From ccc66ab22be8244d70206b93cd8be027303057e3 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 2 Apr 2024 16:55:28 +0200
Subject: [PATCH 1/2] Fix unsupported WOPI file button for inventory files
 [SCI-10546]

---
 .../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 298679e2f..c758cd8fc 100644
--- a/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
+++ b/app/javascript/vue/shared/content/attachments/open_locally_menu.vue
@@ -1,6 +1,6 @@
 <template>
   <div class="sn-open-locally-menu" @mouseenter="fetchLocalAppInfo">
-    <div v-if="!canOpenLocally && (attachment.attributes.wopi && attachment.attributes.urls.edit_asset)">
+    <div v-if="(!canOpenLocally || disableLocalOpen) && (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="{ 'disabled': !editWopiSupported }"

From 4cf0c7ac007b0a584ca0ae291ea186c3c0c4faa5 Mon Sep 17 00:00:00 2001
From: Andrej <andrej.jugovic7@gmail.com>
Date: Tue, 2 Apr 2024 17:26:03 +0200
Subject: [PATCH 2/2] Fix project export [SCI-10527]

---
 app/helpers/reports_helper.rb   |  2 +-
 app/jobs/team_zip_export_job.rb | 29 +++++++-----
 app/jobs/zip_export_job.rb      | 12 +++--
 app/models/project.rb           | 78 ++++++++++++++++++---------------
 app/models/report.rb            |  2 +-
 5 files changed, 67 insertions(+), 56 deletions(-)

diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 48a276c2f..07e3eec42 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -21,7 +21,7 @@ module ReportsHelper
     children_html = ''.html_safe
     # First, recursively render element's children
     if element.children.active.present?
-      element.children.active.each do |child|
+      element.children.active.find_each do |child|
         children_html.safe_concat render_report_element(child, provided_locals)
       end
     end
diff --git a/app/jobs/team_zip_export_job.rb b/app/jobs/team_zip_export_job.rb
index bb3c02af4..504e4a7b8 100644
--- a/app/jobs/team_zip_export_job.rb
+++ b/app/jobs/team_zip_export_job.rb
@@ -4,6 +4,7 @@ require 'fileutils'
 require 'csv'
 require 'vips'
 
+# rubocop:disable Metrics/BlockLength
 class TeamZipExportJob < ZipExportJob
   include StringUtility
 
@@ -51,13 +52,13 @@ class TeamZipExportJob < ZipExportJob
 
       # Include all experiments
       ex_idx = ex_archive_idx = 0
-      project.experiments.each do |experiment|
+      project.experiments.find_each do |experiment|
         idx = experiment.archived ? (ex_archive_idx += 1) : (ex_idx += 1)
         experiment_path = make_model_dir(project_path, experiment, idx)
 
         # Include all modules
         mod_pos = mod_archive_pos = 0
-        experiment.my_modules.order(:workflow_order).each do |my_module|
+        experiment.my_modules.order(:workflow_order).find_each do |my_module|
           pos = my_module.archived ? (mod_archive_pos += 1) : (mod_pos += 1)
           my_module_path = make_model_dir(experiment_path, my_module, pos)
 
@@ -153,19 +154,21 @@ class TeamZipExportJob < ZipExportJob
     directory = create_archived_results_folder(directory) if archived && elements.present?
 
     asset_indexes = {}
-    elements.each_with_index do |element, i|
+    index = 1
+    elements.find_each do |element|
       asset = element.asset
       preview = prepare_preview(asset)
       if type == :step
         name = "#{directory}/" \
-               "#{append_file_suffix(asset.file_name, "_#{i}_Step#{element.step.position_plus_one}")}"
+               "#{append_file_suffix(asset.file_name, "_#{index}_Step#{element.step.position_plus_one}")}"
         if preview
           preview_name = "#{directory}/" \
-                         "#{append_file_suffix(preview[:file_name], "_#{i}_Step#{element.step.position_plus_one}_preview")}"
+                         "#{append_file_suffix(preview[:file_name],
+                                               "_#{index}_Step#{element.step.position_plus_one}_preview")}"
         end
       elsif type == :result
-        name = "#{directory}/#{append_file_suffix(asset.file_name, "_#{i}")}"
-        preview_name = "#{directory}/#{append_file_suffix(preview[:file_name], "_#{i}_preview")}" if preview
+        name = "#{directory}/#{append_file_suffix(asset.file_name, "_#{index}")}"
+        preview_name = "#{directory}/#{append_file_suffix(preview[:file_name], "_#{index}_preview")}" if preview
       end
 
       if asset.file.attached?
@@ -180,6 +183,7 @@ class TeamZipExportJob < ZipExportJob
         file: name,
         preview: preview_name
       }
+      index += 1
     end
     asset_indexes
   end
@@ -218,14 +222,15 @@ class TeamZipExportJob < ZipExportJob
     directory = create_archived_results_folder(directory) if archived && elements.present?
 
     table_indexes = {}
-    elements.each_with_index do |element, i|
+    index = 0
+    elements.find_each do |element|
       table = element.table
       table_name = table.name.presence || 'Table'
-      table_name += i.to_s
+      table_name += index.to_s
 
       if type == :step
         name = "#{directory}/#{to_filesystem_name(table_name)}" \
-               "_#{i}_Step#{element.step.position_plus_one}.csv"
+               "_#{index}_Step#{element.step.position_plus_one}.csv"
       elsif type == :result
         name = "#{directory}/#{to_filesystem_name(table_name)}.csv"
       end
@@ -233,6 +238,7 @@ class TeamZipExportJob < ZipExportJob
       table_indexes[table.id] = {
         file: name
       }
+      index += 1
     end
 
     table_indexes
@@ -253,7 +259,7 @@ class TeamZipExportJob < ZipExportJob
     # Define headers and columns IDs
     col_ids = [-3, -4, -5, -6]
     col_ids << -9 if Repository.repository_row_connections_enabled?
-    col_ids += repo.repository_columns.map(&:id)
+    col_ids += repo.repository_columns.pluck(:id)
 
     # Define callback function for file name
     assets = {}
@@ -290,3 +296,4 @@ class TeamZipExportJob < ZipExportJob
            item: I18n.t('activejob.failure_notifiable_job.items.project'))
   end
 end
+# rubocop:enable Metrics/BlockLength
diff --git a/app/jobs/zip_export_job.rb b/app/jobs/zip_export_job.rb
index a64d03b28..c28074d8e 100644
--- a/app/jobs/zip_export_job.rb
+++ b/app/jobs/zip_export_job.rb
@@ -9,13 +9,11 @@ class ZipExportJob < ApplicationJob
     zip_input_dir = FileUtils.mkdir_p(Rails.root.join("tmp/temp_zip_#{Time.now.to_i}").to_s).first
     zip_dir = FileUtils.mkdir_p(Rails.root.join('tmp/zip-ready').to_s).first
     full_zip_name = File.join(zip_dir, zip_name)
-    ZipExport.transaction do
-      @zip_export = ZipExport.create!(user: @user)
-      fill_content(zip_input_dir, params)
-      @zip_export.zip!(zip_input_dir, full_zip_name)
-      @zip_export.zip_file.attach(io: File.open(full_zip_name), filename: zip_name)
-      generate_notification!
-    end
+    @zip_export = ZipExport.create!(user: @user)
+    fill_content(zip_input_dir, params)
+    @zip_export.zip!(zip_input_dir, full_zip_name)
+    @zip_export.zip_file.attach(io: File.open(full_zip_name), filename: zip_name)
+    generate_notification!
   rescue Errno::ENOENT => e
     Rails.logger.error(e.message)
   ensure
diff --git a/app/models/project.rb b/app/models/project.rb
index 8540caae5..ab5d8b0a7 100644
--- a/app/models/project.rb
+++ b/app/models/project.rb
@@ -252,6 +252,7 @@ class Project < ApplicationRecord
     project_comments
   end
 
+  # rubocop:disable Metrics/BlockLength
   def generate_teams_export_report_html(
     user, team, html_title, obj_filenames = nil
   )
@@ -260,50 +261,54 @@ class Project < ApplicationRecord
     proxy.set_user(user, scope: :user, store: false)
     ApplicationController.renderer.defaults[:http_host] = Rails.application.routes.default_url_options[:host]
     renderer = ApplicationController.renderer.new(warden: proxy)
+    report = nil
+    parsed_html = ''
 
-    report = Report.generate_whole_project_report(self, user, team)
+    Report.transaction do
+      report = Report.generate_whole_project_report(self, user, team)
 
-    page_html_string =
-      renderer.render 'reports/export',
-                      locals: { report: report, export_all: true },
-                      assigns: { settings: report.settings, obj_filenames: obj_filenames }
-    parsed_page_html = Nokogiri::HTML(page_html_string)
-    parsed_html = parsed_page_html.at_css('#report-content')
+      page_html_string =
+        renderer.render 'reports/export',
+                        locals: { report: report, export_all: true },
+                        assigns: { settings: report.settings, obj_filenames: obj_filenames }
+      parsed_page_html = Nokogiri::HTML(page_html_string)
+      parsed_html = parsed_page_html.at_css('#report-content')
 
-    # Style tables (mimick frontend processing)
+      # Style tables (mimick frontend processing)
 
-    tables = parsed_html.css('.hot-table-contents')
-                        .zip(parsed_html.css('.hot-table-container'), parsed_html.css('.hot-table-metadata'))
-    tables.each do |table_input, table_container, metadata|
-      is_plate_template = JSON.parse(metadata['value'])['plateTemplate'] if metadata && metadata['value'].present?
-      table_vals = JSON.parse(table_input['value'])
-      table_data = table_vals['data']
-      table_headers = table_vals['headers']
-      table_headers ||= Array.new(table_data[0].count) do |index|
-        is_plate_template ? index + 1 : convert_index_to_letter(index)
-      end
+      tables = parsed_html.css('.hot-table-contents')
+                          .zip(parsed_html.css('.hot-table-container'), parsed_html.css('.hot-table-metadata'))
+      tables.each do |table_input, table_container, metadata|
+        is_plate_template = JSON.parse(metadata['value'])['plateTemplate'] if metadata && metadata['value'].present?
+        table_vals = JSON.parse(table_input['value'])
+        table_data = table_vals['data']
+        table_headers = table_vals['headers']
+        table_headers ||= Array.new(table_data[0].count) do |index|
+          is_plate_template ? index + 1 : convert_index_to_letter(index)
+        end
 
-      table_el = table_container.add_child('<table class="handsontable"></table>').first
+        table_el = table_container.add_child('<table class="handsontable"></table>').first
 
-      # Add header row
-      header_cell = '<th><div class="relative"><span>%s</span></div></th>'
+        # Add header row
+        header_cell = '<th><div class="relative"><span>%s</span></div></th>'
 
-      header_el = table_el.add_child('<thead></thead>').first
-      row_el = header_el.add_child('<tr></tr>').first
-      row_el.add_child(format(header_cell, '')).first
-      table_headers.each do |col|
-        row_el.add_child(format(header_cell, col)).first
-      end
+        header_el = table_el.add_child('<thead></thead>').first
+        row_el = header_el.add_child('<tr></tr>').first
+        row_el.add_child(format(header_cell, '')).first
+        table_headers.each do |col|
+          row_el.add_child(format(header_cell, col)).first
+        end
 
-      # Add body rows
-      body_cell = '<td>%s</td>'
-      body_el = table_el.add_child('<tbody></tbody>').first
-      table_data.each.with_index(1) do |row, idx|
-        row_name = is_plate_template ? convert_index_to_letter(idx - 1) : idx
-        row_el = body_el.add_child('<tr></tr>').first
-        row_el.add_child(format(header_cell, row_name)).first
-        row.each do |col|
-          row_el.add_child(format(body_cell, col)).first
+        # Add body rows
+        body_cell = '<td>%s</td>'
+        body_el = table_el.add_child('<tbody></tbody>').first
+        table_data.each.with_index(1) do |row, idx|
+          row_name = is_plate_template ? convert_index_to_letter(idx - 1) : idx
+          row_el = body_el.add_child('<tr></tr>').first
+          row_el.add_child(format(header_cell, row_name)).first
+          row.each do |col|
+            row_el.add_child(format(body_cell, col)).first
+          end
         end
       end
     end
@@ -321,6 +326,7 @@ class Project < ApplicationRecord
   ensure
     report.destroy if report.present?
   end
+  # rubocop:enable Metrics/BlockLength
 
   def archived_branch?
     archived?
diff --git a/app/models/report.rb b/app/models/report.rb
index 5f5ff7fb7..b9989bbdb 100644
--- a/app/models/report.rb
+++ b/app/models/report.rb
@@ -116,7 +116,7 @@ class Report < ApplicationRecord
       'experiments' => [],
       'repositories' => project.assigned_repositories_and_snapshots.pluck(:id)
     }
-    project.experiments.includes(:my_modules).each do |experiment|
+    project.experiments.includes(:my_modules).find_each do |experiment|
       content['experiments'].push(
         { id: experiment.id, my_module_ids: experiment.my_module_ids }
       )