From 5054c44b4dd5f8e4292872da1e1e2ecc54f096a3 Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Mon, 21 Jul 2025 08:47:29 +0200
Subject: [PATCH 01/91] Add data-e2e to confirm item assignment modal and task
 page [SCI-12143]

---
 .../vue/my_module/assigned_items.vue          |  8 +++-
 app/javascript/vue/protocol/container.vue     | 10 ++++-
 ..._repository_records_modal_content.html.erb | 41 +++++++++++++------
 .../_update_repository_records_modal.html.erb |  2 +-
 app/views/my_modules/protocols.html.erb       |  4 +-
 5 files changed, 47 insertions(+), 18 deletions(-)

diff --git a/app/javascript/vue/my_module/assigned_items.vue b/app/javascript/vue/my_module/assigned_items.vue
index fe7f57596..748074f32 100644
--- a/app/javascript/vue/my_module/assigned_items.vue
+++ b/app/javascript/vue/my_module/assigned_items.vue
@@ -1,8 +1,12 @@
 <template>
   <div class="bg-white px-4 my-4 task-section">
     <div class="py-4 flex items-center gap-4">
-      <i ref="openHandler" @click="toggleContainer" class="sn-icon sn-icon-right cursor-pointer"></i>
-      <h2 class="my-0 flex items-center gap-1">
+      <i ref="openHandler"
+        @click="toggleContainer"
+        class="sn-icon sn-icon-right cursor-pointer"
+        data-e2e="e2e-IC-task-assignedItems-visibilityToggle">
+      </i>
+      <h2 class="my-0 flex items-center gap-1" data-e2e="e2e-TX-task-assignedItems-title">
         {{ i18n.t('my_modules.assigned_items.title') }}
         <span class="text-sn-grey-500 font-normal text-base">[{{ totalRows }}]</span>
       </h2>
diff --git a/app/javascript/vue/protocol/container.vue b/app/javascript/vue/protocol/container.vue
index 1553859af..94c4ff60d 100644
--- a/app/javascript/vue/protocol/container.vue
+++ b/app/javascript/vue/protocol/container.vue
@@ -9,7 +9,15 @@
           </div>
         </template>
         <template v-else>
-          <a class="task-section-caret" tabindex="0" role="button" data-toggle="collapse" href="#protocol-content" aria-expanded="true" aria-controls="protocol-content">
+          <a class="task-section-caret"
+            tabindex="0"
+            role="button"
+            data-toggle="collapse"
+            href="#protocol-content"
+            aria-expanded="true"
+            aria-controls="protocol-content"
+            data-e2e="e2e-IC-task-protocol-visibilityToggle"
+          >
             <i class="sn-icon sn-icon-right"></i>
             <div class="task-section-title truncate">
               <h2>{{ i18n.t('Protocol') }}</h2>
diff --git a/app/views/my_modules/modals/_assign_repository_records_modal_content.html.erb b/app/views/my_modules/modals/_assign_repository_records_modal_content.html.erb
index 6403e49f6..7a076fe5f 100644
--- a/app/views/my_modules/modals/_assign_repository_records_modal_content.html.erb
+++ b/app/views/my_modules/modals/_assign_repository_records_modal_content.html.erb
@@ -1,17 +1,30 @@
 <div class="modal-header">
-  <button type="button" class="close self-start" data-dismiss="modal" aria-label="Close">
-          <i class="sn-icon sn-icon-close"></i>
+  <button
+    type="button"
+    class="close self-start"
+    data-dismiss="modal"
+    aria-label="Close"
+    data-e2e="e2e-BT-task-assignItemModal-confirmAssignModal-close"
+  >
+    <i class="sn-icon sn-icon-close"></i>
   </button>
   <% if downstream %>
-    <h4 class="modal-title !line-clamp-3" title="<%= t('my_modules.modals.assign_repository_record.title_downstream',
-             repository_name: repository.name) %>">
+    <h4
+      class="modal-title !line-clamp-3"
+      title="<%= t('my_modules.modals.assign_repository_record.title_downstream', repository_name: repository.name) %>"
+      data-e2e="e2e-TX-task-assignItemModal-confirmAssignModal-titleDownstream"
+    >
       <%= t('my_modules.modals.assign_repository_record.title_downstream',
              repository_name: repository.name) %>
     </h4>
   <% else %>
-    <h4 class="modal-title !line-clamp-3" title="<%= t('my_modules.modals.assign_repository_record.title',
-             repository_name: repository.name,
-             my_module_name: my_module.name) %>">
+    <h4
+      class="modal-title !line-clamp-3"
+      title="<%= t('my_modules.modals.assign_repository_record.title',
+            repository_name: repository.name,
+            my_module_name: my_module.name) %>"
+      data-e2e="e2e-TX-task-assignItemModal-confirmAssignModal-title"
+    >
       <%= t('my_modules.modals.assign_repository_record.title',
            repository_name: repository.name,
            my_module_name: my_module.name) %>
@@ -19,7 +32,7 @@
   <% end %>
 </div>
 <div class="modal-body">
-  <p>
+  <p data-e2e="e2e-TX-task-assignItemModal-confirmAssignModal-message">
     <% if downstream %>
       <%= t('my_modules.modals.assign_repository_record.message_downstream', size: selected_rows.count) %>
     <% else %>
@@ -27,7 +40,7 @@
     <% end %>
   </p>
   <% if downstream %>
-    <div class='my-modules-to-assign'>
+    <div class='my-modules-to-assign' data-e2e="e2e-TX-task-assignItemModal-confirmAssignModal-taskList">
       <% visible_modules = 0
          downstream_modules = my_module.downstream_modules
          downstream_modules.each do |m| %>
@@ -52,15 +65,19 @@
 </div>
 <div class="modal-footer">
   <div class="sci-btn-group">
-    <a class="btn btn-secondary hide-assign-repo-modal" data-dismiss="modal">
+    <a
+      class="btn btn-secondary hide-assign-repo-modal"
+      data-dismiss="modal"
+      data-e2e="e2e-BT-task-assignItemModal-confirmAssignModal-cancel"
+    >
       <%= t('general.cancel') %>
     </a>
     <% if downstream %>
-      <a class="btn btn-primary downstream-action">
+      <a class="btn btn-primary downstream-action" data-e2e="e2e-BT-task-assignItemModal-confirmAssignModal-assignDownstream">
         <%= t('my_modules.modals.assign_repository_record.task_and_downstream') %>
       </a>
     <% else %>
-      <a class="btn btn-primary task-action">
+      <a class="btn btn-primary task-action" data-e2e="e2e-BT-task-assignItemModal-confirmAssignModal-assign">
         <%= t('my_modules.modals.assign_repository_record.task') %>
       </a>
     <% end %>
diff --git a/app/views/my_modules/modals/_update_repository_records_modal.html.erb b/app/views/my_modules/modals/_update_repository_records_modal.html.erb
index ca5b38c7a..ce403ab37 100644
--- a/app/views/my_modules/modals/_update_repository_records_modal.html.erb
+++ b/app/views/my_modules/modals/_update_repository_records_modal.html.erb
@@ -1,6 +1,6 @@
 <div id="updateRepositoryRecordModal" class="modal update-repository-record-modal" tabindex="-1" role="dialog" data-dismiss="modal">
   <div class="modal-dialog">
-    <div class="modal-content">
+    <div class="modal-content" data-e2e="e2e-MD-task-assignItemModal-confirmAssign">
     </div>
   </div>
 </div>
diff --git a/app/views/my_modules/protocols.html.erb b/app/views/my_modules/protocols.html.erb
index 96e59f542..8f6ac492a 100644
--- a/app/views/my_modules/protocols.html.erb
+++ b/app/views/my_modules/protocols.html.erb
@@ -36,7 +36,7 @@
       <div id="task-details" class="task-section-header">
         <div class="flex items-center mr-auto">
           <a class="task-section-caret collapsed" role="button" data-toggle="collapse" href="#details-container" aria-expanded="false" aria-controls="details-container">
-            <i class="sn-icon sn-icon-right"></i>
+            <i class="sn-icon sn-icon-right" data-e2e="e2e-IC-task-details-visibilityToggle"></i>
             <span id="taskDetailsLabel" class="task-section-title">
               <h2 data-e2e="e2e-TX-task-details-title">
                 <%= t('my_modules.details.title') %>
@@ -69,7 +69,7 @@
     <div class="task-section hidden">
       <div class="task-section-header">
         <a class="task-section-caret" role="button" data-toggle="collapse" href="#notes-container" aria-expanded="true" aria-controls="notes-container">
-          <i class="sn-icon sn-icon-right"></i>
+          <i class="sn-icon sn-icon-right" data-e2e="e2e-IC-task-notes-visibilityToggle"></i>
           <span class="task-section-title">
             <h2 data-e2e="e2e-TX-task-notes-title"><%= t('my_modules.notes.title') %></h2>
           </span>

From d1f4adb00aa6413d7d1712af04e45a4699213628 Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Mon, 21 Jul 2025 08:49:13 +0200
Subject: [PATCH 02/91] Add data-e2e to add column stock dropdown option
 [SCI-12143]

---
 .../repository_columns/_manage_column_modal_content.html.erb  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/app/views/repository_columns/_manage_column_modal_content.html.erb b/app/views/repository_columns/_manage_column_modal_content.html.erb
index c3e09ef2c..d8add6e89 100644
--- a/app/views/repository_columns/_manage_column_modal_content.html.erb
+++ b/app/views/repository_columns/_manage_column_modal_content.html.erb
@@ -109,6 +109,10 @@
                         text_description: 'Only one per inventory allowed',
                         data_e2e: 'e2e-DO-invItems-manageColumns-columnType-stock'
                       }.to_json %>"
+                    <% else %>
+                        data-params="<%= {
+                          data_e2e: 'e2e-DO-invItems-manageColumns-columnType-stock'
+                        }.to_json %>"
                     <% end %>
                     <%= 'selected' if @repository_column.repository_stock_value? %> >
               <%= t('libraries.manange_modal_column.select.repository_stock_value') %>

From 536dfe5ef7811998421999d04a38f6ffe8757edc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 22 Jul 2025 03:19:48 +0000
Subject: [PATCH 03/91] Bump thor from 1.3.2 to 1.4.0

Bumps [thor](https://github.com/rails/thor) from 1.3.2 to 1.4.0.
- [Release notes](https://github.com/rails/thor/releases)
- [Commits](https://github.com/rails/thor/compare/v1.3.2...v1.4.0)

---
updated-dependencies:
- dependency-name: thor
  dependency-version: 1.4.0
  dependency-type: indirect
...

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

diff --git a/Gemfile.lock b/Gemfile.lock
index 1deaf8d0f..5ea9c5013 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -750,7 +750,7 @@ GEM
       railties (>= 6.0.0)
     tailwindcss-rails (2.4.0-x86_64-linux)
       railties (>= 6.0.0)
-    thor (1.3.2)
+    thor (1.4.0)
     tilt (2.4.0)
     timecop (0.9.6)
     timeout (0.4.3)

From 73914c1d0de3aafc49fc6dca77c4569a45e5a589 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 22 Jul 2025 10:01:30 +0200
Subject: [PATCH 04/91] Update team/export import script [SCI-11839]

---
 .../model_exporters/experiment_exporter.rb    | 15 ++++++++
 app/services/model_exporters/team_exporter.rb | 31 ++++++++++++++---
 app/services/team_importer.rb                 | 34 ++++++++++++++-----
 3 files changed, 67 insertions(+), 13 deletions(-)

diff --git a/app/services/model_exporters/experiment_exporter.rb b/app/services/model_exporters/experiment_exporter.rb
index c82a0192f..0c7c256b4 100644
--- a/app/services/model_exporters/experiment_exporter.rb
+++ b/app/services/model_exporters/experiment_exporter.rb
@@ -47,6 +47,9 @@ module ModelExporters
         user_assignments: @experiment.user_assignments.map do |ua|
           user_assignment(ua)
         end,
+        team_assignments: @experiment.team_assignments.map do |ta|
+          team_assignment(ta)
+        end,
         my_modules: my_modules.map { |m| my_module(m) },
         my_module_groups: my_module_groups
       }, @assets_to_copy
@@ -61,12 +64,24 @@ module ModelExporters
       }
     end
 
+    def team_assignment(team_assignment)
+      {
+        team_id: team_assignment.team_id,
+        assigned_by_id: team_assignment.assigned_by_id,
+        role_name: team_assignment.user_role.name,
+        assigned: team_assignment.assigned
+      }
+    end
+
     def my_module(my_module)
       {
         my_module: my_module,
         user_assignments: my_module.user_assignments.map do |ua|
           user_assignment(ua)
         end,
+        team_assignments: my_module.team_assignments.map do |ta|
+          team_assignment(ta)
+        end,
         my_module_status_name: my_module.my_module_status&.name,
         outputs: my_module.outputs,
         my_module_tags: my_module.my_module_tags,
diff --git a/app/services/model_exporters/team_exporter.rb b/app/services/model_exporters/team_exporter.rb
index 0f992a497..92ab28ddd 100644
--- a/app/services/model_exporters/team_exporter.rb
+++ b/app/services/model_exporters/team_exporter.rb
@@ -51,9 +51,14 @@ module ModelExporters
         tiny_mce_assets: team.tiny_mce_assets.map { |tma| tiny_mce_asset_data(tma) },
         protocols: team.protocols.where(my_module: nil).map do |pr|
           protocol(pr).merge(
-            user_assignments: pr.user_assignments.map do |ua|
-              user_assignment(ua)
-            end
+            {
+              user_assignments: pr.user_assignments.map do |ua|
+                user_assignment(ua)
+              end,
+              team_assignments: pr.team_assignments.map do |ta|
+                team_assigment(ta)
+              end
+            }
           )
         end,
         protocol_keywords: team.protocol_keywords,
@@ -102,7 +107,9 @@ module ModelExporters
         user_assignments: project.user_assignments.map do |ua|
           user_assignment(ua)
         end,
-        user_projects: project.user_projects,
+        team_assignments: project.team_assignments.map do |ta|
+          team_assigment(ta)
+        end,
         activities: project.activities,
         project_comments: project.project_comments,
         reports: project.reports.map { |r| report(r) },
@@ -121,12 +128,24 @@ module ModelExporters
       }
     end
 
+    def team_assigment(team_assignment)
+      {
+        team_id: team_assignment.team_id,
+        assigned_by_id: team_assignment.assigned_by_id,
+        role_name: team_assignment.user_role.name,
+        assigned: team_assignment.assigned
+      }
+    end
+
     def report(report)
       {
         report: report,
         user_assignments: report.user_assignments.map do |ua|
           user_assignment(ua)
         end,
+        team_assignments: report.team_assignments.map do |ta|
+          team_assigment(ta)
+        end,
         report_elements: report.report_elements
       }
     end
@@ -146,6 +165,10 @@ module ModelExporters
           repository.user_assignments.where(team: repository.team, user: repository.team.users).map do |ua|
             user_assignment(ua)
           end
+        result[:team_assignments] =
+          repository.team_assignments.where(team: repository.team).map do |ta|
+            team_assigment(ta)
+          end
         result[:repository_snapshots] = repository.repository_snapshots.map { |r| repository(r) }
       end
       result
diff --git a/app/services/team_importer.rb b/app/services/team_importer.rb
index 7a90d4b86..d0e501cc9 100644
--- a/app/services/team_importer.rb
+++ b/app/services/team_importer.rb
@@ -428,10 +428,12 @@ class TeamImporter
       repository.archived_by_id = find_user(repository.archived_by_id)
       repository.restored_by_id = find_user(repository.restored_by_id)
       repository.discarded_by_id = find_user(repository.discarded_by_id)
+      repository.repository_template_id = nil
       repository.skip_user_assignments = true
       repository.save!
 
       create_user_assignments(repository_json['user_assignments'], repository)
+      create_team_assignments(repository_json['team_assignments'], repository)
 
       @repository_mappings[orig_repository_id] = repository.id
       @repository_counter += 1
@@ -498,6 +500,7 @@ class TeamImporter
       orig_rep_row_id = repository_row.id
       repository_row.id = nil
       repository_row.repository = repository
+      repository_row.my_module_id = @my_module_mappings[repository_row.my_module_id]
       repository_row.created_by_id = find_user(repository_row.created_by_id)
       repository_row.archived_by_id = find_user(repository_row.archived_by_id)
       repository_row.restored_by_id = find_user(repository_row.restored_by_id)
@@ -578,20 +581,14 @@ class TeamImporter
       project.restored_by_id = find_user(project.restored_by_id)
       project.skip_user_assignments = true
       project.project_folder_id = @project_folder_mappings[project.project_folder_id]
+      project.supervised_by_id = find_user(project.supervised_by_id) if project.supervised_by_id
       project.save!
       @project_mappings[orig_project_id] = project.id
       @project_counter += 1
       puts 'Creating project user_assignments...'
       create_user_assignments(project_json['user_assignments'], project)
-      puts 'Creating user_projects...'
-      project_json['user_projects'].each do |user_project_json|
-        user_project = UserProject.new(user_project_json)
-        user_project.id = nil
-        user_project.project = project
-        user_project.user_id = find_user(user_project.user_id)
-        user_project.assigned_by_id = find_user(user_project.assigned_by_id)
-        user_project.save!
-      end
+      puts 'Creating project team_assignments...'
+      create_team_assignments(project_json['team_assignments'], project)
       puts 'Creating project_comments...'
       project_json['project_comments'].each do |project_comment_json|
         project_comment = ProjectComment.new(project_comment_json)
@@ -641,6 +638,7 @@ class TeamImporter
     @experiment_mappings[orig_experiment_id] = experiment.id
 
     create_user_assignments(experiment_json['user_assignments'], experiment)
+    create_team_assignments(experiment_json['team_assignments'], experiment)
 
     experiment_json['my_module_groups'].each do |my_module_group_json|
       my_module_group = MyModuleGroup.new(my_module_group_json)
@@ -687,6 +685,7 @@ class TeamImporter
       @my_module_counter += 1
 
       create_user_assignments(my_module_json['user_assignments'], my_module)
+      create_team_assignments(my_module_json['team_assignments'], my_module)
 
       unless @is_template
         my_module_json['my_module_tags'].each do |my_module_tag_json|
@@ -777,6 +776,7 @@ class TeamImporter
       protocol.save!
 
       create_user_assignments(protocol_json['user_assignments'], protocol) if protocol.in_repository?
+      create_team_assignments(protocol_json['team_assignments'], protocol) if protocol.in_repository?
 
       @protocol_counter += 1
       @protocol_mappings[orig_protocol_id] = protocol.id
@@ -841,6 +841,7 @@ class TeamImporter
         elsif element_json['checklist']
           orderable = create_step_checklist(element_json['checklist'], step, user_id)
         end
+
         StepOrderableElement.create!(
           position: element_json['position'],
           step: step,
@@ -980,6 +981,7 @@ class TeamImporter
       report.save!
 
       create_user_assignments(report_json['user_assignments'], report)
+      create_team_assignments(report_json['team_assignments'], report)
 
       @report_mappings[orig_report_id] = report.id
       @report_counter += 1
@@ -1059,6 +1061,20 @@ class TeamImporter
     end
   end
 
+  def create_team_assignments(team_assignments_json, assignable)
+    return if team_assignments_json.blank?
+
+    team_assignments_json.each do |team_assignment_json|
+      team_assignment = TeamAssignment.new
+      team_assignment.assignable = assignable
+      team_assignment.team_id = @team_id
+      team_assignment.user_role = @user_roles.find { |role| role.name == team_assignment_json['role_name'] }
+      team_assignment.assigned = team_assignment_json['assigned']
+      team_assignment.assigned_by_id = find_user(team_assignment_json['assigned_by_id'])
+      team_assignment.save!
+    end
+  end
+
   def create_cell_value(repository_cell, value_json, team)
     cell_json = value_json['repository_value']
     case repository_cell.value_type

From 99b232e19e46baa7477a9aa4c8b7083d8901372f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 22 Jul 2025 08:44:48 +0000
Subject: [PATCH 05/91] Bump nokogiri from 1.18.8 to 1.18.9

Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.18.8 to 1.18.9.
- [Release notes](https://github.com/sparklemotion/nokogiri/releases)
- [Changelog](https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md)
- [Commits](https://github.com/sparklemotion/nokogiri/compare/v1.18.8...v1.18.9)

---
updated-dependencies:
- dependency-name: nokogiri
  dependency-version: 1.18.9
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Gemfile      | 2 +-
 Gemfile.lock | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Gemfile b/Gemfile
index 64d0d3293..69ed0c7e9 100644
--- a/Gemfile
+++ b/Gemfile
@@ -58,7 +58,7 @@ gem 'jbuilder' # JSON structures via a Builder-style DSL
 gem 'logging', '~> 2.0.0'
 gem 'mime-types', '~> 3.4'
 gem 'nested_form_fields'
-gem 'nokogiri', '~> 1.18.8' # HTML/XML parser
+gem 'nokogiri', '~> 1.18.9' # HTML/XML parser
 gem 'noticed'
 gem 'oj'
 gem 'rails_autolink', '~> 1.1', '>= 1.1.6'
diff --git a/Gemfile.lock b/Gemfile.lock
index 5ea9c5013..99f845814 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -486,9 +486,9 @@ GEM
       net-protocol
     newrelic_rpm (9.14.0)
     nio4r (2.7.4)
-    nokogiri (1.18.8-arm64-darwin)
+    nokogiri (1.18.9-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.18.8-x86_64-linux-gnu)
+    nokogiri (1.18.9-x86_64-linux-gnu)
       racc (~> 1.4)
     noticed (1.6.3)
       http (>= 4.0.0)
@@ -866,7 +866,7 @@ DEPENDENCIES
   mime-types (~> 3.4)
   nested_form_fields
   newrelic_rpm
-  nokogiri (~> 1.18.8)
+  nokogiri (~> 1.18.9)
   noticed
   oj
   omniauth (~> 2.1)

From f857744fe7f12063c0710d98ea39dc96c4432921 Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Wed, 23 Jul 2025 14:20:49 +0200
Subject: [PATCH 06/91] Add data-e2e to task protocol and linked modals
 [SCI-12154]

---
 app/javascript/vue/protocol/container.vue     | 42 +++++++++++++++----
 .../protocol/modals/add_protocol_steps.vue    | 34 ++++++++++++---
 .../vue/protocol/modals/delete_steps.vue      | 38 +++++++++++++----
 .../vue/protocol/protocolOptions.vue          |  9 ++++
 .../_confirm_link_update_modal.html.erb       | 39 +++++++++++++----
 .../_load_from_repository_modal.html.erb      | 36 +++++++++++++---
 .../_load_from_repository_modal_body.html.erb |  4 +-
 .../protocols/_protocol_status_bar.html.erb   |  4 +-
 8 files changed, 170 insertions(+), 36 deletions(-)

diff --git a/app/javascript/vue/protocol/container.vue b/app/javascript/vue/protocol/container.vue
index 1553859af..8ba4c8848 100644
--- a/app/javascript/vue/protocol/container.vue
+++ b/app/javascript/vue/protocol/container.vue
@@ -12,7 +12,7 @@
           <a class="task-section-caret" tabindex="0" role="button" data-toggle="collapse" href="#protocol-content" aria-expanded="true" aria-controls="protocol-content">
             <i class="sn-icon sn-icon-right"></i>
             <div class="task-section-title truncate">
-              <h2>{{ i18n.t('Protocol') }}</h2>
+              <h2 data-e2e="e2e-TX-task-protocol-sectionTitle">{{ i18n.t('Protocol') }}</h2>
             </div>
           </a>
         </template>
@@ -29,16 +29,30 @@
              :title="i18n.t('protocols.steps.new_step_title')"
              @keyup.enter="addStep(steps.length)"
              @click="addStep(steps.length)"
-             tabindex="0">
+             tabindex="0"
+             data-e2e="e2e-BT-task-protocol-newStep">
               <span class="sn-icon sn-icon-new-task" aria-hidden="true"></span>
               <span class="tw-hidden xl:inline">{{ i18n.t("protocols.steps.new_step") }}</span>
           </a>
           <template v-if="steps.length > 0">
-            <button :title="i18n.t('protocols.steps.collapse_label')" v-if="!stepCollapsed" class="btn btn-secondary icon-btn xl:!px-4" @click="collapseSteps" tabindex="0">
+            <button
+              :title="i18n.t('protocols.steps.collapse_label')"
+              v-if="!stepCollapsed"
+              class="btn btn-secondary icon-btn xl:!px-4"
+              @click="collapseSteps"
+              tabindex="0"
+              data-e2e="e2e-BT-task-protocol-collapseAll"
+            >
               <i class="sn-icon sn-icon-collapse-all"></i>
               <span class="tw-hidden xl:inline">{{ i18n.t("protocols.steps.collapse_label") }}</span>
             </button>
-            <button v-else  :title="i18n.t('protocols.steps.expand_label')" class="btn btn-secondary icon-btn xl:!px-4" @click="expandSteps" tabindex="0">
+            <button v-else
+              :title="i18n.t('protocols.steps.expand_label')"
+              class="btn btn-secondary icon-btn xl:!px-4"
+              @click="expandSteps"
+              tabindex="0"
+              data-e2e="e2e-BT-task-protocol-expandAll"
+            >
               <i class="sn-icon sn-icon-expand-all"></i>
               <span class="tw-hidden xl:inline">{{ i18n.t("protocols.steps.expand_label") }}</span>
             </button>
@@ -51,7 +65,13 @@
             @protocol:add_protocol_steps="addSteps"
             :canDeleteSteps="steps.length > 0 && urls.delete_steps_url !== null"
           />
-          <button class="btn btn-light icon-btn" data-toggle="modal" data-target="#print-protocol-modal" tabindex="0">
+          <button
+            class="btn btn-light icon-btn"
+            data-toggle="modal"
+            data-target="#print-protocol-modal"
+            tabindex="0"
+            data-e2e="e2e-BT-task-protocol-print"
+          >
             <span class="sn-icon sn-icon-printer" aria-hidden="true"></span>
           </button>
           <a v-if="steps.length > 0 && urls.reorder_steps_url"
@@ -60,13 +80,20 @@
             @click="startStepReorder"
             @keyup.enter="startStepReorder"
             :class="{'disabled': steps.length == 1}"
-            tabindex="0" >
+            tabindex="0"
+            data-e2e="e2e-BT-task-protocol-reorderSteps"
+          >
               <i class="sn-icon sn-icon-sort" aria-hidden="true"></i>
           </a>
         </div>
       </div>
     </div>
-    <div id="protocol-content" class="protocol-content collapse in" aria-expanded="true">
+    <div
+      id="protocol-content"
+      class="protocol-content collapse in"
+      aria-expanded="true"
+      data-e2e="e2e-CO-task-protocol-content"
+    >
       <div class="sci-divider" v-if="!inRepository"></div>
       <div class="mb-4">
         <div class="protocol-name mt-4" v-if="!inRepository">
@@ -78,6 +105,7 @@
             :allowBlank="!inRepository"
             :attributeName="`${i18n.t('Protocol')} ${i18n.t('name')}`"
             @update="updateName"
+            :dataE2e="'task-protocol-title'"
           />
           <span v-else>
             {{ protocol.attributes.name }}
diff --git a/app/javascript/vue/protocol/modals/add_protocol_steps.vue b/app/javascript/vue/protocol/modals/add_protocol_steps.vue
index 2fe01adee..684367b64 100644
--- a/app/javascript/vue/protocol/modals/add_protocol_steps.vue
+++ b/app/javascript/vue/protocol/modals/add_protocol_steps.vue
@@ -1,18 +1,26 @@
 <template>
   <div ref="modal" class="modal" tabindex="-1" role="dialog">
-    <div class="modal-dialog" role="document">
+    <div class="modal-dialog" role="document" data-e2e="e2e-MD-protocol-addProtocolSteps">
       <form @submit.prevent="submit">
         <div class="modal-content">
           <div class="modal-header">
-            <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+            <button
+              type="button"
+              class="close"
+              data-dismiss="modal"
+              aria-label="Close"
+              data-e2e="e2e-BT-protocol-addProtocolStepsModal-close"
+            >
               <i class="sn-icon sn-icon-close"></i>
             </button>
-            <h4 class="modal-title truncate !block" >
+            <h4 class="modal-title truncate !block" data-e2e="e2e-TX-protocol-addProtocolStepsModal-title">
               {{ i18n.t('protocols.steps.modals.add_protocol_steps.title') }}
             </h4>
           </div>
           <div class="modal-body">
-            <p class="mb-6">{{ i18n.t('protocols.steps.modals.add_protocol_steps.description')}}</p>
+            <p class="mb-6" data-e2e="e2e-TX-protocol-addProtocolStepsModal-description">
+              {{ i18n.t('protocols.steps.modals.add_protocol_steps.description')}}
+            </p>
             <div class="mb-6">
               <label class="sci-label">{{ i18n.t('protocols.steps.modals.add_protocol_steps.protocol_label') }}</label>
               <SelectDropdown
@@ -21,6 +29,7 @@
                 :searchable="true"
                 :value="selectedProtocol"
                 @change="selectedProtocol = $event"
+                :e2eValue="'e2e-DD-protocol-addProtocolStepsModal-selectProtocol'"
               ></SelectDropdown>
             </div>
             <div class="relative">
@@ -36,12 +45,25 @@
                 :searchable="true"
                 :value="selectedSteps"
                 @change="selectedSteps= $event"
+                :e2eValue="'e2e-DD-protocol-addProtocolStepsModal-selectSteps'"
               ></SelectDropdown>
             </div>
           </div>
           <div class="modal-footer">
-            <button type="button" class="btn btn-secondary" data-dismiss="modal">{{ i18n.t('general.cancel') }}</button>
-            <button class="btn btn-primary" :disabled="submitting || !validObject" type="submit">
+            <button
+              type="button"
+              class="btn btn-secondary"
+              data-dismiss="modal"
+              data-e2e="e2e-BT-protocol-addProtocolStepsModal-cancel"
+            >
+              {{ i18n.t('general.cancel') }}
+            </button>
+            <button
+              class="btn btn-primary"
+              :disabled="submitting || !validObject"
+              type="submit"
+              data-e2e="e2e-BT-protocol-addProtocolStepsModal-addSteps"
+            >
               {{ i18n.t('protocols.steps.modals.add_protocol_steps.confirm') }}
             </button>
           </div>
diff --git a/app/javascript/vue/protocol/modals/delete_steps.vue b/app/javascript/vue/protocol/modals/delete_steps.vue
index 33d035ba7..604765295 100644
--- a/app/javascript/vue/protocol/modals/delete_steps.vue
+++ b/app/javascript/vue/protocol/modals/delete_steps.vue
@@ -1,20 +1,44 @@
 <template>
   <div ref="modal" @keydown.esc="cancel" class="modal delete-steps-modal" tabindex="-1" role="dialog">
     <div class="modal-dialog" role="document">
-      <div class="modal-content">
+      <div class="modal-content" data-e2e="e2e-MD-task-protocol-deleteAllSteps">
         <div class="modal-header">
-          <button type="button" class="close" data-dismiss="modal" aria-label="Close"><i class="sn-icon sn-icon-close"></i></button>
-          <h4 class="modal-title">
+          <button
+            type="button"
+            class="close"
+            data-dismiss="modal"
+            aria-label="Close"
+            data-e2e="e2e-BT-task-protocol-deleteAllStepsModal-close"
+          >
+            <i class="sn-icon sn-icon-close"></i>
+          </button>
+          <h4 class="modal-title" data-e2e="e2e-TX-task-protocol-deleteAllStepsModal-title">
             {{ i18n.t('protocols.steps.modals.delete_steps.title')}}
           </h4>
         </div>
         <div class="modal-body">
-          <p>{{ i18n.t('protocols.steps.modals.delete_steps.description_1')}}</p>
-          <p class="warning">{{ i18n.t('protocols.steps.modals.delete_steps.description_2')}}</p>
+          <p data-e2e="e2e-TX-task-protocol-deleteAllStepsModal-description">
+            {{ i18n.t('protocols.steps.modals.delete_steps.description_1')}}
+          </p>
+          <p class="warning" data-e2e="e2e-TX-task-protocol-deleteAllStepsModal-warning">
+            {{ i18n.t('protocols.steps.modals.delete_steps.description_2')}}
+          </p>
         </div>
         <div class="modal-footer">
-          <button class="btn btn-secondary" @click="cancel">{{ i18n.t('general.cancel') }}</button>
-          <button class="btn btn-danger" @click="confirm">{{ i18n.t('protocols.steps.modals.delete_steps.confirm')}}</button>
+          <button
+            class="btn btn-secondary"
+            @click="cancel"
+            data-e2e="e2e-BT-task-protocol-deleteAllStepsModal-cancel"
+          >
+            {{ i18n.t('general.cancel') }}
+          </button>
+          <button
+            class="btn btn-danger"
+            @click="confirm"
+            data-e2e="e2e-BT-task-protocol-deleteAllStepsModal-delete"
+          >
+            {{ i18n.t('protocols.steps.modals.delete_steps.confirm')}}
+          </button>
         </div>
       </div>
     </div>
diff --git a/app/javascript/vue/protocol/protocolOptions.vue b/app/javascript/vue/protocol/protocolOptions.vue
index 4b71cd715..5ad38d2f7 100644
--- a/app/javascript/vue/protocol/protocolOptions.vue
+++ b/app/javascript/vue/protocol/protocolOptions.vue
@@ -9,6 +9,7 @@
         aria-haspopup="true"
         aria-expanded="true"
         tabindex="0"
+        data-e2e="e2e-DD-task-protocol-actions"
       >
         <span>{{ i18n.t("my_modules.protocol.options_dropdown.title") }}</span>
         <span class="sn-icon sn-icon-down"></span>
@@ -22,6 +23,7 @@
             ref="loadProtocol"
             data-action="load-from-repository"
             @click="loadProtocol"
+            data-e2e="e2e-DO-task-protocol-actions-loadFromRepository"
           >
             <span>{{ i18n.t("my_modules.protocol.options_dropdown.load_from_repo") }}</span>
           </a>
@@ -30,6 +32,7 @@
           <a class="!px-3 !py-2.5 hover:!bg-sn-super-light-blue !text-sn-blue"
             data-turbolinks="false"
             @click.prevent="openAddStepsModal()"
+            data-e2e="e2e-DO-task-protocol-actions-addProtocolSteps"
           >
             <span>{{
               i18n.t("my_modules.protocol.options_dropdown.add_protocol_steps")
@@ -42,6 +45,7 @@
             data-target="#newProtocolModal"
             v-bind:data-protocol-name="protocol.attributes.name"
             :class="{ disabled: !protocol.attributes.urls.save_to_repo_url }"
+            data-e2e="e2e-DO-task-protocol-actions-saveAsNewTemplate"
           >
             <span>{{
               i18n.t("my_modules.protocol.options_dropdown.save_to_repo")
@@ -53,6 +57,7 @@
             data-turbolinks="false"
             :href="protocol.attributes.urls.export_url"
             :class="{ disabled: !protocol.attributes.urls.export_url }"
+            data-e2e="e2e-DO-task-protocol-actions-exportProtocol"
           >
             <span>{{
               i18n.t("my_modules.protocol.options_dropdown.export")
@@ -64,6 +69,7 @@
             ref="updateProtocol"
             data-action="update-self"
             @click="updateProtocol"
+            data-e2e="e2e-DO-task-protocol-actions-updateProtocol"
           >
             <span>{{
               i18n.t("my_modules.protocol.options_dropdown.update_protocol")
@@ -75,6 +81,7 @@
             ref="unlinkProtocol"
             data-action="unlink"
             @click="unlinkProtocol"
+            data-e2e="e2e-DO-task-protocol-actions-unlinkProtocol"
           >
             <span>{{
               i18n.t("my_modules.protocol.options_dropdown.unlink")
@@ -86,6 +93,7 @@
             ref="revertProtocol"
             data-action="revert"
             @click="revertProtocol"
+            data-e2e="e2e-DO-task-protocol-actions-revertProtocol"
           >
             <span>{{
               i18n.t("my_modules.protocol.options_dropdown.revert_protocol")
@@ -96,6 +104,7 @@
           <a class="!px-3 !py-2.5 hover:!bg-sn-super-light-blue !text-sn-blue"
             data-turbolinks="false"
             @click.prevent="openStepsDeletingModal()"
+            data-e2e="e2e-DO-task-protocol-actions-deleteAllSteps"
           >
             <span>{{
               i18n.t("my_modules.protocol.options_dropdown.delete_steps")
diff --git a/app/views/my_modules/protocols/_confirm_link_update_modal.html.erb b/app/views/my_modules/protocols/_confirm_link_update_modal.html.erb
index d606f0f09..673482a5c 100644
--- a/app/views/my_modules/protocols/_confirm_link_update_modal.html.erb
+++ b/app/views/my_modules/protocols/_confirm_link_update_modal.html.erb
@@ -1,17 +1,42 @@
 <div class="modal" id="confirm-link-update-modal" tabindex="-1" role="dialog" aria-labelledby="confirm-link-update-modal-label">
   <div class="modal-dialog" role="document">
-    <div class="modal-content">
+    <div class="modal-content" data-e2e="e2e-MD-task-protocol-updateRevertFromTemplates">
       <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><i class="sn-icon sn-icon-close"></i></button>
-        <h4 class="modal-title" id="confirm-link-update-modal-label"></h4>
+        <button
+          type="button"
+          class="close"
+          data-dismiss="modal"
+          aria-label="Close"
+          data-e2e="e2e-BT-task-protocol-updateRevertFromTemplatesModal-close"
+        >
+          <i class="sn-icon sn-icon-close"></i>
+        </button>
+        <h4
+          class="modal-title"
+          id="confirm-link-update-modal-label"
+          data-e2e="e2e-TX-task-protocol-updateRevertFromTemplatesModal-title"
+        ></h4>
       </div>
       <div class="modal-body">
-        <p class="message"></p>
-        <p class="warning"><%= t('my_modules.protocols.confirm_link_update_modal.warning') %></p>
+        <p class="message" data-e2e="e2e-TX-task-protocol-updateRevertFromTemplates-description"></p>
+        <p class="warning" data-e2e="e2e-TX-task-protocol-updateRevertFromTemplates-warning">
+          <%= t('my_modules.protocols.confirm_link_update_modal.warning') %>
+        </p>
       </div>
       <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal"><%= t("general.cancel") %></button>
-        <button type="button" class="btn btn-success" data-action="submit"></button>
+        <button
+          type="button"
+          class="btn btn-secondary"
+          data-dismiss="modal"
+          data-e2e="e2e-BT-task-protocol-updateRevertFromTemplatesModal-cancel">
+            <%= t("general.cancel") %>
+        </button>
+        <button
+          type="button"
+          class="btn btn-success"
+          data-action="submit"
+          data-e2e="e2e-BT-task-protocol-updateRevertFromTemplatesModal-confirm"
+        ></button>
       </div>
     </div>
   </div>
diff --git a/app/views/my_modules/protocols/_load_from_repository_modal.html.erb b/app/views/my_modules/protocols/_load_from_repository_modal.html.erb
index df9c024e8..c71564399 100644
--- a/app/views/my_modules/protocols/_load_from_repository_modal.html.erb
+++ b/app/views/my_modules/protocols/_load_from_repository_modal.html.erb
@@ -1,16 +1,42 @@
 <div class="modal" id="load-from-repository-modal" tabindex="-1" role="dialog" aria-labelledby="load-from-repository-modal-label" data-url="<%= load_from_repository_protocol_path(@protocol) %>">
   <div class="modal-dialog modal-lg" role="document">
-    <div class="modal-content">
+    <div class="modal-content" data-e2e="e2e-MD-task-protocol-loadTemplate">
       <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><i class="sn-icon sn-icon-close"></i></button>
-        <h2 class="modal-title" id="load-from-repository-modal-label">
+        <button
+          type="button"
+          class="close"
+          data-dismiss="modal"
+          aria-label="Close"
+          data-e2e="e2e-BT-task-protocol-loadTemplateModal-close"
+        >
+          <i class="sn-icon sn-icon-close"></i>
+        </button>
+        <h2
+          class="modal-title"
+          id="load-from-repository-modal-label"
+          data-e2e="e2e-TX-task-protocol-loadTemplateModal-title"
+        >
           <%= t("my_modules.protocols.load_from_repository_modal.title") %>
         </h2>
       </div>
       <div class="modal-body"></div>
       <div class="modal-footer">
-        <button type="button" class="btn btn-secondary" data-dismiss="modal"><%= t("general.cancel") %></button>
-        <button type="button" class="btn btn-primary" data-action="submit"><%= t("my_modules.protocols.load_from_repository_modal.load") %></button>
+        <button
+          type="button"
+          class="btn btn-secondary"
+          data-dismiss="modal"
+          data-e2e="e2e-BT-task-protocol-loadTemplateModal-cancel"
+        >
+          <%= t("general.cancel") %>
+        </button>
+        <button
+          type="button"
+          class="btn btn-primary"
+          data-action="submit"
+          data-e2e="e2e-BT-task-protocol-loadTemplateModal-load"
+        >
+          <%= t("my_modules.protocols.load_from_repository_modal.load") %>
+        </button>
       </div>
     </div>
   </div>
diff --git a/app/views/my_modules/protocols/_load_from_repository_modal_body.html.erb b/app/views/my_modules/protocols/_load_from_repository_modal_body.html.erb
index b713feb29..ce728d8f7 100644
--- a/app/views/my_modules/protocols/_load_from_repository_modal_body.html.erb
+++ b/app/views/my_modules/protocols/_load_from_repository_modal_body.html.erb
@@ -9,7 +9,7 @@
            data-role="datatable"
            data-source="<%= load_from_repository_datatable_protocol_path(@protocol) %>">
       <thead>
-          <tr>
+        <tr>
             <th class="all" id="protocol-name"><%= t("my_modules.protocols.load_from_repository_modal.thead_name") %></th>
             <th class="min-tablet-p" id="protocol-versions"><%= t("my_modules.protocols.load_from_repository_modal.thead_version") %></th>
             <th class="min-tablet-l" id="protocol-id"><%= t("my_modules.protocols.load_from_repository_modal.thead_id") %></th>
@@ -18,7 +18,7 @@
             <th class="min-desktop" id="protocol-published-on"><%= t("my_modules.protocols.load_from_repository_modal.thead_published_on") %></th>
           </tr>
         </thead>
-      <tbody></tbody>
+      <tbody data-e2e="e2e-CO-task-protocol-loadTemplateModal-table"></tbody>
     </table>
   </div>
 </div>
diff --git a/app/views/my_modules/protocols/_protocol_status_bar.html.erb b/app/views/my_modules/protocols/_protocol_status_bar.html.erb
index 1fd9457c1..2ba8ea424 100644
--- a/app/views/my_modules/protocols/_protocol_status_bar.html.erb
+++ b/app/views/my_modules/protocols/_protocol_status_bar.html.erb
@@ -1,10 +1,10 @@
 <div class="flex items-center dropdown my-module-protocol-status whitespace-nowrap">
   <% if @protocol.linked? %>
-    <span class="status-label linked">
+    <span class="status-label linked" data-e2e="e2e-TX-task-protocol-statusLinked">
       [<%= t("my_modules.protocols.protocol_status_bar.linked") %>]
     </span>
   <% else %>
-    <span class="status-label">
+    <span class="status-label" data-e2e="e2e-TX-task-protocol-statusUnlinked">
       [<%= t("my_modules.protocols.protocol_status_bar.unlinked") %>]
     </span>
   <% end %>

From c573aa32db36cdc05aaf0e5d33607ea27603e878 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Thu, 24 Jul 2025 11:18:36 +0200
Subject: [PATCH 07/91] Upgrade form-data JS package to version 4.0.4
 [SCI-12163]

---
 yarn.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/yarn.lock b/yarn.lock
index 4b8505785..b3bfb6899 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -2570,9 +2570,9 @@ form-data@^3.0.0:
     mime-types "^2.1.35"
 
 form-data@^4.0.0:
-  version "4.0.3"
-  resolved "https://registry.yarnpkg.com/form-data/-/form-data-4.0.3.tgz#608b1b3f3e28be0fccf5901fc85fb3641e5cf0ae"
-  integrity sha512-qsITQPfmvMOSAdeyZ+12I1c+CKSstAFAwu+97zrnWAbIr5u8wfsExUzCesVLC8NgHuRUqNN4Zy6UPWUTRGslcA==
+  version "4.0.4"
+  resolved "https://registry.yarnpkg.com/form-data/-/form-data-4.0.4.tgz#784cdcce0669a9d68e94d11ac4eea98088edd2c4"
+  integrity sha512-KrGhL9Q4zjj0kiUt5OO4Mr/A/jlI2jDYs5eHBpYHPcBEVSiipAvn2Ko2HnPe20rmcuuvMHNdZFp+4IlGTMF0Ow==
   dependencies:
     asynckit "^0.4.0"
     combined-stream "^1.0.8"

From d030bb8a6b4504aad7de1e63c6ad6e7f67b79e3a Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Thu, 24 Jul 2025 11:39:30 +0200
Subject: [PATCH 08/91] Bump version to 1.43.0.2

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

diff --git a/VERSION b/VERSION
index c798851e9..758e98242 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.43.0.1
+1.43.0.2

From f56d0aef8b3f3c641f76434f6dc609c46a331694 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 24 Jul 2025 12:22:08 +0200
Subject: [PATCH 09/91] Fix password reset for core [SCI-12091]

---
 app/controllers/users/passwords_controller.rb | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/app/controllers/users/passwords_controller.rb b/app/controllers/users/passwords_controller.rb
index 9b9644ab8..f10e61f31 100644
--- a/app/controllers/users/passwords_controller.rb
+++ b/app/controllers/users/passwords_controller.rb
@@ -5,9 +5,19 @@ class Users::PasswordsController < Devise::PasswordsController
   # end
 
   # POST /resource/password
-  # def create
-  #   super
-  # end
+  def create
+    self.resource = resource_class.send_reset_password_instructions(resource_params)
+    yield resource if block_given?
+
+    if resource.errors.added?(:email, :blank)
+      flash.now[:alert] = I18n.t('devise.errors.email.empty')
+      self.resource = resource_class.new
+      render :new
+    else
+      set_flash_message!(:notice, :send_instructions)
+      respond_with({}, location: after_sending_reset_password_instructions_path_for(resource_name))
+    end
+  end
 
   # GET /resource/password/edit?reset_password_token=abcdef
   # def edit

From 684bb91604778d12e07b2d50c34eec80f04e8246 Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Thu, 24 Jul 2025 13:35:42 +0200
Subject: [PATCH 10/91] Add data-e2e to task status dropdown [SCI-12154]

---
 .../status_flow/_task_flow_button.html.erb         | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/app/views/my_modules/status_flow/_task_flow_button.html.erb b/app/views/my_modules/status_flow/_task_flow_button.html.erb
index 1d20e37a2..4da7142bd 100644
--- a/app/views/my_modules/status_flow/_task_flow_button.html.erb
+++ b/app/views/my_modules/status_flow/_task_flow_button.html.erb
@@ -45,7 +45,12 @@
         <% unless status.initial_status? %>
           <% previous_s = status.previous_status %>
           <% previous_s_errors = previous_s.conditions_errors(my_module) %>
-          <li data-state-id="<%= previous_s.id %>" id="previousStatusSelector" class="<%= 'disabled' if previous_s_errors.any? %>">
+          <li
+              data-state-id="<%= previous_s.id %>"
+              id="previousStatusSelector"
+              class="<%= 'disabled' if previous_s_errors.any? %>"
+              data-e2e="e2e-DO-tasks-taskStatus-previousStatus"
+          >
             <span><%= t('my_module_statuses.dropdown.return_label') %></span>
             <i class="fas fa-long-arrow-alt-right"></i>
             <div class="status-container">
@@ -61,7 +66,12 @@
         <% unless status.final_status? %>
           <% next_s = status.next_status %>
           <% next_s_errors = next_s.conditions_errors(my_module) %>
-          <li data-state-id="<%= next_s.id %>" id="nextStatusSelector" class="<%= 'disabled' if next_s_errors.any? %>">
+          <li
+              data-state-id="<%= next_s.id %>"
+              id="nextStatusSelector"
+              class="<%= 'disabled' if next_s_errors.any? %>"
+              data-e2e="e2e-DO-tasks-taskStatus-nextStatus"
+          >
             <span><%= t('my_module_statuses.dropdown.move_label') %></span>
             <i class="fas fa-long-arrow-alt-right"></i>
             <div class="status-container">

From 4581edd78ae9e8d1cf1f7aa4fdcec63f037ea477 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Thu, 17 Jul 2025 13:41:53 +0200
Subject: [PATCH 11/91] Fix start due date in serializer [SCI-12130]

---
 app/serializers/lists/experiment_serializer.rb | 18 ++++--------------
 .../lists/project_and_folder_serializer.rb     |  4 ++--
 2 files changed, 6 insertions(+), 16 deletions(-)

diff --git a/app/serializers/lists/experiment_serializer.rb b/app/serializers/lists/experiment_serializer.rb
index 1fd5a52f6..5f68c2f02 100644
--- a/app/serializers/lists/experiment_serializer.rb
+++ b/app/serializers/lists/experiment_serializer.rb
@@ -102,8 +102,8 @@ module Lists
 
     def due_date_cell
       {
-        value: due_date,
-        value_formatted: due_date,
+        value: object.due_date,
+        value_formatted: (I18n.l(object.due_date, format: :full_date) if object.due_date),
         editable: can_manage_experiment?(object),
         icon: (if object.one_day_prior? && !object.done?
                  'sn-icon sn-icon-alert-warning text-sn-alert-brittlebush'
@@ -115,8 +115,8 @@ module Lists
 
     def start_date_cell
       {
-        value: start_date,
-        value_formatted: start_date,
+        value: object.start_date,
+        value_formatted: (I18n.l(object.start_date, format: :full_date) if object.start_date),
         editable: can_manage_experiment?(object)
       }
     end
@@ -126,15 +126,5 @@ module Lists
         manage: can_manage_experiment?(object)
       }
     end
-
-    private
-
-    def due_date
-      I18n.l(object.due_date, format: :full_date) if object.due_date
-    end
-
-    def start_date
-      I18n.l(object.start_date, format: :full_date) if object.start_date
-    end
   end
 end
diff --git a/app/serializers/lists/project_and_folder_serializer.rb b/app/serializers/lists/project_and_folder_serializer.rb
index 9765601e2..d9b686bb8 100644
--- a/app/serializers/lists/project_and_folder_serializer.rb
+++ b/app/serializers/lists/project_and_folder_serializer.rb
@@ -106,7 +106,7 @@ module Lists
     def due_date_cell
       if project?
         {
-          value: (I18n.l(object.due_date, format: :default) if object.due_date),
+          value: object.due_date,
           value_formatted: (I18n.l(object.due_date, format: :full_date) if object.due_date),
           editable: can_manage_project?(@object),
           icon: (if object.one_day_prior? && !object.done?
@@ -121,7 +121,7 @@ module Lists
     def start_date_cell
       if project?
         {
-          value: (I18n.l(object.start_date, format: :default) if object.start_date),
+          value: object.start_date,
           value_formatted: (I18n.l(object.start_date, format: :full_date) if object.start_date),
           editable: can_manage_project?(@object)
         }

From 2bc84a71eb39096f2d008be754efce6c1f787704 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 24 Jul 2025 12:22:08 +0200
Subject: [PATCH 12/91] Fix password reset for core [SCI-12091]

---
 app/controllers/users/passwords_controller.rb | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/app/controllers/users/passwords_controller.rb b/app/controllers/users/passwords_controller.rb
index 9b9644ab8..f10e61f31 100644
--- a/app/controllers/users/passwords_controller.rb
+++ b/app/controllers/users/passwords_controller.rb
@@ -5,9 +5,19 @@ class Users::PasswordsController < Devise::PasswordsController
   # end
 
   # POST /resource/password
-  # def create
-  #   super
-  # end
+  def create
+    self.resource = resource_class.send_reset_password_instructions(resource_params)
+    yield resource if block_given?
+
+    if resource.errors.added?(:email, :blank)
+      flash.now[:alert] = I18n.t('devise.errors.email.empty')
+      self.resource = resource_class.new
+      render :new
+    else
+      set_flash_message!(:notice, :send_instructions)
+      respond_with({}, location: after_sending_reset_password_instructions_path_for(resource_name))
+    end
+  end
 
   # GET /resource/password/edit?reset_password_token=abcdef
   # def edit

From d2d24624af7f69ec30bff589504017b24f644030 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Mon, 28 Jul 2025 17:28:10 +0200
Subject: [PATCH 13/91] Set a correct event type on sign in after successful
 password reset [SCI-12135]

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

diff --git a/app/controllers/users/passwords_controller.rb b/app/controllers/users/passwords_controller.rb
index 9b9644ab8..113a6a97a 100644
--- a/app/controllers/users/passwords_controller.rb
+++ b/app/controllers/users/passwords_controller.rb
@@ -25,7 +25,7 @@ class Users::PasswordsController < Devise::PasswordsController
         flash_message = resource.active_for_authentication? ? :updated : :updated_not_active
         set_flash_message!(:notice, flash_message)
         resource.after_database_authentication if check_database_authentication?(resource)
-        sign_in(resource_name, resource)
+        sign_in(resource_name, resource, event: :authentication)
       else
         set_flash_message!(:notice, :updated_not_active)
       end

From 7dc0dfdd74be2348f0f39cf5ec5a9b195fb25479 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 30 Jul 2025 13:23:23 +0000
Subject: [PATCH 14/91] Bump ruby-saml from 1.18.0 to 1.18.1

Bumps [ruby-saml](https://github.com/saml-toolkits/ruby-saml) from 1.18.0 to 1.18.1.
- [Release notes](https://github.com/saml-toolkits/ruby-saml/releases)
- [Changelog](https://github.com/SAML-Toolkits/ruby-saml/blob/master/CHANGELOG.md)
- [Commits](https://github.com/saml-toolkits/ruby-saml/compare/v1.18.0...v1.18.1)

---
updated-dependencies:
- dependency-name: ruby-saml
  dependency-version: 1.18.1
  dependency-type: indirect
...

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

diff --git a/Gemfile.lock b/Gemfile.lock
index 99f845814..ef1db5197 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -698,7 +698,7 @@ GEM
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
     ruby-progressbar (1.13.0)
-    ruby-saml (1.18.0)
+    ruby-saml (1.18.1)
       nokogiri (>= 1.13.10)
       rexml
     ruby-vips (2.1.4)

From 1c17218dc1cda19d0e707585255704f85017b898 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Fri, 1 Aug 2025 12:44:07 +0200
Subject: [PATCH 15/91] Fix tables infinite scroll [SCI-12176]

---
 app/javascript/vue/shared/datatable/table.vue | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/app/javascript/vue/shared/datatable/table.vue b/app/javascript/vue/shared/datatable/table.vue
index d3138ad23..30246b731 100644
--- a/app/javascript/vue/shared/datatable/table.vue
+++ b/app/javascript/vue/shared/datatable/table.vue
@@ -537,9 +537,10 @@ export default {
 
           this.handleScroll();
         })
-        .catch(() => {
+        .catch((e) => {
           this.dataLoading = false;
           this.$emit('tableReloaded', [], { filtered: this.searchValue.length > 0 });
+          console.error(e);
           window.HelperModule.flashAlertMsg(this.i18n.t('general.error'), 'danger');
         });
     },
@@ -554,6 +555,9 @@ export default {
       this.rowData = newRows;
       if (this.gridApi) {
         const viewport = document.querySelector('.ag-body-viewport');
+
+        if (!viewport) return;
+
         const { scrollTop } = viewport;
         this.gridApi.setRowData(this.rowData);
         this.$nextTick(() => {

From 7b8d24a0848e5656d7c84f75ee2454b00899b7b5 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Wed, 30 Jul 2025 11:39:20 +0200
Subject: [PATCH 16/91] Add OpenTelemetery gem [SCI-12179]

---
 Gemfile                              |   7 +-
 Gemfile.lock                         | 111 +++++++++++++++++++++------
 config/initializers/opentelemetry.rb |  18 +++++
 3 files changed, 112 insertions(+), 24 deletions(-)
 create mode 100644 config/initializers/opentelemetry.rb

diff --git a/Gemfile b/Gemfile
index 69ed0c7e9..726fb046d 100644
--- a/Gemfile
+++ b/Gemfile
@@ -70,7 +70,6 @@ gem 'rubyzip', '>= 2.3.0' # will load new rubyzip version
 gem 'scenic', '~> 1.4'
 gem 'sdoc', '~> 1.0', group: :doc
 gem 'silencer' # Silence certain Rails logs
-gem 'sneaky-save', git: 'https://github.com/einzige/sneaky-save'
 gem 'turbolinks', '~> 5.2.0'
 gem 'underscore-rails'
 gem 'wicked_pdf'
@@ -95,8 +94,12 @@ gem 'js-routes'
 gem 'tailwindcss-rails', '~> 2.4'
 
 gem 'base62' # Used for smart annotations
-gem 'datadog'
 gem 'newrelic_rpm'
+gem 'opentelemetry-exporter-otlp'
+gem 'opentelemetry-instrumentation-pg'
+gem 'opentelemetry-instrumentation-rails'
+gem 'opentelemetry-propagator-xray'
+gem 'opentelemetry-sdk'
 
 # Permission helper Gem
 gem 'canaid', git: 'https://github.com/scinote-eln/canaid'
diff --git a/Gemfile.lock b/Gemfile.lock
index 99f845814..8614dcd46 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,10 +1,3 @@
-GIT
-  remote: https://github.com/einzige/sneaky-save
-  revision: ee71d0a00cd4ecdd575bd2a9aa8b8693915f4871
-  specs:
-    sneaky-save (0.1.3)
-      activerecord (>= 3.2.0)
-
 GIT
   remote: https://github.com/scinote-eln/canaid
   revision: bba1b817d1c9b0c7e0440a83d0f62848aabc0a1b
@@ -292,13 +285,6 @@ GEM
       activerecord (>= 5.a)
       database_cleaner-core (~> 2.0.0)
     database_cleaner-core (2.0.1)
-    datadog (2.14.0)
-      datadog-ruby_core_source (~> 3.4)
-      libdatadog (~> 16.0.1.1.0)
-      libddwaf (~> 1.21.0.0.1)
-      logger
-      msgpack
-    datadog-ruby_core_source (3.4.0)
     date (3.4.1)
     debug_inspector (1.1.0)
     deface (1.9.0)
@@ -361,6 +347,14 @@ GEM
       raabro (~> 1.4)
     globalid (1.2.1)
       activesupport (>= 6.1)
+    google-protobuf (4.31.1-arm64-darwin)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.31.1-x86_64-linux-gnu)
+      bigdecimal
+      rake (>= 13)
+    googleapis-common-protos-types (1.20.0)
+      google-protobuf (>= 3.18, < 5.a)
     graphviz (1.2.1)
       process-pipeline
     grover (1.2.3)
@@ -430,12 +424,6 @@ GEM
       activerecord
       kaminari-core (= 1.2.2)
     kaminari-core (1.2.2)
-    libdatadog (16.0.1.1.0)
-    libdatadog (16.0.1.1.0-x86_64-linux)
-    libddwaf (1.21.0.0.1-arm64-darwin)
-      ffi (~> 1.0)
-    libddwaf (1.21.0.0.1-x86_64-linux)
-      ffi (~> 1.0)
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
@@ -536,6 +524,82 @@ GEM
       validate_email
       validate_url
       webfinger (~> 2.0)
+    opentelemetry-api (1.5.0)
+    opentelemetry-common (0.22.0)
+      opentelemetry-api (~> 1.0)
+    opentelemetry-exporter-otlp (0.30.0)
+      google-protobuf (>= 3.18)
+      googleapis-common-protos-types (~> 1.3)
+      opentelemetry-api (~> 1.1)
+      opentelemetry-common (~> 0.20)
+      opentelemetry-sdk (~> 1.2)
+      opentelemetry-semantic_conventions
+    opentelemetry-helpers-sql (0.1.1)
+      opentelemetry-api (~> 1.0)
+    opentelemetry-helpers-sql-obfuscation (0.3.0)
+      opentelemetry-common (~> 0.21)
+    opentelemetry-instrumentation-action_mailer (0.4.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-active_support (~> 0.7)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-action_pack (0.12.3)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+      opentelemetry-instrumentation-rack (~> 0.21)
+    opentelemetry-instrumentation-action_view (0.9.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-active_support (~> 0.7)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-active_job (0.8.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-active_record (0.9.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-active_storage (0.1.1)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-active_support (~> 0.7)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-active_support (0.8.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-base (0.23.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-common (~> 0.21)
+      opentelemetry-registry (~> 0.1)
+    opentelemetry-instrumentation-concurrent_ruby (0.22.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-pg (0.30.1)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-helpers-sql
+      opentelemetry-helpers-sql-obfuscation
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-rack (0.26.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+    opentelemetry-instrumentation-rails (0.36.0)
+      opentelemetry-api (~> 1.0)
+      opentelemetry-instrumentation-action_mailer (~> 0.4.0)
+      opentelemetry-instrumentation-action_pack (~> 0.12.0)
+      opentelemetry-instrumentation-action_view (~> 0.9.0)
+      opentelemetry-instrumentation-active_job (~> 0.8.0)
+      opentelemetry-instrumentation-active_record (~> 0.9.0)
+      opentelemetry-instrumentation-active_storage (~> 0.1.0)
+      opentelemetry-instrumentation-active_support (~> 0.8.0)
+      opentelemetry-instrumentation-base (~> 0.23.0)
+      opentelemetry-instrumentation-concurrent_ruby (~> 0.22.0)
+    opentelemetry-propagator-xray (0.24.0)
+      opentelemetry-api (~> 1.0)
+    opentelemetry-registry (0.4.0)
+      opentelemetry-api (~> 1.1)
+    opentelemetry-sdk (1.8.0)
+      opentelemetry-api (~> 1.1)
+      opentelemetry-common (~> 0.20)
+      opentelemetry-registry (~> 0.2)
+      opentelemetry-semantic_conventions
+    opentelemetry-semantic_conventions (1.11.0)
+      opentelemetry-api (~> 1.0)
     orm_adapter (0.5.0)
     ostruct (0.6.0)
     overcommit (0.60.0)
@@ -836,7 +900,6 @@ DEPENDENCIES
   cssbundling-rails
   cucumber-rails
   database_cleaner
-  datadog
   deface (~> 1.9)
   delayed_job_active_record
   devise (~> 4.9.4)
@@ -876,6 +939,11 @@ DEPENDENCIES
   omniauth-rails_csrf_protection (~> 1.0)
   omniauth-saml
   omniauth_openid_connect
+  opentelemetry-exporter-otlp (~> 0.30.0)
+  opentelemetry-instrumentation-pg (~> 0.30.1)
+  opentelemetry-instrumentation-rails (~> 0.36.0)
+  opentelemetry-propagator-xray (~> 0.24.0)
+  opentelemetry-sdk (~> 1.8)
   overcommit
   pg (~> 1.5)
   pg_search
@@ -907,7 +975,6 @@ DEPENDENCIES
   shoulda-matchers
   silencer
   simplecov
-  sneaky-save!
   sprockets-rails
   tailwindcss-rails (~> 2.4)
   timecop
diff --git a/config/initializers/opentelemetry.rb b/config/initializers/opentelemetry.rb
new file mode 100644
index 000000000..07b9edd72
--- /dev/null
+++ b/config/initializers/opentelemetry.rb
@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+if ENV['OTEL_ENABLED'] == 'true'
+  require 'opentelemetry/sdk'
+  require 'opentelemetry/instrumentation/rails'
+
+  OpenTelemetry::SDK.configure do |config|
+    if ENV['OTEL_XRAY_ENABLED'] == 'true'
+      require 'opentelemetry-propagator-xray'
+      # The X-Ray ID Generator generates spans with X-Ray backend compliant IDs
+      config.id_generator = OpenTelemetry::Propagator::XRay::IDGenerator
+      # The X-Ray Propagator injects the X-Ray Tracing Header into downstream calls
+      config.propagators = [OpenTelemetry::Propagator::XRay::TextMapPropagator.new]
+    end
+
+    config.use_all # enables all instrumentation!
+  end
+end

From 3dae83e9b814930dab279bb92b60891c5884351b Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Mon, 4 Aug 2025 09:54:26 +0200
Subject: [PATCH 17/91] Remove grant access from create and edit screens
 [SCI-12183]

---
 .../javascripts/protocols/new_protocol.js     | 16 ------
 .../javascripts/protocols/protocolsio.js      | 27 ---------
 .../external_protocols_controller.rb          |  2 +-
 app/controllers/projects_controller.rb        | 41 +-------------
 app/controllers/protocols_controller.rb       |  2 +-
 app/javascript/vue/projects/list.vue          |  4 +-
 app/javascript/vue/projects/modals/form.vue   | 51 +----------------
 app/javascript/vue/protocols/modals/new.vue   | 55 +------------------
 app/javascript/vue/protocols/table.vue        |  1 -
 .../_preview_modal_footer.html.erb            | 19 -------
 .../index/_new_protocol_modal.html.erb        | 17 ------
 spec/controllers/projects_controller_spec.rb  |  7 ---
 12 files changed, 11 insertions(+), 231 deletions(-)

diff --git a/app/assets/javascripts/protocols/new_protocol.js b/app/assets/javascripts/protocols/new_protocol.js
index 1b8735365..70493cdf7 100644
--- a/app/assets/javascripts/protocols/new_protocol.js
+++ b/app/assets/javascripts/protocols/new_protocol.js
@@ -3,17 +3,6 @@
   const protocolModal = '#newProtocolModal';
   const submitButton = $('.create-protocol-button');
 
-  let roleSelector = `${protocolModal} #protocol_role_selector`;
-  dropdownSelector.init(roleSelector, {
-    noEmptyOption: true,
-    singleSelect: true,
-    closeOnSelect: true,
-    selectAppearance: 'simple',
-    onChange: function() {
-      $('#protocol_default_public_user_role_id').val(dropdownSelector.getValues(roleSelector));
-    }
-  });
-
   $(protocolModal)
     .on('input', '#protocol_name', function() {
       if ($(this).val().length >= GLOBAL_CONSTANTS.NAME_MIN_LENGTH) {
@@ -22,11 +11,6 @@
         submitButton.attr('disabled', 'disabled');
       }
     })
-    .on('change', '#protocol_visibility', function() {
-      let checked = $(this)[0].checked;
-      $('#roleSelectWrapper').toggleClass('hidden', !checked);
-      $('#protocol_default_public_user_role_id').prop('disabled', !checked);
-    })
     .on('submit', function() {
       submitButton.attr('disabled', 'disabled');
     })
diff --git a/app/assets/javascripts/protocols/protocolsio.js b/app/assets/javascripts/protocols/protocolsio.js
index 65dde90dd..ad2c1cda9 100644
--- a/app/assets/javascripts/protocols/protocolsio.js
+++ b/app/assets/javascripts/protocols/protocolsio.js
@@ -198,15 +198,6 @@ var protocolsIO = function() {
       e.stopPropagation();
       animateSpinner(modal, true);
 
-      const visibility = $('#protocol-preview-modal .modal-footer #visibility').prop('checked');
-      const defaultPublicUserRoleId = $('#protocol-preview-modal .modal-footer #default_public_user_role_id')
-        .prop('value');
-      const visibilityField = $('#protocol-preview-modal #protocol_visibility');
-      const defaultPublicUserRoleIdField = $('#protocol-preview-modal #protocol_default_public_user_role_id');
-
-      visibilityField.prop('value', visibility ? 'visible' : 'hidden');
-      defaultPublicUserRoleIdField.prop('value', defaultPublicUserRoleId);
-
       $.ajax({
         type: 'POST',
         url: url,
@@ -291,24 +282,6 @@ var protocolsIO = function() {
   $('form.protocols-search-bar').submit();
 
   function initProtocolModalPreview() {
-    $('#protocol-preview-modal').on('change', '#visibility', function() {
-      const checkbox = this;
-      $('#protocol-preview-modal #roleSelectWrapper').toggleClass('hidden', !checkbox.checked);
-    });
-
-
-    const roleSelector = '#protocol-preview-modal #role_selector';
-
-    dropdownSelector.init(roleSelector, {
-      noEmptyOption: true,
-      singleSelect: true,
-      closeOnSelect: true,
-      selectAppearance: 'simple',
-      onChange: function() {
-        $('#protocol-preview-modal #default_public_user_role_id').val(dropdownSelector.getValues(roleSelector));
-      }
-    });
-
     $('#protocol-preview-modal')
       .on('ajax:error', 'form', function(e, error) {
         let msg = error.responseJSON.error;
diff --git a/app/controllers/external_protocols_controller.rb b/app/controllers/external_protocols_controller.rb
index c38826e5f..8bfe34f37 100644
--- a/app/controllers/external_protocols_controller.rb
+++ b/app/controllers/external_protocols_controller.rb
@@ -118,7 +118,7 @@ class ExternalProtocolsController < ApplicationController
   def create_protocol_params
     params
       .require(:protocol)
-      .permit(:name, :authors, :published_on, :protocol_type, :description, :visibility, :default_public_user_role_id)
+      .permit(:name, :authors, :published_on, :protocol_type, :description)
       .except(:steps)
   end
 
diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb
index b89a7a110..a864845a2 100644
--- a/app/controllers/projects_controller.rb
+++ b/app/controllers/projects_controller.rb
@@ -86,7 +86,6 @@ class ProjectsController < ApplicationController
   end
 
   def update
-    default_public_user_role_name_before_update = @project.default_public_user_role&.name
     old_status = @project.status
     @project.assign_attributes(project_update_params)
     return_error = false
@@ -105,14 +104,6 @@ class ProjectsController < ApplicationController
     end
 
     message_edited = @project.name_changed? || @project.description_changed?
-    message_visibility = if !@project.visibility_changed?
-                           nil
-                         elsif @project.visible?
-                           t('projects.activity.visibility_visible')
-                         else
-                           t('projects.activity.visibility_hidden')
-                         end
-
     message_archived = if !@project.archived_changed?
                          nil
                        elsif @project.archived?
@@ -124,41 +115,14 @@ class ProjectsController < ApplicationController
     start_date_changes = @project.changes[:start_date]
     due_date_changes = @project.changes[:due_date]
 
-    default_public_user_role_name = nil
-    if !@project.visibility_changed? && @project.default_public_user_role_id_changed?
-      @project.visibility_will_change! # triggers assignment sync
-      default_public_user_role_name = UserRole.find(project_params[:default_public_user_role_id]).name
-    end
-
     @project.last_modified_by = current_user
     if !return_error && @project.save
 
       # Add activities if needed
-      if message_visibility.present? && @project.visible?
-        log_activity(:project_grant_access_to_all_team_members,
-                     @project,
-                     { visibility: message_visibility,
-                       role: @project.default_public_user_role.name,
-                       team: @project.team.id })
-      end
-      if message_visibility.present? && !@project.visible?
-        log_activity(:project_remove_access_from_all_team_members,
-                     @project,
-                     { visibility: message_visibility,
-                       role: default_public_user_role_name_before_update,
-                       team: @project.team.id })
-      end
-
       log_activity(:edit_project) if message_edited.present?
       log_activity(:archive_project) if message_archived == 'archive'
       log_activity(:restore_project) if message_archived == 'restore'
 
-      if default_public_user_role_name.present?
-        log_activity(:project_access_changed_all_team_members,
-                     @project,
-                     { team: @project.team.id, role: default_public_user_role_name })
-      end
-
       if supervised_by_id_changes.present?
         log_activity(:remove_head_of_project, @project, { user_target: supervised_by_id_changes[0] }) if supervised_by_id_changes[0].present? # remove head of project
         log_activity(:set_head_of_project, @project, { user_target: supervised_by_id_changes[1] }) if supervised_by_id_changes[1].present? # add head of project
@@ -320,9 +284,8 @@ class ProjectsController < ApplicationController
   def project_params
     params.require(:project)
           .permit(
-            :name, :visibility,
+            :name,
             :archived, :project_folder_id,
-            :default_public_user_role_id,
             :due_date,
             :start_date,
             :description
@@ -331,7 +294,7 @@ class ProjectsController < ApplicationController
 
   def project_update_params
     params.require(:project)
-          .permit(:name, :visibility, :archived, :default_public_user_role_id, :due_date, :start_date, :description, :status, :supervised_by_id)
+          .permit(:name, :archived, :due_date, :start_date, :description, :status, :supervised_by_id)
   end
 
   def view_type_params
diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index 1bf70f38b..a96270be6 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -1092,7 +1092,7 @@ class ProtocolsController < ApplicationController
   end
 
   def create_params
-    params.require(:protocol).permit(:name, :default_public_user_role_id, :visibility)
+    params.require(:protocol).permit(:name)
   end
 
   def check_protocolsio_import_permissions
diff --git a/app/javascript/vue/projects/list.vue b/app/javascript/vue/projects/list.vue
index 4506ace1c..f69ae2160 100644
--- a/app/javascript/vue/projects/list.vue
+++ b/app/javascript/vue/projects/list.vue
@@ -55,12 +55,12 @@
     @update="updateDescription"
     @close="descriptionModalObject = null"/>
   <ExportLimitExceededModal v-if="exportLimitExceded" :description="exportDescription" @close="exportLimitExceded = false"/>
-  <ProjectFormModal v-if="editProject" :userRolesUrl="userRolesUrl"
+  <ProjectFormModal v-if="editProject"
                     :project="editProject" @close="editProject = null" @update="updateTable(); updateNavigator()" />
   <EditFolderModal v-if="editFolder" :folder="editFolder"
                    @close="editFolder = null" @update="updateTable(); updateNavigator()" />
   <ProjectFormModal v-if="newProject" :createUrl="createUrl"
-                   :currentFolderId="currentFolderId" :userRolesUrl="userRolesUrl"
+                   :currentFolderId="currentFolderId"
                    @close="newProject = false" @create="updateTable(); updateNavigator()" />
   <NewFolderModal v-if="newFolder" :createFolderUrl="createFolderUrl"
                   :currentFolderId="currentFolderId" :viewMode="currentViewMode"
diff --git a/app/javascript/vue/projects/modals/form.vue b/app/javascript/vue/projects/modals/form.vue
index 1b87f3c77..3fca65100 100644
--- a/app/javascript/vue/projects/modals/form.vue
+++ b/app/javascript/vue/projects/modals/form.vue
@@ -51,22 +51,6 @@
                 :placeholder="i18n.t('projects.index.add_description')"
               ></TinymceEditor>
             </div>
-            <div class="flex gap-2 text-xs items-center">
-              <div class="sci-checkbox-container">
-                <input type="checkbox" class="sci-checkbox" v-model="visible" value="visible" data-e2e="e2e-CB-projects-newProjectModal-access"/>
-                <span class="sci-checkbox-label"></span>
-              </div>
-              <span v-html="i18n.t('projects.index.modal_new_project.visibility_html')"></span>
-            </div>
-            <div class="mt-6" :class="{'hidden': !visible}">
-              <label class="sci-label">{{ i18n.t("user_assignment.select_default_user_role") }}</label>
-              <SelectDropdown
-                :options="userRoles"
-                :value="defaultRole"
-                @change="changeRole"
-                :e2eValue="'e2e-DD-projects-newProjectModal-defaultRole'"
-              />
-            </div>
           </div>
           <div class="modal-footer">
             <button
@@ -80,7 +64,7 @@
             <button
               class="btn btn-primary"
               type="submit"
-              :disabled="submitting || (visible && !defaultRole) || !validName"
+              :disabled="submitting || !validName"
               data-e2e="e2e-BT-projects-newProjectModal-create"
             >
               {{ submitButtonLabel }}
@@ -94,7 +78,6 @@
 
 <script>
 
-import SelectDropdown from '../../shared/select_dropdown.vue';
 import DateTimePicker from '../../shared/date_time_picker.vue';
 import TinymceEditor from '../../shared/tinymce_editor.vue';
 import axios from '../../../packs/custom_axios.js';
@@ -104,25 +87,14 @@ export default {
   name: 'ProjectFormModal',
   props: {
     project: Object,
-    userRolesUrl: String,
     currentFolderId: String,
     createUrl: String
   },
   mixins: [modalMixin],
   components: {
-    SelectDropdown,
     DateTimePicker,
     TinymceEditor
   },
-  watch: {
-    visible(newValue) {
-      if (newValue) {
-        [this.defaultRole] = this.userRoles.find((role) => role[1] === 'Viewer');
-      } else {
-        this.defaultRole = null;
-      }
-    }
-  },
   computed: {
     validName() {
       return this.name.length >= GLOBAL_CONSTANTS.NAME_MIN_LENGTH;
@@ -142,16 +114,10 @@ export default {
       return this.i18n.t('projects.index.modal_edit_project.submit');
     }
   },
-  mounted() {
-    this.fetchUserRoles();
-  },
   data() {
     return {
       name: this.project?.name || '',
-      visible: this.project ? !this.project.hidden : false,
-      defaultRole: this.project?.default_public_user_role_id,
       error: null,
-      userRoles: [],
       submitting: false,
       startDate: null,
       dueDate: null,
@@ -175,9 +141,7 @@ export default {
         name: this.name,
         start_date: this.startDate,
         due_date: this.dueDate,
-        description: this.description,
-        visibility: (this.visible ? 'visible' : 'hidden'),
-        default_public_user_role_id: this.defaultRole
+        description: this.description
       };
 
       if (this.createUrl) {
@@ -209,23 +173,12 @@ export default {
       });
       this.submitting = false;
     },
-    changeRole(role) {
-      this.defaultRole = role;
-    },
     updateStartDate(startDate) {
       this.startDate = this.stripTime(startDate);
     },
     updateDueDate(dueDate) {
       this.dueDate = this.stripTime(dueDate);
     },
-    fetchUserRoles() {
-      if (this.userRolesUrl) {
-        axios.get(this.userRolesUrl)
-          .then((response) => {
-            this.userRoles = response.data.data;
-          });
-      }
-    },
     stripTime(date) {
       if (date) {
         return new Date(Date.UTC(
diff --git a/app/javascript/vue/protocols/modals/new.vue b/app/javascript/vue/protocols/modals/new.vue
index 08496d913..2f43ea5b8 100644
--- a/app/javascript/vue/protocols/modals/new.vue
+++ b/app/javascript/vue/protocols/modals/new.vue
@@ -22,26 +22,10 @@
                        :placeholder="i18n.t('protocols.new_protocol_modal.name_placeholder')" />
               </div>
             </div>
-            <div class="flex gap-2 text-xs items-center">
-              <div class="sci-checkbox-container">
-                <input type="checkbox" class="sci-checkbox" v-model="visible" value="visible" data-e2e="e2e-CB-newProtocolModal-grantAccess"/>
-                <span class="sci-checkbox-label"></span>
-              </div>
-              <span v-html="i18n.t('protocols.new_protocol_modal.access_label')" data-e2e="e2e-TX-newProtocolModal-grantAccess"></span>
-            </div>
-            <div class="mt-6" :class="{'hidden': !visible}">
-              <label class="sci-label">{{ i18n.t("protocols.new_protocol_modal.role_label") }}</label>
-              <SelectDropdown
-                :options="userRoles"
-                :value="defaultRole"
-                :data-e2e="`e2e-DD-newProtocolModal-defaultUserRole`"
-                @change="changeRole"
-              />
-            </div>
           </div>
           <div class="modal-footer">
             <button type="button" class="btn btn-secondary" data-dismiss="modal" data-e2e="e2e-BT-newProtocolModal-cancel">{{ i18n.t('general.cancel') }}</button>
-            <button class="btn btn-primary" type="submit" :disabled="submitting || (visible && !defaultRole) || !validName" data-e2e="e2e-BT-newProtocolModal-create">
+            <button class="btn btn-primary" type="submit" :disabled="submitting || !validName" data-e2e="e2e-BT-newProtocolModal-create">
               {{ i18n.t('protocols.new_protocol_modal.create_new') }}
             </button>
           </div>
@@ -54,32 +38,15 @@
 <script>
 /* global GLOBAL_CONSTANTS */
 
-import SelectDropdown from '../../shared/select_dropdown.vue';
 import axios from '../../../packs/custom_axios.js';
 import modalMixin from '../../shared/modal_mixin';
 
 export default {
   name: 'NewProtocolModal',
   props: {
-    createUrl: String,
-    userRolesUrl: String
+    createUrl: String
   },
   mixins: [modalMixin],
-  components: {
-    SelectDropdown
-  },
-  watch: {
-    visible(newValue) {
-      if (newValue) {
-        [this.defaultRole] = this.userRoles.find((role) => role[1] === 'Viewer');
-      } else {
-        this.defaultRole = null;
-      }
-    }
-  },
-  mounted() {
-    this.fetchUserRoles();
-  },
   computed: {
     validName() {
       return this.name.length >= GLOBAL_CONSTANTS.NAME_MIN_LENGTH;
@@ -88,9 +55,6 @@ export default {
   data() {
     return {
       name: '',
-      visible: false,
-      defaultRole: null,
-      userRoles: [],
       error: null,
       submitting: false
     };
@@ -101,9 +65,7 @@ export default {
 
       axios.post(this.createUrl, {
         protocol: {
-          name: this.name,
-          visibility: (this.visible ? 'visible' : 'hidden'),
-          default_public_user_role_id: this.defaultRole
+          name: this.name
         }
       }).then(() => {
         this.error = null;
@@ -113,17 +75,6 @@ export default {
         this.submitting = false;
         this.error = error.response.data.error;
       });
-    },
-    changeRole(role) {
-      this.defaultRole = role;
-    },
-    fetchUserRoles() {
-      if (this.userRolesUrl) {
-        axios.get(this.userRolesUrl)
-          .then((response) => {
-            this.userRoles = response.data.data;
-          });
-      }
     }
   }
 };
diff --git a/app/javascript/vue/protocols/table.vue b/app/javascript/vue/protocols/table.vue
index 715d408d2..66ec4765e 100644
--- a/app/javascript/vue/protocols/table.vue
+++ b/app/javascript/vue/protocols/table.vue
@@ -25,7 +25,6 @@
     />
   </div>
   <NewProtocolModal v-if="newProtocol" :createUrl="createUrl"
-                   :userRolesUrl="userRolesUrl"
                    @close="newProtocol = false" @create="updateTable" />
   <AccessModal v-if="accessModalParams" :params="accessModalParams"
                @close="accessModalParams = null" @refresh="this.reloadingTable = true" />
diff --git a/app/views/protocol_importers/_preview_modal_footer.html.erb b/app/views/protocol_importers/_preview_modal_footer.html.erb
index 28a91a1b3..84cbf20f9 100644
--- a/app/views/protocol_importers/_preview_modal_footer.html.erb
+++ b/app/views/protocol_importers/_preview_modal_footer.html.erb
@@ -1,23 +1,4 @@
 <div class="footer">
-  <div class="left-section">
-    <div class="default-role-container">
-      <div class="sci-checkbox-container" data-e2e="e2e-CB-protocolTemplates-previewProtocolsIo-grantAccess">
-        <%= check_box_tag "visibility", "visible", false, class: "sci-checkbox" %>
-        <span class="sci-checkbox-label"></span>
-      </div>
-      <div class="default-role-description" data-e2e="e2e-TX-protocolTemplates-previewProtocolsIo-grantAccess">
-        <%= t("protocols.new_protocol_modal.access_label") %>
-      </div>
-    </div>
-    <div class="hidden" id="roleSelectWrapper" data-e2e="e2e-DD-protocolTemplates-previewProtocolsIo-userRole">
-      <div class="sci-input-container">
-        <%= label_tag :default_public_user_role_id, t("protocols.new_protocol_modal.role_label") %>
-        <% default_role = UserRole.find_by(name: I18n.t('user_roles.predefined.viewer')).id %>
-        <%= hidden_field_tag :default_public_user_role_id, value: default_role %>
-        <%= select_tag :role_selector, options_for_select(user_roles_collection(@protocol), default_role) %>
-      </div>
-    </div>
-  </div>
   <div class="right-section">
     <button type="button" class="btn btn-secondary" data-dismiss="modal" 
             data-e2e="e2e-BT-protocolTemplates-previewProtocolsIo-cancel">
diff --git a/app/views/protocols/index/_new_protocol_modal.html.erb b/app/views/protocols/index/_new_protocol_modal.html.erb
index 76b29537b..40f6cc54f 100644
--- a/app/views/protocols/index/_new_protocol_modal.html.erb
+++ b/app/views/protocols/index/_new_protocol_modal.html.erb
@@ -21,23 +21,6 @@
             <%= t("protocols.new_protocol_modal.description") %>
           </p>
           <% end %>
-          <div class="default-role-container">
-            <div class="sci-checkbox-container">
-              <%= f.check_box :visibility, { class: 'sci-checkbox'},:visible, :hidden %>
-              <span class="sci-checkbox-label"></span>
-            </div>
-            <div class="default-role-description">
-              <%= t("protocols.new_protocol_modal.access_label") %>
-            </div>
-          </div>
-          <div class="hidden" id="roleSelectWrapper">
-            <div class="sci-input-container">
-              <%= f.label :default_public_user_role_id, t("protocols.new_protocol_modal.role_label") %>
-              <% default_role = UserRole.find_by(name: I18n.t('user_roles.predefined.viewer')).id %>
-              <%= f.hidden_field :default_public_user_role_id, value: nil, disabled: true %>
-              <%= f.select :role_selector, options_for_select(team_user_roles_for_select, default_role) %>
-            </div>
-          </div>
         </div>
         <div class="modal-footer">
           <button type="button" class="btn btn-secondary" data-dismiss="modal"><%= t('general.cancel') %></button>
diff --git a/spec/controllers/projects_controller_spec.rb b/spec/controllers/projects_controller_spec.rb
index 74d76acb2..f00db1ec3 100644
--- a/spec/controllers/projects_controller_spec.rb
+++ b/spec/controllers/projects_controller_spec.rb
@@ -69,13 +69,6 @@ describe ProjectsController, type: :controller do
         expect(response.media_type).to eq 'text/html'
       end
 
-      it 'calls create activity service (project_grant_access_to_all_team_members)' do
-        params[:project][:visibility] = 'visible'
-        expect(Activities::CreateActivityService).to receive(:call)
-          .with(hash_including(activity_type: :project_grant_access_to_all_team_members))
-        action
-      end
-
       it 'adds activity in DB' do
         params[:project][:archived] = true
         expect { action }

From 4cbc54a73e462631b85b542a229554dda55de95c Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 5 Aug 2025 09:52:27 +0200
Subject: [PATCH 18/91] Fix user management for shared repositories [SCI-12197]

---
 app/controllers/access_permissions/repositories_controller.rb | 2 +-
 app/permissions/repository.rb                                 | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/app/controllers/access_permissions/repositories_controller.rb b/app/controllers/access_permissions/repositories_controller.rb
index 82a72fd53..7a1b6a136 100644
--- a/app/controllers/access_permissions/repositories_controller.rb
+++ b/app/controllers/access_permissions/repositories_controller.rb
@@ -15,7 +15,7 @@ module AccessPermissions
     end
 
     def check_read_permissions
-      render_403 unless can_read_repository?(@model) || can_manage_team?(@model.team)
+      render_403 unless can_manage_repository_users?(@model) || can_read_repository?(@model)
     end
   end
 end
diff --git a/app/permissions/repository.rb b/app/permissions/repository.rb
index b686da635..934a5a95d 100644
--- a/app/permissions/repository.rb
+++ b/app/permissions/repository.rb
@@ -131,8 +131,7 @@ Canaid::Permissions.register_for(Repository) do
   end
 
   can :manage_repository_users do |user, repository|
-    repository.team.permission_granted?(user, TeamPermissions::MANAGE) ||
-      repository.can_manage_shared?(user) ||
+    repository.can_manage_shared?(user) ||
       repository.permission_granted?(user, RepositoryPermissions::USERS_MANAGE)
   end
 end

From fa7558e2b603ab82b92abb24ecff4475e438f0d7 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Tue, 5 Aug 2025 10:31:43 +0200
Subject: [PATCH 19/91] Fix initial user assignments creation [SCI-12187]

---
 app/models/concerns/assignable.rb             | 53 +++++++++++--------
 app/models/experiment.rb                      |  6 +--
 app/models/protocol.rb                        |  2 +-
 .../experiments/move_to_project_service.rb    | 18 +------
 4 files changed, 35 insertions(+), 44 deletions(-)

diff --git a/app/models/concerns/assignable.rb b/app/models/concerns/assignable.rb
index d7b73a712..9dbdb330b 100644
--- a/app/models/concerns/assignable.rb
+++ b/app/models/concerns/assignable.rb
@@ -24,7 +24,7 @@ module Assignable
              class_name: 'TeamAssignment',
              inverse_of: :assignable
 
-    after_create :create_users_assignments
+    after_create :create_user_assignments!, unless: -> { skip_user_assignments }
 
     def users
       direct_user_ids = user_assignments.select(:user_id)
@@ -53,12 +53,11 @@ module Assignable
       false
     end
 
-    def role_for_user(user, team)
-      user_assignments.find_by(user: user, team: team)&.user_role ||
-        user_group_assignments.joins(user_group: :user_group_memberships)
-                              .where(team: team, user_groups: { user_group_memberships: { user_id: user.id } })
-                              .last&.user_role ||
-        team_assignments.find_by(team: team)&.user_role
+    def reset_all_users_assignments!(assigned_by)
+      user_assignments.destroy_all
+      user_group_assignments.destroy_all
+      team_assignments.destroy_all
+      create_user_assignments!(assigned_by)
     end
 
     def manually_assigned_users
@@ -114,23 +113,31 @@ module Assignable
       # Will be called when an assignment is changed (save/destroy) for the assignable model.
     end
 
-    def create_users_assignments
-      return if skip_user_assignments
+    def create_user_assignments!(user = created_by)
+      # First create initial assignments for the object's creator
+      if top_level_assignable?
+        user_assignments.create!(user: user, assigned: :manually, user_role: UserRole.find_predefined_owner_role)
+      else
+        parent_assignment = permission_parent.user_assignments.find_by(user: user, team: team)
+        if parent_assignment.present?
+          user_assignments.create!(user: user, user_role: parent_assignment.user_role)
+        else
+          parent_group_assignments = permission_parent.user_group_assignments
+                                                      .joins(user_group: :user_group_memberships)
+                                                      .where(team: team, user_groups: { user_group_memberships: { user_id: user.id } })
+          if parent_group_assignments.present?
+            parent_group_assignments.each do |parent_group_assignment|
+              user_group_assignments.create!(user_group: parent_group_assignment.user_group, user_role: parent_group_assignment.user_role)
+            end
+          else
+            parent_team_assignment = permission_parent.team_assignments.find_by(team: team)
+            team_assignments.create!(team: team, user_role: parent_team_assignment.user_role) if parent_team_assignment.present?
+          end
+        end
+      end
 
-      role = if top_level_assignable?
-               UserRole.find_predefined_owner_role
-             else
-               permission_parent.role_for_user(created_by, team)
-             end
-
-      UserAssignment.create!(
-        user: created_by,
-        assignable: self,
-        assigned: top_level_assignable? ? :manually : :automatically,
-        user_role: role
-      )
-
-      UserAssignments::GenerateUserAssignmentsJob.perform_later(self, created_by.id)
+      # Generate assignments for the rest of users in the background
+      UserAssignments::GenerateUserAssignmentsJob.perform_later(self, user.id)
     end
   end
 end
diff --git a/app/models/experiment.rb b/app/models/experiment.rb
index 77c397a7c..19ae4cb5b 100644
--- a/app/models/experiment.rb
+++ b/app/models/experiment.rb
@@ -348,8 +348,7 @@ class Experiment < ApplicationRecord
       next unless my_module.save
 
       # regenerate user assignments
-      my_module.user_assignments.destroy_all
-      UserAssignments::GenerateUserAssignmentsJob.perform_later(my_module, current_user.id)
+      my_module.reset_all_users_assignments!(current_user)
 
       Activities::CreateActivityService.call(activity_type: :move_task,
                                              owner: current_user,
@@ -405,8 +404,7 @@ class Experiment < ApplicationRecord
             m.save!
 
             # regenerate user assignments
-            m.user_assignments.destroy_all
-            UserAssignments::GenerateUserAssignmentsJob.new(m, current_user.id).perform_now
+            m.reset_all_users_assignments!(current_user)
 
             # Add activity
             Activities::CreateActivityService.call(
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 92e3fc6fb..2c8941c20 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -17,7 +17,7 @@ class Protocol < ApplicationRecord
   include PermissionCheckableModel
   include TinyMceImages
 
-  skip_callback :create, :after, :create_users_assignments, if: -> { in_module? }
+  before_create -> { self.skip_user_assignments = true }, if: -> { in_module? }
 
   enum visibility: { hidden: 0, visible: 1 }
   enum protocol_type: {
diff --git a/app/services/experiments/move_to_project_service.rb b/app/services/experiments/move_to_project_service.rb
index 94d3dc9d0..8785db846 100644
--- a/app/services/experiments/move_to_project_service.rb
+++ b/app/services/experiments/move_to_project_service.rb
@@ -25,14 +25,14 @@ module Experiments
 
       ActiveRecord::Base.transaction do
         @exp.project = @project
-        sync_user_assignments(@exp)
+        @exp.reset_all_users_assignments!(@user)
 
         @exp.my_modules.each do |my_module|
           unless can_move_my_module?(@user, my_module)
             @errors[:main] = I18n.t('move_to_project_service.my_modules_permission_error')
             raise
           end
-          sync_user_assignments(my_module)
+          my_module.reset_all_users_assignments!(@user)
           clean_up_user_my_modules(my_module)
           move_tags!(my_module)
         end
@@ -107,20 +107,6 @@ module Experiments
       end
     end
 
-    def sync_user_assignments(object)
-      # remove user assignments where the user are not present on the project
-      object.user_assignments.destroy_all
-
-      UserAssignment.create!(
-        user: @user,
-        assignable: object,
-        assigned: :automatically,
-        user_role: @project.user_assignments.find_by(user: @user).user_role
-      )
-
-      UserAssignments::GenerateUserAssignmentsJob.perform_later(object, @user.id)
-    end
-
     def clean_up_user_my_modules(my_module)
       my_module.user_my_modules.where.not(user_id: @project.users.select(:id)).destroy_all
     end

From 85d78f357a8a086c94a17fb878f49d1dee9c9d6a Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 5 Aug 2025 14:26:14 +0200
Subject: [PATCH 20/91] Fix protocol team assignment propagation [SCI-12199]

---
 .../experiment_user_assignments_controller.rb |  7 +----
 .../v1/project_user_assignments_controller.rb |  5 +---
 .../project_group_assignment_job.rb           |  7 +----
 app/models/concerns/assignable.rb             |  5 ++++
 app/models/protocol.rb                        | 29 ++++++++++++-------
 app/models/team_assignment.rb                 |  7 +++++
 6 files changed, 33 insertions(+), 27 deletions(-)

diff --git a/app/controllers/api/v1/experiment_user_assignments_controller.rb b/app/controllers/api/v1/experiment_user_assignments_controller.rb
index 65b0e238b..6ef48346c 100644
--- a/app/controllers/api/v1/experiment_user_assignments_controller.rb
+++ b/app/controllers/api/v1/experiment_user_assignments_controller.rb
@@ -35,12 +35,7 @@ module Api
 
           @user_assignment.update!(user_assignment_params.merge(assigned: :manually))
 
-          UserAssignments::PropagateAssignmentJob.perform_later(
-            @experiment,
-            @user_assignment.user_id,
-            @user_assignment.user_role,
-            current_user.id
-          )
+          UserAssignments::PropagateAssignmentJob.perform_later(@user_assignment)
 
           log_change_activity
 
diff --git a/app/controllers/api/v1/project_user_assignments_controller.rb b/app/controllers/api/v1/project_user_assignments_controller.rb
index a51814181..ba3218cab 100644
--- a/app/controllers/api/v1/project_user_assignments_controller.rb
+++ b/app/controllers/api/v1/project_user_assignments_controller.rb
@@ -110,10 +110,7 @@ module Api
 
       def propagate_job(user_assignment, destroy: false)
         UserAssignments::PropagateAssignmentJob.perform_later(
-          @project,
-          user_assignment.user.id,
-          user_assignment.user_role,
-          current_user.id,
+          user_assignment,
           destroy: destroy
         )
       end
diff --git a/app/jobs/user_assignments/project_group_assignment_job.rb b/app/jobs/user_assignments/project_group_assignment_job.rb
index 52cca8bc6..a1aefa375 100644
--- a/app/jobs/user_assignments/project_group_assignment_job.rb
+++ b/app/jobs/user_assignments/project_group_assignment_job.rb
@@ -28,12 +28,7 @@ module UserAssignments
           next unless project.experiments.any?
 
           # make sure all related experiments and my modules are assigned
-          UserAssignments::PropagateAssignmentJob.perform_later(
-            project,
-            user.id,
-            project.default_public_user_role || UserRole.find_predefined_viewer_role,
-            @assigned_by&.id
-          )
+          UserAssignments::PropagateAssignmentJob.perform_later(user_assignment)
         end
       end
     end
diff --git a/app/models/concerns/assignable.rb b/app/models/concerns/assignable.rb
index 9dbdb330b..d21ba3a1e 100644
--- a/app/models/concerns/assignable.rb
+++ b/app/models/concerns/assignable.rb
@@ -113,6 +113,11 @@ module Assignable
       # Will be called when an assignment is changed (save/destroy) for the assignable model.
     end
 
+    def after_team_assignment_changed(team_assignment = nil)
+      # Optional, redefine in the assignable model.
+      # Will be called when an assignment is changed (save/destroy) for the assignable model.
+    end
+
     def create_user_assignments!(user = created_by)
       # First create initial assignments for the object's creator
       if top_level_assignable?
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 2c8941c20..00ff966fd 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -601,11 +601,11 @@ class Protocol < ApplicationRecord
     end
 
     parent_protocol.user_assignments.each do |parent_user_assignment|
-      parent_protocol.sync_child_protocol_user_assignment(parent_user_assignment, draft.id)
+      parent_protocol.sync_child_protocol_assignment(parent_user_assignment, draft.id)
     end
 
     parent_protocol.user_group_assignments.each do |parent_user_group_assignment|
-      parent_protocol.sync_child_protocol_user_assignment(parent_user_group_assignment, draft.id)
+      parent_protocol.sync_child_protocol_assignment(parent_user_group_assignment, draft.id)
     end
     draft
   end
@@ -678,29 +678,30 @@ class Protocol < ApplicationRecord
     published_versions.or(Protocol.where(id: draft&.id))
   end
 
-  def sync_child_protocol_user_assignment(user_assignment, child_protocol_id = nil)
+  def sync_child_protocol_assignment(assignment, child_protocol_id = nil)
     # Copy user assignments to child protocol(s)
 
     Protocol.transaction(requires_new: true) do
       # Reload to ensure a potential new draft is also included in child versions
       reload
-      assignment_type = user_assignment.respond_to?(:user_group) ? 'user_group' : 'user'
-      assignment_key = "#{assignment_type}_id".to_sym
+      assignment_key = assignment.model_name.param_key
+      assignable_id_key = assignment_key.gsub('assignment', 'id')
+
       (
         # all or single child version protocol
         child_protocol_id ? child_version_protocols.where(id: child_protocol_id) : child_version_protocols
       ).find_each do |child_protocol|
-        child_assignment = child_protocol.public_send("#{assignment_type}_assignments").find_or_initialize_by(
-          assignment_key => user_assignment.public_send(assignment_key)
+        child_assignment = child_protocol.public_send(assignment_key.pluralize).find_or_initialize_by(
+          assignable_id_key => assignment.public_send(assignable_id_key)
         )
 
-        if user_assignment.destroyed?
+        if assignment.destroyed?
           child_assignment.destroy! if child_assignment.persisted?
           next
         end
 
         child_assignment.update!(
-          user_assignment.attributes.slice(
+          assignment.attributes.slice(
             'user_role_id',
             'assigned',
             'assigned_by_id',
@@ -716,13 +717,19 @@ class Protocol < ApplicationRecord
   def after_user_assignment_changed(user_assignment)
     return unless in_repository_published_original?
 
-    sync_child_protocol_user_assignment(user_assignment)
+    sync_child_protocol_assignment(user_assignment)
   end
 
   def after_user_group_assignment_changed(user_group_assignment)
     return unless in_repository_published_original?
 
-    sync_child_protocol_user_assignment(user_group_assignment)
+    sync_child_protocol_assignment(user_group_assignment)
+  end
+
+  def after_team_assignment_changed(user_group_assignment)
+    return unless in_repository_published_original?
+
+    sync_child_protocol_assignment(user_group_assignment)
   end
 
   def deep_clone(clone, current_user, include_file_versions: false)
diff --git a/app/models/team_assignment.rb b/app/models/team_assignment.rb
index 7d1b3d036..bc69b8fd7 100644
--- a/app/models/team_assignment.rb
+++ b/app/models/team_assignment.rb
@@ -14,4 +14,11 @@ class TeamAssignment < ApplicationRecord
   scope :as_viewers, -> { where(user_role: UserRole.find_predefined_viewer_role) }
 
   validates :team, uniqueness: { scope: :assignable }
+
+  after_destroy :call_team_assignment_changed_hook
+  after_save :call_team_assignment_changed_hook
+
+  def call_team_assignment_changed_hook
+    assignable.__send__(:after_team_assignment_changed, self)
+  end
 end

From b31f8638c5498aaca18d29dcb262567ae459204c Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Tue, 5 Aug 2025 15:41:08 +0200
Subject: [PATCH 21/91] Add data-e2e to result page [SCI-12198]

---
 app/javascript/vue/results/result.vue | 124 ++++++++++++++++++++------
 app/views/results/index.html.erb      |   2 +-
 2 files changed, 97 insertions(+), 29 deletions(-)

diff --git a/app/javascript/vue/results/result.vue b/app/javascript/vue/results/result.vue
index ce8e89413..48713f334 100644
--- a/app/javascript/vue/results/result.vue
+++ b/app/javascript/vue/results/result.vue
@@ -6,6 +6,7 @@
        @dragover.prevent
        :data-id="result.id"
        :class="{ 'bg-sn-super-light-blue': dragingFile, 'bg-white': !dragingFile, 'locked': locked, 'pointer-events-none': addingContent }"
+       :data-e2e="`e2e-CO-task-result${result.id}`"
   >
     <div class="text-xl items-center flex flex-col text-sn-blue h-full justify-center left-0 absolute top-0 w-full"
          v-if="dragingFile"
@@ -20,6 +21,7 @@
               :href="'#resultBody' + result.id"
               data-toggle="collapse"
               data-remote="true"
+              :data-e2e="`e2e-BT-task-result${result.id}-visibilityToggle`"
               @click="toggleCollapsed">
             <span class="sn-icon sn-icon-right "></span>
           </a>
@@ -35,6 +37,7 @@
             :placeholder="i18n.t('my_modules.results.placeholder')"
             :defaultValue="i18n.t('my_modules.results.default_name')"
             :timestamp="i18n.t('protocols.steps.timestamp', {date: result.attributes.created_at, user: result.attributes.created_by })"
+            :data-e2e="`task-result${result.id}`"
             @editingEnabled="editingName = true"
             @editingDisabled="editingName = false"
             :editOnload="result.newResult == true"
@@ -48,6 +51,7 @@
             :btnText="i18n.t('my_modules.results.insert.button')"
             :position="'right'"
             :caret="true"
+            :data-e2e="`e2e-DD-task-result${result.id}-insertContent`"
             @create:custom_well_plate="openCustomWellPlateModal"
             @create:table="(...args) => this.createElement('table', ...args)"
             @create:checklist="createElement('checklist')"
@@ -65,14 +69,26 @@
             :data-object-type="result.attributes.type"
             tabindex="0"
           ></span> <!-- Hidden element to support legacy code -->
-          <tempplate v-if="result.attributes.steps.length == 0">
-            <button v-if="urls.update_url" ref="linkButton" :title="i18n.t('my_modules.results.link_steps')" class="btn btn-light icon-btn" @click="this.openLinkStepsModal = true">
+          <template v-if="result.attributes.steps.length == 0">
+            <button
+              v-if="urls.update_url"
+              ref="linkButton"
+              :title="i18n.t('my_modules.results.link_steps')"
+              class="btn btn-light icon-btn"
+              @click="this.openLinkStepsModal = true"
+              :data-e2e="`e2e-BT-task-result${result.id}-linkStep`"
+            >
               {{ i18n.t('my_modules.results.link_to_step') }}
             </button>
-          </tempplate>
+          </template>
           <GeneralDropdown v-else ref="linkedStepsDropdown"  position="right">
             <template v-slot:field>
-              <button ref="linkButton" class="btn btn-light icon-btn" :title="i18n.t('my_modules.results.linked_steps')">
+              <button
+                ref="linkButton"
+                class="btn btn-light icon-btn"
+                :title="i18n.t('my_modules.results.linked_steps')"
+                :data-e2e="`e2e-DD-task-result${result.id}-linkStep-showLinked`"
+              >
                 <i class="sn-icon sn-icon-steps"></i>
                 <span class="absolute top-1 -right-1 h-4 min-w-4 bg-sn-science-blue text-white flex items-center justify-center rounded-full text-[10px]">
                   {{ result.attributes.steps.length }}
@@ -86,14 +102,18 @@
                   :title="step.name"
                   :href="protocolUrl(step.id)"
                   class="py-2.5 px-3 hover:bg-sn-super-light-grey cursor-pointer block hover:no-underline text-sn-blue truncate"
+                  :data-e2e="`e2e-BT-task-result${result.id}-linkStep-step${step.id}`"
                 >
                   {{ step.name }}
                 </a>
               </div>
               <template v-if="urls.update_url">
                 <hr class="my-0">
-                <div class="py-2.5 px-3 hover:bg-sn-super-light-grey cursor-pointer text-sn-blue"
-                    @click="this.openLinkStepsModal = true; $refs.linkedStepsDropdown.closeMenu()">
+                <div
+                  class="py-2.5 px-3 hover:bg-sn-super-light-grey cursor-pointer text-sn-blue"
+                  @click="this.openLinkStepsModal = true; $refs.linkedStepsDropdown.closeMenu()"
+                  :data-e2e="`e2e-BT-task-result${result.id}-linkStep-manage`"
+                >
                   {{ i18n.t('protocols.steps.manage_links') }}
                 </div>
               </template>
@@ -104,7 +124,9 @@
             class="open-comments-sidebar btn icon-btn btn-light"
             data-turbolinks="false"
             data-object-type="Result"
-            :data-object-id="result.id">
+            :data-object-id="result.id"
+            :data-e2e="`e2e-BT-task-result${result.id}-comments`"
+          >
             <i class="sn-icon sn-icon-comments"></i>
             <span class="comments-counter" :class="{ 'hidden': !result.attributes.comments_count }"
                   :id="`comment-count-${result.id}`">
@@ -118,6 +140,7 @@
             :btnClasses="'btn btn-light icon-btn'"
             :position="'right'"
             :btnIcon="'sn-icon sn-icon-more-hori'"
+            :data-e2e="`e2e-DD-task-result${result.id}-optionsMenu`"
             @reorder="openReorderModal"
             @duplicate="duplicateResult"
             @archive="archiveResult"
@@ -243,14 +266,46 @@ export default {
       customWellPlate: false,
       openLinkStepsModal: false,
       wellPlateOptions: [
-        { text: I18n.t('protocols.steps.insert.well_plate_options.custom'), emit: 'create:custom_well_plate'},
-        { text: I18n.t('protocols.steps.insert.well_plate_options.32_x_48'), emit: 'create:table', params: [32, 48] },
-        { text: I18n.t('protocols.steps.insert.well_plate_options.16_x_24'), emit: 'create:table', params: [16, 24] },
-        { text: I18n.t('protocols.steps.insert.well_plate_options.8_x_12'), emit: 'create:table', params: [8, 12] },
-        { text: I18n.t('protocols.steps.insert.well_plate_options.6_x_8'), emit: 'create:table', params: [6, 8] },
-        { text: I18n.t('protocols.steps.insert.well_plate_options.4_x_6'), emit: 'create:table', params: [4, 6] },
-        { text: I18n.t('protocols.steps.insert.well_plate_options.3_x_4'), emit: 'create:table', params: [3, 4] },
-        { text: I18n.t('protocols.steps.insert.well_plate_options.2_x_3'), emit: 'create:table', params: [2, 3] }
+        {
+          text: I18n.t('protocols.steps.insert.well_plate_options.custom'),
+          emit: 'create:custom_well_plate',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate-custom`
+        },
+        {
+          text: I18n.t('protocols.steps.insert.well_plate_options.32_x_48'), emit: 'create:table', 
+          params: [32, 48],
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate-32`
+        },
+        {
+          text: I18n.t('protocols.steps.insert.well_plate_options.16_x_24'), emit: 'create:table',
+          params: [16, 24],
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate-16`
+        },
+        {
+          text: I18n.t('protocols.steps.insert.well_plate_options.8_x_12'), emit: 'create:table',
+          params: [8, 12],
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate-8`
+        },
+        {
+          text: I18n.t('protocols.steps.insert.well_plate_options.6_x_8'), emit: 'create:table',
+          params: [6, 8],
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate-6`
+        },
+        {
+          text: I18n.t('protocols.steps.insert.well_plate_options.4_x_6'), emit: 'create:table',
+          params: [4, 6],
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate-4`
+        },
+        {
+          text: I18n.t('protocols.steps.insert.well_plate_options.3_x_4'), emit: 'create:table',
+          params: [3, 4],
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate-3`
+        },
+        {
+          text: I18n.t('protocols.steps.insert.well_plate_options.2_x_3'), emit: 'create:table',
+          params: [2, 3],
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate-2`
+        }
       ],
       editingName: false,
       confirmingDelete: false,
@@ -328,25 +383,29 @@ export default {
       if (this.urls.upload_attachment_url) {
         menu = menu.concat([{
           text: this.i18n.t('my_modules.results.insert.add_file'),
-          emit: 'create:file'
+          emit: 'create:file',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-file-addFromPc`
         }]);
       }
       if (this.result.attributes.wopi_enabled) {
         menu = menu.concat([{
           text: this.i18n.t('assets.create_wopi_file.button_text'),
-          emit: 'create:wopi_file'
+          emit: 'create:wopi_file',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-file-wopi`
         }]);
       }
       if (this.result.attributes.open_vector_editor_context.new_sequence_asset_url) {
         menu = menu.concat([{
           text: this.i18n.t('open_vector_editor.new_sequence_file'),
-          emit: 'create:ove_file'
+          emit: 'create:ove_file',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-file-sequence`
         }]);
       }
       if (this.result.attributes.marvinjs_enabled) {
         menu = menu.concat([{
           text: this.i18n.t('marvinjs.new_button'),
-          emit: 'create:marvinjs_file'
+          emit: 'create:marvinjs_file',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-file-chemical`
         }]);
       }
       return menu;
@@ -357,21 +416,25 @@ export default {
         menu = menu.concat([{
           text: this.i18n.t('my_modules.results.insert.text'),
           icon: 'sn-icon sn-icon-result-text',
-          emit: 'create:text'
+          emit: 'create:text',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-text`
         }, {
           text: this.i18n.t('my_modules.results.insert.attachment'),
           submenu: this.filesMenu,
           icon: 'sn-icon sn-icon-file',
-          position: 'left'
+          position: 'left',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-file`
         }, {
           text: this.i18n.t('my_modules.results.insert.table'),
           icon: 'sn-icon sn-icon-tables',
-          emit: 'create:table'
+          emit: 'create:table',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-table`
         }, {
           text: this.i18n.t('my_modules.results.insert.well_plate'),
           icon: 'sn-icon sn-icon-tables',
           submenu: this.wellPlateOptions,
-          position: 'left'
+          position: 'left',
+          data_e2e: `e2e-DO-task-result${this.result.id}-insertMenu-wellPlate`
         }]);
       }
 
@@ -382,31 +445,36 @@ export default {
       if (this.urls.reorder_elements_url && this.elements.length > 1) {
         menu = menu.concat([{
           text: this.i18n.t('my_modules.results.actions.rearrange'),
-          emit: 'reorder'
+          emit: 'reorder',
+          data_e2e: `e2e-DO-task-result${this.result.id}-optionsMenu-reorder`
         }]);
       }
       if (this.urls.duplicate_url && !this.result.attributes.archived) {
         menu = menu.concat([{
           text: this.i18n.t('my_modules.results.actions.duplicate'),
-          emit: 'duplicate'
+          emit: 'duplicate',
+          data_e2e: `e2e-DO-task-result${this.result.id}-optionsMenu-duplicate`
         }]);
       }
       if (this.urls.archive_url) {
         menu = menu.concat([{
           text: this.i18n.t('my_modules.results.actions.archive'),
-          emit: 'archive'
+          emit: 'archive',
+          data_e2e: `e2e-DO-task-result${this.result.id}-optionsMenu-archive`
         }]);
       }
       if (this.urls.restore_url) {
         menu = menu.concat([{
           text: this.i18n.t('my_modules.results.actions.restore'),
-          emit: 'restore'
+          emit: 'restore',
+          data_e2e: `e2e-DO-task-result${this.result.id}-optionsMenu-restore`
         }]);
       }
       if (this.urls.delete_url) {
         menu = menu.concat([{
           text: this.i18n.t('my_modules.results.actions.delete'),
-          emit: 'delete'
+          emit: 'delete',
+          data_e2e: `e2e-DO-task-result${this.result.id}-optionsMenu-delete`
         }]);
       }
       return menu;
diff --git a/app/views/results/index.html.erb b/app/views/results/index.html.erb
index ed20fc2c9..a18556733 100644
--- a/app/views/results/index.html.erb
+++ b/app/views/results/index.html.erb
@@ -17,7 +17,7 @@
   <%= render partial: 'my_modules/header' %>
   <%= render partial: 'my_modules/header_actions' %>
 
-  <div id="results" data-behaviour="vue">
+  <div id="results" data-behaviour="vue" data-e2e="e2e-CO-task-results">
     <results url="<%= my_module_results_url(@my_module, view_mode: params[:view_mode]) %>"
              active_url="<%= my_module_results_url(@my_module) %>"
              protocol-id="<%= @my_module.protocol.id %>"

From 6c551774413c028bc8a40835bf43539cc1a680bd Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Wed, 6 Aug 2025 10:40:39 +0200
Subject: [PATCH 22/91] Add data-e2e to comments, new result button [SCI-12198]

---
 .../vue/results/results_toolbar.vue           |  9 +++++-
 app/views/my_modules/protocols.html.erb       | 24 +++++++++++---
 .../comments/_comments_sidebar.html.erb       | 32 +++++++++++++------
 3 files changed, 50 insertions(+), 15 deletions(-)

diff --git a/app/javascript/vue/results/results_toolbar.vue b/app/javascript/vue/results/results_toolbar.vue
index 57446c891..f4d296179 100644
--- a/app/javascript/vue/results/results_toolbar.vue
+++ b/app/javascript/vue/results/results_toolbar.vue
@@ -8,7 +8,14 @@
     </div>
 
     <div class="result-toolbar__left flex items-center">
-      <button v-if="canCreate" :title="i18n.t('my_modules.results.add_title')" class="btn btn-secondary" :class="{'mr-3': headerSticked}" @click="$emit('newResult')">
+      <button
+        v-if="canCreate" 
+        :title="i18n.t('my_modules.results.add_title')"
+        class="btn btn-secondary"
+        :class="{'mr-3': headerSticked}"
+        @click="$emit('newResult')"
+        data-e2e="e2e-BT-task-results-createNew"
+      >
         <i class="sn-icon sn-icon-new-task"></i>
         {{ i18n.t('my_modules.results.add_label') }}
       </button>
diff --git a/app/views/my_modules/protocols.html.erb b/app/views/my_modules/protocols.html.erb
index 8f6ac492a..8e723c9f9 100644
--- a/app/views/my_modules/protocols.html.erb
+++ b/app/views/my_modules/protocols.html.erb
@@ -35,8 +35,16 @@
     <div class="task-section task-information hidden" data-e2e="e2e-CO-task-details">
       <div id="task-details" class="task-section-header">
         <div class="flex items-center mr-auto">
-          <a class="task-section-caret collapsed" role="button" data-toggle="collapse" href="#details-container" aria-expanded="false" aria-controls="details-container">
-            <i class="sn-icon sn-icon-right" data-e2e="e2e-IC-task-details-visibilityToggle"></i>
+          <a
+            class="task-section-caret collapsed"
+            role="button"
+            data-toggle="collapse"
+            href="#details-container"
+            aria-expanded="false"
+            aria-controls="details-container"
+            data-e2e="e2e-BT-task-details-visibilityToggle"
+          >
+            <i class="sn-icon sn-icon-right"></i>
             <span id="taskDetailsLabel" class="task-section-title">
               <h2 data-e2e="e2e-TX-task-details-title">
                 <%= t('my_modules.details.title') %>
@@ -68,8 +76,16 @@
     <!-- Notes -->
     <div class="task-section hidden">
       <div class="task-section-header">
-        <a class="task-section-caret" role="button" data-toggle="collapse" href="#notes-container" aria-expanded="true" aria-controls="notes-container">
-          <i class="sn-icon sn-icon-right" data-e2e="e2e-IC-task-notes-visibilityToggle"></i>
+        <a
+           class="task-section-caret"
+           role="button"
+           data-toggle="collapse"
+           href="#notes-container"
+           aria-expanded="true"
+           aria-controls="notes-container"
+           data-e2e="e2e-BT-task-notes-visibilityToggle"
+        >
+          <i class="sn-icon sn-icon-right"></i>
           <span class="task-section-title">
             <h2 data-e2e="e2e-TX-task-notes-title"><%= t('my_modules.notes.title') %></h2>
           </span>
diff --git a/app/views/shared/comments/_comments_sidebar.html.erb b/app/views/shared/comments/_comments_sidebar.html.erb
index 5bf58bbbe..b44929974 100644
--- a/app/views/shared/comments/_comments_sidebar.html.erb
+++ b/app/views/shared/comments/_comments_sidebar.html.erb
@@ -1,8 +1,11 @@
-<div class="comments-sidebar" data-comments-url="<%= comments_path %>">
+<div class="comments-sidebar" data-comments-url="<%= comments_path %>" data-e2e="e2e-CO-comments">
   <div class="sidebar-content">
     <div class="sidebar-header">
-      <div class="comments-subject-title"></div>
-      <div class="btn btn-light icon-btn close-btn !bg-transparent">
+      <div class="comments-subject-title" data-e2e="e2e-TX-comments-title"></div>
+      <div
+        class="btn btn-light icon-btn close-btn !bg-transparent"
+        data-e2e="e2e-BT-comments-close"
+      >
         <i class="sn-icon sn-icon-close"></i>
       </div>
       <div class="comments-subject-url">
@@ -14,9 +17,11 @@
       <div class="no-comments-placeholder">
         <%= image_tag 'comments/placeholder.svg', class: 'no-comments-image' %>
         <h1><%= t('comments.empty_state.title') %></h1>
-        <p class="description"><%= t('comments.empty_state.description') %></p>
+        <p class="description" data-e2e="e2e-TX-comments-noCommentDescription">
+          <%= t('comments.empty_state.description') %>
+        </p>
       </div>
-      <div class="loading-placeholder">
+      <div class="loading-placeholder" data-e2e="e2e-CO-comments-commentPlaceholder">
         <% 5.times do |i| %>
           <div class="comment-placeholder <%= i.even? ? 'left' : 'right' %>">
             <div class="comment-user-placeholder"></div>
@@ -27,14 +32,21 @@
     </div>
     <div class="sidebar-footer">
       <div class="comment-input-container !pr-0 grid grid-flow-row">
-        <textarea class="comment-input-field smart-text-area textarea-sm"
-                  placeholder="<%= t('comments.placeholder') %>"></textarea>
-        <i class="sn-icon sn-icon-send send-comment"></i>
+        <textarea
+          class="comment-input-field smart-text-area textarea-sm"
+          placeholder="<%= t('comments.placeholder') %>"
+          data-e2e="e2e-IF-comments-addNew"
+        ></textarea>
+        <i class="sn-icon sn-icon-send send-comment" data-e2e="e2e-BT-comments-send"></i>
       </div>
       <div class="error-container"></div>
       <div class="update-buttons sci-btn-group">
-        <button class="btn btn-secondary cancel-button"><%= t('general.cancel') %></button>
-        <button class="btn btn-primary update-comment"><%= t('comments.save_changes') %></button>
+        <button class="btn btn-secondary cancel-button" data-e2e="e2e-BT-comments-cancel">
+          <%= t('general.cancel') %>
+        </button>
+        <button class="btn btn-primary update-comment" data-e2e="e2e-BT-comments-saveChanges">
+          <%= t('comments.save_changes') %>
+        </button>
       </div>
     </div>
   </div>

From 4db3a8171e4c0215ea7cc3f41e22c8e745f38497 Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Wed, 6 Aug 2025 11:33:21 +0200
Subject: [PATCH 23/91] Add data-e2e to delete result modal, new team
 [SCI-12198]

---
 app/javascript/vue/results/delete_result.vue  | 32 +++++++++++++++----
 app/views/users/settings/teams/index.html.erb |  2 +-
 app/views/users/settings/teams/new.html.erb   | 21 +++++++++---
 3 files changed, 44 insertions(+), 11 deletions(-)

diff --git a/app/javascript/vue/results/delete_result.vue b/app/javascript/vue/results/delete_result.vue
index a527e324d..6c71b5b81 100644
--- a/app/javascript/vue/results/delete_result.vue
+++ b/app/javascript/vue/results/delete_result.vue
@@ -1,21 +1,41 @@
 <template>
   <div ref="modal" @keydown.esc="cancel" class="modal" tabindex="-1" role="dialog">
     <div class="modal-dialog modal-sm" role="document">
-      <div class="modal-content">
+      <div class="modal-content" data-e2e="e2e-MD-task-result-deleteResult">
         <div class="modal-header">
-          <button type="button" class="close" data-dismiss="modal" aria-label="Close"><i class="sn-icon sn-icon-close"></i></button>
-          <h4 class="modal-title">
+          <button
+            type="button"
+            class="close"
+            data-dismiss="modal"
+            aria-label="Close"
+            data-e2e="e2e-BT-task-result-deleteResultModal-close"
+          >
+            <i class="sn-icon sn-icon-close">
+          </i></button>
+          <h4 class="modal-title" data-e2e="e2e-TX-task-result-deleteResultModal-title">
             {{ i18n.t("my_modules.results.delete_modal.title") }}
           </h4>
         </div>
-        <div class="modal-body">
+        <div class="modal-body" data-e2e="e2e-TX-task-result-deleteResultModal-description">
           <p>{{ i18n.t("my_modules.results.delete_modal.description_1") }}</p>
           <p><b>{{ i18n.t("my_modules.results.delete_modal.description_2") }}</b></p>
 
         </div>
         <div class="modal-footer">
-          <button class="btn btn-secondary" @click="cancel">{{ i18n.t('general.cancel') }}</button>
-          <button class="btn btn-danger" @click="confirm">{{ i18n.t("my_modules.results.delete_modal.confirm") }}</button>
+          <button
+            class="btn btn-secondary"
+            @click="cancel"
+            data-e2e="e2e-BT-task-result-deleteResultModal-cancel"
+          >
+            {{ i18n.t('general.cancel') }}
+          </button>
+          <button
+            class="btn btn-danger"
+            @click="confirm"
+            data-e2e="e2e-BT-task-result-deleteResultModal-delete"
+          >
+            {{ i18n.t("my_modules.results.delete_modal.confirm") }}
+          </button>
         </div>
       </div>
     </div>
diff --git a/app/views/users/settings/teams/index.html.erb b/app/views/users/settings/teams/index.html.erb
index 979e49f75..afc21a3c4 100644
--- a/app/views/users/settings/teams/index.html.erb
+++ b/app/views/users/settings/teams/index.html.erb
@@ -21,7 +21,7 @@
         <em><%= t("users.settings.teams.index.no_teams") %></em>
       <% end %>
       <% if can_create_teams? %>
-        <span id="new-team-button">
+        <span id="new-team-button" data-e2e="e2e-BT-settings-workspaces-newWorkspace">
           <%= link_to new_team_path, class: "btn btn-primary", style: "margin-left: 30px;" do %>
             <span class="sn-icon sn-icon-new-task"></span>
             <span class="hidden-xs">
diff --git a/app/views/users/settings/teams/new.html.erb b/app/views/users/settings/teams/new.html.erb
index c12e24504..8cce67c77 100644
--- a/app/views/users/settings/teams/new.html.erb
+++ b/app/views/users/settings/teams/new.html.erb
@@ -11,7 +11,9 @@
         <%= f.text_field :name,
                          autofocus: true,
                          class: 'sci-input-field',
-                         placeholder: t('users.settings.teams.new.name_placeholder') %>
+                         placeholder: t('users.settings.teams.new.name_placeholder'),
+                         data: {'e2e'=>'e2e-IF-settings-workspaces-newWorkspace-name'}
+                       %>
         <br>
         <small>
           <%=t 'users.settings.teams.new.name_sublabel' %>
@@ -19,15 +21,26 @@
       </div>
 
       <div class="sci-input-container mb-4 max-w-lg" style="display: block !important">
-        <%= f.text_area :description, class: "sci-input-field textarea", label: t('users.settings.teams.new.description_label') %>
+        <%= f.text_area :description,
+                        class: "sci-input-field textarea",
+                        label: t('users.settings.teams.new.description_label'),
+                        data: {'e2e'=>'e2e-IF-settings-workspaces-newWorkspace-description'}
+                      %>
         <br>
         <small>
           <%=t 'users.settings.teams.new.description_sublabel' %>
         </small>
       </div>
 
-      <%= link_to t('general.cancel'), teams_path, class: 'btn btn-secondary' %>
-      <%= f.submit t('users.settings.teams.new.create'), class: 'btn btn-success' %>
+      <%= link_to t('general.cancel'),
+                  teams_path,
+                  class: 'btn btn-secondary',
+                  data: {'e2e'=>'e2e-BT-settings-workspaces-newWorkspace-cancel'}
+                %>
+      <%= f.submit t('users.settings.teams.new.create'),
+                   class: 'btn btn-success',
+                   data: {'e2e'=>'e2e-BT-settings-workspaces-newWorkspace-create'} 
+      %>
 
     <% end %>
   </div>

From 44af63d1c8f381b7f61d825d9a479c08349fff41 Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Wed, 6 Aug 2025 12:10:34 +0200
Subject: [PATCH 24/91] Add data e2e to settings dropdown and team dropdown
 [SCI-12198]

---
 app/javascript/vue/navigation/top_menu.vue    | 12 +++++++++---
 app/javascript/vue/shared/select_dropdown.vue |  5 +++--
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/app/javascript/vue/navigation/top_menu.vue b/app/javascript/vue/navigation/top_menu.vue
index 4fb5497c5..74162b052 100644
--- a/app/javascript/vue/navigation/top_menu.vue
+++ b/app/javascript/vue/navigation/top_menu.vue
@@ -5,11 +5,12 @@
       <img :src="logoUrl" alt="SciNote" class="h-full block">
     </a>
   </div>
-    <div v-if="currentTeam" class="w-64" :data-e2e="'e2e-DD-topMenu-teams'">
+    <div v-if="currentTeam" class="w-64">
       <SelectDropdown
         :value="currentTeam"
         :options="teams"
         @change="switchTeam"
+        :e2eValue="'e2e-DD-topMenu-teams'"
       ></SelectDropdown>
     </div>
     <QuickSearch
@@ -144,11 +145,16 @@ export default {
   },
   computed: {
     settingsMenuItems() {
-      return this.settingsMenu.map((item) => ({ text: item.name, url: item.url })).concat(
+      return this.settingsMenu.map((item) => ({ 
+        text: item.name,
+        url: item.url,
+        data_e2e: `e2e-DO-topMenu-settings-${item.name.replace(' ','').toLowerCase()}`
+      })).concat(
         {
           text: this.i18n.t('left_menu_bar.support_links.core_version'),
           modalTarget: '#aboutModal',
-          url: ''
+          url: '',
+          data_e2e: `e2e-DO-topMenu-settings-scinoteVersion`
         }
       );
     }
diff --git a/app/javascript/vue/shared/select_dropdown.vue b/app/javascript/vue/shared/select_dropdown.vue
index 7b46aa045..ab6e4ee66 100644
--- a/app/javascript/vue/shared/select_dropdown.vue
+++ b/app/javascript/vue/shared/select_dropdown.vue
@@ -60,8 +60,9 @@
     <template v-if="isOpen">
       <teleport to="body">
         <div ref="flyout"
-            class="sn-select-dropdown bg-white inline-block sn-shadow-menu-sm rounded w-full
-                    fixed z-[3000]">
+          class="sn-select-dropdown bg-white inline-block sn-shadow-menu-sm rounded w-full fixed z-[3000]"
+          :data-e2e="`${e2eValue}-dropdownOptions`"
+        >
           <div v-if="multiple && withCheckboxes" class="p-2.5 pb-0">
             <div @click="selectAll" :class="sizeClass"
                 class="border border-x-0 !border-transparent border-solid !border-b-sn-light-grey

From 72faf51747a5b3d5b0eadbfbed36035bf11e1f6b Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Wed, 6 Aug 2025 13:03:11 +0200
Subject: [PATCH 25/91] Add data-e2e to invite members button and dialog
 [SCI-12198]

---
 app/views/shared/_invite_users_modal.html.erb | 38 ++++++++++++++-----
 app/views/users/settings/teams/show.html.erb  |  9 ++++-
 2 files changed, 36 insertions(+), 11 deletions(-)

diff --git a/app/views/shared/_invite_users_modal.html.erb b/app/views/shared/_invite_users_modal.html.erb
index e41292dcd..84af73e3a 100644
--- a/app/views/shared/_invite_users_modal.html.erb
+++ b/app/views/shared/_invite_users_modal.html.erb
@@ -41,11 +41,19 @@ invite_with_team_selector = type.in?(%w(invite_new_members invite_with_team_sele
   <%= "data-team-role=#{role}" if type.in?(%w(invite_with_team_selector_and_role)) %>
 >
   <div class="modal-dialog" role="document">
-    <div class="modal-content">
+    <div class="modal-content" data-e2e="e2e-MD-settings-members-invite">
 
       <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><i class="sn-icon sn-icon-close"></i></button>
-        <h4 class="modal-title">
+        <button
+          type="button"
+          class="close"
+          data-dismiss="modal"
+          aria-label="Close"
+          data-e2e="e2e-BT-settings-members-inviteModal-close"
+        >
+          <i class="sn-icon sn-icon-close"></i>
+        </button>
+        <h4 class="modal-title" data-e2e="e2e-TX-settings-members-inviteModal-title">
           <% if text_title %>
             <%= text_title %>
           <% else %>
@@ -77,8 +85,8 @@ invite_with_team_selector = type.in?(%w(invite_new_members invite_with_team_sele
             <h4 class="heading">
               <span><%= t('invite_users.new_members.input_label') %></span>
             </h4>
-            <div class="emails-selector" >
-              <div class="select-container">
+            <div class="emails-selector">
+              <div class="select-container" data-e2e="e2e-IF-settings-members-inviteModal-emails">
                 <select name="emails[]" class="emails-input"></select>
               </div>
               <p><small><%= t('invite_users.new_members.input_subtitle') %></small></p>
@@ -122,6 +130,7 @@ invite_with_team_selector = type.in?(%w(invite_new_members invite_with_team_sele
                     data-select-all = "false"
                     data-toggle-target = "#role-select-container"
                     data-ajax-url = "<%= invitable_teams_path %>"
+                    data-e2e="e2e-DD-settings-members-inviteModal-team"
                   ></select>
                 </div>
 
@@ -129,7 +138,7 @@ invite_with_team_selector = type.in?(%w(invite_new_members invite_with_team_sele
                   <h4 class="heading">
                     <span><%= t('invite_users.select_team_role') %></span>
                   </h4>
-                  <div class="relative">
+                  <div class="relative" data-e2e="e2e-DD-settings-members-inviteModal-role">
                     <% normal_user_role = UserRole.find_predefined_normal_user_role %>
                     <%= select_tag "role-id",
                       options_for_select(
@@ -155,14 +164,23 @@ invite_with_team_selector = type.in?(%w(invite_new_members invite_with_team_sele
 
       <div class="modal-footer">
         <div data-role="step-form">
-          <button type="button" class="btn btn-secondary" data-dismiss="modal">
+          <button
+            type="button"
+            class="btn btn-secondary"
+            data-dismiss="modal"
+            data-e2e="e2e-BT-settings-members-inviteModal-cancel"
+          >
             <%= t('general.cancel') %>
           </button>
 
           <!-- Invite buttons -->
-          <button type="button" class="btn btn-primary"
-                  data-role="invite-btn" data-action="invite"
-                  disabled="disabled">
+          <button type="button"
+                  class="btn btn-primary"
+                  data-role="invite-btn"
+                  data-action="invite"
+                  disabled="disabled"
+                  data-e2e="e2e-BT-settings-members-inviteModal-invite"
+          >
             <%= t('invite_users.invite_btn') %>
           </button>
 
diff --git a/app/views/users/settings/teams/show.html.erb b/app/views/users/settings/teams/show.html.erb
index e71126147..9eb7fe0e2 100644
--- a/app/views/users/settings/teams/show.html.erb
+++ b/app/views/users/settings/teams/show.html.erb
@@ -92,7 +92,14 @@
     <div class="users-datatable">
       <% if can_invite_team_users?(@team) %>
         <div id="add-new-team-members-button" class="hidden">
-          <a href="#" class="btn btn-primary" data-trigger="invite-users" data-turbolinks="false" data-modal-id="team-invite-users-modal">
+          <a
+            href="#"
+            class="btn btn-primary"
+            data-trigger="invite-users"
+            data-turbolinks="false"
+            data-modal-id="team-invite-users-modal"
+            data-e2e="e2e-BT-settings-members-invite"
+          >
             <span class="sn-icon sn-icon-new-task"></span>
             <%= I18n.t('users.settings.teams.edit.add_user') %>
           </a>

From 84b796756f382ad89160184fbf77538e285939b3 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 6 Aug 2025 15:03:03 +0200
Subject: [PATCH 26/91] Add team and user_group assignment relations
 [SCI-12204]

---
 app/models/team.rb       | 1 +
 app/models/user_group.rb | 1 +
 2 files changed, 2 insertions(+)

diff --git a/app/models/team.rb b/app/models/team.rb
index 6edec7c03..78eb99da8 100644
--- a/app/models/team.rb
+++ b/app/models/team.rb
@@ -61,6 +61,7 @@ class Team < ApplicationRecord
   has_many :shareable_links, inverse_of: :team, dependent: :destroy
   has_many :storage_locations, dependent: :destroy
   has_many :forms, dependent: :destroy
+  has_many :team_assignments, dependent: :destroy
 
   attr_accessor :without_templates
 
diff --git a/app/models/user_group.rb b/app/models/user_group.rb
index af608ef52..9b8c9994b 100644
--- a/app/models/user_group.rb
+++ b/app/models/user_group.rb
@@ -14,6 +14,7 @@ class UserGroup < ApplicationRecord
   belongs_to :last_modified_by, class_name: 'User', optional: true
   has_many :user_group_memberships, dependent: :destroy
   has_many :users, through: :user_group_memberships, dependent: :destroy
+  has_many :user_group_assignments, dependent: :destroy
 
   accepts_nested_attributes_for :user_group_memberships
 

From cdabf0b199e90f360d7c2abfeedf61ee7a7d9c1e Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Wed, 6 Aug 2025 15:03:58 +0200
Subject: [PATCH 27/91] Fix automatic creation of user group assignments for
 new objects [SCI-12187]

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

diff --git a/app/models/user_group_assignment.rb b/app/models/user_group_assignment.rb
index 1beb65d9c..fb6b103ec 100644
--- a/app/models/user_group_assignment.rb
+++ b/app/models/user_group_assignment.rb
@@ -7,7 +7,7 @@ class UserGroupAssignment < ApplicationRecord
   belongs_to :team
   belongs_to :user_group
   belongs_to :user_role
-  belongs_to :assigned_by, class_name: 'User'
+  belongs_to :assigned_by, class_name: 'User', optional: true
 
   enum :assigned, { automatically: 0, manually: 1 }, suffix: true
 

From 18ad2a8a933be57859b8285d6ad3af08591fd2a4 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 6 Aug 2025 15:41:24 +0200
Subject: [PATCH 28/91] Fix team assignments for new protocol drafts
 [SCI-12199]

---
 app/models/protocol.rb | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 00ff966fd..0e2715aea 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -607,6 +607,11 @@ class Protocol < ApplicationRecord
     parent_protocol.user_group_assignments.each do |parent_user_group_assignment|
       parent_protocol.sync_child_protocol_assignment(parent_user_group_assignment, draft.id)
     end
+
+    parent_protocol.team_assignments.each do |parent_team_assignment|
+      parent_protocol.sync_child_protocol_assignment(parent_team_assignment, draft.id)
+    end
+
     draft
   end
 

From 492bff1a443514f4d47f3f7533a0a45617c39b46 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 7 Aug 2025 10:51:51 +0200
Subject: [PATCH 29/91] Fix assigned user dropdown on task create [SCI-12207]

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

diff --git a/app/controllers/experiments_controller.rb b/app/controllers/experiments_controller.rb
index acb418e61..67cc028e6 100644
--- a/app/controllers/experiments_controller.rb
+++ b/app/controllers/experiments_controller.rb
@@ -47,7 +47,7 @@ class ExperimentsController < ApplicationController
   end
 
   def assigned_users
-    render json: User.where(id: @experiment.user_assignments.select(:user_id)),
+    render json: @experiment.users,
            each_serializer: UserSerializer,
            user: current_user
   end

From c457f276dbe44c2ac71ea8f50187187fdcb681b1 Mon Sep 17 00:00:00 2001
From: Klemen Benedicic <klemen.benedicic@scinote.net>
Date: Thu, 7 Aug 2025 14:27:27 +0200
Subject: [PATCH 30/91] Add data-e2e to members tab in workspace [SCI-12198]

---
 app/views/users/settings/teams/members.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/users/settings/teams/members.html.erb b/app/views/users/settings/teams/members.html.erb
index ef061b753..bd8946494 100644
--- a/app/views/users/settings/teams/members.html.erb
+++ b/app/views/users/settings/teams/members.html.erb
@@ -9,7 +9,7 @@
   <%= render partial: 'header' %>
 
   <!-- USERS TABLE -->
-  <div class="users-datatable">
+  <div class="users-datatable" data-e2e="e2e-CO-settings-workspace-usersTable">
     <% if can_invite_team_users?(@team) %>
       <div id="add-new-team-members-button" class="hidden">
         <a href="#" class="btn btn-primary" data-trigger="invite-users" data-turbolinks="false" data-modal-id="team-invite-users-modal">

From 90f779462f851eb68aed2a8fd36496b5cf14aa47 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 7 Aug 2025 14:43:05 +0200
Subject: [PATCH 31/91] Disable workspace tabs if you do not have permission
 [SCI-12212]

---
 app/controllers/users/settings/teams_controller.rb | 6 ++++++
 app/views/users/settings/teams/_header.html.erb    | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/app/controllers/users/settings/teams_controller.rb b/app/controllers/users/settings/teams_controller.rb
index dce1104b2..43b55723a 100644
--- a/app/controllers/users/settings/teams_controller.rb
+++ b/app/controllers/users/settings/teams_controller.rb
@@ -28,6 +28,8 @@ module Users
         members
       )
 
+      before_action :check_read_permissions, only: :show
+
       before_action :check_create_team_permission,
                     only: %i(new create)
 
@@ -138,6 +140,10 @@ module Users
         render_403 unless can_create_teams?
       end
 
+      def check_read_permissions
+        render_403 unless can_read_team?(@team)
+      end
+
       def load_user
         @user = current_user
       end
diff --git a/app/views/users/settings/teams/_header.html.erb b/app/views/users/settings/teams/_header.html.erb
index c30852006..d0b90bdf4 100644
--- a/app/views/users/settings/teams/_header.html.erb
+++ b/app/views/users/settings/teams/_header.html.erb
@@ -18,7 +18,7 @@
   </div>
 </div>
 <div class="flex items-center gap-4 p-2 mb-4 bg-white">
-  <%= link_to t("users.settings.teams.navigation.details"), team_path(@team), class: "p-2.5 hover:no-underline #{ @active_tab == :details ? "text-sn-blue" : "text-sn-grey" }"%>
+  <%= link_to t("users.settings.teams.navigation.details"), team_path(@team), class: "p-2.5 hover:no-underline #{ 'disabled' unless can_read_team?(@team) } #{ @active_tab == :details ? "text-sn-blue" : "text-sn-grey" }"%>
   <%= link_to t("users.settings.teams.navigation.members"), members_users_settings_team_path(@team), class: "p-2.5 hover:no-underline #{ @active_tab == :members ? "text-sn-blue" : "text-sn-grey" }"%>
-  <%= link_to t("users.settings.teams.navigation.groups"), users_settings_team_user_groups_path(@team), class: "p-2.5 hover:no-underline #{ @active_tab == :user_groups ? "text-sn-blue" : "text-sn-grey" }"%>
+  <%= link_to t("users.settings.teams.navigation.groups"), users_settings_team_user_groups_path(@team), class: "p-2.5 hover:no-underline  #{ 'disabled' unless can_read_team?(@team) } #{ @active_tab == :user_groups ? "text-sn-blue" : "text-sn-grey" }"%>
 </div>

From 5623ccc164fc23f5d0a889fc0174465050349829 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Fri, 8 Aug 2025 11:13:02 +0200
Subject: [PATCH 32/91] Fix experiment status and replace group icon
 [SCI-12219]

---
 .../vue/experiments/renderers/status.vue          |   9 ++++++++-
 .../vue/shared/access_modal/assign_flyout.vue     |   2 +-
 app/javascript/vue/shared/access_modal/edit.vue   |   2 +-
 public/images/icon/group.png                      | Bin 935 -> 0 bytes
 public/images/icon/group.svg                      |   5 +++++
 5 files changed, 15 insertions(+), 3 deletions(-)
 delete mode 100644 public/images/icon/group.png
 create mode 100644 public/images/icon/group.svg

diff --git a/app/javascript/vue/experiments/renderers/status.vue b/app/javascript/vue/experiments/renderers/status.vue
index 78fe66385..ef31f362a 100644
--- a/app/javascript/vue/experiments/renderers/status.vue
+++ b/app/javascript/vue/experiments/renderers/status.vue
@@ -39,9 +39,16 @@ export default {
   },
   methods: {
     optionRenderer(option) {
+      let color = 'bg-sn-grey-500';
+      if (option[0] === 'in_progress') {
+        color = 'bg-sn-science-blue';
+      } else if (option[0] === 'done') {
+        color = 'bg-sn-alert-green';
+      }
+
       return `
         <div class="flex items-center gap-2">
-          <div class="${this.statusColor(option[0])} w-3 h-3 rounded-full"></div>
+          <div class="${color} w-3 h-3 rounded-full"></div>
           <span>${option[1]}</span>
         </div>`;
     },
diff --git a/app/javascript/vue/shared/access_modal/assign_flyout.vue b/app/javascript/vue/shared/access_modal/assign_flyout.vue
index 439e1cab1..61c2c8959 100644
--- a/app/javascript/vue/shared/access_modal/assign_flyout.vue
+++ b/app/javascript/vue/shared/access_modal/assign_flyout.vue
@@ -37,7 +37,7 @@
         <perfect-scrollbar class="max-h-80 relative">
           <div v-for="userGroup in filteredUserGroups" :key="userGroup.id" class="py-2 flex items-center w-full">
             <div>
-              <img src="/images/icon/group.png" class="rounded-full w-8 h-8">
+              <img src="/images/icon/group.svg" class="rounded-full w-8 h-8">
             </div>
             <div
               class="truncate ml-2"
diff --git a/app/javascript/vue/shared/access_modal/edit.vue b/app/javascript/vue/shared/access_modal/edit.vue
index 262392d44..03f9ab002 100644
--- a/app/javascript/vue/shared/access_modal/edit.vue
+++ b/app/javascript/vue/shared/access_modal/edit.vue
@@ -50,7 +50,7 @@
         <div>
           <img
             class="rounded-full w-8 h-8"
-            src="/images/icon/group.png"
+            src="/images/icon/group.svg"
           >
         </div>
         <div class="truncate">
diff --git a/public/images/icon/group.png b/public/images/icon/group.png
deleted file mode 100644
index a099fbb8d9ba7f5ac6b75f808b593304f9c6c63b..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 935
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JPDHLkV1mD_qnQ8z

diff --git a/public/images/icon/group.svg b/public/images/icon/group.svg
new file mode 100644
index 000000000..e7057628d
--- /dev/null
+++ b/public/images/icon/group.svg
@@ -0,0 +1,5 @@
+<svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg">
+<rect x="0.5" y="0.5" width="23" height="23" rx="11.5" fill="#F9F9F9"/>
+<rect x="0.5" y="0.5" width="23" height="23" rx="11.5" stroke="#EAECF0"/>
+<path d="M4.50001 17.8331V16.6663C4.50001 16.2744 4.60001 15.9412 4.80001 15.6662C5.00001 15.3912 5.26689 15.1663 5.60001 14.9994C6.32501 14.6494 7.04189 14.3744 7.75814 14.1744C8.47439 13.9744 9.33314 13.8744 10.3331 13.8744C11.3331 13.8744 12.1913 13.9744 12.9081 14.1744C13.625 14.3744 14.3413 14.6494 15.0663 14.9994C15.3994 15.1663 15.6663 15.3912 15.8663 15.6662C16.0663 15.9412 16.1663 16.2744 16.1663 16.6663V17.8331H4.50001ZM10.3331 12C9.64126 12 9.05001 11.7581 8.56626 11.2669C8.08314 10.7837 7.83314 10.1919 7.83314 9.5C7.83314 8.80813 8.07501 8.23313 8.56626 7.74188C9.04939 7.25 9.64126 7 10.3331 7C11.025 7 11.6 7.25 12.0913 7.74188C12.5831 8.23375 12.8331 8.825 12.8331 9.5C12.8331 10.175 12.5831 10.7831 12.0913 11.2669C11.5994 11.75 11.0081 12 10.3331 12ZM16.3919 9.5C16.3919 10.1919 16.1419 10.7831 15.65 11.2669C15.1581 11.7506 14.5669 12 13.8919 12C13.85 12 13.8 12 13.75 11.9919C13.6919 11.9919 13.65 11.9837 13.625 11.9837C13.9 11.6337 14.1169 11.2506 14.275 10.8256C14.425 10.4006 14.5 9.95875 14.5 9.50063C14.5 9.0425 14.4169 8.62563 14.2581 8.20875C14.1 7.79188 13.8831 7.40063 13.625 7.04188C13.6669 7.025 13.7081 7.01687 13.75 7.00875C13.7919 7.00875 13.8419 7.00063 13.8919 7.00063C14.575 7.00063 15.1588 7.25062 15.65 7.7425C16.1413 8.23437 16.3919 8.82563 16.3919 9.50063V9.5ZM5.33314 17H15.3331V16.6669C15.3331 16.475 15.2831 16.3 15.1831 16.1587C15.0831 16.0087 14.9163 15.8669 14.6663 15.7338C14.0413 15.4006 13.3831 15.1506 12.6994 14.9756C12.0075 14.8006 11.2244 14.7175 10.3325 14.7175C9.44064 14.7175 8.65752 14.8006 7.96564 14.9756C7.27376 15.1506 6.62376 15.4006 5.99876 15.7338C5.74876 15.8756 5.57376 16.0169 5.48189 16.1587C5.38189 16.3006 5.34001 16.4756 5.34001 16.6669V17H5.33314ZM10.3331 11.1669C10.7913 11.1669 11.1831 11 11.5081 10.675C11.8331 10.35 12 9.95812 12 9.5C12 9.04188 11.8331 8.65 11.5081 8.325C11.1831 8 10.7913 7.83313 10.3331 7.83313C9.87501 7.83313 9.48314 8 9.15814 8.325C8.83314 8.65 8.66627 9.04188 8.66627 9.5C8.66627 9.95812 8.83314 10.35 9.15814 10.675C9.48314 11 9.87501 11.1669 10.3331 11.1669ZM17.25 16.3169V17.8337H19.5V16.3169C19.5 15.9587 19.4 15.6337 19.2081 15.325C19.0163 15.025 18.7413 14.775 18.3913 14.575C18.0331 14.3831 17.6663 14.2 17.2994 14.0419C16.9325 13.875 16.5494 13.75 16.1663 13.6669C16.5163 13.9919 16.7831 14.3837 16.9663 14.85C17.1494 15.3081 17.25 15.8 17.25 16.3169Z" fill="#1D2939"/>
+</svg>

From d35da236cda5b9883be28145a8f7d259b1196273 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Fri, 8 Aug 2025 11:57:47 +0200
Subject: [PATCH 33/91] Fix user leaving the workspace [SCI-12211]

---
 app/assets/javascripts/users/settings/teams/show.js     | 6 +++++-
 app/controllers/users/settings/user_teams_controller.rb | 4 +++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/app/assets/javascripts/users/settings/teams/show.js b/app/assets/javascripts/users/settings/teams/show.js
index d9a887b2a..cd213e4b6 100644
--- a/app/assets/javascripts/users/settings/teams/show.js
+++ b/app/assets/javascripts/users/settings/teams/show.js
@@ -150,7 +150,11 @@
             if (data.status === 'done') {
               // Reload the whole table
               HelperModule.flashAlertMsg(jobData.success_message, 'success');
-              usersDatatable.ajax.reload();
+              if(jobData.redirect_url) {
+                window.location.href = jobData.redirect_url;
+              } else {
+                usersDatatable.ajax.reload();
+              }
               animateSpinner(null, false);
               $('#destroy-user-team-modal').modal('hide');
               clearInterval(jobStatusInterval);
diff --git a/app/controllers/users/settings/user_teams_controller.rb b/app/controllers/users/settings/user_teams_controller.rb
index ebf1ccbe4..f316ee7a6 100644
--- a/app/controllers/users/settings/user_teams_controller.rb
+++ b/app/controllers/users/settings/user_teams_controller.rb
@@ -109,11 +109,13 @@ module Users
                               )
                             end
 
+          redirect_url = teams_path if params[:leave]
+
           generate_notification(current_user,
                                 @user_assignment.user,
                                 @user_assignment.assignable,
                                 false)
-          render json: { status: :ok, job_id: job_id, success_message: success_message }
+          render json: { status: :ok, job_id: job_id, success_message: success_message, redirect_url: redirect_url }
         end
       end
 

From 10e831b88240cb868b61731c4d423aa572f24e4b Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 8 Aug 2025 12:00:39 +0200
Subject: [PATCH 34/91] Fix assignment propagation and favorite, designation
 clenaup [SCI-12220]

---
 .../propagate_assignment_job.rb               | 34 ++++++++-----------
 app/models/team_assignment.rb                 |  2 +-
 app/models/user_group_assignment.rb           |  1 +
 3 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/app/jobs/user_assignments/propagate_assignment_job.rb b/app/jobs/user_assignments/propagate_assignment_job.rb
index eff3ae8ca..3d99152b6 100644
--- a/app/jobs/user_assignments/propagate_assignment_job.rb
+++ b/app/jobs/user_assignments/propagate_assignment_job.rb
@@ -2,6 +2,8 @@
 
 module UserAssignments
   class PropagateAssignmentJob < ApplicationJob
+    include Canaid::Helpers::PermissionsHelper
+
     queue_as :high_priority
 
     def perform(assignment, destroy: false, remove_from_team: false)
@@ -13,6 +15,7 @@ module UserAssignments
 
       ActiveRecord::Base.transaction do
         @assignment.destroy! if destroy && !@assignment.destroyed?
+        cleanup!(@assignment)
         sync_resource_user_associations(@resource)
       end
     end
@@ -39,7 +42,7 @@ module UserAssignments
 
       child_associations.find_each do |child_association|
         if @destroy
-          destroy_or_update_assignment(child_association)
+          destroy_assignment(child_association)
         else
           create_or_update_assignment(child_association)
         end
@@ -47,7 +50,7 @@ module UserAssignments
         sync_resource_user_associations(child_association)
       end
 
-      destroy_or_update_assignment(resource) if resource.is_a?(Project) && @destroy
+      destroy_assignment(resource) if resource.is_a?(Project) && @destroy
     end
 
     def create_or_update_assignment(resource)
@@ -66,31 +69,24 @@ module UserAssignments
       )
     end
 
-    def destroy_or_update_assignment(resource)
-      # also destroy user designations if it's a MyModule
-      resource.user_my_modules.where(user: @user).destroy_all if resource.is_a?(MyModule)
-
+    def destroy_assignment(resource)
       assignment = resource.public_send(:"#{@type}_assignments").find_by(
         "#{@type}_id" => @assignment.public_send(@type).id
       )
 
       return unless assignment
 
-      project = resource.is_a?(Project) ? resource : resource.project
+      assignment.destroy!
 
-      if project.default_public_user_role_id && !@remove_from_team
-        # if project is public, the assignment
-        # will reset to the default public role
+      cleanup!(assignment)
+    end
 
-        assignment.update!(
-          user_role_id: project.default_public_user_role_id,
-          assigned: :automatically,
-          assigned_by: @assignment.assigned_by
-        )
-      else
-        resource.favorites.where(user: @user).destroy_all if resource.respond_to?(:favorites)
-        assignment.destroy!
-      end
+    def cleanup!(assignment)
+      # clean up designations and favorites if user is no longer assigned
+      assigned_users = assignment.assignable.users
+
+      assignment.assignable.favorites.where.not(user: assigned_users).destroy_all if assignment.assignable.respond_to?(:favorites)
+      assignment.assignable.user_my_modules.where.not(user: assigned_users).destroy_all if assignment.assignable.is_a?(MyModule)
     end
   end
 end
diff --git a/app/models/team_assignment.rb b/app/models/team_assignment.rb
index bc69b8fd7..3a3fd4abc 100644
--- a/app/models/team_assignment.rb
+++ b/app/models/team_assignment.rb
@@ -5,7 +5,7 @@ class TeamAssignment < ApplicationRecord
   belongs_to :team
   belongs_to :user_role
   belongs_to :assigned_by, class_name: 'User', optional: true
-  has_many :users, through: :team
+  delegate :users, to: :team
 
   enum :assigned, { automatically: 0, manually: 1 }, suffix: true
 
diff --git a/app/models/user_group_assignment.rb b/app/models/user_group_assignment.rb
index fb6b103ec..1050046fa 100644
--- a/app/models/user_group_assignment.rb
+++ b/app/models/user_group_assignment.rb
@@ -8,6 +8,7 @@ class UserGroupAssignment < ApplicationRecord
   belongs_to :user_group
   belongs_to :user_role
   belongs_to :assigned_by, class_name: 'User', optional: true
+  has_many :users, through: :user_group
 
   enum :assigned, { automatically: 0, manually: 1 }, suffix: true
 

From b5bc880c2f9280dcdeaf817738930a6743ec21ce Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Fri, 8 Aug 2025 12:12:37 +0200
Subject: [PATCH 35/91] FIx assigned user dropdown on task create on canvas
 [SCI-12207]

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

diff --git a/app/controllers/my_modules_controller.rb b/app/controllers/my_modules_controller.rb
index 2a0883402..781e4f3d5 100644
--- a/app/controllers/my_modules_controller.rb
+++ b/app/controllers/my_modules_controller.rb
@@ -47,7 +47,7 @@ class MyModulesController < ApplicationController
 
   def new
     @my_module = @experiment.my_modules.new
-    assigned_users = User.where(id: @experiment.user_assignments.select(:user_id))
+    assigned_users = @experiment.users
 
     render json: {
       html: render_to_string(

From 3fb55af206dad80f63ca3f7a46f730742ba45914 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 8 Aug 2025 15:58:29 +0200
Subject: [PATCH 36/91] Don't revert to viewer role for roles with no read
 permission [SCI-12210]

---
 .../team_shared_objects_controller.rb         |  8 ++-----
 app/models/concerns/shareable.rb              | 22 +++++++++++++++++++
 app/models/team_shared_object.rb              |  8 ++-----
 3 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/app/controllers/team_shared_objects_controller.rb b/app/controllers/team_shared_objects_controller.rb
index fbbb25509..1132bb993 100644
--- a/app/controllers/team_shared_objects_controller.rb
+++ b/app/controllers/team_shared_objects_controller.rb
@@ -25,13 +25,9 @@ class TeamSharedObjectsController < ApplicationController
 
           case global_permission_level
           when :shared_read
-            UserAssignment.where(assignable: @model).where.not(team: @model.team).update!(user_role: UserRole.find_predefined_viewer_role)
-            TeamAssignment.where(assignable: @model).where.not(team: @model.team).update!(user_role: UserRole.find_predefined_viewer_role)
-            UserGroupAssignment.where(assignable: @model).where.not(team: @model.team).update!(user_role: UserRole.find_predefined_viewer_role)
+            @model.demote_all_sharing_assignments_to_viewer!
           when :not_shared
-            UserAssignment.where(assignable: @model).where.not(team: @model.team).destroy_all
-            TeamAssignment.where(assignable: @model).where.not(team: @model.team).destroy_all
-            UserGroupAssignment.where(assignable: @model).where.not(team: @model.team).destroy_all
+            @model.destroy_all_sharing_assignments!
           end
 
           case @model
diff --git a/app/models/concerns/shareable.rb b/app/models/concerns/shareable.rb
index 1da4e1762..3649f2fb3 100644
--- a/app/models/concerns/shareable.rb
+++ b/app/models/concerns/shareable.rb
@@ -99,4 +99,26 @@ module Shareable
 
     shared_read? || team_shared_objects.exists?(team: team, permission_level: :shared_read)
   end
+
+  def demote_all_sharing_assignments_to_viewer!(for_team: nil)
+    # take into account special roles with no read permission, and do not upgrade them to viewer
+    read_permission = "#{self.class.permission_class}Permissions".constantize::READ
+
+    teams = for_team ? Team.where(id: for_team.id).where.not(id: team.id) : Team.where.not(id: team.id)
+
+    [user_assignments, user_group_assignments, team_assignments].each do |assignments|
+      assignments.joins(:user_role)
+                 .where(team_id: teams.select(:id))
+                 .where(['user_roles.permissions @> ARRAY[?]::varchar[]', [read_permission]])
+                 .update!(user_role: UserRole.find_predefined_viewer_role)
+    end
+  end
+
+  def destroy_all_sharing_assignments!(for_team: nil)
+    teams = for_team ? Team.where(id: for_team.id).where.not(id: team.id) : Team.where.not(id: team.id)
+
+    user_assignments.where(team_id: teams.select(:id)).destroy_all
+    user_group_assignments.where.not(team_id: teams.select(:id)).destroy_all
+    team_assignments.where.not(team_id: teams.select(:id)).destroy_all
+  end
 end
diff --git a/app/models/team_shared_object.rb b/app/models/team_shared_object.rb
index 3e3181ec7..c2ef157d7 100644
--- a/app/models/team_shared_object.rb
+++ b/app/models/team_shared_object.rb
@@ -26,15 +26,11 @@ class TeamSharedObject < ApplicationRecord
   def update_assignments
     return unless saved_change_to_permission_level? && permission_level == 'shared_read'
 
-    shared_object.user_assignments.where(team: team).update!(user_role: UserRole.find_predefined_viewer_role)
-    shared_object.user_group_assignments.where(team: team).update!(user_role: UserRole.find_predefined_viewer_role)
-    shared_object.team_assignments.where(team: team).update!(user_role: UserRole.find_predefined_viewer_role)
+    shared_object.demote_all_sharing_assignments_to_viewer!(for_team: team)
   end
 
   def destroy_assignments
-    shared_object.user_assignments.where(team: team).destroy_all
-    shared_object.user_group_assignments.where(team: team).destroy_all
-    shared_object.team_assignments.where(team: team).destroy_all
+    shared_object.destroy_all_sharing_assignments!(for_team: team)
   end
 
   def team_cannot_be_the_same

From 2de788542f6626f9b1ecef49497b049028694fb7 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 8 Aug 2025 16:28:05 +0200
Subject: [PATCH 37/91] Fix inherit role for experiments [SCI-12222]

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

diff --git a/app/controllers/access_permissions/experiments_controller.rb b/app/controllers/access_permissions/experiments_controller.rb
index 813b6bb2a..186c856c3 100644
--- a/app/controllers/access_permissions/experiments_controller.rb
+++ b/app/controllers/access_permissions/experiments_controller.rb
@@ -24,7 +24,7 @@ module AccessPermissions
         )
       end
 
-      UserAssignments::PropagateAssignmentJob.perform_later(@assignment, destroy: permitted_params[:user_role_id] == 'reset')
+      UserAssignments::PropagateAssignmentJob.perform_later(@assignment)
 
       case assignment_type
       when :user_group

From 0bd7da79222782cadfa93b3bb850176bbe7088a0 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 15 Jul 2025 18:43:50 +0200
Subject: [PATCH 38/91] Handle project "visibility" property
 backward-compatibility on API [SCI-12041]

---
 app/controllers/api/v1/projects_controller.rb | 57 +++++++++++++------
 app/serializers/api/v1/project_serializer.rb  |  4 ++
 2 files changed, 45 insertions(+), 16 deletions(-)

diff --git a/app/controllers/api/v1/projects_controller.rb b/app/controllers/api/v1/projects_controller.rb
index 19ec39c40..59522a766 100644
--- a/app/controllers/api/v1/projects_controller.rb
+++ b/app/controllers/api/v1/projects_controller.rb
@@ -26,32 +26,57 @@ module Api
       def create
         raise PermissionError.new(Project, :create) unless can_create_projects?(@team)
 
-        project = @team.projects.build(project_params.merge!(created_by: current_user))
+        ActiveRecord::Base.transaction do
+          project = @team.projects.build(project_params.merge!(created_by: current_user))
 
-        if project.visible? # set default viewer role for public projects
-          project.default_public_user_role = UserRole.predefined.find_by(name: I18n.t('user_roles.predefined.viewer'))
+          project.save!
+
+          if project_params[:visibility] == 'visible'
+            project.team_assignments.create!(
+              team: project.team,
+              user_role: UserRole.find_predefined_viewer_role,
+              assigned_by: current_user,
+              assigned: :manually
+            )
+          end
+
+          render jsonapi: project, serializer: ProjectSerializer, scope: { metadata: params['with-metadata'] == 'true' }, status: :created
         end
-
-        project.save!
-
-        render jsonapi: project, serializer: ProjectSerializer, scope: { metadata: params['with-metadata'] == 'true' }, status: :created
       end
 
       def update
         @project.assign_attributes(project_params)
 
-        return render body: nil, status: :no_content unless @project.changed?
+        return render body: nil, status: :no_content if !@project.changed? && project_params[:visibility].blank?
 
-        if @project.archived_changed?
-          if @project.archived?
-            @project.archived_by = current_user
-          else
-            @project.restored_by = current_user
+        ActiveRecord::Base.transaction do
+          if @project.archived_changed?
+            if @project.archived?
+              @project.archived_by = current_user
+            else
+              @project.restored_by = current_user
+            end
           end
+          @project.last_modified_by = current_user
+          @project.save!
+
+          if project_params[:visibility].present?
+            team_assignment = @project.team_assignments.find_by(team: @team)
+
+            if project_params[:visibility] == 'hidden' && team_assignment.present?
+              team_assignment.destroy!
+            elsif project_params[:visibility] == 'visible' && team_assignment.blank?
+              @project.team_assignments.create!(
+                team: @project.team,
+                user_role: UserRole.find_predefined_viewer_role,
+                assigned_by: current_user,
+                assigned: :manually
+              )
+            end
+          end
+
+          render jsonapi: @project, serializer: ProjectSerializer, scope: { metadata: params['with-metadata'] == 'true' }, status: :ok
         end
-        @project.last_modified_by = current_user
-        @project.save!
-        render jsonapi: @project, serializer: ProjectSerializer, scope: { metadata: params['with-metadata'] == 'true' }, status: :ok
       end
 
       def activities
diff --git a/app/serializers/api/v1/project_serializer.rb b/app/serializers/api/v1/project_serializer.rb
index d671e1535..c6d3d2005 100644
--- a/app/serializers/api/v1/project_serializer.rb
+++ b/app/serializers/api/v1/project_serializer.rb
@@ -12,6 +12,10 @@ module Api
       has_many :project_comments, key: :comments, serializer: CommentSerializer
 
       include TimestampableModel
+
+      def visibility
+        object.team_assignments.any? ? 'visible' : 'hidden'
+      end
     end
   end
 end

From c42138e7138e299a2a54681085323904e5f030aa Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 15 Jul 2025 12:09:51 +0200
Subject: [PATCH 39/91] Fix permissions check in repository api [SCI-12136]

---
 .../api/v1/inventories_controller.rb          |  1 +
 .../api/v1/task_inventory_items_controller.rb | 50 ++++++++++---------
 2 files changed, 27 insertions(+), 24 deletions(-)

diff --git a/app/controllers/api/v1/inventories_controller.rb b/app/controllers/api/v1/inventories_controller.rb
index 7c4089615..b148aa520 100644
--- a/app/controllers/api/v1/inventories_controller.rb
+++ b/app/controllers/api/v1/inventories_controller.rb
@@ -13,6 +13,7 @@ module Api
       def index
         inventories =
           timestamps_filter(@team.repositories).active
+                                               .readable_by_user(current_user)
                                                .page(params.dig(:page, :number))
                                                .per(params.dig(:page, :size))
 
diff --git a/app/controllers/api/v1/task_inventory_items_controller.rb b/app/controllers/api/v1/task_inventory_items_controller.rb
index c93ced8e5..21f4265b6 100644
--- a/app/controllers/api/v1/task_inventory_items_controller.rb
+++ b/app/controllers/api/v1/task_inventory_items_controller.rb
@@ -7,16 +7,18 @@ module Api
       before_action :load_project
       before_action :load_experiment
       before_action :load_task
-      before_action :load_my_module_repository_row, only: :update
+      before_action :load_inventory_item, only: %i(show destroy update)
+      before_action :load_task_inventory_item, only: %i(update destroy)
+      before_action :check_repository_view_permissions, only: :show
       before_action :check_stock_consumption_update_permissions, only: :update
       before_action :check_task_assign_permissions, only: %i(create destroy)
 
       def index
-        items =
-          timestamps_filter(@task.repository_rows).includes(repository_cells: :repository_column)
-                                                  .preload(repository_cells: :value)
-                                                  .page(params.dig(:page, :number))
-                                                  .per(params.dig(:page, :size))
+        items = @task.repository_rows.where(repository_id: Repository.readable_by_user(current_user).select(:id))
+        items = timestamps_filter(items).includes(repository_cells: :repository_column)
+                                        .preload(repository_cells: :value)
+                                        .page(params.dig(:page, :number))
+                                        .per(params.dig(:page, :size))
         render jsonapi: items,
                each_serializer: TaskInventoryItemSerializer,
                show_repository: true,
@@ -25,7 +27,7 @@ module Api
       end
 
       def show
-        render jsonapi: @task.repository_rows.find(params.require(:id)),
+        render jsonapi: @inventory_item,
                serializer: TaskInventoryItemSerializer,
                show_repository: true,
                my_module: @task,
@@ -39,7 +41,7 @@ module Api
 
         @task.my_module_repository_rows.create!(repository_row: @inventory_item, assigned_by: current_user)
 
-        render jsonapi: @task.repository_rows,
+        render jsonapi: @inventory_item,
                each_serializer: TaskInventoryItemSerializer,
                show_repository: true,
                my_module: @task,
@@ -47,13 +49,13 @@ module Api
       end
 
       def update
-        @my_module_repository_row.consume_stock(
+        @task_inventory_item.consume_stock(
           current_user,
           repository_row_params[:attributes][:stock_consumption],
           repository_row_params[:attributes][:stock_consumption_comment]
         )
 
-        render jsonapi: @my_module_repository_row.repository_row,
+        render jsonapi: @inventory_item,
                serializer: TaskInventoryItemSerializer,
                show_repository: true,
                my_module: @task,
@@ -61,29 +63,29 @@ module Api
       end
 
       def destroy
-        @inventory_item = @task.repository_rows.find(params.require(:id))
-
-        raise PermissionError.new(Repository, :read) unless @inventory_item && can_read_repository?(@inventory_item.repository)
-
-        @task.my_module_repository_rows.find_by(repository_row: @inventory_item).destroy!
+        @task_inventory_item.destroy!
 
         render body: nil
       end
 
       private
 
-      def load_my_module_repository_row
-        @my_module_repository_row = @task.repository_rows
-                                         .find(params.require(:id))
-                                         .my_module_repository_rows
-                                         .find_by(my_module: @task)
+      def load_inventory_item
+        @inventory_item = @task.repository_rows.find(params.require(:id))
+      end
+
+      def load_task_inventory_item
+        @task_inventory_item = @task.my_module_repository_rows.find_by(repository_row: @inventory_item)
+
+        raise ActiveRecord::RecordNotFound unless @task_inventory_item
+      end
+
+      def check_repository_view_permissions
+        raise PermissionError.new(RepositoryRow, :read_repository) unless can_read_repository?(@inventory_item.repository)
       end
 
       def check_stock_consumption_update_permissions
-        unless can_update_my_module_stock_consumption?(@task) &&
-               can_manage_repository_rows?(@my_module_repository_row.repository_row.repository)
-          raise PermissionError.new(RepositoryRow, :update_stock_consumption)
-        end
+        raise PermissionError.new(RepositoryRow, :update_stock_consumption) unless can_update_my_module_stock_consumption?(@task)
       end
 
       def check_task_assign_permissions

From 30cf08a666000a9796f182f43b7fb125616f5f8c Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Mon, 11 Aug 2025 12:58:17 +0200
Subject: [PATCH 40/91] Prevent experiment row selection on status click
 [SCI-12219]

---
 app/javascript/vue/experiments/list.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/javascript/vue/experiments/list.vue b/app/javascript/vue/experiments/list.vue
index 87e335554..4e08b764c 100644
--- a/app/javascript/vue/experiments/list.vue
+++ b/app/javascript/vue/experiments/list.vue
@@ -171,6 +171,7 @@ export default {
           cellRendererParams: {
             statusesList: this.statusesList
           },
+          notSelectable: true,
           minWidth: 180
         },
         {

From 3c78ab67e13aeb98e0043d9c87ba7ea0b800ee89 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Mon, 11 Aug 2025 13:14:43 +0200
Subject: [PATCH 41/91] Css fixes for user groups [SCI-12218]

---
 app/controllers/users/settings/user_groups_controller.rb | 2 +-
 app/javascript/vue/shared/access_modal/edit.vue          | 4 ++--
 app/javascript/vue/shared/select_dropdown.vue            | 8 ++++----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/app/controllers/users/settings/user_groups_controller.rb b/app/controllers/users/settings/user_groups_controller.rb
index 92dc0c1e5..ec96f9c61 100644
--- a/app/controllers/users/settings/user_groups_controller.rb
+++ b/app/controllers/users/settings/user_groups_controller.rb
@@ -5,7 +5,7 @@ module Users
     class UserGroupsController < ApplicationController
       before_action :load_team
       before_action :set_breadcrumbs_items, only: %i(index show)
-      before_action :check_user_groups_enabled
+      before_action :check_user_groups_enabled, except: :users
       before_action :load_user_group, except: %i(index unassigned_users actions_toolbar create)
       before_action :check_read_permissions, only: %i(index show unassigned_users actions_toolbar users)
       before_action :check_manage_permissions, except: %i(index show unassigned_users actions_toolbar users)
diff --git a/app/javascript/vue/shared/access_modal/edit.vue b/app/javascript/vue/shared/access_modal/edit.vue
index 03f9ab002..be47e43e1 100644
--- a/app/javascript/vue/shared/access_modal/edit.vue
+++ b/app/javascript/vue/shared/access_modal/edit.vue
@@ -54,7 +54,7 @@
           >
         </div>
         <div class="truncate">
-          <div class="flex flex-row gap-2">
+          <div class="flex flex-row gap-2 items-center">
             <div class="truncate"
                 :title="userGroupAssignment.attributes.user_group.name"
             >{{ userGroupAssignment.attributes.user_group.name }}</div>
@@ -114,7 +114,7 @@
           >
         </div>
         <div class="truncate">
-          <div class="flex flex-row gap-2">
+          <div class="flex flex-row gap-2 items-center">
             <div class="truncate"
                 :title="userAssignment.attributes.user.name"
                 :data-e2e="`e2e-TX-${dataE2e}-${userAssignment.attributes.user.name.replace(/\W/g, '')}-name`"
diff --git a/app/javascript/vue/shared/select_dropdown.vue b/app/javascript/vue/shared/select_dropdown.vue
index ab6e4ee66..f95f7a02e 100644
--- a/app/javascript/vue/shared/select_dropdown.vue
+++ b/app/javascript/vue/shared/select_dropdown.vue
@@ -73,7 +73,7 @@
               {{ i18n.t('general.select_all') }}
             </div>
           </div>
-          <perfect-scrollbar ref="scrollContainer" class="p-2.5 flex flex-col max-h-80 relative" :class="{ 'pt-0': withCheckboxes }">
+          <div ref="scrollContainer" class="p-2.5 flex flex-col max-h-80 relative overflow-y-auto" :class="{ 'pt-0': withCheckboxes }">
             <template v-for="(option, i) in filteredOptions" :key="option[0]">
               <div
                 @click.stop="setValue(option[0])"
@@ -99,7 +99,7 @@
             <div v-if="filteredOptions.length === 0" class="text-sn-grey text-center py-2.5">
               {{ noOptionsPlaceholder || this.i18n.t('general.select_dropdown.no_options_placeholder') }}
             </div>
-          </perfect-scrollbar>
+          </div>
         </div>
       </teleport>
     </template>
@@ -276,7 +276,7 @@ export default {
         this.$nextTick(() => {
           this.setPosition();
           this.$refs.search?.focus();
-          this.$refs.scrollContainer.$el.addEventListener('scroll', this.loadNextPage);
+          this.$refs.scrollContainer.addEventListener('scroll', this.loadNextPage);
         });
       }
     },
@@ -296,7 +296,7 @@ export default {
       this.fetchOptions();
     },
     loadNextPage() {
-      const container = this.$refs.scrollContainer.$el;
+      const container = this.$refs.scrollContainer;
       if (this.nextPage && container.scrollTop + container.clientHeight >= container.scrollHeight) {
         this.fetchOptions();
       }

From c76d71f113289a9c92b387485b3d63093a60c4b2 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 11 Aug 2025 13:21:29 +0200
Subject: [PATCH 42/91] Access activity fixes for PET [SCI-12223]

---
 app/controllers/access_permissions/base_controller.rb |  2 +-
 .../access_permissions/experiments_controller.rb      |  2 ++
 .../access_permissions/my_modules_controller.rb       |  2 ++
 config/initializers/extends.rb                        |  8 +++++---
 config/locales/global_activities/en.yml               | 11 ++++++++---
 5 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/app/controllers/access_permissions/base_controller.rb b/app/controllers/access_permissions/base_controller.rb
index 4e0da28db..d45651b9e 100644
--- a/app/controllers/access_permissions/base_controller.rb
+++ b/app/controllers/access_permissions/base_controller.rb
@@ -122,7 +122,7 @@ module AccessPermissions
     private
 
     def model_parameter
-      @model.class.permission_class.name.parameterize.to_sym
+      @model.model_name.param_key
     end
 
     def manage_permission_constant
diff --git a/app/controllers/access_permissions/experiments_controller.rb b/app/controllers/access_permissions/experiments_controller.rb
index 186c856c3..6199c5f89 100644
--- a/app/controllers/access_permissions/experiments_controller.rb
+++ b/app/controllers/access_permissions/experiments_controller.rb
@@ -27,6 +27,8 @@ module AccessPermissions
       UserAssignments::PropagateAssignmentJob.perform_later(@assignment)
 
       case assignment_type
+      when :team
+        log_activity(:experiment_access_changed_all_team_members, team: @assignment.team.id, role: @assignment.user_role.name)
       when :user_group
         log_activity(:experiment_access_changed_user_group, user_group: @assignment.user_group.id, role: @assignment.user_role.name)
       when :user
diff --git a/app/controllers/access_permissions/my_modules_controller.rb b/app/controllers/access_permissions/my_modules_controller.rb
index 9a42e6eb0..c1e57c663 100644
--- a/app/controllers/access_permissions/my_modules_controller.rb
+++ b/app/controllers/access_permissions/my_modules_controller.rb
@@ -26,6 +26,8 @@ module AccessPermissions
       end
 
       case assignment_type
+      when :team
+        log_activity(:my_module_access_changed_all_team_members, team: @assignment.team.id, role: @assignment.user_role.name)
       when :user_group
         log_activity(:my_module_access_changed_user_group, user_group: @assignment.user_group.id, role: @assignment.user_role.name)
       when :user
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index b4a2aef8b..3440eb60e 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -619,18 +619,20 @@ class Extends
     repository_access_revoked_all_team_members: 402,
     repository_access_granted_user_group: 403,
     repository_access_changed_user_group: 404,
-    repository_access_revoked_user_group: 405
+    repository_access_revoked_user_group: 405,
+    experiment_access_changed_all_team_members: 406,
+    my_module_access_changed_all_team_members: 407
   }
 
   ACTIVITY_GROUPS = {
     projects: [*0..7, 32, 33, 34, 95, 108, 65, 109, *158..162, 241, 242, 243, *370..378, *390..392],
     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, 394, 395, 396],
+           148, 166, 394, 395, 396, 407],
     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, 327, *347..352, 359],
     task_inventory: [55, 56, 146, 147, 183],
-    experiment: [*27..31, 57, 141, 165, *363..369, 393],
+    experiment: [*27..31, 57, 141, 165, *363..369, 393, 406],
     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, 329, *397..405],
diff --git a/config/locales/global_activities/en.yml b/config/locales/global_activities/en.yml
index 2303640b3..8c419eb3c 100644
--- a/config/locales/global_activities/en.yml
+++ b/config/locales/global_activities/en.yml
@@ -418,9 +418,12 @@ en:
       repository_access_granted_all_team_members_html: "%{user} granted access to all team members of %{team} team with user role %{role} to inventory %{repository}."
       repository_access_changed_all_team_members_html: "%{user} changed %{team}’s role on inventory %{repository} to %{role}."
       repository_access_revoked_all_team_members_html: "%{user} removed %{team} team members with user role %{role} from inventory %{repository}."
-      repository_access_granted_user_group_html: "%{user} granted access to %{user_group} with user role %{role} to inventory template %{repository}."
-      repository_access_changed_user_group_html: "%{user} changed %{user_group}'s role on inventory template %{repository} to %{role}."
-      repository_access_revoked_user_group_html: "%{user} removed group %{user_group} with user role %{role} from inventory template %{repository}."
+      repository_access_granted_user_group_html: "%{user} granted access to %{user_group} with user role %{role} to inventory %{repository}."
+      repository_access_changed_user_group_html: "%{user} changed %{user_group}'s role on inventory %{repository} to %{role}."
+      repository_access_revoked_user_group_html: "%{user} removed group %{user_group} with user role %{role} from inventory %{repository}."
+      experiment_access_changed_all_team_members_html: "%{user} changed %{team}'s role on experiment %{experiment} to %{role}."
+      my_module_access_changed_all_team_members_html: "%{user} changed %{team}'s role on task %{my_module} to %{role}."
+
     activity_name:
       create_project: "Project created"
       edit_project: "Project edited"
@@ -797,6 +800,8 @@ en:
       repository_access_granted_user_group: "Grant access to group"
       repository_access_changed_user_group: "Change role of group"
       repository_access_revoked_user_group: "Remove access to group"
+      experiment_access_changed_all_team_members: "Change role of all team members"
+      my_module_access_changed_all_team_members: "Change role of all team members"
     activity_group:
       projects: "Projects"
       task_results: "Task results"

From 584ea2ff0531fb4790ace2c4a369801a1aae073c Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Mon, 11 Aug 2025 15:32:36 +0200
Subject: [PATCH 43/91] Fix users role on workspace error [SCI-12228]

---
 app/views/users/settings/teams/_user_dropdown.html.erb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/views/users/settings/teams/_user_dropdown.html.erb b/app/views/users/settings/teams/_user_dropdown.html.erb
index b4c1a25eb..0e980f94d 100644
--- a/app/views/users/settings/teams/_user_dropdown.html.erb
+++ b/app/views/users/settings/teams/_user_dropdown.html.erb
@@ -10,7 +10,8 @@
          id="<%= id %>"
          data-toggle="dropdown"
          aria-haspopup="true"
-         aria-expanded="true">
+         aria-expanded="true"
+          <%= "disabled=disabled" unless can_manage_team_users?(user_assignment.team) %>>
       <span class="sn-icon sn-icon-down"></span>
     </button>
     <ul class="dropdown-menu custom-dropdown-menu dropdown-menu-right" aria-labelledby="<%= id %>">

From c10d641ba4943d359f4f452aff7b0b7f3b249450 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Mon, 11 Aug 2025 17:10:20 +0200
Subject: [PATCH 44/91] Fix cursor for user grup member page [SCI-12234]

---
 app/javascript/vue/user_groups/renderers/members.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/javascript/vue/user_groups/renderers/members.vue b/app/javascript/vue/user_groups/renderers/members.vue
index e9143198c..89dd5b522 100644
--- a/app/javascript/vue/user_groups/renderers/members.vue
+++ b/app/javascript/vue/user_groups/renderers/members.vue
@@ -49,7 +49,7 @@
       </GeneralDropdown>
     </div>
     <div v-else>
-      <div class="flex items-center gap-1 cursor-pointer h-9">
+      <div class="flex items-center gap-1 h-9">
         <div v-for="(user, i) in visibleUsers" :key="i" :title="user.full_name">
           <img :src="user.avatar" class="w-7 h-7 rounded-full" />
         </div>

From ad5856cf2d2d053c2d97dd88753e2acf5697038e Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 12 Aug 2025 11:24:49 +0200
Subject: [PATCH 45/91] Add missing url to my_module list serializer
 [SCI-12204]

---
 app/serializers/lists/my_module_serializer.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/serializers/lists/my_module_serializer.rb b/app/serializers/lists/my_module_serializer.rb
index 6b5e2920a..cefc2fa5d 100644
--- a/app/serializers/lists/my_module_serializer.rb
+++ b/app/serializers/lists/my_module_serializer.rb
@@ -68,7 +68,8 @@ module Lists
         provisioning_status: provisioning_status_my_module_url(object),
         favorite: favorite_my_module_url(object),
         unfavorite: unfavorite_my_module_url(object),
-        user_roles: user_roles_access_permissions_my_module_path(object)
+        user_roles: user_roles_access_permissions_my_module_path(object),
+        user_group_members: users_users_settings_team_user_groups_path(team_id: object.team.id)
       }
 
       if can_manage_project_users?(object.experiment.project)

From 2c036f61997b259fc72dbd90d80f2003c41e1669 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Mon, 11 Aug 2025 16:56:56 +0200
Subject: [PATCH 46/91] Enable details tab on workspace [SCI-12232]

---
 app/controllers/users/settings/teams_controller.rb       | 6 ------
 app/controllers/users/settings/user_groups_controller.rb | 4 ++--
 app/views/users/settings/teams/_header.html.erb          | 4 ++--
 3 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/app/controllers/users/settings/teams_controller.rb b/app/controllers/users/settings/teams_controller.rb
index 43b55723a..dce1104b2 100644
--- a/app/controllers/users/settings/teams_controller.rb
+++ b/app/controllers/users/settings/teams_controller.rb
@@ -28,8 +28,6 @@ module Users
         members
       )
 
-      before_action :check_read_permissions, only: :show
-
       before_action :check_create_team_permission,
                     only: %i(new create)
 
@@ -140,10 +138,6 @@ module Users
         render_403 unless can_create_teams?
       end
 
-      def check_read_permissions
-        render_403 unless can_read_team?(@team)
-      end
-
       def load_user
         @user = current_user
       end
diff --git a/app/controllers/users/settings/user_groups_controller.rb b/app/controllers/users/settings/user_groups_controller.rb
index 92dc0c1e5..845b27ec5 100644
--- a/app/controllers/users/settings/user_groups_controller.rb
+++ b/app/controllers/users/settings/user_groups_controller.rb
@@ -7,8 +7,8 @@ module Users
       before_action :set_breadcrumbs_items, only: %i(index show)
       before_action :check_user_groups_enabled
       before_action :load_user_group, except: %i(index unassigned_users actions_toolbar create)
-      before_action :check_read_permissions, only: %i(index show unassigned_users actions_toolbar users)
-      before_action :check_manage_permissions, except: %i(index show unassigned_users actions_toolbar users)
+      before_action :check_read_permissions, only: %i(users)
+      before_action :check_manage_permissions, except: %i(users)
 
       def index
         respond_to do |format|
diff --git a/app/views/users/settings/teams/_header.html.erb b/app/views/users/settings/teams/_header.html.erb
index d0b90bdf4..2dcd619be 100644
--- a/app/views/users/settings/teams/_header.html.erb
+++ b/app/views/users/settings/teams/_header.html.erb
@@ -18,7 +18,7 @@
   </div>
 </div>
 <div class="flex items-center gap-4 p-2 mb-4 bg-white">
-  <%= link_to t("users.settings.teams.navigation.details"), team_path(@team), class: "p-2.5 hover:no-underline #{ 'disabled' unless can_read_team?(@team) } #{ @active_tab == :details ? "text-sn-blue" : "text-sn-grey" }"%>
+  <%= link_to t("users.settings.teams.navigation.details"), team_path(@team), class: "p-2.5 hover:no-underline #{ @active_tab == :details ? "text-sn-blue" : "text-sn-grey" }"%>
   <%= link_to t("users.settings.teams.navigation.members"), members_users_settings_team_path(@team), class: "p-2.5 hover:no-underline #{ @active_tab == :members ? "text-sn-blue" : "text-sn-grey" }"%>
-  <%= link_to t("users.settings.teams.navigation.groups"), users_settings_team_user_groups_path(@team), class: "p-2.5 hover:no-underline  #{ 'disabled' unless can_read_team?(@team) } #{ @active_tab == :user_groups ? "text-sn-blue" : "text-sn-grey" }"%>
+  <%= link_to t("users.settings.teams.navigation.groups"), users_settings_team_user_groups_path(@team), class: "p-2.5 hover:no-underline  #{ 'disabled' unless can_manage_team?(@team) } #{ @active_tab == :user_groups ? "text-sn-blue" : "text-sn-grey" }"%>
 </div>

From 5cabb444ab927314e43c548c9306b9509b910139 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Tue, 12 Aug 2025 14:01:17 +0200
Subject: [PATCH 47/91] Do not update updated_at in team assignment migration
 [SCI-12231]

---
 ...one_else_assignment_to_team_assignments.rb | 188 +++++++++---------
 1 file changed, 97 insertions(+), 91 deletions(-)

diff --git a/db/migrate/20250707080048_move_every_one_else_assignment_to_team_assignments.rb b/db/migrate/20250707080048_move_every_one_else_assignment_to_team_assignments.rb
index 41ccbcc31..2f9bf367d 100644
--- a/db/migrate/20250707080048_move_every_one_else_assignment_to_team_assignments.rb
+++ b/db/migrate/20250707080048_move_every_one_else_assignment_to_team_assignments.rb
@@ -2,122 +2,128 @@
 
 class MoveEveryOneElseAssignmentToTeamAssignments < ActiveRecord::Migration[7.2]
   def up
-    viewer_role = UserRole.find_predefined_viewer_role
-    normal_user_role = UserRole.find_predefined_normal_user_role
+    # rubocop:disable Metrics/BlockLength
+    ActiveRecord::Base.no_touching do
+      viewer_role = UserRole.find_predefined_viewer_role
+      normal_user_role = UserRole.find_predefined_normal_user_role
 
-    # Shared repositories with read permission
-    TeamSharedObject.where(permission_level: Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_read])
-                    .find_each do |shared_obj|
-                      next if shared_obj.shared_repository.blank?
+      # Shared repositories with read permission
+      TeamSharedObject.where(permission_level: Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_read])
+                      .find_each do |shared_obj|
+                        next if shared_obj.shared_repository.blank?
 
-                      shared_obj.shared_repository.user_assignments.where(team_id: shared_obj.team_id).delete_all
-                      shared_obj.shared_repository.team_assignments.find_or_create_by!(team_id: shared_obj.team_id, user_role: viewer_role)
-                    end
+                        shared_obj.shared_repository.user_assignments.where(team_id: shared_obj.team_id).delete_all
+                        shared_obj.shared_repository.team_assignments.find_or_create_by!(team_id: shared_obj.team_id, user_role: viewer_role)
+                      end
 
-    # Shared repositories with write permission
-    TeamSharedObject.where(permission_level: Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_write])
-                    .find_each do |shared_obj|
-                      next if shared_obj.shared_repository.blank?
+      # Shared repositories with write permission
+      TeamSharedObject.where(permission_level: Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_write])
+                      .find_each do |shared_obj|
+                        next if shared_obj.shared_repository.blank?
 
-                      shared_obj.shared_repository.user_assignments.where(team_id: shared_obj.team_id).update_all(assigned: :manually)
+                        shared_obj.shared_repository.user_assignments.where(team_id: shared_obj.team_id).update_all(assigned: :manually)
 
-                      shared_obj.shared_repository.user_assignments.where(team_id: shared_obj.team_id, user_role: normal_user_role).delete_all
-                      shared_obj.shared_repository.team_assignments.find_or_create_by!(team_id: shared_obj.team_id, user_role: normal_user_role)
-                    end
+                        shared_obj.shared_repository.user_assignments.where(team_id: shared_obj.team_id, user_role: normal_user_role).delete_all
+                        shared_obj.shared_repository.team_assignments.find_or_create_by!(team_id: shared_obj.team_id, user_role: normal_user_role)
+                      end
 
-    # Other repositories
-    Repository.find_each do |repository|
-      repository.user_assignments.where(team_id: repository.team_id).update_all(assigned: :manually)
+      # Other repositories
+      Repository.find_each do |repository|
+        repository.user_assignments.where(team_id: repository.team_id).update_all(assigned: :manually)
 
-      repository.user_assignments.where(team_id: repository.team_id, user_role: normal_user_role).delete_all
-      repository.team_assignments.find_or_create_by!(team_id: repository.team_id, user_role: normal_user_role)
-    end
-
-    # global share
-    Repository.where(permission_level: %i(shared_read shared_write)).find_each do |repository|
-      Team.where.not(id: repository.team_id).find_each do |team|
-        next if repository.private_shared_with?(team) || repository.team_assignments.exists?(team: team)
-
-        repository.user_assignments.where(team: team).delete_all
-
-        if repository.permission_level == 'shared_read'
-          repository.team_assignments.find_or_create_by!(team_id: team.id, user_role: viewer_role)
-        else
-          repository.team_assignments.find_or_create_by!(team_id: team.id, user_role: normal_user_role)
-          team.user_assignments.where.not(user_role: normal_user_role).find_each do |user_assignment|
-            UserAssignment.create!(
-              assignable: repository,
-              team: team,
-              user: user_assignment.user,
-              user_role: user_assignment.user_role,
-              assigned: :manually
-            )
-          end
-        end
+        repository.user_assignments.where(team_id: repository.team_id, user_role: normal_user_role).delete_all
+        repository.team_assignments.find_or_create_by!(team_id: repository.team_id, user_role: normal_user_role)
       end
-    end
 
-    # Forms
-    Form.find_each do |form|
-      replace_automatic_user_assignments_with_team_assignment(record: form, team_id: form.team_id)
-    end
+      # global share
+      Repository.where(permission_level: %i(shared_read shared_write)).find_each do |repository|
+        Team.where.not(id: repository.team_id).find_each do |team|
+          next if repository.private_shared_with?(team) || repository.team_assignments.exists?(team: team)
 
-    # Protocols
-    Protocol.where(protocol_type: %i(in_repository_published_original in_repository_draft in_repository_published_version))
-            .find_each do |protocol|
-              replace_automatic_user_assignments_with_team_assignment(record: protocol, team_id: protocol.team_id)
+          repository.user_assignments.where(team: team).delete_all
+
+          if repository.permission_level == 'shared_read'
+            repository.team_assignments.find_or_create_by!(team_id: team.id, user_role: viewer_role)
+          else
+            repository.team_assignments.find_or_create_by!(team_id: team.id, user_role: normal_user_role)
+            team.user_assignments.where.not(user_role: normal_user_role).find_each do |user_assignment|
+              UserAssignment.create!(
+                assignable: repository,
+                team: team,
+                user: user_assignment.user,
+                user_role: user_assignment.user_role,
+                assigned: :manually
+              )
             end
-
-    # PET
-    Project.visible.preload(:experiments).find_in_batches(batch_size: 100) do |projects|
-      projects.each do |project|
-        project_automatic_user_assignments = project.user_assignments.where(assigned: :automatically)
-        next if project_automatic_user_assignments.blank?
-
-        user_role = project_automatic_user_assignments.first.user_role
-        team_assignment_values = []
-
-        project.experiments.preload(:my_modules).each do |experiment|
-          experiment.my_modules.each do |my_module|
-            team_assignment_values << new_team_assignment(project.team_id, my_module, user_role)
-            my_module.automatic_user_assignments.where(user_id: project_automatic_user_assignments.select(:user_id)).delete_all
           end
-          team_assignment_values << new_team_assignment(project.team_id, experiment, user_role)
-          experiment.automatic_user_assignments.where(user_id: project_automatic_user_assignments.select(:user_id)).delete_all
         end
+      end
 
-        team_assignment_values << new_team_assignment(project.team_id, project, user_role)
-        project_automatic_user_assignments.delete_all
+      # Forms
+      Form.find_each do |form|
+        replace_automatic_user_assignments_with_team_assignment(record: form, team_id: form.team_id)
+      end
 
-        TeamAssignment.import(team_assignment_values, validate: false)
+      # Protocols
+      Protocol.where(protocol_type: %i(in_repository_published_original in_repository_draft in_repository_published_version))
+              .find_each do |protocol|
+                replace_automatic_user_assignments_with_team_assignment(record: protocol, team_id: protocol.team_id)
+              end
+
+      # PET
+      Project.visible.preload(:experiments).find_in_batches(batch_size: 100) do |projects|
+        projects.each do |project|
+          project_automatic_user_assignments = project.user_assignments.where(assigned: :automatically)
+          next if project_automatic_user_assignments.blank?
+
+          user_role = project_automatic_user_assignments.first.user_role
+          team_assignment_values = []
+
+          project.experiments.preload(:my_modules).each do |experiment|
+            experiment.my_modules.each do |my_module|
+              team_assignment_values << new_team_assignment(project.team_id, my_module, user_role)
+              my_module.automatic_user_assignments.where(user_id: project_automatic_user_assignments.select(:user_id)).delete_all
+            end
+            team_assignment_values << new_team_assignment(project.team_id, experiment, user_role)
+            experiment.automatic_user_assignments.where(user_id: project_automatic_user_assignments.select(:user_id)).delete_all
+          end
+
+          team_assignment_values << new_team_assignment(project.team_id, project, user_role)
+          project_automatic_user_assignments.delete_all
+
+          TeamAssignment.import(team_assignment_values, validate: false)
+        end
       end
     end
+    # rubocop:enable Metrics/BlockLength
   end
 
   def down
-    team_shared_read_objects = TeamSharedObject.where(permission_level: Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_read])
+    ActiveRecord::Base.no_touching do
+      team_shared_read_objects = TeamSharedObject.where(permission_level: Extends::SHARED_OBJECTS_PERMISSION_LEVELS[:shared_read])
 
-    team_shared_read_objects.find_each do |team_shared_object|
-      next if team_shared_object.shared_repository.blank?
+      team_shared_read_objects.find_each do |team_shared_object|
+        next if team_shared_object.shared_repository.blank?
 
-      # shared repositories with read permission
-      TeamAssignment.where(assignable: team_shared_object.shared_repository, team_id: team_shared_object.team_id).delete_all
+        # shared repositories with read permission
+        TeamAssignment.where(assignable: team_shared_object.shared_repository, team_id: team_shared_object.team_id).delete_all
 
-      user_assignments = team_shared_object.team.user_assignments
-      user_assignments.find_each do |user_assignment|
-        UserAssignment.create!(assignable: team_shared_object.shared_repository,
-                               team_id: team_shared_object.team_id,
-                               user: user_assignment.user,
-                               user_role: user_assignment.user_role)
+        user_assignments = team_shared_object.team.user_assignments
+        user_assignments.find_each do |user_assignment|
+          UserAssignment.create!(assignable: team_shared_object.shared_repository,
+                                 team_id: team_shared_object.team_id,
+                                 user: user_assignment.user,
+                                 user_role: user_assignment.user_role)
+        end
       end
-    end
 
-    remove_team_assignments(TeamAssignment.where(assignable_type: 'RepositoryBase'))
-    remove_team_assignments(TeamAssignment.where(assignable_type: 'Form'))
-    remove_team_assignments(TeamAssignment.where(assignable_type: 'Protocol'))
-    remove_team_assignments(TeamAssignment.where(assignable_type: 'MyModule'))
-    remove_team_assignments(TeamAssignment.where(assignable_type: 'Experiment'))
-    remove_team_assignments(TeamAssignment.where(assignable_type: 'Project'))
+      remove_team_assignments(TeamAssignment.where(assignable_type: 'RepositoryBase'))
+      remove_team_assignments(TeamAssignment.where(assignable_type: 'Form'))
+      remove_team_assignments(TeamAssignment.where(assignable_type: 'Protocol'))
+      remove_team_assignments(TeamAssignment.where(assignable_type: 'MyModule'))
+      remove_team_assignments(TeamAssignment.where(assignable_type: 'Experiment'))
+      remove_team_assignments(TeamAssignment.where(assignable_type: 'Project'))
+    end
   end
 
   private

From 9a6cccab75626824cc83c7acdfb65a6b57bceeb8 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 12 Aug 2025 12:41:54 +0200
Subject: [PATCH 48/91] Fix css for user groups [SCI-12196]

---
 app/controllers/navigations_controller.rb               | 2 ++
 app/javascript/vue/user_groups/modal/add_member.vue     | 1 +
 app/javascript/vue/user_groups/modal/create_group.vue   | 1 +
 app/services/toolbars/user_group_memberships_service.rb | 2 +-
 app/views/users/settings/teams/_header.html.erb         | 4 ++--
 app/views/users/settings/user_groups/show.html.erb      | 4 ++--
 config/locales/en.yml                                   | 1 +
 7 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/app/controllers/navigations_controller.rb b/app/controllers/navigations_controller.rb
index 964ca12e4..f884be192 100644
--- a/app/controllers/navigations_controller.rb
+++ b/app/controllers/navigations_controller.rb
@@ -63,6 +63,8 @@ class NavigationsController < ApplicationController
     links = [
       {
         name: I18n.t('users.settings.sidebar.teams'), url: teams_path
+      }, {
+        name: I18n.t('users.settings.sidebar.groups'), url: users_settings_team_user_groups_path(current_team)
       }, {
         name: I18n.t('users.settings.sidebar.account_nav.addons'), url: addons_path
       }
diff --git a/app/javascript/vue/user_groups/modal/add_member.vue b/app/javascript/vue/user_groups/modal/add_member.vue
index 2b70dc230..17e5c1caf 100644
--- a/app/javascript/vue/user_groups/modal/add_member.vue
+++ b/app/javascript/vue/user_groups/modal/add_member.vue
@@ -21,6 +21,7 @@
                 :option-renderer="usersRenderer"
                 :label-renderer="usersRenderer"
                 :multiple="true"
+                :searchable="true"
                 :placeholder="i18n.t('user_groups.show.add_members_modal.select_members_placeholder')"
               />
             </div>
diff --git a/app/javascript/vue/user_groups/modal/create_group.vue b/app/javascript/vue/user_groups/modal/create_group.vue
index 0b9aaa0e8..2ff830ca8 100644
--- a/app/javascript/vue/user_groups/modal/create_group.vue
+++ b/app/javascript/vue/user_groups/modal/create_group.vue
@@ -32,6 +32,7 @@
                 :withCheckboxes="true"
                 :option-renderer="usersRenderer"
                 :label-renderer="usersRenderer"
+                :searchable="true"
                 :multiple="true"
                 :placeholder="i18n.t('user_groups.index.create_modal.select_members_placeholder')"
               />
diff --git a/app/services/toolbars/user_group_memberships_service.rb b/app/services/toolbars/user_group_memberships_service.rb
index 191c2ad61..38147e7f9 100644
--- a/app/services/toolbars/user_group_memberships_service.rb
+++ b/app/services/toolbars/user_group_memberships_service.rb
@@ -32,7 +32,7 @@ module Toolbars
       {
         name: 'delete',
         label: 'Remove',
-        icon: 'sn-icon sn-icon-delete',
+        icon: 'sn-icon sn-icon-close',
         path: destroy_multiple_users_settings_team_user_group_user_group_memberships_path(@team, @user_group, membership_ids: @memberships.pluck(:id)),
         type: :emit
       }
diff --git a/app/views/users/settings/teams/_header.html.erb b/app/views/users/settings/teams/_header.html.erb
index 2dcd619be..d32215429 100644
--- a/app/views/users/settings/teams/_header.html.erb
+++ b/app/views/users/settings/teams/_header.html.erb
@@ -17,8 +17,8 @@
     </h1>
   </div>
 </div>
-<div class="flex items-center gap-4 p-2 mb-4 bg-white">
-  <%= link_to t("users.settings.teams.navigation.details"), team_path(@team), class: "p-2.5 hover:no-underline #{ @active_tab == :details ? "text-sn-blue" : "text-sn-grey" }"%>
+<div class="flex items-center gap-4 p-2 mb-4 bg-white rounded-lg">
+  <%= link_to t("users.settings.teams.navigation.details"), team_path(@team), class: "p-2.5 hover:no-underline #{ 'disabled' unless can_read_team?(@team) } #{ @active_tab == :details ? "text-sn-blue" : "text-sn-grey" }"%>
   <%= link_to t("users.settings.teams.navigation.members"), members_users_settings_team_path(@team), class: "p-2.5 hover:no-underline #{ @active_tab == :members ? "text-sn-blue" : "text-sn-grey" }"%>
   <%= link_to t("users.settings.teams.navigation.groups"), users_settings_team_user_groups_path(@team), class: "p-2.5 hover:no-underline  #{ 'disabled' unless can_manage_team?(@team) } #{ @active_tab == :user_groups ? "text-sn-blue" : "text-sn-grey" }"%>
 </div>
diff --git a/app/views/users/settings/user_groups/show.html.erb b/app/views/users/settings/user_groups/show.html.erb
index 779f533a1..c56991364 100644
--- a/app/views/users/settings/user_groups/show.html.erb
+++ b/app/views/users/settings/user_groups/show.html.erb
@@ -7,8 +7,8 @@
 
 <div class="content-pane flexible with-grey-background">
   <%= render partial: 'users/settings/teams/header' %>
-  <div class="flex items-center h-8 gap-4 p-4">
-    <%= link_to users_settings_team_user_groups_path, class: "hover:text-black text-black hover:no-underline" do %>
+  <div class="flex items-center h-8 gap-4 p-4 pl-0">
+    <%= link_to users_settings_team_user_groups_path, class: "btn btn-light btn-black icon-btn" do %>
       <i class="sn-icon sn-icon-arrow-left"></i>
     <% end %>
     <h3 class="m-0 flex gap-0.5 items-center">
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 18b1368a3..4d7595eee 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -3473,6 +3473,7 @@ en:
         account: "Account"
         teams: "Workspaces"
         webhooks: "Webhooks"
+        groups: "Groups"
         account_nav:
           profile: "My profile"
           preferences: "My preferences"

From 1b653057e2a0fc160eccf7940e04905d30b7e236 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Tue, 12 Aug 2025 15:32:45 +0200
Subject: [PATCH 49/91] Fix delete description rendering [SCI-12230]

---
 app/javascript/vue/repositories/table.vue      | 3 ++-
 app/javascript/vue/storage_locations/table.vue | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/repositories/table.vue b/app/javascript/vue/repositories/table.vue
index 90931740c..0890b88a3 100644
--- a/app/javascript/vue/repositories/table.vue
+++ b/app/javascript/vue/repositories/table.vue
@@ -94,6 +94,7 @@ import DataTable from '../shared/datatable/table.vue';
 import NameRenderer from './renderers/name.vue';
 import AccessModal from '../shared/access_modal/modal.vue';
 import UsersRenderer from '../projects/renderers/users.vue';
+import escapeHtml from '../shared/escape_html.js';
 
 export default {
   name: 'RepositoriesTable',
@@ -287,7 +288,7 @@ export default {
       };
       this.deleteModal.title = this.i18n.t('repositories.index.modal_delete.title_html', { name: repository.name });
       this.deleteModal.description = `
-        <p data-e2e="e2e-TX-deleteInventoryModal-info">${this.i18n.t('repositories.index.modal_delete.message_html', { name: repository.name })}</p>
+        <p data-e2e="e2e-TX-deleteInventoryModal-info">${this.i18n.t('repositories.index.modal_delete.message_html', { name: escapeHtml(repository.name) })}</p>
         <div class="alert alert-danger" role="alert" data-e2e="e2e-TX-deleteInventoryModal-warning">
           <span class="fas fa-exclamation-triangle"></span>
           ${this.i18n.t('repositories.index.modal_delete.alert_heading')}
diff --git a/app/javascript/vue/storage_locations/table.vue b/app/javascript/vue/storage_locations/table.vue
index 8f21de22b..d93344e39 100644
--- a/app/javascript/vue/storage_locations/table.vue
+++ b/app/javascript/vue/storage_locations/table.vue
@@ -66,6 +66,7 @@ import ShareObjectModal from '../shared/share_modal.vue';
 import DescriptionRenderer from './renderers/description.vue';
 import NameRenderer from './renderers/storage_name_renderer.vue';
 import FindRowModal from './modals/find_row.vue';
+import escapeHtml from '../shared/escape_html.js';
 
 export default {
   name: 'RepositoriesTable',
@@ -264,7 +265,7 @@ export default {
       const storageLocationType = rows[0].container ? this.i18n.t('storage_locations.container') : this.i18n.t('storage_locations.location');
       const description = `
         <p>${this.i18n.t('storage_locations.index.delete_modal.description_1_html',
-    { name: rows[0].name, type: storageLocationType, num_of_items: event.number_of_items })}</p>
+    { name: escapeHtml(rows[0].name), type: storageLocationType, num_of_items: event.number_of_items })}</p>
         <p>${this.i18n.t('storage_locations.index.delete_modal.description_2_html')}</p>`;
 
       this.storageLocationDeleteDescription = description;

From 08bfa91820d61b7d2e9df540945e4f8c2b20dbd3 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 12 Aug 2025 16:25:19 +0200
Subject: [PATCH 50/91] Fix role reset for team assignments on PET [SCI-12222]

---
 app/controllers/access_permissions/base_controller.rb        | 2 ++
 app/controllers/access_permissions/experiments_controller.rb | 4 ++--
 app/controllers/access_permissions/my_modules_controller.rb  | 4 +++-
 app/javascript/vue/shared/access_modal/edit.vue              | 2 +-
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/app/controllers/access_permissions/base_controller.rb b/app/controllers/access_permissions/base_controller.rb
index d45651b9e..922f47976 100644
--- a/app/controllers/access_permissions/base_controller.rb
+++ b/app/controllers/access_permissions/base_controller.rb
@@ -75,6 +75,8 @@ module AccessPermissions
       end
 
       propagate_job
+
+      render json: { user_role_id: @assignment.user_role_id }, status: :ok
     rescue ActiveRecord::RecordInvalid
       render json: { flash: t('access_permissions.update.failure') }, status: :unprocessable_entity
     end
diff --git a/app/controllers/access_permissions/experiments_controller.rb b/app/controllers/access_permissions/experiments_controller.rb
index 6199c5f89..0f661007e 100644
--- a/app/controllers/access_permissions/experiments_controller.rb
+++ b/app/controllers/access_permissions/experiments_controller.rb
@@ -7,7 +7,7 @@ module AccessPermissions
     def update
       if permitted_params[:user_role_id] == 'reset'
         parent_assignment = @project.public_send(:"#{assignment_type}_assignments").find_or_initialize_by(
-          "#{assignment_type}_id": permitted_params[:"#{assignment_type}_id"],
+          "#{assignment_type}_id": permitted_params[:"#{assignment_type}_id"] || current_team.id,
           team: current_team
         )
 
@@ -35,7 +35,7 @@ module AccessPermissions
         log_activity(:change_user_role_on_experiment, user_target: @assignment.user.id, role: @assignment.user_role.name)
       end
 
-      render json: {}, status: :ok
+      render json: { user_role_id: @assignment.user_role_id }, status: :ok
     end
 
     private
diff --git a/app/controllers/access_permissions/my_modules_controller.rb b/app/controllers/access_permissions/my_modules_controller.rb
index c1e57c663..62cc95a0c 100644
--- a/app/controllers/access_permissions/my_modules_controller.rb
+++ b/app/controllers/access_permissions/my_modules_controller.rb
@@ -8,7 +8,7 @@ module AccessPermissions
     def update
       if permitted_params[:user_role_id] == 'reset'
         parent_assignment = @experiment.public_send(:"#{assignment_type}_assignments").find_or_initialize_by(
-          "#{assignment_type}_id": permitted_params[:"#{assignment_type}_id"],
+          "#{assignment_type}_id": permitted_params[:"#{assignment_type}_id"] || current_team.id,
           team: current_team
         )
 
@@ -33,6 +33,8 @@ module AccessPermissions
       when :user
         log_activity(:change_user_role_on_my_module, user_target: @assignment.user.id, role: @assignment.user_role.name)
       end
+
+      render json: { user_role_id: @assignment.user_role_id }, status: :ok
     end
 
     private
diff --git a/app/javascript/vue/shared/access_modal/edit.vue b/app/javascript/vue/shared/access_modal/edit.vue
index be47e43e1..f08912668 100644
--- a/app/javascript/vue/shared/access_modal/edit.vue
+++ b/app/javascript/vue/shared/access_modal/edit.vue
@@ -329,7 +329,7 @@ export default {
         if (!roleId) {
           this.$emit('changeVisibility', false, null);
         } else {
-          this.$emit('changeVisibility', true, roleId);
+          this.$emit('changeVisibility', true, response.data.user_role_id);
         }
         if (response.data.message) {
           HelperModule.flashAlertMsg(response.data.message, 'success');

From c97d085a990a736ff146316c17df42b097af9298 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 12 Aug 2025 16:33:36 +0200
Subject: [PATCH 51/91] Fix repository user manage permissions for team owner
 [SCI-12245]

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

diff --git a/app/permissions/repository.rb b/app/permissions/repository.rb
index 934a5a95d..b686da635 100644
--- a/app/permissions/repository.rb
+++ b/app/permissions/repository.rb
@@ -131,7 +131,8 @@ Canaid::Permissions.register_for(Repository) do
   end
 
   can :manage_repository_users do |user, repository|
-    repository.can_manage_shared?(user) ||
+    repository.team.permission_granted?(user, TeamPermissions::MANAGE) ||
+      repository.can_manage_shared?(user) ||
       repository.permission_granted?(user, RepositoryPermissions::USERS_MANAGE)
   end
 end

From d40ac5845e3b6590c6050d1ffb0ed8dab7d7a672 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 12 Aug 2025 16:46:35 +0200
Subject: [PATCH 52/91] Replace remaining activity mentions of 'team'
 [SCI-12242]

---
 config/locales/global_activities/en.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/config/locales/global_activities/en.yml b/config/locales/global_activities/en.yml
index 8c419eb3c..393bd5661 100644
--- a/config/locales/global_activities/en.yml
+++ b/config/locales/global_activities/en.yml
@@ -47,7 +47,7 @@ en:
       create_project_html: "%{user} created project %{project}."
       edit_project_html: "%{user} edited project %{project}."
       change_project_visibility_html: "%{user} changed project %{project}'s visibility to %{visibility}."
-      project_grant_access_to_all_team_members_html: "%{user} granted access to all team members of %{team} team with user role %{role} to project %{project}."
+      project_grant_access_to_all_team_members_html: "%{user} granted access to all workspace members of %{team} workspace with user role %{role} to project %{project}."
       project_remove_access_from_all_team_members_html: "%{user} removed %{team} workspace members with user role %{role} from project %{project}."
       archive_project_html: "%{user} archived project %{project}."
       restore_project_html: "%{user} restored project %{project} from archive."
@@ -415,9 +415,9 @@ en:
       repository_access_granted_html: "%{user} granted access to %{user_target} with user role %{role} to inventory %{repository}."
       repository_access_changed_html: "%{user} changed %{user_target}’s role on inventory %{repository} to %{role}."
       repository_access_revoked_html: "%{user} removed %{user_target} with user role %{role} from inventory %{repository}."
-      repository_access_granted_all_team_members_html: "%{user} granted access to all team members of %{team} team with user role %{role} to inventory %{repository}."
+      repository_access_granted_all_team_members_html: "%{user} granted access to all workspace members of %{team} workspace with user role %{role} to inventory %{repository}."
       repository_access_changed_all_team_members_html: "%{user} changed %{team}’s role on inventory %{repository} to %{role}."
-      repository_access_revoked_all_team_members_html: "%{user} removed %{team} team members with user role %{role} from inventory %{repository}."
+      repository_access_revoked_all_team_members_html: "%{user} removed %{team} workspace members with user role %{role} from inventory %{repository}."
       repository_access_granted_user_group_html: "%{user} granted access to %{user_group} with user role %{role} to inventory %{repository}."
       repository_access_changed_user_group_html: "%{user} changed %{user_group}'s role on inventory %{repository} to %{role}."
       repository_access_revoked_user_group_html: "%{user} removed group %{user_group} with user role %{role} from inventory %{repository}."
@@ -794,14 +794,14 @@ en:
       repository_access_granted: "User granted access to inventory"
       repository_access_changed: "User role changed on inventory"
       repository_access_revoked: "User removed from inventory"
-      repository_access_granted_all_team_members: "Grant access to all team members"
-      repository_access_changed_all_team_members: "Change role of all team members"
-      repository_access_revoked_all_team_members: "Remove access from all team members"
+      repository_access_granted_all_team_members: "Grant access to all workspace members"
+      repository_access_changed_all_team_members: "Change role of all workspace members"
+      repository_access_revoked_all_team_members: "Remove access from all workspace members"
       repository_access_granted_user_group: "Grant access to group"
       repository_access_changed_user_group: "Change role of group"
       repository_access_revoked_user_group: "Remove access to group"
-      experiment_access_changed_all_team_members: "Change role of all team members"
-      my_module_access_changed_all_team_members: "Change role of all team members"
+      experiment_access_changed_all_team_members: "Change role of all workspace members"
+      my_module_access_changed_all_team_members: "Change role of all workspace members"
     activity_group:
       projects: "Projects"
       task_results: "Task results"

From f44f66f52cbbfca0f48fd0a3290fa29a2f5f9f59 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Tue, 12 Aug 2025 17:13:15 +0200
Subject: [PATCH 53/91] Fix global search [SCI-12237]

---
 app/controllers/label_templates_controller.rb | 2 +-
 app/models/label_template.rb                  | 2 +-
 app/models/project_folder.rb                  | 2 +-
 app/models/result.rb                          | 3 +--
 4 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/app/controllers/label_templates_controller.rb b/app/controllers/label_templates_controller.rb
index dcb312dac..710b71d42 100644
--- a/app/controllers/label_templates_controller.rb
+++ b/app/controllers/label_templates_controller.rb
@@ -5,7 +5,7 @@ class LabelTemplatesController < ApplicationController
   include TeamsHelper
 
   before_action :check_feature_enabled, except: %i(index zpl_preview list)
-  before_action :load_label_templates, only: %i(index datatable list)
+  before_action :load_label_templates, only: %i(index list)
   before_action :load_label_template, only: %i(show set_default update template_tags)
   before_action :check_view_permissions, except: %i(create duplicate set_default delete update)
   before_action :check_manage_permissions, only: %i(create duplicate set_default delete update)
diff --git a/app/models/label_template.rb b/app/models/label_template.rb
index a272cb057..784b9f8bf 100644
--- a/app/models/label_template.rb
+++ b/app/models/label_template.rb
@@ -23,7 +23,7 @@ class LabelTemplate < ApplicationRecord
   scope :predefined, -> { where(predefined: true) }
 
   def self.readable_by_user(user, teams)
-    where(team: teams.with_granted_permissions(user, TeamPermissions::LABEL_TEMPLATES_READ, teams))
+    where(team: Team.with_granted_permissions(user, TeamPermissions::LABEL_TEMPLATES_READ, teams))
   end
 
   def self.enabled?
diff --git a/app/models/project_folder.rb b/app/models/project_folder.rb
index a926d45b5..dbce95bbc 100644
--- a/app/models/project_folder.rb
+++ b/app/models/project_folder.rb
@@ -35,7 +35,7 @@ class ProjectFolder < ApplicationRecord
   scope :top_level, -> { where(parent_folder: nil) }
 
   def self.readable_by_user(user, teams)
-    joins(team: :users)
+    joins(team: :user_assignments)
       .where(teams: { user_assignments: { user: user } })
       .where(team: teams)
   end
diff --git a/app/models/result.rb b/app/models/result.rb
index f3bff42b6..0b0368aff 100644
--- a/app/models/result.rb
+++ b/app/models/result.rb
@@ -54,8 +54,7 @@ class Result < ApplicationRecord
     new_query = joins(:my_module)
                 .where(
                   my_modules: {
-                    id: MyModule.with_granted_permissions(user, MyModulePermissions::READ)
-                                .where(user_assignments: { team: teams }).select(:id)
+                    id: MyModule.with_granted_permissions(user, MyModulePermissions::READ, teams).select(:id)
                   }
                 )
 

From 98d1ac89f3d73d85bf2b35e0dbf115e1affa1436 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 13 Aug 2025 11:12:59 +0200
Subject: [PATCH 54/91] Fix displaying user groups from other teams on shared
 repositories [SCI-12249]

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

diff --git a/app/controllers/access_permissions/base_controller.rb b/app/controllers/access_permissions/base_controller.rb
index 922f47976..5495d6c00 100644
--- a/app/controllers/access_permissions/base_controller.rb
+++ b/app/controllers/access_permissions/base_controller.rb
@@ -108,7 +108,7 @@ module AccessPermissions
     end
 
     def show_user_group_assignments
-      render json: @model.user_group_assignments.includes(:user_role, :user_group).order('user_groups.name ASC'),
+      render json: @model.user_group_assignments.where(team: current_team).includes(:user_role, :user_group).order('user_groups.name ASC'),
              each_serializer: UserGroupAssignmentSerializer, user: current_user
     end
 

From 1ad62d084025f74c01763a8a42dff0dcd2ff23ec Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 13 Aug 2025 11:19:09 +0200
Subject: [PATCH 55/91] Fix displaying members of user group on shared
 repositories [SCI-12249]

---
 app/serializers/lists/repository_serializer.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/serializers/lists/repository_serializer.rb b/app/serializers/lists/repository_serializer.rb
index ca88aee3c..47b2f6724 100644
--- a/app/serializers/lists/repository_serializer.rb
+++ b/app/serializers/lists/repository_serializer.rb
@@ -58,7 +58,7 @@ module Lists
         show_access: access_permissions_repository_path(object),
         share: team_shared_objects_path(current_user.current_team, object_id: object.id, object_type: 'Repository'),
         user_roles: user_roles_access_permissions_repository_path(object),
-        user_group_members: users_users_settings_team_user_groups_path(team_id: object.team.id)
+        user_group_members: users_users_settings_team_user_groups_path(team_id: current_user.current_team_id)
       }
 
       urls[:show] = repository_path(object) if can_read?

From 6a02cbae255980b3244079168031e54b2a9137cc Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 13 Aug 2025 11:36:34 +0200
Subject: [PATCH 56/91] Show inventory activities based on access (just show
 deleted inventories) [SCI-12224]

---
 app/services/activities_service.rb | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/app/services/activities_service.rb b/app/services/activities_service.rb
index b2485b334..2fdc8a454 100644
--- a/app/services/activities_service.rb
+++ b/app/services/activities_service.rb
@@ -36,23 +36,33 @@ class ActivitiesService
     visible_projects = Project.readable_by_user(user, teams)
     visible_my_modules = MyModule.readable_by_user(user, teams)
     visible_forms = Form.readable_by_user(user, teams)
-    # Temporary solution until handling of deleted subjects is fully implemented
-    visible_repository_teams = user.teams.with_granted_permissions(user, RepositoryPermissions::READ, teams)
+    visible_repositories = Repository.readable_by_user(user, teams)
+
+    deleted_repository_activities =
+      activities.where(subject_type: %w(RepositoryBase RepositoryRow))
+                .joins("LEFT OUTER JOIN repositories ON (activities.subject_id = repositories.id AND activities.subject_type = 'RepositoryBase')")
+                .joins("LEFT OUTER JOIN repository_rows ON (activities.subject_id = repository_rows.id AND activities.subject_type = 'RepositoryRow')")
+                .where("(activities.subject_type = 'RepositoryBase' AND repositories.id IS NULL) OR
+                        (activities.subject_type = 'RepositoryRow' AND repository_rows.id IS NULL)")
 
     activities = Activity.from(activities, 'activities')
     activities = activities.where(project: nil, team_id: teams).where.not(subject_type: %w(RepositoryBase RepositoryRow Protocol Form))
-                           .or(activities.where(subject_type: %w(RepositoryBase RepositoryRow), team_id: visible_repository_teams.select(:id)))
+                           .or(activities.where(id: deleted_repository_activities.select(:id)))
                            .or(activities.where(subject_type: 'Protocol', subject_id: Protocol.readable_by_user(user, teams).select(:id)))
                            .or(activities.where(project_id: visible_projects.select(:id)).where.not(subject_type: %w(Experiment MyModule Result Protocol)))
                            .or(activities.where(subject_type: 'Experiment', subject_id: Experiment.readable_by_user(user, teams).select(:id)))
                            .or(activities.where("subject_id IN (?) AND subject_type = 'MyModule' OR " \
                                                 "subject_id IN (?) AND subject_type = 'Result' OR " \
                                                 "subject_id IN (?) AND subject_type = 'Protocol' OR " \
-                                                "subject_id IN (?) AND subject_type = 'Form'",
+                                                "subject_id IN (?) AND subject_type = 'Form' OR " \
+                                                "subject_id IN (?) AND subject_type = 'RepositoryBase' OR " \
+                                                "subject_id IN (?) AND subject_type = 'RepositoryRow'",
                                                 visible_my_modules.select(:id),
                                                 Result.with_discarded.where(my_module: visible_my_modules).select(:id),
                                                 Protocol.where(my_module: visible_my_modules).select(:id),
-                                                visible_forms.select(:id)))
+                                                visible_forms.select(:id),
+                                                visible_repositories.select(:id),
+                                                RepositoryRow.where(repository_id: visible_repositories).select(:id)))
 
     activities.order(created_at: :desc)
               .page(filters[:page])

From fff571c63544a3d24c030e6f99fbffb98499f573 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Wed, 13 Aug 2025 12:49:32 +0200
Subject: [PATCH 57/91] User groups error handling fix and pagination fix
 [SCI-12243]

---
 .../users/settings/user_groups_controller.rb          |  2 +-
 app/services/lists/user_groups_service.rb             | 11 ++++-------
 app/views/users/settings/user_groups/show.html.erb    |  2 +-
 3 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/app/controllers/users/settings/user_groups_controller.rb b/app/controllers/users/settings/user_groups_controller.rb
index d6c04e0cc..12e8530f7 100644
--- a/app/controllers/users/settings/user_groups_controller.rb
+++ b/app/controllers/users/settings/user_groups_controller.rb
@@ -58,7 +58,7 @@ module Users
           end
           render json: { message: t('user_groups.create.success') }, status: :created
         else
-          render json: { errors: t('user_groups.create.error') }, status: :unprocessable_entity
+          render json: { error: @user_group.errors.full_messages.join(", ") }, status: :unprocessable_entity
         end
       end
 
diff --git a/app/services/lists/user_groups_service.rb b/app/services/lists/user_groups_service.rb
index 162ca5d29..57c29b482 100644
--- a/app/services/lists/user_groups_service.rb
+++ b/app/services/lists/user_groups_service.rb
@@ -5,14 +5,11 @@ module Lists
     private
 
     def fetch_records
-      @records = @raw_data.joins(
-        'LEFT OUTER JOIN users AS creators ' \
-        'ON user_groups.created_by_id = creators.id'
-      ).left_joins(:user_group_memberships).includes(:users)
-                          .select('user_groups.* as user_groups')
-                          .select('creators.full_name AS created_by_user')
+      @records = @raw_data.left_joins(:created_by).left_joins(:user_group_memberships).includes(:users)
+                          .select('user_groups.*')
+                          .select('array_agg(users.full_name) AS created_by_user')
                           .select('COUNT(user_groups.id) AS members_count')
-                          .group('user_groups.id, creators.full_name')
+                          .group('user_groups.id')
     end
 
     def filter_records
diff --git a/app/views/users/settings/user_groups/show.html.erb b/app/views/users/settings/user_groups/show.html.erb
index c56991364..0fcd54bb3 100644
--- a/app/views/users/settings/user_groups/show.html.erb
+++ b/app/views/users/settings/user_groups/show.html.erb
@@ -11,7 +11,7 @@
     <%= link_to users_settings_team_user_groups_path, class: "btn btn-light btn-black icon-btn" do %>
       <i class="sn-icon sn-icon-arrow-left"></i>
     <% end %>
-    <h3 class="m-0 flex gap-0.5 items-center">
+    <h3 class="m-0 flex gap-0.5 items-center grow">
       <% if can_manage_team?(@team) %>
         <%= render partial: "shared/inline_editing",
                     locals: {

From 001e0f8d27447afd97c344da683a5bd48d664c8e Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Wed, 13 Aug 2025 13:32:12 +0200
Subject: [PATCH 58/91] Fix SA notifications on step and item card [SCI-12247]

---
 app/controllers/form_field_values_controller.rb | 2 +-
 app/controllers/repository_rows_controller.rb   | 2 ++
 app/helpers/comment_helper.rb                   | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/controllers/form_field_values_controller.rb b/app/controllers/form_field_values_controller.rb
index 4b4f577e7..5bbeffd08 100644
--- a/app/controllers/form_field_values_controller.rb
+++ b/app/controllers/form_field_values_controller.rb
@@ -52,7 +52,7 @@ class FormFieldValuesController < ApplicationController
     smart_annotation_notification(
       old_text: @form_field_value.text_previously_was,
       new_text: @form_field_value.text,
-      subject: step.protocol,
+      subject: step,
       title: t('notifications.form_field_value_title',
                user: current_user.full_name,
                field: @form_field_value.form_field.name,
diff --git a/app/controllers/repository_rows_controller.rb b/app/controllers/repository_rows_controller.rb
index 1366d2331..bb9aabde5 100644
--- a/app/controllers/repository_rows_controller.rb
+++ b/app/controllers/repository_rows_controller.rb
@@ -213,6 +213,8 @@ class RepositoryRowsController < ApplicationController
                      { repository_row: @repository_row.id,
                        repository_column: update_params['repository_cells']&.keys&.first ||
                        I18n.t('repositories.table.row_name') })
+
+        record_annotation_notification(@repository_row, row_cell_update.cell) if row_cell_update.cell.value_type == 'RepositoryTextValue'
       end
       @reminders_present = @repository_row.repository_cells.with_active_reminder(@current_user).any?
 
diff --git a/app/helpers/comment_helper.rb b/app/helpers/comment_helper.rb
index 81aa82646..ba6dc2566 100644
--- a/app/helpers/comment_helper.rb
+++ b/app/helpers/comment_helper.rb
@@ -162,7 +162,7 @@ module CommentHelper
     smart_annotation_notification(
       old_text: old_text,
       new_text: comment.message,
-      subject: step.protocol,
+      subject: step,
       title: t('notifications.step_comment_annotation_title',
                step: step.name,
                user: current_user.full_name),

From a5cc736bf00bd4c39471a901603568ec210c7cd5 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 13 Aug 2025 16:23:08 +0200
Subject: [PATCH 59/91] Fix showing group icons for groups from other teams in
 tables [SCI-12249]

---
 app/serializers/concerns/assignments_helper.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/serializers/concerns/assignments_helper.rb b/app/serializers/concerns/assignments_helper.rb
index 65cc4a523..6cb8001c8 100644
--- a/app/serializers/concerns/assignments_helper.rb
+++ b/app/serializers/concerns/assignments_helper.rb
@@ -11,7 +11,7 @@ module AssignmentsHelper
       }
     end
 
-    user_groups = object.user_group_assignments.map do |ua|
+    user_groups = object.user_group_assignments.where(team: current_user.current_team).map do |ua|
       {
         avatar: ActionController::Base.helpers.asset_path('icon/group.svg'),
         full_name: ua.user_group_name_with_role

From aaf100792c5e64ef93df2634f764f6f8cf13627f Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 13 Aug 2025 16:39:45 +0200
Subject: [PATCH 60/91] Properly scope permission check to current team for
 user_group_assignments [SCI-12249]

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

diff --git a/app/models/concerns/permission_checkable_model.rb b/app/models/concerns/permission_checkable_model.rb
index b02172d6b..f1a571941 100644
--- a/app/models/concerns/permission_checkable_model.rb
+++ b/app/models/concerns/permission_checkable_model.rb
@@ -50,7 +50,7 @@ module PermissionCheckableModel
     end
 
     user_roles = UserRole.left_outer_joins(:team_assignments, user_group_assignments: { user_group: :users })
-    user_roles.where(user_group_assignments: { assignable: self, user_groups: { users: user } })
+    user_roles.where(user_group_assignments: { assignable: self, user_groups: { users: user }, team: permission_team })
               .or(user_roles.where(team_assignments: { assignable: self, team: permission_team }))
               .exists?(['user_roles.permissions @> ARRAY[?]::varchar[]', [permission]])
   end

From 82964535ba55bc453281c5a0a40e9b6e83a6e2f5 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 13 Aug 2025 17:01:19 +0200
Subject: [PATCH 61/91] Add back unlinking and unassigning unshared repository
 rows [SCI-12055]

---
 app/models/team_shared_object.rb | 39 ++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/app/models/team_shared_object.rb b/app/models/team_shared_object.rb
index c2ef157d7..28404f287 100644
--- a/app/models/team_shared_object.rb
+++ b/app/models/team_shared_object.rb
@@ -19,10 +19,49 @@ class TeamSharedObject < ApplicationRecord
 
   # ifs needed for StorageLocations, which currently do not have assignments
   after_update :update_assignments, if: -> { shared_object.respond_to?(:user_assignments) }
+  before_destroy :unassign_unshared_items, if: -> { shared_object.is_a?(Repository) }
+  before_destroy :unlink_unshared_items, if: -> { shared_object.is_a?(Repository) }
   after_destroy :destroy_assignments, if: -> { shared_object.respond_to?(:user_assignments) }
 
   private
 
+  def unassign_unshared_items
+    return if shared_object.shared_read? || shared_object.shared_write?
+
+    MyModuleRepositoryRow.joins(my_module: { experiment: { project: :team } })
+                         .joins(repository_row: :repository)
+                         .where(my_module: { experiment: { projects: { team: team } } })
+                         .where(repository_rows: { repository: shared_object })
+                         .destroy_all
+  end
+
+  def unlink_unshared_items
+    # We keep all the other teams shared with and the repository's own team
+    teams_ids = shared_object.teams_shared_with.where.not(id: team).pluck(:id)
+    teams_ids << shared_object.team_id
+    repository_rows_ids = shared_object.repository_rows.select(:id)
+    rows_to_unlink = RepositoryRow.joins("LEFT JOIN repository_row_connections \
+                                         ON repository_rows.id = repository_row_connections.parent_id \
+                                         OR repository_rows.id = repository_row_connections.child_id")
+                                  .where("repository_row_connections.parent_id IN (?) \
+                                         OR repository_row_connections.child_id IN (?)",
+                                         repository_rows_ids,
+                                         repository_rows_ids)
+                                  .joins(:repository)
+                                  .where.not(repositories: { team: teams_ids })
+                                  .select(:id)
+
+    RepositoryRowConnection.where("(repository_row_connections.parent_id IN (?) \
+                                   AND repository_row_connections.child_id IN (?)) \
+                                   OR (repository_row_connections.parent_id IN (?) \
+                                   AND repository_row_connections.child_id IN (?))",
+                                  repository_rows_ids,
+                                  rows_to_unlink,
+                                  rows_to_unlink,
+                                  repository_rows_ids)
+                           .destroy_all
+  end
+
   def update_assignments
     return unless saved_change_to_permission_level? && permission_level == 'shared_read'
 

From f4fdf8e78c451c4d8fa717a014c727b567be4204 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 13 Aug 2025 22:48:25 +0000
Subject: [PATCH 62/91] Bump activerecord from 7.2.2.1 to 7.2.2.2

Bumps [activerecord](https://github.com/rails/rails) from 7.2.2.1 to 7.2.2.2.
- [Release notes](https://github.com/rails/rails/releases)
- [Changelog](https://github.com/rails/rails/blob/v8.0.2.1/activerecord/CHANGELOG.md)
- [Commits](https://github.com/rails/rails/compare/v7.2.2.1...v7.2.2.2)

---
updated-dependencies:
- dependency-name: activerecord
  dependency-version: 7.2.2.2
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Gemfile.lock | 122 +++++++++++++++++++++++++--------------------------
 1 file changed, 61 insertions(+), 61 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 1b1f3a776..7d2ec2351 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -36,29 +36,29 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actioncable (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
       zeitwerk (~> 2.6)
-    actionmailbox (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activejob (= 7.2.2.1)
-      activerecord (= 7.2.2.1)
-      activestorage (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actionmailbox (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activejob (= 7.2.2.2)
+      activerecord (= 7.2.2.2)
+      activestorage (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       mail (>= 2.8.0)
-    actionmailer (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      actionview (= 7.2.2.1)
-      activejob (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actionmailer (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      actionview (= 7.2.2.2)
+      activejob (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       mail (>= 2.8.0)
       rails-dom-testing (~> 2.2)
-    actionpack (7.2.2.1)
-      actionview (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actionpack (7.2.2.2)
+      actionview (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       nokogiri (>= 1.8.5)
       racc
       rack (>= 2.2.4, < 3.2)
@@ -67,15 +67,15 @@ GEM
       rails-dom-testing (~> 2.2)
       rails-html-sanitizer (~> 1.6)
       useragent (~> 0.16)
-    actiontext (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activerecord (= 7.2.2.1)
-      activestorage (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actiontext (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activerecord (= 7.2.2.2)
+      activestorage (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.2.2.1)
-      activesupport (= 7.2.2.1)
+    actionview (7.2.2.2)
+      activesupport (= 7.2.2.2)
       builder (~> 3.1)
       erubi (~> 1.11)
       rails-dom-testing (~> 2.2)
@@ -85,14 +85,14 @@ GEM
       activemodel (>= 4.1)
       case_transform (>= 0.2)
       jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
-    activejob (7.2.2.1)
-      activesupport (= 7.2.2.1)
+    activejob (7.2.2.2)
+      activesupport (= 7.2.2.2)
       globalid (>= 0.3.6)
-    activemodel (7.2.2.1)
-      activesupport (= 7.2.2.1)
-    activerecord (7.2.2.1)
-      activemodel (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    activemodel (7.2.2.2)
+      activesupport (= 7.2.2.2)
+    activerecord (7.2.2.2)
+      activemodel (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       timeout (>= 0.4.0)
     activerecord-import (2.2.0)
       activerecord (>= 4.2)
@@ -103,13 +103,13 @@ GEM
       multi_json (~> 1.11, >= 1.11.2)
       rack (>= 2.0.8, < 4)
       railties (>= 6.1)
-    activestorage (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activejob (= 7.2.2.1)
-      activerecord (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    activestorage (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activejob (= 7.2.2.2)
+      activerecord (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       marcel (~> 1.0)
-    activesupport (7.2.2.1)
+    activesupport (7.2.2.2)
       base64
       benchmark (>= 0.3)
       bigdecimal
@@ -188,14 +188,14 @@ GEM
     aws-sigv4 (1.12.1)
       aws-eventstream (~> 1, >= 1.0.2)
     base62 (1.0.0)
-    base64 (0.2.0)
+    base64 (0.3.0)
     bcrypt (3.1.18)
-    benchmark (0.4.0)
+    benchmark (0.4.1)
     better_errors (2.10.1)
       erubi (>= 1.0.0)
       rack (>= 0.9.0)
       rouge (>= 1.0.0)
-    bigdecimal (3.2.0)
+    bigdecimal (3.2.2)
     bindata (2.5.0)
     binding_of_caller (1.0.0)
       debug_inspector (>= 0.0.1)
@@ -661,20 +661,20 @@ GEM
     rackup (1.0.1)
       rack (< 3)
       webrick
-    rails (7.2.2.1)
-      actioncable (= 7.2.2.1)
-      actionmailbox (= 7.2.2.1)
-      actionmailer (= 7.2.2.1)
-      actionpack (= 7.2.2.1)
-      actiontext (= 7.2.2.1)
-      actionview (= 7.2.2.1)
-      activejob (= 7.2.2.1)
-      activemodel (= 7.2.2.1)
-      activerecord (= 7.2.2.1)
-      activestorage (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    rails (7.2.2.2)
+      actioncable (= 7.2.2.2)
+      actionmailbox (= 7.2.2.2)
+      actionmailer (= 7.2.2.2)
+      actionpack (= 7.2.2.2)
+      actiontext (= 7.2.2.2)
+      actionview (= 7.2.2.2)
+      activejob (= 7.2.2.2)
+      activemodel (= 7.2.2.2)
+      activerecord (= 7.2.2.2)
+      activestorage (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       bundler (>= 1.15.0)
-      railties (= 7.2.2.1)
+      railties (= 7.2.2.2)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -690,9 +690,9 @@ GEM
       actionview (> 3.1)
       activesupport (> 3.1)
       railties (> 3.1)
-    railties (7.2.2.1)
-      actionpack (= 7.2.2.1)
-      activesupport (= 7.2.2.1)
+    railties (7.2.2.2)
+      actionpack (= 7.2.2.2)
+      activesupport (= 7.2.2.2)
       irb (~> 1.13)
       rackup (>= 1.0.0)
       rake (>= 12.2)
@@ -939,11 +939,11 @@ DEPENDENCIES
   omniauth-rails_csrf_protection (~> 1.0)
   omniauth-saml
   omniauth_openid_connect
-  opentelemetry-exporter-otlp (~> 0.30.0)
-  opentelemetry-instrumentation-pg (~> 0.30.1)
-  opentelemetry-instrumentation-rails (~> 0.36.0)
-  opentelemetry-propagator-xray (~> 0.24.0)
-  opentelemetry-sdk (~> 1.8)
+  opentelemetry-exporter-otlp
+  opentelemetry-instrumentation-pg
+  opentelemetry-instrumentation-rails
+  opentelemetry-propagator-xray
+  opentelemetry-sdk
   overcommit
   pg (~> 1.5)
   pg_search

From 304bbdcb94f8733010a6f7e67e79df97b7d21e29 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 14 Aug 2025 09:53:15 +0200
Subject: [PATCH 63/91] Fix error in sync scheduler [SCI-12206]

---
 config/initializers/scheduler.rb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/config/initializers/scheduler.rb b/config/initializers/scheduler.rb
index 19d8e7179..706c21056 100644
--- a/config/initializers/scheduler.rb
+++ b/config/initializers/scheduler.rb
@@ -22,7 +22,6 @@ if ENV['WORKER'].present?
       Rails.logger.info(
         "Templates, total number of updated projects: #{updated} out of #{total}}"
       )
-      Rails.logger.flush
     end
   end
 

From dc4e4bcae847e582bf49798bb1b3dc0ba458525c Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Thu, 14 Aug 2025 11:09:41 +0200
Subject: [PATCH 64/91] Fix nested general dropdown [SCI-12250]

---
 app/javascript/vue/shared/general_dropdown.vue | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/shared/general_dropdown.vue b/app/javascript/vue/shared/general_dropdown.vue
index 1e40ba43b..bb12c9b21 100644
--- a/app/javascript/vue/shared/general_dropdown.vue
+++ b/app/javascript/vue/shared/general_dropdown.vue
@@ -6,6 +6,7 @@
     <template v-if="isOpen">
       <teleport to="body">
         <div @click="closeOnClick && closeMenu()" ref="flyout"
+            :id="randomId"
             class="sn-dropdown fixed z-[3000] bg-sn-white inline-block
                   rounded p-2.5 sn-shadow-menu-sm"
             :class="{
@@ -42,7 +43,8 @@ export default {
   },
   data() {
     return {
-      isOpen: false
+      isOpen: false,
+      randomId: `dropdown-${Math.random().toString(36).substring(2, 15)}`,
     };
   },
   directives: {
@@ -70,7 +72,7 @@ export default {
       }
     },
     closeMenu(e) {
-      if (e && e.target.closest('.sn-dropdown, .sn-select-dropdown, .sn-menu-dropdown, .dp__instance_calendar')) return;
+      if (e && e.target.closest(`.sn-dropdown#${this.randomId}, .sn-select-dropdown, .sn-menu-dropdown, .dp__instance_calendar`)) return;
       this.isOpen = false;
     }
   }

From 7894a7b374cee03bb2839b57929cfaa016d3926c Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 14 Aug 2025 11:38:53 +0200
Subject: [PATCH 65/91] Fix serialization when creating form field values
 [SCI-12259]

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

diff --git a/app/controllers/form_field_values_controller.rb b/app/controllers/form_field_values_controller.rb
index 5bbeffd08..6fb2b6305 100644
--- a/app/controllers/form_field_values_controller.rb
+++ b/app/controllers/form_field_values_controller.rb
@@ -18,7 +18,7 @@ class FormFieldValuesController < ApplicationController
     log_form_field_value_create_activity
     form_field_value_annotation if @form_field_value.is_a?(FormTextFieldValue)
 
-    render json: @form_field_value, serializer: FormFieldValueSerializer, user: current_user
+    render json: @form_field_value, serializer: FormFieldValueSerializer, scope: { user: current_user }
   end
 
   private

From 6a2ecf8f6fa8cb5273fb8412bb1a63de69694890 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 14 Aug 2025 11:39:41 +0200
Subject: [PATCH 66/91] Fix settings menu link and order [SCI-12255]

---
 app/controllers/navigations_controller.rb | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/app/controllers/navigations_controller.rb b/app/controllers/navigations_controller.rb
index f884be192..b11fa6f9d 100644
--- a/app/controllers/navigations_controller.rb
+++ b/app/controllers/navigations_controller.rb
@@ -60,24 +60,16 @@ class NavigationsController < ApplicationController
   end
 
   def settings_menu_links
-    links = [
-      {
-        name: I18n.t('users.settings.sidebar.teams'), url: teams_path
-      }, {
-        name: I18n.t('users.settings.sidebar.groups'), url: users_settings_team_user_groups_path(current_team)
-      }, {
-        name: I18n.t('users.settings.sidebar.account_nav.addons'), url: addons_path
-      }
-    ]
-
-    if can_create_acitivity_filters?
-      links.push({ name: I18n.t('users.settings.sidebar.webhooks'), url: users_settings_webhooks_path })
-    end
+    links = [{ name: I18n.t('users.settings.sidebar.teams'), url: teams_path }]
+    links << { name: I18n.t('users.settings.sidebar.groups'), url: users_settings_team_user_groups_path(current_team) } if can_manage_team?(current_team)
+    links << { name: I18n.t('users.settings.sidebar.account_nav.addons'), url: addons_path }
 
     private_methods.select { |i| i.to_s[/^settings_menu_links_[a-z]*_extension$/] }.each do |method|
       links = __send__(method, links)
     end
 
+    links << { name: I18n.t('users.settings.sidebar.webhooks'), url: users_settings_webhooks_path } if can_create_acitivity_filters?
+
     links
   end
 

From 00124430d012c246a8ad27d9ac6283b16e5ba8cd Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Thu, 14 Aug 2025 11:50:18 +0200
Subject: [PATCH 67/91] Fix row name update [SCI-12260]

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

diff --git a/app/controllers/repository_rows_controller.rb b/app/controllers/repository_rows_controller.rb
index bb9aabde5..3b5f0866d 100644
--- a/app/controllers/repository_rows_controller.rb
+++ b/app/controllers/repository_rows_controller.rb
@@ -214,7 +214,7 @@ class RepositoryRowsController < ApplicationController
                        repository_column: update_params['repository_cells']&.keys&.first ||
                        I18n.t('repositories.table.row_name') })
 
-        record_annotation_notification(@repository_row, row_cell_update.cell) if row_cell_update.cell.value_type == 'RepositoryTextValue'
+        record_annotation_notification(@repository_row, row_cell_update.cell) if row_cell_update.cell && row_cell_update.cell.value_type == 'RepositoryTextValue'
       end
       @reminders_present = @repository_row.repository_cells.with_active_reminder(@current_user).any?
 

From dabeb0650fa7665d4fec2318c27e0a60c833a95c Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Thu, 14 Aug 2025 14:00:09 +0200
Subject: [PATCH 68/91] Fix search in select dropdown [SCI-12261]

---
 app/javascript/vue/shared/select_dropdown.vue | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/app/javascript/vue/shared/select_dropdown.vue b/app/javascript/vue/shared/select_dropdown.vue
index f95f7a02e..ae7e8eeaa 100644
--- a/app/javascript/vue/shared/select_dropdown.vue
+++ b/app/javascript/vue/shared/select_dropdown.vue
@@ -149,7 +149,8 @@ export default {
       fixedWidth: true,
       focusedOption: null,
       skipQueryCallback: false,
-      nextPage: 1
+      nextPage: 1,
+      totalOptionsCount: this.options.length
     };
   },
   mixins: [FixedFlyoutMixin],
@@ -226,11 +227,11 @@ export default {
       if (this.newValue.length === 0) {
         return false;
       }
-      if (this.newValue.length === 1 && this.rawOptions.length > 1) {
+      if (this.newValue.length === 1 && this.totalOptionsCount > 1) {
         this.selectAllState = 'indeterminate';
         return this.renderLabel(this.rawOptions.find((option) => option[0] === this.newValue[0]));
       }
-      if (this.newValue.length === this.rawOptions.length) {
+      if (this.newValue.length === this.totalOptionsCount) {
         this.selectAllState = 'checked';
         return this.allOptionsPlaceholder || this.i18n.t('general.select_dropdown.all_options_placeholder');
       }
@@ -264,7 +265,6 @@ export default {
     if (!this.newValue && this.multiple) {
       this.newValue = [];
     }
-    this.fetchOptions();
   },
   watch: {
     value(newValue) {
@@ -318,6 +318,7 @@ export default {
     },
     open() {
       if (!this.disabled) this.isOpen = true;
+      this.fetchOptions();
     },
     clear() {
       this.newValue = this.multiple ? [] : null;
@@ -391,6 +392,11 @@ export default {
             } else {
               this.fetchedOptions = response.data.data;
             }
+
+            if (this.fetchedOptions.length > this.totalOptionsCount) {
+              this.totalOptionsCount = this.fetchedOptions.length;
+            }
+
             this.$nextTick(() => {
               this.setPosition();
             });

From 6d54188b386e11bc81cde233e8b2b491083d873b Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 14 Aug 2025 14:17:19 +0200
Subject: [PATCH 69/91] Fix use of beforeDestroy, which is invalid in Vue3
 [SCI-12259]

---
 app/javascript/vue/repositories/modals/new.vue                  | 2 +-
 app/javascript/vue/repository/state_menu.vue                    | 2 +-
 .../vue/repository_item_sidebar/repository_values/ScrollSpy.vue | 2 +-
 app/javascript/vue/repository_row/manage_stock_value_modal.vue  | 2 +-
 app/javascript/vue/shared/breadcrumbs.vue                       | 2 +-
 app/javascript/vue/shared/repository_row_selector.vue           | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/app/javascript/vue/repositories/modals/new.vue b/app/javascript/vue/repositories/modals/new.vue
index d1534efdb..9e306def7 100644
--- a/app/javascript/vue/repositories/modals/new.vue
+++ b/app/javascript/vue/repositories/modals/new.vue
@@ -108,7 +108,7 @@ export default {
   mounted() {
     document.addEventListener('mouseover', this.loadColumnsInfo);
   },
-  beforeDestroy() {
+  beforeUnmount() {
     document.removeEventListener('mouseover', this.loadColumnsInfo);
   },
   computed: {
diff --git a/app/javascript/vue/repository/state_menu.vue b/app/javascript/vue/repository/state_menu.vue
index 015a1cf81..df47f39e7 100644
--- a/app/javascript/vue/repository/state_menu.vue
+++ b/app/javascript/vue/repository/state_menu.vue
@@ -23,7 +23,7 @@ export default {
     archivedUrl: { type: String, required: true },
     disabled: { type: String, default: 'false' }
   },
-  beforeDestroy() {
+  beforeUnmount() {
     delete window.initRepositoryStateMenu;
   },
   computed: {
diff --git a/app/javascript/vue/repository_item_sidebar/repository_values/ScrollSpy.vue b/app/javascript/vue/repository_item_sidebar/repository_values/ScrollSpy.vue
index 07d8b936e..333f3cde4 100644
--- a/app/javascript/vue/repository_item_sidebar/repository_values/ScrollSpy.vue
+++ b/app/javascript/vue/repository_item_sidebar/repository_values/ScrollSpy.vue
@@ -60,7 +60,7 @@ export default {
       }
     });
   },
-  beforeDestroy() {
+  beforeUnmount() {
     window.removeEventListener('resize', this.handleResize);
     this.removeScrollListener();
   },
diff --git a/app/javascript/vue/repository_row/manage_stock_value_modal.vue b/app/javascript/vue/repository_row/manage_stock_value_modal.vue
index 87f26c404..b015df92e 100644
--- a/app/javascript/vue/repository_row/manage_stock_value_modal.vue
+++ b/app/javascript/vue/repository_row/manage_stock_value_modal.vue
@@ -222,7 +222,7 @@ export default {
   created() {
     window.manageStockModalComponent = this;
   },
-  beforeDestroy() {
+  beforeUnmount() {
     delete window.manageStockModalComponent;
   },
   mounted() {
diff --git a/app/javascript/vue/shared/breadcrumbs.vue b/app/javascript/vue/shared/breadcrumbs.vue
index 7764b31c0..b421f881c 100644
--- a/app/javascript/vue/shared/breadcrumbs.vue
+++ b/app/javascript/vue/shared/breadcrumbs.vue
@@ -94,7 +94,7 @@ export default {
     this.setContainerSize();
     window.addEventListener('resize', this.setContainerSize);
   },
-  beforeDestroy() {
+  beforeUnmount() {
     window.removeEventListener('resize', this.setContainerSize);
   },
   methods: {
diff --git a/app/javascript/vue/shared/repository_row_selector.vue b/app/javascript/vue/shared/repository_row_selector.vue
index 4a57fb44a..8e1f5b37d 100644
--- a/app/javascript/vue/shared/repository_row_selector.vue
+++ b/app/javascript/vue/shared/repository_row_selector.vue
@@ -97,7 +97,7 @@ export default {
   mounted() {
     document.addEventListener('mouseover', this.loadColumnsInfo);
   },
-  beforeDestroy() {
+  beforeUnmount() {
     document.removeEventListener('mouseover', this.loadColumnsInfo);
   },
   watch: {

From 88bf0562e89dea63935b9653f111e4a5aaa419c3 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 14 Aug 2025 14:33:39 +0200
Subject: [PATCH 70/91] Fix ambiguous column error in activities_service
 [SCI-12224]

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

diff --git a/app/services/activities_service.rb b/app/services/activities_service.rb
index 2fdc8a454..c8d850c8c 100644
--- a/app/services/activities_service.rb
+++ b/app/services/activities_service.rb
@@ -22,13 +22,13 @@ class ActivitiesService
 
     activities =
       if filters[:from_date].present? && filters[:to_date].present?
-        activities.where('created_at <= :from AND created_at >= :to',
+        activities.where('activities.created_at <= :from AND activities.created_at >= :to',
                          from: Time.zone.parse(filters[:from_date]).end_of_day.utc,
                          to: Time.zone.parse(filters[:to_date]).beginning_of_day.utc)
       elsif filters[:from_date].present? && filters[:to_date].blank?
-        activities.where('created_at <= :from', from: Time.zone.parse(filters[:from_date]).end_of_day.utc)
+        activities.where('activities.created_at <= :from', from: Time.zone.parse(filters[:from_date]).end_of_day.utc)
       elsif filters[:from_date].blank? && filters[:to_date].present?
-        activities.where(created_at: Time.zone.parse(filters[:to_date]).beginning_of_day.utc..)
+        activities.where('activities.created_at' => Time.zone.parse(filters[:to_date]).beginning_of_day.utc..)
       else
         activities
       end

From 67541a79dba28c74507a46f9e84206f648f47760 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 14 Aug 2025 14:48:01 +0200
Subject: [PATCH 71/91] Allow creating columns in shared inventories
 [SCI-12264]

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

diff --git a/app/permissions/repository.rb b/app/permissions/repository.rb
index b686da635..fbb452a75 100644
--- a/app/permissions/repository.rb
+++ b/app/permissions/repository.rb
@@ -113,8 +113,7 @@ Canaid::Permissions.register_for(Repository) do
 
   # repository: create field
   can :create_repository_columns do |user, repository|
-    !repository.shared_with?(user.current_team) &&
-      repository.permission_granted?(user, RepositoryPermissions::COLUMNS_CREATE)
+    repository.permission_granted?(user, RepositoryPermissions::COLUMNS_CREATE)
   end
 
   can :manage_repository_columns do |user, repository|

From 24757ddc1925c70d0e4619a021ade2f3831eea0f Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Thu, 14 Aug 2025 14:53:04 +0200
Subject: [PATCH 72/91] Fix access management for STI models [SCI-12252]

---
 app/controllers/access_permissions/base_controller.rb | 2 +-
 app/helpers/user_roles_helper.rb                      | 2 +-
 app/models/repository.rb                              | 4 ++++
 app/models/repository_base.rb                         | 4 ----
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/app/controllers/access_permissions/base_controller.rb b/app/controllers/access_permissions/base_controller.rb
index 5495d6c00..4b493fbee 100644
--- a/app/controllers/access_permissions/base_controller.rb
+++ b/app/controllers/access_permissions/base_controller.rb
@@ -124,7 +124,7 @@ module AccessPermissions
     private
 
     def model_parameter
-      @model.model_name.param_key
+      @model.class.permission_class.model_name.param_key
     end
 
     def manage_permission_constant
diff --git a/app/helpers/user_roles_helper.rb b/app/helpers/user_roles_helper.rb
index 7b03ebdbf..94f24db15 100644
--- a/app/helpers/user_roles_helper.rb
+++ b/app/helpers/user_roles_helper.rb
@@ -7,7 +7,7 @@ module UserRolesHelper
       viewer_role = UserRole.find_predefined_viewer_role
       roles = [[viewer_role.name, viewer_role.id]]
     else
-      permission_group = "#{object.class.name}Permissions".constantize
+      permission_group = "#{object.class.permission_class}Permissions".constantize
       permissions = permission_group.constants.map { |const| permission_group.const_get(const) }
 
       roles = user_roles_subset_by_permissions(permissions).order(id: :asc).pluck(:name, :id)
diff --git a/app/models/repository.rb b/app/models/repository.rb
index 98dfe4bf3..822e1ac12 100644
--- a/app/models/repository.rb
+++ b/app/models/repository.rb
@@ -53,6 +53,10 @@ class Repository < RepositoryBase
           .where(team: teams)
   }
 
+  def self.permission_class
+    Repository
+  end
+
   def top_level_assignable
     true
   end
diff --git a/app/models/repository_base.rb b/app/models/repository_base.rb
index 3f61ec831..95190312e 100644
--- a/app/models/repository_base.rb
+++ b/app/models/repository_base.rb
@@ -27,10 +27,6 @@ class RepositoryBase < ApplicationRecord
   # Not discarded
   default_scope -> { kept }
 
-  def self.permission_class
-    Repository
-  end
-
   def self.stock_management_enabled?
     ApplicationSettings.instance.values['stock_management_enabled']
   end

From ef3870855f20db9bfbbaf4f8b81cd174576815a0 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 14 Aug 2025 15:28:08 +0200
Subject: [PATCH 73/91] Fix returning repositories list [SCI-12254]

---
 app/controllers/repositories_controller.rb                  | 5 +++--
 .../item_relationships/RepositoryItemRelationshipsModal.vue | 1 +
 app/javascript/vue/shared/repository_row_selector.vue       | 6 +++++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index d56dfd84e..a98205547 100644
--- a/app/controllers/repositories_controller.rb
+++ b/app/controllers/repositories_controller.rb
@@ -12,7 +12,7 @@ class RepositoriesController < ApplicationController
   before_action :switch_team_with_param, only: %i(index)
   before_action :load_repository, except: %i(index create create_modal archive restore actions_toolbar
                                              export_repositories list)
-  before_action :load_repositories, only: %i(index list actions_toolbar)
+  before_action :load_repositories, only: %i(index actions_toolbar)
   before_action :load_repositories_for_archiving, only: :archive
   before_action :load_repositories_for_restoring, only: :restore
   before_action :check_view_permissions, except: %i(index create_modal create update destroy parse_sheet
@@ -44,7 +44,8 @@ class RepositoriesController < ApplicationController
   end
 
   def list
-    results = @repositories.select(:id, :name, 'LOWER(repositories.name)')
+    repositories = params[:manageable] == 'true' ? Repository.managable_by_user(current_user, current_team) : Repository.readable_by_user(current_user, current_team)
+    results = repositories.select(:id, :name, 'LOWER(repositories.name)')
     results = results.name_like(params[:query]) if params[:query].present?
     results = results.joins(:repository_rows).distinct if params[:non_empty].present?
     results = results.active if params[:active].present?
diff --git a/app/javascript/vue/item_relationships/RepositoryItemRelationshipsModal.vue b/app/javascript/vue/item_relationships/RepositoryItemRelationshipsModal.vue
index 6e1d1bc1a..c641e324a 100644
--- a/app/javascript/vue/item_relationships/RepositoryItemRelationshipsModal.vue
+++ b/app/javascript/vue/item_relationships/RepositoryItemRelationshipsModal.vue
@@ -33,6 +33,7 @@
         <div class="modal-body flex flex-col gap-6" :class="{ '!pb-3': notification }">
           <RepositoryRowSelector
             :multiple="true"
+            :manageableRepositoriesOnly="true"
             @change="selectedItemValues = $event"
             @repositoryChange="changeSelectedInventory"
           />
diff --git a/app/javascript/vue/shared/repository_row_selector.vue b/app/javascript/vue/shared/repository_row_selector.vue
index 4a57fb44a..26115bb7c 100644
--- a/app/javascript/vue/shared/repository_row_selector.vue
+++ b/app/javascript/vue/shared/repository_row_selector.vue
@@ -79,6 +79,10 @@ export default {
     excludeRows: {
       type: Array,
       default: () => []
+    },
+    manageableRepositoriesOnly: {
+      type: Boolean,
+      default: false
     }
   },
   created() {
@@ -116,7 +120,7 @@ export default {
   },
   computed: {
     repositoriesUrl() {
-      return list_team_repositories_path(this.teamId, { non_empty: true, active: true });
+      return list_team_repositories_path(this.teamId, { non_empty: true, active: true, manageable: this.manageableRepositoriesOnly });
     },
     rowsUrl() {
       if (!this.selectedRepository) {

From 1b189062a622142c592dc4f2bf4c239929dc1e7b Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Thu, 14 Aug 2025 16:21:05 +0200
Subject: [PATCH 74/91] Fix team assignment user list

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

diff --git a/app/models/concerns/assignable.rb b/app/models/concerns/assignable.rb
index d21ba3a1e..582d75340 100644
--- a/app/models/concerns/assignable.rb
+++ b/app/models/concerns/assignable.rb
@@ -85,7 +85,7 @@ module Assignable
 
       team_assignment = team_assignments.find_by(team: team)
       if team_assignment
-        User.where.not(id: user_assignments.select(:user_id)).where(id: team_assignment.team.users.select(:id)).find_each do |user|
+        User.where.not(id: user_assignments.select(:user_id).where(team: team)).where(id: team_assignment.team.users.select(:id)).find_each do |user|
           users << {
             user: user,
             role: team_assignment.user_role,

From d5fc3847d45e8d60fad2483368b3c336df2db277 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Thu, 14 Aug 2025 17:14:03 +0200
Subject: [PATCH 75/91] Fix list selected repositories for list [SCI-12254]

---
 app/controllers/repositories_controller.rb | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index a98205547..34c01b9c7 100644
--- a/app/controllers/repositories_controller.rb
+++ b/app/controllers/repositories_controller.rb
@@ -44,7 +44,11 @@ class RepositoriesController < ApplicationController
   end
 
   def list
-    repositories = params[:manageable] == 'true' ? Repository.managable_by_user(current_user, current_team) : Repository.readable_by_user(current_user, current_team)
+    repositories = if params[:manageable] == 'true'
+                     Repository.with_granted_permissions(current_user, RepositoryPermissions::ROWS_UPDATE, current_team)
+                   else
+                     Repository.readable_by_user(current_user, current_team)
+                   end
     results = repositories.select(:id, :name, 'LOWER(repositories.name)')
     results = results.name_like(params[:query]) if params[:query].present?
     results = results.joins(:repository_rows).distinct if params[:non_empty].present?

From 8c4f406d8e076fadb0c759c844a8f9edbe18f7b2 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 18 Aug 2025 09:30:13 +0200
Subject: [PATCH 76/91] Fix unassigning unshared repositories [SCI-12269]

---
 app/models/concerns/shareable.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/models/concerns/shareable.rb b/app/models/concerns/shareable.rb
index 3649f2fb3..53aec9752 100644
--- a/app/models/concerns/shareable.rb
+++ b/app/models/concerns/shareable.rb
@@ -118,7 +118,7 @@ module Shareable
     teams = for_team ? Team.where(id: for_team.id).where.not(id: team.id) : Team.where.not(id: team.id)
 
     user_assignments.where(team_id: teams.select(:id)).destroy_all
-    user_group_assignments.where.not(team_id: teams.select(:id)).destroy_all
-    team_assignments.where.not(team_id: teams.select(:id)).destroy_all
+    user_group_assignments.where(team_id: teams.select(:id)).destroy_all
+    team_assignments.where(team_id: teams.select(:id)).destroy_all
   end
 end

From e7da50f180b25f44faa8bcda7a07f8b6be75e95b Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 18 Aug 2025 09:37:43 +0200
Subject: [PATCH 77/91] Add back unassignment/unlinking logic for global
 repositroy sharing [SCI-12270]

---
 app/models/repository.rb | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/app/models/repository.rb b/app/models/repository.rb
index 822e1ac12..6aac3071f 100644
--- a/app/models/repository.rb
+++ b/app/models/repository.rb
@@ -32,6 +32,8 @@ class Repository < RepositoryBase
 
   before_save :sync_name_with_snapshots, if: :name_changed?
   before_destroy :refresh_report_references_on_destroy, prepend: true
+  after_save :unassign_unshared_items, if: :saved_change_to_permission_level
+  after_save :unlink_unshared_items, if: -> { saved_change_to_permission_level? && !globally_shared? }
 
   validates :name,
             presence: true,
@@ -176,6 +178,26 @@ class Repository < RepositoryBase
                          .destroy_all
   end
 
+  def unlink_unshared_items
+    repository_rows_ids = repository_rows.select(:id)
+    rows_to_unlink = RepositoryRow.joins("LEFT JOIN repository_row_connections \
+                                         ON repository_rows.id = repository_row_connections.parent_id \
+                                         OR repository_rows.id = repository_row_connections.child_id")
+                                  .where("repository_row_connections.parent_id IN (?) \
+                                         OR repository_row_connections.child_id IN (?)",
+                                         repository_rows_ids,
+                                         repository_rows_ids)
+                                  .joins(:repository)
+                                  .where.not(repository: self)
+                                  .where.not(repositories: { team: team })
+                                  .distinct
+
+    RepositoryRowConnection.where(parent: repository_rows_ids, child: rows_to_unlink)
+                           .destroy_all
+    RepositoryRowConnection.where(child: repository_rows_ids, parent: rows_to_unlink)
+                           .destroy_all
+  end
+
   def archived_branch?
     archived?
   end

From 4e8622d0c8c6026a25cc21ac3f775b9e953cdf5b Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 18 Aug 2025 09:44:28 +0200
Subject: [PATCH 78/91] Fix logic parenthesis in .can_manage_shared?
 [SCI-12271]

---
 app/models/concerns/shareable.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/models/concerns/shareable.rb b/app/models/concerns/shareable.rb
index 3649f2fb3..dde2b6ec1 100644
--- a/app/models/concerns/shareable.rb
+++ b/app/models/concerns/shareable.rb
@@ -50,8 +50,8 @@ module Shareable
   end
 
   def can_manage_shared?(user)
-    globally_shared? ||
-      (shared_with?(user.current_team) && user.current_team.permission_granted?(user, TeamPermissions::MANAGE))
+    (globally_shared? || shared_with?(user.current_team)) &&
+      user.current_team.permission_granted?(user, TeamPermissions::MANAGE)
   end
 
   def shareable_write?

From c85e7ce1e212e992bb4ca803e434b5de426c0bd1 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Mon, 18 Aug 2025 10:26:36 +0200
Subject: [PATCH 79/91] Fix double items in dropdown [SCI-12267]

---
 app/javascript/vue/shared/select_dropdown.vue | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/shared/select_dropdown.vue b/app/javascript/vue/shared/select_dropdown.vue
index ae7e8eeaa..a559f1e6c 100644
--- a/app/javascript/vue/shared/select_dropdown.vue
+++ b/app/javascript/vue/shared/select_dropdown.vue
@@ -317,8 +317,15 @@ export default {
       return this.newValue === value;
     },
     open() {
-      if (!this.disabled) this.isOpen = true;
-      this.fetchOptions();
+      if (this.disabled || this.isOpen) return;
+
+      this.isOpen = true;
+
+      if (this.optionsUrl) {
+        this.fetchedOptions = [];
+        this.nextPage = 1;
+        this.fetchOptions();
+      }
     },
     clear() {
       this.newValue = this.multiple ? [] : null;

From 1362ce08ec60d2787d17b8433235a7859306f6a1 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Mon, 18 Aug 2025 10:35:56 +0200
Subject: [PATCH 80/91] Fix unlink for inventory items [SCI-12256]

---
 .../vue/repository_item_sidebar/RepositoryItemSidebar.vue     | 4 ++--
 app/views/repository_rows/show.json.jbuilder                  | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/repository_item_sidebar/RepositoryItemSidebar.vue b/app/javascript/vue/repository_item_sidebar/RepositoryItemSidebar.vue
index 82f3dbcbb..54a8b7ef6 100644
--- a/app/javascript/vue/repository_item_sidebar/RepositoryItemSidebar.vue
+++ b/app/javascript/vue/repository_item_sidebar/RepositoryItemSidebar.vue
@@ -192,7 +192,7 @@
                             <span>{{ i18n.t('repositories.item_card.relationships.item') }}</span>
                             <a v-if="parent.path" :href="parent.path" class="record-info-link btn-text-link !text-sn-science-blue">{{ parent.name }}</a>
                             <span v-else>{{ parent.name }}</span>
-                            <button v-if="permissions.can_connect_rows" @click="openUnlinkModal(parent)"
+                            <button v-if="permissions.can_connect_rows && parent.can_connect_rows" @click="openUnlinkModal(parent)"
                                     class=" ml-2 bg-transparent border-none opacity-0 group-hover:opacity-100 cursor-pointer">
                               <img :src="icons.unlink_path" />
                             </button>
@@ -243,7 +243,7 @@
                             <span>{{ i18n.t('repositories.item_card.relationships.item') }}</span>
                             <a v-if="child.path" :href="child.path" class="record-info-link btn-text-link !text-sn-science-blue">{{ child.name }}</a>
                             <span v-else>{{ child.name }}</span>
-                            <button v-if="permissions.can_connect_rows" @click="openUnlinkModal(child)"
+                            <button v-if="permissions.can_connect_rows && child.can_connect_rows" @click="openUnlinkModal(child)"
                                     class="ml-2 bg-transparent border-none opacity-0 group-hover:opacity-100 cursor-pointer">
                               <img :src="icons.unlink_path" />
                             </button>
diff --git a/app/views/repository_rows/show.json.jbuilder b/app/views/repository_rows/show.json.jbuilder
index e765098c5..4761121f2 100644
--- a/app/views/repository_rows/show.json.jbuilder
+++ b/app/views/repository_rows/show.json.jbuilder
@@ -95,6 +95,7 @@ json.relationships do
       else
         json.name I18n.t('repositories.item_card.relationships.private_item_name')
       end
+      json.can_connect_rows can_connect_repository_rows?(parent.repository) if parent.repository.is_a?(Repository) && !parent.repository.is_a?(SoftLockedRepository)
       json.unlink_path repository_repository_row_repository_row_connection_path(parent.repository,
                                                                                 parent,
                                                                                 @repository_row.parent_connections
@@ -113,6 +114,7 @@ json.relationships do
       else
         json.name I18n.t('repositories.item_card.relationships.private_item_name')
       end
+      json.can_connect_rows can_connect_repository_rows?(child.repository) if child.repository.is_a?(Repository) && !child.repository.is_a?(SoftLockedRepository)
       json.unlink_path repository_repository_row_repository_row_connection_path(child.repository,
                                                                                 child,
                                                                                 @repository_row.child_connections

From ebdba39445870b4007a5b7967e8a2fc86e099d04 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Mon, 18 Aug 2025 10:53:52 +0200
Subject: [PATCH 81/91] Fix private inventory item when adding new item
 relationship [SCI-12253]

---
 .../repository_row_connections_controller.rb  | 30 +++++++++++--------
 .../RepositoryItemSidebar.vue                 |  4 +--
 config/locales/en.yml                         |  2 +-
 3 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/app/controllers/repository_row_connections_controller.rb b/app/controllers/repository_row_connections_controller.rb
index d05d47913..3e6955ae7 100644
--- a/app/controllers/repository_row_connections_controller.rb
+++ b/app/controllers/repository_row_connections_controller.rb
@@ -145,19 +145,23 @@ class RepositoryRowConnectionsController < ApplicationController
 
     repository_connections.map do |connection|
       repository_row = @relation_type == 'parent' ? connection.parent : connection.child
-
-      {
-        name: repository_row.name_with_label,
-        code: repository_row.code,
-        path: repository_repository_row_path(repository_row.repository, repository_row),
-        repository_name: repository_row.repository.name_with_label,
-        repository_path: repository_path(repository_row.repository),
-        unlink_path: repository_repository_row_repository_row_connection_path(
-          repository_row.repository,
-          repository_row,
-          connection
-        )
-      }
+      if can_read_repository?(repository_row.repository)
+        {
+          name: repository_row.name_with_label,
+          code: repository_row.code,
+          path: repository_repository_row_path(repository_row.repository, repository_row),
+          repository_name: repository_row.repository.name_with_label,
+          repository_path: repository_path(repository_row.repository),
+          can_connect_rows: can_connect_repository_rows?(repository_row.repository),
+          unlink_path: repository_repository_row_repository_row_connection_path(
+            repository_row.repository,
+            repository_row,
+            connection
+          )
+        }
+      else
+        { name: I18n.t('repositories.item_card.relationships.private_item_name') }
+      end
     end
   end
 
diff --git a/app/javascript/vue/repository_item_sidebar/RepositoryItemSidebar.vue b/app/javascript/vue/repository_item_sidebar/RepositoryItemSidebar.vue
index 54a8b7ef6..bdfcef902 100644
--- a/app/javascript/vue/repository_item_sidebar/RepositoryItemSidebar.vue
+++ b/app/javascript/vue/repository_item_sidebar/RepositoryItemSidebar.vue
@@ -184,7 +184,7 @@
                       </a>
                     </div>
                     <div v-if="parentsCount">
-                      <details v-for="(parent) in parents" @toggle="updateOpenState(parent.code, $event.target.open)" :key="parent.code" class="flex flex-col font-normal gap-4 group cursor-default">
+                      <details v-for="(parent) in parents" @toggle="updateOpenState(parent.code, $event.target.open)" :key="parent.code" class="flex flex-col font-normal group cursor-default">
                         <summary class="flex flex-row gap-3 mb-4 relative group">
                           <img :src="icons.delimiter_path" class="w-3 h-3 cursor-pointer flex-shrink-0 relative top-1"
                                :class="{ 'rotate-90': relationshipDetailsState[parent.code] }" />
@@ -234,7 +234,7 @@
                     </div>
                     <div v-if="childrenCount">
                       <details v-for="(child) in children" :key="child.code" @toggle="updateOpenState(child.code, $event.target.open)"
-                               class="flex flex-col font-normal gap-4 group-last-of-type:[&>p:last-child]:mb-0">
+                               class="flex flex-col font-normal group-last-of-type:[&>p:last-child]:mb-0">
                         <summary class="flex flex-row gap-3 mb-4 relative group"
                                  :class="{ 'group-last-of-type:mb-0': !relationshipDetailsState[child.code] }">
                           <img :src="icons.delimiter_path" class="w-3 h-3 flex-shrink-0 cursor-pointer relative top-1"
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 4d7595eee..52f4f649b 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -2919,7 +2919,7 @@ en:
           select_valid_value: 'Select a valid date or date-time value'
           browser_alert_message: 'You have made some changes, are you sure you want to leave this page?'
       errors:
-        load_error_header: 'Your workspace does not have the necessary permissions to view the details of this item.'
+        load_error_header: 'You do not have the necessary permissions to view the details of this item.'
         load_error_description: 'To obtain access, reach out to your workspace administrator.'
     highlight_component:
       information_label: 'Information'

From c121daa4b50e499e4f0ff599d4942a7339219c71 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 18 Aug 2025 11:56:38 +0200
Subject: [PATCH 82/91] Fix group assignment url for non-manage roles on
 repository [SCI-12271]

---
 app/serializers/lists/repository_serializer.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/serializers/lists/repository_serializer.rb b/app/serializers/lists/repository_serializer.rb
index 47b2f6724..9eec6b7e6 100644
--- a/app/serializers/lists/repository_serializer.rb
+++ b/app/serializers/lists/repository_serializer.rb
@@ -58,7 +58,8 @@ module Lists
         show_access: access_permissions_repository_path(object),
         share: team_shared_objects_path(current_user.current_team, object_id: object.id, object_type: 'Repository'),
         user_roles: user_roles_access_permissions_repository_path(object),
-        user_group_members: users_users_settings_team_user_groups_path(team_id: current_user.current_team_id)
+        user_group_members: users_users_settings_team_user_groups_path(team_id: current_user.current_team_id),
+        show_user_group_assignments_access: show_user_group_assignments_access_permissions_repository_path(object)
       }
 
       urls[:show] = repository_path(object) if can_read?
@@ -68,7 +69,6 @@ module Lists
         urls[:new_access] = new_access_permissions_repository_path(id: object.id)
         urls[:create_access] = access_permissions_repositories_path(id: object.id)
         urls[:unassigned_user_groups] = unassigned_user_groups_access_permissions_repository_path(id: object.id)
-        urls[:show_user_group_assignments_access] = show_user_group_assignments_access_permissions_repository_path(object)
       end
 
       urls

From 7c8fe34db5cefe190d3a9e682385223193c367f2 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 18 Aug 2025 14:04:16 +0200
Subject: [PATCH 83/91] Fix notification recipients [SCI-12273]

---
 app/models/concerns/assignable.rb             | 24 +++++++++++++++++++
 .../recipients/due_date_recipients.rb         |  5 +---
 .../recipients/repository_item_recipients.rb  |  4 ++--
 3 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/app/models/concerns/assignable.rb b/app/models/concerns/assignable.rb
index 582d75340..42f8e511f 100644
--- a/app/models/concerns/assignable.rb
+++ b/app/models/concerns/assignable.rb
@@ -41,6 +41,30 @@ module Assignable
       User.where(id: direct_user_ids).or(User.where(id: group_user_ids)).or(User.where(id: team_user_ids))
     end
 
+    def users_with_permission(permission, teams = Team.all)
+      permitted_individual_assignments = user_assignments.joins(:user_role).where(team: teams).where(
+        'user_roles.permissions @> ARRAY[?]::varchar[]', [permission]
+      )
+
+      disallowed_assignments = user_assignments.joins(:user_role).where(team: teams).where(
+        'NOT(user_roles.permissions @> ARRAY[?]::varchar[])', [permission]
+      )
+
+      permitted_user_group_assignments = user_group_assignments.joins(:user_role, user_group: { user_group_memberships: :user }).where(team: teams).where(
+        'user_roles.permissions @> ARRAY[?]::varchar[]', [permission]
+      )
+
+      permitted_team_assignments = team_assignments.joins(:user_role, team: { user_assignments: :user }).where(team: teams).where(
+        'user_roles.permissions @> ARRAY[?]::varchar[]', [permission]
+      )
+
+      User.where(id: permitted_individual_assignments.select(:user_id)).or(
+        User.where(id: permitted_user_group_assignments.select('user_group_memberships.user_id')).or(
+          User.where(id: permitted_team_assignments.select('user_assignments.user_id'))
+        )
+      ).where.not(id: disallowed_assignments.select(:user_id))
+    end
+
     def default_public_user_role_id(current_team = nil)
       if team_assignments.loaded?
         team_assignments.find { |ta| ta.team_id == (current_team || team).id }&.user_role_id
diff --git a/app/notifications/recipients/due_date_recipients.rb b/app/notifications/recipients/due_date_recipients.rb
index 38c206637..7f568f360 100644
--- a/app/notifications/recipients/due_date_recipients.rb
+++ b/app/notifications/recipients/due_date_recipients.rb
@@ -14,10 +14,7 @@ module Recipients
                            end
       return User.none unless record
 
-      User.where(id: record.user_assignments
-                           .joins(:user_role)
-                           .where('? = ANY(user_roles.permissions)', permission)
-                           .select(:user_id))
+      record.users_with_permission(permission)
     end
   end
 end
diff --git a/app/notifications/recipients/repository_item_recipients.rb b/app/notifications/recipients/repository_item_recipients.rb
index bf1f0ad85..f89a0ab28 100644
--- a/app/notifications/recipients/repository_item_recipients.rb
+++ b/app/notifications/recipients/repository_item_recipients.rb
@@ -6,7 +6,7 @@ class Recipients::RepositoryItemRecipients
   end
 
   def recipients
-    repository_row = RepositoryRow.find(@repository_row_id)
-    repository_row.repository.team.users
+    repository = RepositoryRow.find(@repository_row_id).repository
+    repository.users_with_permission(RepositoryPermissions::READ, repository.team)
   end
 end

From d30e1a0a7b90e8ed0f99b9239f739e4fb4156c22 Mon Sep 17 00:00:00 2001
From: Martin Artnik <85488244+artoscinote@users.noreply.github.com>
Date: Tue, 19 Aug 2025 13:38:14 +0200
Subject: [PATCH 84/91] Bump version to 1.44.0

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

diff --git a/VERSION b/VERSION
index 758e98242..372cf402c 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.43.0.2
+1.44.0

From 8bb21d3eabc7a111c124203e27a645eb92ab8a97 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Tue, 19 Aug 2025 15:20:57 +0200
Subject: [PATCH 85/91] Update sorting by access column [SCI-12275]

---
 app/services/lists/forms_service.rb        | 10 ++++++++--
 app/services/lists/protocols_service.rb    | 16 +++++++++-------
 app/services/lists/repositories_service.rb | 17 +++++++++++++----
 3 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/app/services/lists/forms_service.rb b/app/services/lists/forms_service.rb
index b3b14c08c..ddc6e99e2 100644
--- a/app/services/lists/forms_service.rb
+++ b/app/services/lists/forms_service.rb
@@ -3,7 +3,13 @@
 module Lists
   class FormsService < BaseService
     def fetch_records
-      @records = @raw_data.left_outer_joins(:user_assignments)
+      user_assignments = @raw_data.joins(:user_assignments).select(:assignable_id, :user_id)
+      user_group_assignments = @raw_data.joins(user_group_assignments: { user_group: :user_group_memberships })
+                                        .select('user_group_assignments.assignable_id, user_group_memberships.user_id')
+      team_assignments = @raw_data.joins(team_assignments: { team: :user_assignments }).select('team_assignments.assignable_id, user_assignments.user_id')
+
+      @records = @raw_data.joins("LEFT JOIN (#{user_assignments.to_sql} UNION #{team_assignments.to_sql} UNION #{user_group_assignments.to_sql})
+                                  all_assigned_users ON all_assigned_users.assignable_id = forms.id")
                           .left_outer_joins(:form_responses)
                           .joins(
                             'LEFT OUTER JOIN users AS publishers ' \
@@ -12,7 +18,7 @@ module Lists
                             'forms.* AS forms',
                             'publishers.full_name AS published_by_user',
                             'COUNT(DISTINCT form_responses.id) AS used_in_protocols_count',
-                            'COUNT(DISTINCT user_assignments.id) AS user_assignment_count'
+                            'COUNT(DISTINCT all_assigned_users.user_id) AS user_assignment_count'
                           ).group('forms.id', 'publishers.full_name')
 
       view_mode = @params[:view_mode] || 'active'
diff --git a/app/services/lists/protocols_service.rb b/app/services/lists/protocols_service.rb
index b74c68e55..629f1789e 100644
--- a/app/services/lists/protocols_service.rb
+++ b/app/services/lists/protocols_service.rb
@@ -22,6 +22,11 @@ module Lists
       @records = Protocol.where('protocols.id IN (?) OR protocols.id IN (?) OR protocols.id IN (?)',
                                 original_without_versions, published_versions, new_drafts)
 
+      user_assignments = @records.joins(:user_assignments).select(:assignable_id, :user_id)
+      user_group_assignments = @records.joins(user_group_assignments: { user_group: :user_group_memberships })
+                                       .select('user_group_assignments.assignable_id, user_group_memberships.user_id')
+      team_assignments = @records.joins(team_assignments: { team: :user_assignments }).select('team_assignments.assignable_id, user_assignments.user_id')
+
       @records = @records.preload(:parent, :latest_published_version, :draft,
                                   :protocol_keywords, user_assignments: %i(user user_role))
                          .joins("LEFT OUTER JOIN protocols protocol_versions " \
@@ -48,9 +53,8 @@ module Lists
                                 'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
                          .joins('LEFT OUTER JOIN "users" "archived_users" ON "archived_users"."id" = "protocols"."archived_by_id"')
                          .joins('LEFT OUTER JOIN "users" ON "users"."id" = "protocols"."published_by_id"')
-                         .joins('LEFT OUTER JOIN "user_assignments" "all_user_assignments" ' \
-                                'ON "all_user_assignments"."assignable_type" = \'Protocol\' ' \
-                                'AND "all_user_assignments"."assignable_id" = "protocols"."id"')
+                         .joins("LEFT JOIN (#{user_assignments.to_sql} UNION #{team_assignments.to_sql} UNION #{user_group_assignments.to_sql})
+                                 all_assigned_users ON all_assigned_users.assignable_id = protocols.id")
                          .group('"protocols"."id"')
                          .select(
                            '"protocols".*',
@@ -61,7 +65,7 @@ module Lists
                            "THEN 0 ELSE COUNT(DISTINCT(\"protocol_versions\".\"id\")) + 1 " \
                            "END AS nr_of_versions",
                            'COUNT(DISTINCT("linked_task_protocols"."id")) AS nr_of_linked_tasks',
-                           'COUNT(DISTINCT("all_user_assignments"."id")) AS "nr_of_assigned_users"',
+                           'COUNT(DISTINCT all_assigned_users.user_id) AS "nr_of_assigned_users"',
                            'MAX("users"."full_name") AS "full_username_str"', # "Hack" to get single username
                            'MAX("archived_users"."full_name") AS "archived_full_username_str"'
                          )
@@ -107,9 +111,7 @@ module Lists
         @records = @records.where(protocols: { published_by_id: @filters[:published_by].values })
       end
 
-      if @filters[:members].present?
-        @records = @records.where(all_user_assignments: { user_id: @filters[:members].values })
-      end
+      @records = @records.where(all_assigned_users: { user_id: @filters[:members].values }) if @filters[:members].present?
 
       if @filters[:has_draft].present?
         @records =
diff --git a/app/services/lists/repositories_service.rb b/app/services/lists/repositories_service.rb
index e9ecca151..19edf93f6 100644
--- a/app/services/lists/repositories_service.rb
+++ b/app/services/lists/repositories_service.rb
@@ -5,15 +5,23 @@ module Lists
     private
 
     def fetch_records
+      user_assignments = @raw_data.joins(:user_assignments).select(:assignable_id, :user_id)
+      user_group_assignments = @raw_data.joins(user_group_assignments: { user_group: :user_group_memberships })
+                                        .select('user_group_assignments.assignable_id, user_group_memberships.user_id')
+      team_assignments = @raw_data.joins(team_assignments: { team: :user_assignments }).select('team_assignments.assignable_id, user_assignments.user_id')
+
       @records = @raw_data.joins('LEFT OUTER JOIN users AS creators ' \
                                  'ON repositories.created_by_id = creators.id')
                           .joins('LEFT OUTER JOIN users AS archivers ' \
                                  'ON repositories.archived_by_id = archivers.id')
-                          .joins(:team)
+                          .joins("LEFT OUTER JOIN (#{user_assignments.to_sql} UNION #{team_assignments.to_sql} UNION #{user_group_assignments.to_sql})
+                                 all_assigned_users ON all_assigned_users.assignable_id = repositories.id")
+                          .joins('INNER JOIN teams AS teams_repositories ON teams_repositories.id = repositories.team_id')
                           .select('repositories.*')
-                          .select('MAX(teams.name) AS team_name')
+                          .select('MAX(teams_repositories.name) AS team_name')
                           .select('MAX(creators.full_name) AS created_by_user')
                           .select('MAX(archivers.full_name) AS archived_by_user')
+                          .select('COUNT(DISTINCT all_assigned_users.user_id) AS "assigned_users_count"')
                           .select(shared_sql_select)
                           .preload(:team_assignments, :user_group_assignments, user_assignments: %i(user user_role))
                           .group('repositories.id')
@@ -30,7 +38,7 @@ module Lists
       @records = @records.where_attributes_like(
         [
           'repositories.name',
-          'teams.name',
+          'teams_repositories.name',
           'creators.full_name',
           'archivers.full_name'
         ],
@@ -48,7 +56,8 @@ module Lists
         archived_by: 'archived_by_user',
         nr_of_rows: 'repository_rows_count',
         code: 'repositories.id',
-        shared_label: 'shared'
+        shared_label: 'shared',
+        assigned_users: 'assigned_users_count'
       }
     end
 

From ee32a7369495b7532bb1f474bcf9aa8c3eddd28c Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <oleksii@scinote.net>
Date: Tue, 19 Aug 2025 16:28:55 +0200
Subject: [PATCH 86/91] Fix migration of protocol template assignments
 [SCI-12283]

---
 app/models/protocol.rb                                      | 6 +++---
 ...48_move_every_one_else_assignment_to_team_assignments.rb | 4 ++++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 0e2715aea..a97bd55c3 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -720,19 +720,19 @@ class Protocol < ApplicationRecord
   private
 
   def after_user_assignment_changed(user_assignment)
-    return unless in_repository_published_original?
+    return if skip_user_assignments || !in_repository_published_original?
 
     sync_child_protocol_assignment(user_assignment)
   end
 
   def after_user_group_assignment_changed(user_group_assignment)
-    return unless in_repository_published_original?
+    return if skip_user_assignments || !in_repository_published_original?
 
     sync_child_protocol_assignment(user_group_assignment)
   end
 
   def after_team_assignment_changed(user_group_assignment)
-    return unless in_repository_published_original?
+    return if skip_user_assignments || !in_repository_published_original?
 
     sync_child_protocol_assignment(user_group_assignment)
   end
diff --git a/db/migrate/20250707080048_move_every_one_else_assignment_to_team_assignments.rb b/db/migrate/20250707080048_move_every_one_else_assignment_to_team_assignments.rb
index 2f9bf367d..098d0bcdb 100644
--- a/db/migrate/20250707080048_move_every_one_else_assignment_to_team_assignments.rb
+++ b/db/migrate/20250707080048_move_every_one_else_assignment_to_team_assignments.rb
@@ -1,5 +1,8 @@
 # frozen_string_literal: true
 
+require 'activerecord-import/base'
+require 'activerecord-import/active_record/adapters/postgresql_adapter'
+
 class MoveEveryOneElseAssignmentToTeamAssignments < ActiveRecord::Migration[7.2]
   def up
     # rubocop:disable Metrics/BlockLength
@@ -141,6 +144,7 @@ class MoveEveryOneElseAssignmentToTeamAssignments < ActiveRecord::Migration[7.2]
 
     return if scope.blank?
 
+    record.skip_user_assignments = true
     record.team_assignments.create!(team_id: team_id, user_role: scope.first.user_role)
     scope.delete_all
   end

From 5aa4a7142dd83a40897c3b98041facf9474d103a Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Wed, 20 Aug 2025 08:45:21 +0200
Subject: [PATCH 87/91] Fix repositories list dropdown list for create item
 from task [SCI-12279]

---
 app/controllers/repositories_controller.rb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index 34c01b9c7..37b2466d5 100644
--- a/app/controllers/repositories_controller.rb
+++ b/app/controllers/repositories_controller.rb
@@ -44,7 +44,9 @@ class RepositoriesController < ApplicationController
   end
 
   def list
-    repositories = if params[:manageable] == 'true'
+    repositories = if params[:appendable] == 'true'
+                     Repository.appendable_by_user(current_user)
+                   elsif params[:manageable] == 'true'
                      Repository.with_granted_permissions(current_user, RepositoryPermissions::ROWS_UPDATE, current_team)
                    else
                      Repository.readable_by_user(current_user, current_team)
@@ -487,9 +489,7 @@ class RepositoriesController < ApplicationController
 
   def load_repositories
     @repositories =
-      if params[:appendable] == 'true'
-        Repository.appendable_by_user(current_user)
-      elsif can_manage_team?(current_team)
+      if can_manage_team?(current_team)
         # Team owners see all repositories in the team
         current_team.repositories.or(Repository.shared_with_team(current_team))
       else

From 84f806f623893b588f75986e858d8edd853863f1 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Wed, 20 Aug 2025 08:36:06 +0200
Subject: [PATCH 88/91] Fix dashboard filters for tasks [SCI-12278]

---
 .../dashboard/calendars_controller.rb         | 26 +++++++++----------
 .../dashboard/current_tasks_controller.rb     |  4 +--
 app/models/user.rb                            |  2 --
 spec/models/user_spec.rb                      |  1 -
 4 files changed, 15 insertions(+), 18 deletions(-)

diff --git a/app/controllers/dashboard/calendars_controller.rb b/app/controllers/dashboard/calendars_controller.rb
index 8242ee40f..6bed36ca3 100644
--- a/app/controllers/dashboard/calendars_controller.rb
+++ b/app/controllers/dashboard/calendars_controller.rb
@@ -9,13 +9,13 @@ module Dashboard
       date = params[:date].to_date
       start_date = date.beginning_of_month - 8.days
       end_date = date.end_of_month + 15.days
-      due_dates = current_user.my_modules.readable_by_user(current_user).active.uncomplete
-                              .joins(experiment: :project)
-                              .where(experiments: { archived: false })
-                              .where(projects: { archived: false })
-                              .where(my_modules: { due_date: start_date..end_date })
-                              .joins(:protocols).where(protocols: { team_id: current_team.id })
-                              .pluck(:due_date)
+      due_dates = MyModule.readable_by_user(current_user).active.uncomplete
+                          .joins(experiment: :project)
+                          .where(experiments: { archived: false })
+                          .where(projects: { archived: false })
+                          .where(my_modules: { due_date: start_date..end_date })
+                          .joins(:protocols).where(protocols: { team_id: current_team.id })
+                          .pluck(:due_date)
       render json: { events: due_dates.map { |i| { date: i.to_date } } }
     end
 
@@ -23,12 +23,12 @@ module Dashboard
       date = params[:date].to_date
       start_date = date.beginning_of_day
       end_date = date.end_of_day
-      my_modules = current_user.my_modules.readable_by_user(current_user).active.uncomplete
-                               .joins(experiment: :project)
-                               .where(experiments: { archived: false })
-                               .where(projects: { archived: false })
-                               .where(my_modules: { due_date: start_date..end_date })
-                               .where(projects: { team_id: current_team.id })
+      my_modules = MyModule.readable_by_user(current_user).active.uncomplete
+                           .joins(experiment: :project)
+                           .where(experiments: { archived: false })
+                           .where(projects: { archived: false })
+                           .where(my_modules: { due_date: start_date..end_date })
+                           .where(projects: { team_id: current_team.id })
       render json: {
         html: render_to_string(partial: 'shared/my_modules_list_partial',
                                locals: { my_modules: my_modules },
diff --git a/app/controllers/dashboard/current_tasks_controller.rb b/app/controllers/dashboard/current_tasks_controller.rb
index a61a2c787..85cbd1b46 100644
--- a/app/controllers/dashboard/current_tasks_controller.rb
+++ b/app/controllers/dashboard/current_tasks_controller.rb
@@ -34,7 +34,7 @@ module Dashboard
                              .search_by_name(current_user, current_team, params[:query]).select(:id, :name)
 
       unless params[:mode] == 'team'
-        projects = projects.where(id: current_user.my_modules.joins(:experiment)
+        projects = projects.where(id: MyModule.readable_by_user(current_user).joins(:experiment)
           .group(:project_id).select(:project_id).pluck(:project_id))
       end
       render json: projects.map { |i| { value: i.id, label: escape_input(i.name) } }, status: :ok
@@ -51,7 +51,7 @@ module Dashboard
                             .search_by_name(current_user, current_team, params[:query]).select(:id, :name)
 
       unless params[:mode] == 'team'
-        experiments = experiments.where(id: current_user.my_modules
+        experiments = experiments.where(id: MyModule.readable_by_user(current_user)
           .group(:experiment_id).select(:experiment_id).pluck(:experiment_id))
       end
       render json: experiments.map { |i| { value: i.id, label: escape_input(i.name) } }, status: :ok
diff --git a/app/models/user.rb b/app/models/user.rb
index 195d3710d..8cc04cb92 100644
--- a/app/models/user.rb
+++ b/app/models/user.rb
@@ -62,9 +62,7 @@ class User < ApplicationRecord
   has_many :user_group_memberships, dependent: :destroy
   has_many :user_groups, through: :user_group_memberships
   has_many :teams, through: :user_assignments, source: :assignable, source_type: 'Team'
-  has_many :projects, through: :user_assignments, source: :assignable, source_type: 'Project'
   has_many :user_my_modules, inverse_of: :user
-  has_many :my_modules, through: :user_assignments, source: :assignable, source_type: 'MyModule'
   has_many :comments, inverse_of: :user
   has_many :activities, inverse_of: :owner, foreign_key: 'owner_id'
   has_many :results, inverse_of: :user
diff --git a/spec/models/user_spec.rb b/spec/models/user_spec.rb
index 9a784d61e..d2fa9ff1f 100644
--- a/spec/models/user_spec.rb
+++ b/spec/models/user_spec.rb
@@ -47,7 +47,6 @@ describe User, type: :model do
 
   describe 'Relations' do
     it { should have_many :teams }
-    it { should have_many :projects }
     it { should have_many :user_my_modules }
     it { should have_many :comments }
     it { should have_many :activities }

From 807f0458b92072902316091fc633127e37d36297 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Wed, 20 Aug 2025 10:46:56 +0200
Subject: [PATCH 89/91] Add unique constraint to user assignments [SCI-12284]

---
 ...d_unique_constraint_to_user_assignments.rb | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 db/migrate/20250707080046_add_unique_constraint_to_user_assignments.rb

diff --git a/db/migrate/20250707080046_add_unique_constraint_to_user_assignments.rb b/db/migrate/20250707080046_add_unique_constraint_to_user_assignments.rb
new file mode 100644
index 000000000..90e615d96
--- /dev/null
+++ b/db/migrate/20250707080046_add_unique_constraint_to_user_assignments.rb
@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+class AddUniqueConstraintToUserAssignments < ActiveRecord::Migration[7.2]
+  def up
+    # delete the duplicates
+    execute(
+      'WITH uniq AS
+      (SELECT DISTINCT ON (user_id, assignable_type, assignable_id, team_id) * FROM user_assignments)
+      DELETE FROM user_assignments WHERE user_assignments.id NOT IN
+        (SELECT id FROM uniq)'
+    )
+
+    remove_index :user_assignments, name: 'index_user_assignments_on_assignable'
+    add_index :user_assignments,
+              %i(assignable_type assignable_id user_id team_id),
+              unique: true,
+              name: 'index_user_assignments_on_unique_assignable_in_team'
+  end
+
+  def down
+    add_index :user_assignments, %i(assignable_type assignable_id), name: 'index_user_assignments_on_assignable'
+    remove_index :user_assignments, name: 'index_user_assignments_on_unique_assignable_in_team'
+  end
+end

From 98a402ca325c91decf6266d000a97979050e6200 Mon Sep 17 00:00:00 2001
From: Andrej <andrej@scinote.net>
Date: Wed, 20 Aug 2025 15:43:37 +0200
Subject: [PATCH 90/91] Fix opening my profile page [SCI-12278]

---
 app/models/user.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/models/user.rb b/app/models/user.rb
index 8cc04cb92..6e6169cf9 100644
--- a/app/models/user.rb
+++ b/app/models/user.rb
@@ -463,6 +463,7 @@ class User < ApplicationRecord
   # Returns a hash with user statistics
   def statistics
     statistics = {}
+    projects = Project.readable_by_user(self, teams)
     statistics[:number_of_teams] = teams.count
     statistics[:number_of_projects] = projects.count
     number_of_experiments = 0

From 7381eff0d4c62032514b7e9e5d51e30581911868 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Thu, 21 Aug 2025 10:16:31 +0200
Subject: [PATCH 91/91] Properly scope assignments to team in
 GenerateUserAssignmentsJob [SCI-12284]

---
 app/jobs/user_assignments/generate_user_assignments_job.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/jobs/user_assignments/generate_user_assignments_job.rb b/app/jobs/user_assignments/generate_user_assignments_job.rb
index 49253da17..6d9ae0a0e 100644
--- a/app/jobs/user_assignments/generate_user_assignments_job.rb
+++ b/app/jobs/user_assignments/generate_user_assignments_job.rb
@@ -88,7 +88,8 @@ module UserAssignments
 
       new_assignment = parent_assignment.class.find_or_initialize_by(
         "#{type}_id": parent_assignment.public_send(type).id,
-        assignable: resource
+        assignable: resource,
+        team_id: parent_assignment.team_id
       )
 
       return if new_assignment.manually_assigned?