diff --git a/.gitignore b/.gitignore
index d3fd6cc3ab..5c5f043efe 100644
--- a/.gitignore
+++ b/.gitignore
@@ -66,6 +66,7 @@ public/javascripts/i18n.js
 public/javascripts/translations.js
 public/stylesheets/*_cached.css
 public/system/
+public/sitemaps/*
 
 public/assets/
 public/assets_dev/
diff --git a/Gemfile b/Gemfile
index fd40d4e720..619ca2babd 100644
--- a/Gemfile
+++ b/Gemfile
@@ -109,6 +109,7 @@ gem 'ransack'
 
 gem 'terser', '~> 1.1', '>= 1.1.1'
 
+
 # Rails 4 upgrade
 gem 'activerecord-session_store'
 gem 'rails-observers'
@@ -177,6 +178,8 @@ group :development do
 
   gem 'web-console', '>= 4.1.0'
   gem 'rack-mini-profiler', '~> 2.0'
+  gem "flamegraph", "~> 0.9.5"
+  gem "stackprof", "~> 0.2.25"
   gem 'listen', '~> 3.3'
 end
 
@@ -202,3 +205,5 @@ group :test, :development do
   gem 'teaspoon'
   gem 'teaspoon-mocha'
 end
+
+gem "sitemap_generator", "~> 6.3"
diff --git a/Gemfile.lock b/Gemfile.lock
index b2797432af..192e716d39 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -286,6 +286,7 @@ GEM
       loofah (>= 2.3.1)
       sax-machine (>= 1.0)
     ffi (1.15.5)
+    flamegraph (0.9.5)
     fssm (0.2.10)
     gem-licenses (0.2.2)
     gitlab_omniauth-ldap (2.2.0)
@@ -828,6 +829,8 @@ GEM
       simplecov_json_formatter (~> 0.1)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.3)
+    sitemap_generator (6.3.0)
+      builder (~> 3.0)
     slop (3.6.0)
     snaky_hash (2.0.0)
       hashie
@@ -852,6 +855,7 @@ GEM
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
     sqlite3 (1.4.2)
+    stackprof (0.2.25)
     stringio (3.0.1)
     sunspot (2.6.0)
       pr_geohash (~> 1.0)
@@ -990,6 +994,7 @@ DEPENDENCIES
   exception_notification
   factory_bot (~> 6.2.1)
   feedjira
+  flamegraph (~> 0.9.5)
   fleximage!
   fssm
   gem-licenses
@@ -1073,8 +1078,10 @@ DEPENDENCIES
   seedbank
   simple-spreadsheet-extractor (~> 0.18.0)
   simplecov
+  sitemap_generator (~> 6.3)
   sprockets-rails
   sqlite3 (~> 1.4)
+  stackprof (~> 0.2.25)
   stringio (= 3.0.1)
   sunspot_matchers
   sunspot_rails
diff --git a/app/controllers/assays_controller.rb b/app/controllers/assays_controller.rb
index 48c13e0dd1..796642c82d 100644
--- a/app/controllers/assays_controller.rb
+++ b/app/controllers/assays_controller.rb
@@ -6,6 +6,7 @@ class AssaysController < ApplicationController
   before_action :assays_enabled?
   before_action :find_assets, :only=>[:index]
   before_action :find_and_authorize_requested_item, :only=>[:edit, :update, :destroy, :manage, :manage_update, :show, :new_object_based_on_existing_one]
+  before_action :delete_linked_sample_types, only: [:destroy]
 
   #project_membership_required_appended is an alias to project_membership_required, but is necessary to include the actions
   #defined in the application controller
@@ -18,7 +19,7 @@ class AssaysController < ApplicationController
   api_actions :index, :show, :create, :update, :destroy
 
   def new_object_based_on_existing_one
-    @existing_assay =  Assay.find(params[:id])
+    @existing_assay = Assay.find(params[:id])
     @assay = @existing_assay.clone_with_associations
 
     if @existing_assay.can_view?
@@ -62,9 +63,7 @@ def new_object_based_on_existing_one
       flash[:error]="You do not have the necessary permissions to copy this #{t('assays.assay')}"
       redirect_to @existing_assay
     end
-
-
-   end
+  end
 
   def new
     @assay=setup_new_asset
@@ -112,6 +111,13 @@ def create
     end
   end
 
+
+  def delete_linked_sample_types
+    return unless is_single_page_assay?
+
+    @assay.sample_type.destroy
+  end
+
   def update
     update_assay_organisms @assay, params
     update_assay_human_diseases @assay, params
@@ -177,4 +183,10 @@ def assay_params
       assay_params[:model_ids].select! { |id| Model.find_by_id(id).try(:can_view?) } if assay_params.key?(:model_ids)
     end
   end
+
+  def is_single_page_assay?
+    return false unless params.key?(:return_to)
+
+    params[:return_to].start_with? '/single_pages/'
+  end
 end
diff --git a/app/controllers/studies_controller.rb b/app/controllers/studies_controller.rb
index 2aed0d36a1..bec5ef69fc 100644
--- a/app/controllers/studies_controller.rb
+++ b/app/controllers/studies_controller.rb
@@ -6,6 +6,7 @@ class StudiesController < ApplicationController
   before_action :studies_enabled?
   before_action :find_assets, only: [:index]
   before_action :find_and_authorize_requested_item, only: %i[edit update destroy manage manage_update show new_object_based_on_existing_one]
+  before_action :delete_linked_sample_types, only: [:destroy]
 
   # project_membership_required_appended is an alias to project_membership_required, but is necesary to include the actions
   # defined in the application controller
@@ -88,6 +89,16 @@ def update
     end
   end
 
+  def delete_linked_sample_types
+    return unless is_single_page_study?
+
+    # The study sample types must be destroyed in reversed order
+    # otherwise the first sample type won't be removed becaused it is linked from the second
+    study_st_ids = @study.sample_types.map(&:id).sort { |a, b| b <=> a }
+    SampleType.destroy(study_st_ids)
+  end
+
+
   def show
     @study = Study.find(params[:id])
 
@@ -201,7 +212,7 @@ def batch_create
       study_params = {
         title: params[:studies][:title][index],
         description: params[:studies][:description][index],
-        investigation_id: params[:study][:investigation_id],        
+        investigation_id: params[:study][:investigation_id],
         custom_metadata: CustomMetadata.new(
           custom_metadata_type: metadata_types,
           data: metadata
@@ -351,3 +362,9 @@ def study_params
                                   { custom_metadata_attributes: determine_custom_metadata_keys })
   end
 end
+
+def is_single_page_study?
+  return false unless params.key?(:return_to)
+
+  params[:return_to].start_with? '/single_pages/'
+end
diff --git a/app/controllers/templates_controller.rb b/app/controllers/templates_controller.rb
index 53d070285a..dcb5dace04 100644
--- a/app/controllers/templates_controller.rb
+++ b/app/controllers/templates_controller.rb
@@ -87,7 +87,7 @@ def task_status
 
   def populate_template
     uploaded_file = params[:template_json_file]
-    dir = Rails.root.join('config', 'default_data', 'source_types')
+    dir = Seek::Config.append_filestore_path('source_types')
 
     if Dir.exist?(dir)
       `rm #{dir}/*`
@@ -146,11 +146,11 @@ def set_status
   end
 
   def lockfile
-    Rails.root.join('tmp', 'populate_templates.lock')
+    Rails.root.join(Seek::Config.temporary_filestore_path, 'populate_templates.lock')
   end
 
   def resultfile
-    Rails.root.join('tmp', 'populate_templates.result')
+    Rails.root.join(Seek::Config.temporary_filestore_path, 'populate_templates.result')
   end
 
   def running!
diff --git a/app/models/assay.rb b/app/models/assay.rb
index d8bb9b9a68..13b2b9279e 100644
--- a/app/models/assay.rb
+++ b/app/models/assay.rb
@@ -77,7 +77,7 @@ def short_description
   end
 
   def state_allows_delete?(*args)
-    assets.empty? && publications.empty? && super
+    assets.empty? && publications.empty? && associated_samples_through_sample_type.empty? && super
   end
 
   # returns true if this is a modelling class of assay
@@ -90,6 +90,10 @@ def is_experimental?
     !assay_class.nil? && assay_class.key == 'EXP'
   end
 
+  def associated_samples_through_sample_type
+    (sample_type.nil? || sample_type.samples.nil?) ? [] : sample_type.samples
+  end
+
   # Create or update relationship of this assay to another, with a specific relationship type and version
   def associate(asset, options = {})
     if asset.is_a?(Organism)
diff --git a/app/models/study.rb b/app/models/study.rb
index 944373fc9b..bc1691852e 100644
--- a/app/models/study.rb
+++ b/app/models/study.rb
@@ -2,7 +2,7 @@ class Study < ApplicationRecord
 
   enum status: [:planned, :running, :completed, :cancelled, :failed]
   belongs_to :assignee, class_name: 'Person'
-  
+
   searchable(:auto_index => false) do
     text :experimentalists
   end if Seek::Config.solr_enabled
@@ -22,7 +22,7 @@ class Study < ApplicationRecord
   has_many :sop_versions, through: :assays
 
   has_one :external_asset, as: :seek_entity, dependent: :destroy
-  
+
   has_and_belongs_to_many :sops
 
   has_and_belongs_to_many :sample_types
@@ -41,7 +41,16 @@ def assets
   end
 
   def state_allows_delete? *args
-    assays.empty? && super
+    assays.empty? && associated_samples_through_sample_type.empty? && super
+  end
+
+  def associated_samples_through_sample_type
+    return [] if sample_types.nil?
+    st_samples = []
+    sample_types.map do |st|
+      st.samples.map { |sts| st_samples.push sts }
+    end
+    st_samples
   end
 
   def clone_with_associations
diff --git a/app/views/general/_index.html.erb b/app/views/general/_index.html.erb
index 574ef2ffc1..37f9ff69e2 100644
--- a/app/views/general/_index.html.erb
+++ b/app/views/general/_index.html.erb
@@ -5,10 +5,14 @@
   show_new_button = true unless local_assigns.has_key?(:show_new_button)
   title ||= nil
   subtitle ||= nil
+	isa_templates_enabled = Seek::Config.sample_type_template_enabled && Seek::Config.project_single_page_advanced_enabled
 %>
 
 <div class="pull-right">
   <% if show_new_button && controller_model.can_create? %>
+    <% if isa_templates_enabled %>
+      <%= link_to "Query by #{t('template').pluralize}", query_form_samples_path, class: "btn btn-default btn" %>
+    <% end %>
     <%= button_link_to(new_item_label, "new", new_item_path) %>
   <% end %>
 
diff --git a/app/views/programmes/activation_review.html.erb b/app/views/programmes/activation_review.html.erb
index b7562f03b1..d373da2cd8 100644
--- a/app/views/programmes/activation_review.html.erb
+++ b/app/views/programmes/activation_review.html.erb
@@ -1,4 +1,4 @@
-<%= render :partial => "general/item_title",:locals => {:item=>@programme, :title_prefix=>"Acitivation required for: "} %>
+<%= render :partial => "general/item_title",:locals => {:item=>@programme, :title_prefix=>"Activation required for: "} %>
 
 <p>
   A <%= t('programme') %> has been created by a user, and requires activation. The <%= t('programme') %> created is <%= link_to @programme.title, @programme %>.
diff --git a/config/schedule.rb b/config/schedule.rb
index 5216b0f962..743d0d60ed 100644
--- a/config/schedule.rb
+++ b/config/schedule.rb
@@ -71,6 +71,11 @@ def offset(off_hours)
   runner "Seek::BioSchema::DataDump.generate_dumps"
 end
 
+# Generate a new sitemap...
+every 1.day, at: '12:45 am' do
+  rake "-s sitemap:refresh"
+end
+
 # not safe to automatically add in a non containerised environment
 if Seek::Docker.using_docker?
   every 10.minutes do
diff --git a/config/sitemap.rb b/config/sitemap.rb
new file mode 100644
index 0000000000..90cfab2813
--- /dev/null
+++ b/config/sitemap.rb
@@ -0,0 +1,19 @@
+# https://github.com/kjvarga/sitemap_generator#sitemapgenerator
+SitemapGenerator::Sitemap.sitemaps_path = "sitemaps"
+SitemapGenerator::Sitemap.create_index = "auto"
+SitemapGenerator::Sitemap.compress = false
+SitemapGenerator::Sitemap.default_host = URI.parse(Seek::Config.site_base_url)
+
+SitemapGenerator::Sitemap.create do
+  Seek::Util.searchable_types.each do |type|
+    add  polymorphic_path(type), lastmod: type.maximum(:updated_at), changefreq: 'daily', priority: 0.7
+  end
+end
+
+Seek::Util.searchable_types.each do |type|
+  SitemapGenerator::Sitemap.create(filename: type.table_name, include_root: false) do
+    type.authorized_for('view', nil).find_all do |obj|
+      add polymorphic_path(obj), lastmod: obj.updated_at, changefreq: 'daily', priority: 0.7
+    end
+  end
+end
diff --git a/lib/seek/isa_templates/template_extractor.rb b/lib/seek/isa_templates/template_extractor.rb
index b0487a7e24..236b8d5606 100644
--- a/lib/seek/isa_templates/template_extractor.rb
+++ b/lib/seek/isa_templates/template_extractor.rb
@@ -12,7 +12,7 @@ def self.extract_templates
         disable_authorization_checks do
           client = Ebi::OlsClient.new
           project = Project.find_or_create_by(title: 'Default Project')
-          directory = Rails.root.join('config', 'default_data', 'source_types')
+          directory = Seek::Config.append_filestore_path('source_types')
           directory_files = Dir.exist?(directory) ? Dir.glob("#{directory}/*.json") : []
           raise '<ul><li>Make sure to upload files that have the ".json" extension.</li></ul>' if directory_files == []
 
@@ -172,11 +172,11 @@ def self.seed_isa_tags
       end
 
       def self.lockfile
-        Rails.root.join('tmp', 'populate_templates.lock')
+        Rails.root.join(Seek::Config.temporary_filestore_path, 'populate_templates.lock')
       end
 
       def self.resultfile
-        Rails.root.join('tmp', 'populate_templates.result')
+        Rails.root.join(Seek::Config.temporary_filestore_path, 'populate_templates.result')
       end
     end
   end
diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index ca6b6e607a..51ef422a1c 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/lib/tasks/seek_upgrades.rake
@@ -8,28 +8,6 @@ namespace :seek do
   # these are the tasks required for this version upgrade
   task upgrade_version_tasks: %i[
     environment
-    db:seed:007_sample_attribute_types
-    update_missing_openbis_istest
-    update_missing_publication_versions
-    update_edam_controlled_vocab_keys
-    db:seed:011_topics_controlled_vocab
-    db:seed:012_operations_controlled_vocab
-    db:seed:013_formats_controlled_vocab
-    db:seed:014_data_controlled_vocab
-    db:seed:015_isa_tags
-    db:seed:003_model_formats
-    db:seed:004_model_recommended_environments
-    remove_orphaned_versions
-    refresh_workflow_internals
-    remove_scale_annotations
-    remove_spreadsheet_annotations
-    remove_node_annotations
-    convert_roles
-    update_edam_annotation_attributes
-    remove_orphaned_project_subscriptions
-    remove_node_activity_logs
-    remove_node_asset_creators
-    set_default_sample_type_creators
   ]
 
   # these are the tasks that are executes for each upgrade as standard, and rarely change
@@ -66,201 +44,6 @@ namespace :seek do
     end
   end
 
-  task(update_missing_openbis_istest: :environment) do
-    puts '... creating missing is_test for OpenbisEndpoint...'
-    create = 0
-    disable_authorization_checks do
-      OpenbisEndpoint.find_each do |openbis_endpoint|
-        # check if the publication has a version
-        # then create one if missing
-        if openbis_endpoint.is_test.nil?
-          openbis_endpoint.is_test = false # default -> prod, https
-          openbis_endpoint.save
-          unless openbis_endpoint.is_test.nil?
-            create += 1
-          end
-        end
-        # publication.save
-      end
-    end
-    puts " ... finished creating missing is_test for #{create.to_s} OpenbisEndpoint(s)"
-  end
-
-  task(update_missing_publication_versions: :environment) do
-    puts '... creating missing publications versions ...'
-    create = 0
-    disable_authorization_checks do
-      Publication.find_each do |publication|
-        # check if the publication has a version
-        # then create one if missing
-        if publication.latest_version.nil?
-          publication.save_as_new_version 'Version for legacy entries'
-          unless publication.latest_version.nil?
-            create += 1
-          end
-        end
-        # publication.save
-      end
-    end
-    puts " ... finished creating missing publications versions for #{create.to_s} publications"
-  end
-
-  task(remove_orphaned_versions: [:environment]) do
-    puts 'Removing orphaned versions ...'
-    count = 0
-    types = [DataFile::Version, Document::Version, Sop::Version, Model::Version, Presentation::Version,
-             Sop::Version, Workflow::Version]
-    disable_authorization_checks do
-      types.each do |type|
-        found = type.where.missing(:parent)
-        count += found.length
-        found.each(&:destroy)
-      end
-    end
-    puts "... finished removing #{count} orphaned versions"
-  end
-
-  task(remove_scale_annotations: [:environment]) do
-    a = Annotation.joins(:annotation_attribute).where(annotation_attribute: { name: ['additional_scale_info', 'scale'] })
-    count = a.count
-    a.destroy_all
-    AnnotationAttribute.where(name:['scale','additional_scale_info']).destroy_all
-    puts "Removed #{count} scale related annotations" if count > 0
-  end
-
-  task(remove_spreadsheet_annotations: [:environment]) do
-    annotations = Annotation.where(annotatable_type: 'CellRange')
-    count = annotations.count
-    values = TextValue.joins(:annotations).where(annotations: { annotatable_type: 'CellRange' })
-    values.select{|v| v.annotations.count == 1}.each(&:destroy)
-    annotations.destroy_all
-    AnnotationAttribute.where(name:'annotation').destroy_all
-    puts "Removed #{count} spreadsheet related annotations" if count > 0
-  end
-
-  task(remove_node_annotations: [:environment]) do
-    annotations = Annotation.where(annotatable_type: 'Node')
-    count = annotations.count
-    values = TextValue.joins(:annotations).where(annotations: { annotatable_type: 'Node' })
-    values.select{|v| v.annotations.count == 1}.each(&:destroy)
-    annotations.destroy_all
-    puts "Removed #{count} Node related annotations" if count > 0
-  end
-
-  task(convert_roles: [:environment]) do
-    puts 'Converting roles...'
-    disable_authorization_checks do
-      Person.find_each do |person|
-        RoleType.for_system.each do |rt|
-          mask = rt.id
-          if (person.roles_mask & mask) != 0
-            Role.where(role_type_id: rt.id, person_id: person.id, scope: nil).first_or_create!
-          end
-        end
-      end
-
-      class AdminDefinedRoleProject < ActiveRecord::Base; end
-
-      AdminDefinedRoleProject.find_each do |role|
-        RoleType.for_projects.each do |rt|
-          mask = rt.id
-          if (role.role_mask & mask) != 0
-            Role.where(role_type_id: rt.id, person_id: role.person_id,
-                       scope_type: 'Project', scope_id: role.project_id).first_or_create!
-          end
-        end
-      end
-
-      class AdminDefinedRoleProgramme < ActiveRecord::Base; end
-
-      AdminDefinedRoleProgramme.find_each do |role|
-        RoleType.for_programmes.each do |rt|
-          mask = rt.id
-          if (role.role_mask & mask) != 0
-            Role.where(role_type_id: rt.id, person_id: role.person_id,
-                       scope_type: 'Programme', scope_id: role.programme_id).first_or_create!
-          end
-        end
-      end
-    end
-  end
-
-  task(update_edam_annotation_attributes: [:environment]) do
-    defs = {
-      "edam_formats": "data_format_annotations",
-      "edam_topics": "topic_annotations",
-      "edam_operations": "operation_annotations",
-      "edam_data": "data_type_annotations"
-    }
-    defs.each do |old_name,new_name|
-      query = AnnotationAttribute.where(name: old_name)
-      if query.any?
-        puts "Updating EDAM based #{old_name} Annotation Attributes"
-        query.update_all(name: new_name)
-      end
-    end
-  end
-
-  task(update_edam_controlled_vocab_keys: [:environment]) do
-    defs = {
-      topics: 'edam_topics',
-      operations: 'edam_operations',
-      data_formats: 'edam_formats',
-      data_types: 'edam_data'
-    }
-
-    defs.each do |property, old_key|
-      new_key = SampleControlledVocab::SystemVocabs.database_key_for_property(property)
-      query = SampleControlledVocab.where(key: old_key)
-      if query.any?
-        puts "Updating key for #{old_key} controlled vocabulary"
-        query.update_all(key: new_key)
-      end
-    end
-  end
-
-  task(remove_orphaned_project_subscriptions: [:environment]) do
-    disable_authorization_checks do
-      ProjectSubscription.where.missing(:project).destroy_all
-    end
-  end
-
-  task(remove_node_activity_logs: [:environment]) do
-    logs = ActivityLog.where(activity_loggable_type: 'Node')
-    puts "Removing #{logs.count} Node related activity logs" if logs.count > 0
-    logs.delete_all
-  end
-
-  task(remove_node_asset_creators: [:environment]) do
-    creators = AssetsCreator.where(asset_type: 'Node')
-    puts "Removing #{creators.count} Node related asset creators" if creators.count > 0
-    creators.delete_all
-  end
-
-  task(refresh_workflow_internals: [:environment]) do |task|
-    ran = only_once(task) do
-      Rake::Task['seek:rebuild_workflow_internals'].invoke
-    end
-
-    puts "Skipping workflow internals rebuild, already done" unless ran
-  end
-
-  task(set_default_sample_type_creators: [:environment]) do
-    ran = only_once('set_default_sample_type_creators') do
-      puts "Setting default Sample Type creators"
-      count = 0
-      SampleType.all.each do |sample_type|
-        if sample_type.assets_creators.empty?
-          sample_type.assets_creators.build(creator: sample_type.contributor).save!
-          count += 1
-        end
-      end
-      puts "#{count} Sample Types updated"
-    end
-
-    puts "Skipping setting default Sample Type creators, as already set" unless ran
-  end
-
   private
 
   ##
diff --git a/test/functional/assays_controller_test.rb b/test/functional/assays_controller_test.rb
index 41b1d850d1..86b8c10ef0 100644
--- a/test/functional/assays_controller_test.rb
+++ b/test/functional/assays_controller_test.rb
@@ -1921,4 +1921,20 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links
     assert_select 'span.updated_last_by a', false, 'Last editor should not be shown if editor user has been deleted'
   end
 
+  test 'should delete empty assay with linked sample type' do
+    person = FactoryBot.create(:person)
+    assay_sample_type = FactoryBot.create :linked_sample_type, contributor: person
+    assay = FactoryBot.create(:assay,
+                              policy:FactoryBot.create(:private_policy, permissions:[FactoryBot.create(:permission,contributor: person, access_type:Policy::EDITING)]),
+                              sample_type: assay_sample_type,
+                              contributor: person)
+
+    login_as(person)
+
+    assert_difference('SampleType.count', -1) do
+      assert_difference('Assay.count', -1) do
+        delete :destroy, params: { id: assay.id, return_to: '/single_pages/' }
+      end
+    end
+  end
 end
diff --git a/test/functional/studies_controller_test.rb b/test/functional/studies_controller_test.rb
index 70db123ffd..4810d31a41 100644
--- a/test/functional/studies_controller_test.rb
+++ b/test/functional/studies_controller_test.rb
@@ -11,7 +11,7 @@ class StudiesControllerTest < ActionController::TestCase
   def setup
     login_as FactoryBot.create(:admin).user
   end
-  
+
   test 'should get index' do
     FactoryBot.create :study, policy: FactoryBot.create(:public_policy)
     get :index
@@ -1229,7 +1229,7 @@ def test_should_show_investigation_tab
                             policy: FactoryBot.create(:public_policy),
                             contributor: person)
     get :show, params: { id: study.id }
-    
+
     assert_response :success
     assert_select 'a[href=?]',
                   order_assays_study_path(study), count: 0
@@ -1394,4 +1394,22 @@ def test_should_show_investigation_tab
     assert_equal 'my_tag', assigns(:study).tags_as_text_array.first
   end
 
+  test 'should delete empty study with linked sample type' do
+    person = FactoryBot.create(:person)
+    study_source_sample_type = FactoryBot.create :linked_sample_type, contributor: person
+    study_sample_sample_type = FactoryBot.create :linked_sample_type, contributor: person
+    study = FactoryBot.create(:study,
+                              policy:FactoryBot.create(:private_policy, permissions:[FactoryBot.create(:permission,contributor: person, access_type:Policy::EDITING)]),
+                              sample_types: [study_source_sample_type, study_sample_sample_type],
+                              contributor: person)
+
+    login_as(person)
+
+    assert_difference('SampleType.count', -2) do
+      assert_difference('Study.count', -1) do
+        delete :destroy, params: { id: study.id, return_to: '/single_pages/' }
+      end
+    end
+  end
+
 end
diff --git a/test/unit/assay_test.rb b/test/unit/assay_test.rb
index 106f225503..1a948b9a21 100644
--- a/test/unit/assay_test.rb
+++ b/test/unit/assay_test.rb
@@ -260,6 +260,25 @@ class AssayTest < ActiveSupport::TestCase
     assert !one_assay_with_publication.can_delete?(User.current_user.person)
   end
 
+  # Users shouldn't be able to delete assays populated with samples through their linked sample types
+  test 'can only delete assays with empty sample types' do
+    assay_sample_type = FactoryBot.create(:simple_sample_type, title: "Assay Sample Type with samples")
+    empty_sample_type = FactoryBot.create(:simple_sample_type, title: "Empty assay Sample Type")
+    assay_samples = (0..4).map do |i|
+      FactoryBot.create(:sample, title: "DNA Extract nr. #{i}", sample_type: assay_sample_type)
+    end
+
+    assay = FactoryBot.create(:assay, title: "First Assay", sample_type: assay_sample_type)
+    empty_assay = FactoryBot.create(:assay, title: "Empty assay", sample_type:empty_sample_type)
+
+    assert_equal(assay.sample_type.samples.size, 5)
+    assert(empty_assay.sample_type.samples.none?)
+
+    assert_equal(assay.state_allows_delete?, false)
+    assert_equal(empty_assay.state_allows_delete?, true)
+  end
+
+
   test 'assets' do
     assay = assays(:metabolomics_assay)
     assert_equal 3, assay.assets.size, 'should be 2 sops and 1 data file'
diff --git a/test/unit/study_test.rb b/test/unit/study_test.rb
index d22ded3792..593a12b45e 100644
--- a/test/unit/study_test.rb
+++ b/test/unit/study_test.rb
@@ -45,6 +45,24 @@ class StudyTest < ActiveSupport::TestCase
     assert !study.can_delete?(study.contributor)
   end
 
+  # Users shouldn't be able to delete studies populated with samples through their linked sample types
+  test 'can only delete studies with empty sample types' do
+    study_source_sample_type = FactoryBot.create(:simple_sample_type, title: "Source Sample Type")
+    empty_sample_type = FactoryBot.create(:simple_sample_type, title: "Empty study Sample Type")
+    sources = (0..4).map do |i|
+      FactoryBot.create(:sample, title: "Source nr. #{i}", sample_type: study_source_sample_type)
+    end
+
+    study = FactoryBot.create(:study, title: "First study", sample_types: [study_source_sample_type])
+    empty_study = FactoryBot.create(:study, title: "Empty study", sample_types:[empty_sample_type])
+
+    assert_equal(study.sample_types.first.samples.size, 5)
+    assert(empty_study.sample_types.first.samples.none?)
+
+    assert_equal(study.state_allows_delete?, false)
+    assert_equal(empty_study.state_allows_delete?, true)
+  end
+
   test 'publications through assays' do
     assay1 = FactoryBot.create(:assay)
     study = assay1.study