |  4 ++--
 app/helpers/form_tag_helper.rb |  2 +-
 config/initializers/extends.rb | 13 +++----------
 4 files changed, 7 insertions(+), 14 deletions(-)

diff --git a/Gemfile b/Gemfile
index e68cc2312..8943e018c 100644
--- a/Gemfile
+++ b/Gemfile
@@ -13,7 +13,7 @@ gem 'pg', '~> 1.5'
 gem 'pg_search' # PostgreSQL full text search
 gem 'psych', '< 4.0'
 gem 'rails', '~> 7.0.8'
-gem 'recaptcha', require: 'recaptcha/rails'
+gem 'recaptcha'
 gem 'sanitize'
 gem 'sprockets-rails'
 gem 'view_component'
diff --git a/Gemfile.lock b/Gemfile.lock
index 4ed5dbebe..07911f921 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -50,7 +50,7 @@ GIT
       mime-types (>= 1.23)
 
 GEM
-  remote: http://rubygems.org/
+  remote: https://rubygems.org/
   specs:
     actioncable (7.0.8.5)
       actionpack (= 7.0.8.5)
@@ -608,7 +608,7 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rdoc (6.3.4.1)
-    recaptcha (5.14.0)
+    recaptcha (5.17.0)
     regexp_parser (2.8.1)
     responders (3.1.1)
       actionpack (>= 5.2)
diff --git a/app/helpers/form_tag_helper.rb b/app/helpers/form_tag_helper.rb
index 71235c154..be9532ee7 100644
--- a/app/helpers/form_tag_helper.rb
+++ b/app/helpers/form_tag_helper.rb
@@ -9,7 +9,7 @@ module FormTagHelper
         res << label_tag(:recaptcha_label, I18n.t('users.registrations.new.captcha_description'))
       end
 
-      res << recaptcha_tags
+      res << recaptcha_tags(nonce: content_security_policy_nonce)
       if flash[:recaptcha_error]
         res << "<span class='help-block'>"
         res << flash[:recaptcha_error]
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index c8ce4798f..8f8854f46 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -643,16 +643,9 @@ class Extends
     'FluicsLabelTemplate' => 'Fluics'
   }
 
-  EXTERNAL_SCRIPT_SERVICES =
-    if Rails.application.config.x.no_external_csp_exceptions
-      []
-    else
-      %w(
-        https://marvinjs.chemicalize.com/
-        www.recaptcha.net/
-        www.gstatic.com/recaptcha/
-      )
-    end
+  # If Rails.application.config.x.no_external_csp_exceptions is set, than this should be empty,
+  # but first try to use nonces before adding exceptions here
+  EXTERNAL_SCRIPT_SERVICES = []
 
   EXTERNAL_CONNECT_SERVICES =
     if Rails.application.config.x.no_external_csp_exceptions

From 718fafdec8a20d1579ee8be2dedb4734cd92b7f2 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Fri, 15 Nov 2024 14:03:14 +0100
Subject: [PATCH 92/96] Fix file versions for api flies [SCI-11288]

---
 app/javascript/vue/shared/file_versions_modal.vue | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/app/javascript/vue/shared/file_versions_modal.vue b/app/javascript/vue/shared/file_versions_modal.vue
index 1a0553e97..6d4765066 100644
--- a/app/javascript/vue/shared/file_versions_modal.vue
+++ b/app/javascript/vue/shared/file_versions_modal.vue
@@ -32,7 +32,9 @@
                   </div>
                   <div class="flex text-xs text-sn-grey justify-start">
                     <div class="mr-3">{{ fileVersion.attributes.created_at }}</div>
-                    <div class="mr-3 text-nowrap text-ellipsis overflow-hidden max-w-52">{{ fileVersion.attributes.created_by.full_name }}</div>
+                    <div v-if="fileVersion.attributes.created_by" class="mr-3 text-nowrap text-ellipsis overflow-hidden max-w-52">
+                      {{ fileVersion.attributes.created_by.full_name }}
+                    </div>
                     <div>{{ i18n.t("assets.file_versions_modal.size") }}: {{ Math.round(fileVersion.attributes.byte_size/1024) }}KB</div>
                   </div>
                 </div>

From 7e0a9bb092ba0caf962c55c5bdf7c89531d48740 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Sun, 17 Nov 2024 12:35:15 +0100
Subject: [PATCH 93/96] Fix generating of reports [SCI-11291][SCI-11292]

---
 app/controllers/reports_controller.rb | 20 ++++++++++++--------
 app/helpers/reports_helper.rb         | 18 +++++++++++-------
 app/models/report.rb                  |  4 +++-
 3 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index 3a0dcbc73..3b97e8b00 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -9,6 +9,7 @@ class ReportsController < ApplicationController
   before_action :load_vars_nested, only: %i(create edit update generate_pdf
                                             generate_docx new_template_values new_docx_template_values project_contents)
   before_action :load_wizard_vars, only: %i(new edit)
+  before_action :load_repositories_vars, only: %i(new edit create update)
   before_action :load_available_repositories, only: %i(index save_pdf_to_inventory_modal available_repositories)
   before_action :check_project_read_permissions, only: %i(create edit update generate_pdf
                                                           generate_docx new_template_values new_docx_template_values project_contents)
@@ -355,13 +356,6 @@ class ReportsController < ApplicationController
   def load_wizard_vars
     @templates = Extends::REPORT_TEMPLATES
     @docx_templates = Extends::DOCX_REPORT_TEMPLATES
-    live_repositories = Repository.viewable_by_user(current_user).sort_by { |r| r.name.downcase }
-    snapshots_of_deleted = RepositorySnapshot.left_outer_joins(:original_repository)
-                                             .where(team: current_team)
-                                             .where.not(original_repository: live_repositories)
-                                             .select('DISTINCT ON ("repositories"."parent_id") "repositories".*')
-                                             .sort_by { |r| r.name.downcase }
-    @repositories = live_repositories + snapshots_of_deleted
     @visible_projects = current_team.projects
                                     .active
                                     .joins(experiments: :my_modules)
@@ -375,6 +369,16 @@ class ReportsController < ApplicationController
     @default_docx_template = Extends::DOCX_REPORT_TEMPLATES.keys.first.to_s if Extends::DOCX_REPORT_TEMPLATES.one? && custom_templates(Extends::DOCX_REPORT_TEMPLATES)
   end
 
+  def load_repositories_vars
+    live_repositories = Repository.viewable_by_user(current_user).sort_by { |r| r.name.downcase }
+    snapshots_of_deleted = RepositorySnapshot.left_outer_joins(:original_repository)
+                                             .where(team: current_team)
+                                             .where.not(original_repository: live_repositories)
+                                             .select('DISTINCT ON ("repositories"."parent_id") "repositories".*')
+                                             .sort_by { |r| r.name.downcase }
+    @repositories = live_repositories + snapshots_of_deleted
+  end
+
   def check_project_read_permissions
     render_403 unless can_read_project?(@project)
   end
@@ -407,7 +411,7 @@ class ReportsController < ApplicationController
 
   def report_params
     params.require(:report)
-          .permit(:name, :description, :grouped_by, :report_contents, settings: permit_report_settings_structure(Report::DEFAULT_SETTINGS))
+          .permit(:name, :description, :grouped_by, :report_contents, settings: permit_report_settings_structure(Report::DEFAULT_SETTINGS, @repositories))
   end
 
   def search_params
diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 47a49e6cf..7d7df14cc 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -107,15 +107,19 @@ module ReportsHelper
     end
   end
 
-  def permit_report_settings_structure(settings_definition)
+  def permit_report_settings_structure(settings_definition, repositories)
     settings_definition.each_with_object([]) do |(key, value), permitted|
-      permitted << case value
-                   when Hash
-                     { key => permit_report_settings_structure(value) }
-                   when Array
-                     { key => [] }
+      permitted << if key == :excluded_repository_columns && repositories.present?
+                     { key => repositories.each_with_object({}) { |repository, hash| hash[repository.id.to_s] = [] } }
                    else
-                     key
+                     case value
+                     when Hash
+                       { key => permit_report_settings_structure(value, repositories) }
+                     when Array
+                       { key => [] }
+                     else
+                       key
+                     end
                    end
     end
   end
diff --git a/app/models/report.rb b/app/models/report.rb
index 61f092e33..87d159e6a 100644
--- a/app/models/report.rb
+++ b/app/models/report.rb
@@ -66,7 +66,9 @@ class Report < ApplicationRecord
       activities: true,
       repositories: [],
       excluded_repository_columns: {}
-    }
+    },
+    template: 'scinote_template',
+    docx_template: 'scinote_template'
   }.freeze
 
   def self.search(

From 2e9887a59a329f6ea1d94c78eb1fe95edc412c3e Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 18 Nov 2024 14:56:30 +0100
Subject: [PATCH 94/96] Fix recording of asset authors when duplicating stuff
 and restoring versions [SCI-11295]

---
 app/controllers/assets_controller.rb              |  7 ++++++-
 app/models/asset.rb                               | 10 ++++++++--
 app/models/concerns/versioned_attachments.rb      |  4 ++--
 app/models/step.rb                                |  2 +-
 app/services/repository_actions/duplicate_cell.rb |  2 +-
 5 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/app/controllers/assets_controller.rb b/app/controllers/assets_controller.rb
index 5f4914759..64000acb1 100644
--- a/app/controllers/assets_controller.rb
+++ b/app/controllers/assets_controller.rb
@@ -361,7 +361,8 @@ class AssetsController < ApplicationController
       when Step, Result
         new_asset = @asset.duplicate(
           new_name:
-            "#{@asset.file.filename.base} (1).#{@asset.file.filename.extension}"
+            "#{@asset.file.filename.base} (1).#{@asset.file.filename.extension}",
+          created_by: current_user
         )
 
         @asset.parent.assets << new_asset
@@ -416,6 +417,8 @@ class AssetsController < ApplicationController
   def restore_version
     render_403 unless VersionedAttachments.enabled?
 
+    @asset.last_modified_by = current_user
+
     @asset.restore_file_version(params[:version].to_i)
     @asset.restore_preview_image_version(params[:version].to_i) if @asset.preview_image.attached?
 
@@ -445,6 +448,8 @@ class AssetsController < ApplicationController
                            @repository.team, nil, message_items)
     end
 
+    @asset.save!
+
     render json: @asset.file.blob
   end
 
diff --git a/app/models/asset.rb b/app/models/asset.rb
index 6f0f2632f..6841a795a 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -145,10 +145,15 @@ class Asset < ApplicationRecord
     file&.blob&.content_type
   end
 
-  def duplicate(new_name: nil, include_file_versions: false)
+  def duplicate(new_name: nil, include_file_versions: false, created_by: nil)
     new_asset = dup
     file.filename = new_name if new_name
 
+    if created_by
+      new_asset.created_by = created_by
+      new_asset.last_modified_by = created_by
+    end
+
     return unless new_asset.save
 
     duplicate_file(new_asset, new_name: new_name, include_file_versions: include_file_versions)
@@ -163,7 +168,7 @@ class Asset < ApplicationRecord
       new_blob = ActiveStorage::Blob.create_and_upload!(
         io: tmp_file,
         filename: blob.filename,
-        metadata: metadata || blob.metadata
+        metadata: (metadata || blob.metadata)
       )
 
       attach_method.call(new_blob)
@@ -194,6 +199,7 @@ class Asset < ApplicationRecord
     unless include_file_versions
       metadata.delete('version')
       metadata.delete('restored_from_version')
+      metadata['created_by_id'] = to_asset.created_by_id
     end
 
     duplicate_file_versions(to_asset) if include_file_versions
diff --git a/app/models/concerns/versioned_attachments.rb b/app/models/concerns/versioned_attachments.rb
index b999fc501..5ec8f501c 100644
--- a/app/models/concerns/versioned_attachments.rb
+++ b/app/models/concerns/versioned_attachments.rb
@@ -14,7 +14,7 @@ module VersionedAttachments
           __send__(name).attach(*args, **options)
 
           new_blob = __send__(name).blob
-          new_blob.metadata['created_by_id'] = last_modified_by_id
+          new_blob.metadata['created_by_id'] ||= last_modified_by_id
 
           # set version of current latest file if previous versions exist
           new_blob.save! and next unless __send__(:"previous_#{name.to_s.pluralize}").any?
@@ -36,7 +36,7 @@ module VersionedAttachments
             new_blob = ActiveStorage::Blob.create_and_upload!(
               io: tmp_file,
               filename: blob.filename,
-              metadata: blob.metadata.merge({ 'restored_from_version' => version })
+              metadata: blob.metadata.merge({ 'restored_from_version' => version, 'created_by_id' => last_modified_by_id })
             )
 
             __send__(:"attach_#{name}_version", new_blob)
diff --git a/app/models/step.rb b/app/models/step.rb
index b777c7694..395dfbc55 100644
--- a/app/models/step.rb
+++ b/app/models/step.rb
@@ -142,7 +142,7 @@ class Step < ApplicationRecord
       # "Shallow" Copy assets
       assets.each do |asset|
         new_asset = asset.dup
-        new_asset.save!
+        new_asset.update!(created_by: user, last_modified_by: user)
         new_step.assets << new_asset
         assets_to_clone << [asset.id, new_asset.id]
       end
diff --git a/app/services/repository_actions/duplicate_cell.rb b/app/services/repository_actions/duplicate_cell.rb
index e33cebaf6..4c370f7e7 100644
--- a/app/services/repository_actions/duplicate_cell.rb
+++ b/app/services/repository_actions/duplicate_cell.rb
@@ -25,7 +25,7 @@ module RepositoryActions
     private
 
     def repository_asset_value_extra_attributes(value)
-      new_asset = @cell.value.asset.duplicate
+      new_asset = @cell.value.asset.duplicate(created_by: @user)
       value.asset = new_asset
     end
 

From 956813c66c7680c2df98f1dafa5d142d7c59c8d8 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Tue, 19 Nov 2024 12:52:12 +0100
Subject: [PATCH 95/96] Add defulat docx template if nothing is selected
 [SCI-11300]

---
 app/controllers/reports_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index 3b97e8b00..fab290fd7 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -144,7 +144,7 @@ class ReportsController < ApplicationController
   def edit
     @edit = true
     @active_template = @report.settings[:template]
-    @active_docx_template = @report.settings[:docx_template]
+    @active_docx_template = @report.settings[:docx_template].presence || 'scinote_template'
     @report.settings = Report::DEFAULT_SETTINGS if @report.settings.blank?
 
     @project_contents = {

From b7f8956887dad42f7d82803db34a655bbf0a9a21 Mon Sep 17 00:00:00 2001
From: Martin Artnik <85488244+artoscinote@users.noreply.github.com>
Date: Wed, 20 Nov 2024 10:46:03 +0100
Subject: [PATCH 96/96] Bump version to 1.38.0

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

diff --git a/VERSION b/VERSION
index bf50e910e..ebeef2f2d 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.37.0
+1.38.0