diff --git a/Gemfile b/Gemfile
index 89b42534ce..bdad189046 100644
--- a/Gemfile
+++ b/Gemfile
@@ -52,7 +52,7 @@ gem 'will_paginate', '~> 3.1'
 gem 'yaml_db'
 gem 'rails_autolink'
 gem 'rfc-822'
-gem 'nokogiri', '~> 1.16.2'
+gem 'nokogiri', '~> 1.16.5'
 #necessary for newer hashie dependency, original api_smith is no longer active
 gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b'
 gem 'rdf-virtuoso', '>= 0.2.0'
@@ -134,7 +134,7 @@ gem 'request_store'
 
 gem 'bundler', '>= 1.8.4'
 
-gem 'ro-crate', '~> 0.5.1'
+gem 'ro-crate', '~> 0.5.2'
 
 gem 'rugged'
 gem 'i18n-js'
diff --git a/Gemfile.lock b/Gemfile.lock
index d3e795ca4e..946308413a 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -460,7 +460,7 @@ GEM
       nokogiri (~> 1)
       rake
     mini_mime (1.1.5)
-    mini_portile2 (2.8.5)
+    mini_portile2 (2.8.6)
     minitest (5.20.0)
     minitest-reporters (1.5.0)
       ansi
@@ -492,7 +492,7 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.0)
-    nokogiri (1.16.2)
+    nokogiri (1.16.5)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     nori (1.1.5)
@@ -737,7 +737,7 @@ GEM
       json (~> 2.3.0)
       ucf (~> 2.0.2)
       uuid (~> 2.3)
-    ro-crate (0.5.1)
+    ro-crate (0.5.2)
       addressable (>= 2.7, < 2.9)
       rubyzip (~> 2.0.0)
     rsolr (2.5.0)
@@ -1028,7 +1028,7 @@ DEPENDENCIES
   my_responds_to_parent!
   mysql2
   net-ftp
-  nokogiri (~> 1.16.2)
+  nokogiri (~> 1.16.5)
   omniauth (~> 2.1.0)
   omniauth-github
   omniauth-rails_csrf_protection
@@ -1069,7 +1069,7 @@ DEPENDENCIES
   rfc-822
   rmagick (= 5.3.0)
   ro-bundle (~> 0.3.0)
-  ro-crate (~> 0.5.1)
+  ro-crate (~> 0.5.2)
   rspec-rails (~> 5.1)
   rubocop
   ruby-prof
diff --git a/app/assets/javascripts/objects_input.js b/app/assets/javascripts/objects_input.js
index 3bcb08fd06..ad421c1ae1 100644
--- a/app/assets/javascripts/objects_input.js
+++ b/app/assets/javascripts/objects_input.js
@@ -32,9 +32,8 @@ var ObjectsInput = {
 
             const template = $j(this).data('typeahead-template') || 'typeahead/hint';
             opts.templateResult = HandlebarsTemplates[template];
-            opts.escapeMarkup = function (m) {
-                return m;
-            }
+            opts.escapeMarkup = ObjectsInput.doNothing;
+            opts.templateSelection = ObjectsInput.escapeSelectionMarkup;
 
             if ($j(this).data('typeahead-query-url')) {
                 opts.ajax={
@@ -47,6 +46,12 @@ var ObjectsInput = {
                 opts
             );
         });
+    },
+    doNothing: function (m) {
+        return m;
+    },
+    escapeSelectionMarkup: function (m) {
+        return jQuery.fn.select2.defaults.defaults.escapeMarkup(m.text);
     }
 }
 $j(document).ready(function () {
diff --git a/app/assets/javascripts/single_page/dynamic_table.js.erb b/app/assets/javascripts/single_page/dynamic_table.js.erb
index 0827ff286a..ae1a9cc598 100644
--- a/app/assets/javascripts/single_page/dynamic_table.js.erb
+++ b/app/assets/javascripts/single_page/dynamic_table.js.erb
@@ -19,6 +19,33 @@ const defaultCols = [{
   }
 }];
 
+// Sanitizes input data to prevent XSS attacks
+// https://cheatsheetseries.owasp.org/cheatsheets/Cross_Site_Scripting_Prevention_Cheat_Sheet.html
+function sanitizeHTML(str) {
+    return str.replace(/[&<>"']/g, function(match) {
+        return {
+            '&': '&amp;',
+            '<': '&lt;',
+            '>': '&gt;',
+            '"': '&quot;',
+            "'": '&#x27;'
+        }[match];
+    });
+}
+
+function sanitizeData(data) {
+    if (typeof data === 'string' && data !== "") {
+        return sanitizeHTML(data);
+    } else if(typeof data === 'array'){
+        return data.forEach((e) => {
+            sanitizeData(e);
+        });
+    } else {
+        // Handle other data types or nested objects/arrays if necessary
+        return data;
+    }
+}
+
 const objectInputTemp = '<input type="hidden" name="_NAME_[]" id="inpt-_NAME_" value="" autocomplete="off" />' +
   '<select name="_NAME_[]" id="select-_NAME_" class="form-control _EXTRACLASS_" title="_TITLE_" data-role="seek-objectsinput" ' +
   'data-tags-limit="100" _MULTIPLE?_ style="background-color: coral;" data-typeahead-template="_TYPEHEAD_"' +
@@ -59,12 +86,13 @@ const handleSelect = (e) => {
         }
 
         c["render"] = function(data_, type, full, meta) {
+          sanitizedData = sanitizeData(data_);
           if(c.linked_sample_type){
-            data = data_ && Array.isArray(data_) ? data_ : [data_];
+            data = sanitizedData && Array.isArray(sanitizedData) ? sanitizedData : [sanitizedData];
             data = data[0]?.id ? data : [];
             return inputObjectsInput(c, data, options, linkedSamplesUrl);
-          } else if(c.is_cv_list && data_ !== "#HIDDEN"){
-              data = data_ && Array.isArray(data_) ? data_ : [data_];
+          } else if(c.is_cv_list && sanitizedData !== "#HIDDEN"){
+              data = sanitizedData && Array.isArray(sanitizedData) ? sanitizedData : [sanitizedData];
               data = data.map((e) => {
                 if (e?.id){
                   return e.id
@@ -73,10 +101,10 @@ const handleSelect = (e) => {
                 }
               });
               return cvListObjectsInput(c, data, options, cvUrl);
-          } else if (data_ === "#HIDDEN") {
+          } else if (sanitizedData === "#HIDDEN") {
             return "<em><small>Hidden</small></em>";
           } else {
-            return data_;
+            return sanitizedData;
           }
         };
         c["createdCell"] = function(td, cellData, rowData, row, col) {
@@ -162,7 +190,7 @@ const handleSelect = (e) => {
         $j.each(sampleTypes, (i, s) => {
           if (!isNaN(s)) {
             const colIdxs = this.table.columns(`${s}:name`)[0];
-            if (colIdxs.length) colIdxs.push(colIdxs[0] - 1);
+            if (colIdxs.length) colIdxs.push(colIdxs[0] - 1, colIdxs[0] - 2);
             this.table.column(function(idx, data, node) {
               if (colIdxs.includes(idx)) $j(node).addClass(`sp-variant-${i % 2}`);
             });
@@ -435,6 +463,7 @@ const handleSelect = (e) => {
   };
 })(jQuery);
 
+// Highlights the column if the attribute is a title
 function highlightTitleCol(table) {
   table.settings()[0].aoColumns.forEach((c, i) => {
     if (c.is_title) $j(table.column(i).nodes()).addClass("highlight");
@@ -546,11 +575,11 @@ function inputObjectsInput(column, data, options, url){
     if (isHiddenInput) {
       return `<option selected="selected" title="ID: hidden" value="hidden">hidden</option>`
     } else {
-      return `<option selected="selected" title="ID: ${e.id}" value="${e.id}">${e.title}</option>`
+      return `<option selected="selected" title="ID: ${e.id}" value="${e.id}">${sanitizeData(e.title)}</option>`
     }
   }).join("");
   if (options.readonly) {
-    return data.map((e) => `<span title="ID: ${e.id}" class="badge">${e.title}</span>`).join(" ");
+    return data.map((e) => `<span title="ID: ${e.id}" class="badge">${sanitizeData(e.title)}</span>`).join(" ");
   } else {
     const typeaheadTemplate = 'typeahead/single_pages_samples'
     const objectInputName = data.map((e) => e.id).join('-') + '-' + crypto.randomUUID();
@@ -582,16 +611,16 @@ function inputObjectsInput(column, data, options, url){
 }
 
 function cvListObjectsInput(column, data, options, url){
-  const existingOptions = data.map((e) => `<option selected="selected" value="${e}">${e}</option>`);
-  if (options.readonly) {
-    return data.map((e) => `<span title="ID: ${e}" class="badge">${e}</span>`).join(" ");
-  } else {
-    const typeaheadTemplate = 'typeahead/controlled_vocab_term';
-    const objectInputName = data.map((e) => e.title).join('-') + '-' + crypto.randomUUID();
-    const extraClass = '';
-    const titleText = '';
-    const allowNewItems = column.cv_allows_free_text;
-    setTimeout(ObjectsInput.init);
+  const existingOptions = data.map((e) => `<option selected="selected" value="${sanitizeData(e)}">${sanitizeData(e)}</option>`);
+    if (options.readonly) {
+        return data.map((e) => `<span title="ID: ${sanitizeData(e)}" class="badge">${sanitizeData(e)}</span>`).join(" ");
+    } else {
+        const typeaheadTemplate = 'typeahead/controlled_vocab_term';
+        const objectInputName = data.map((e) => sanitizeData(e)).join('-') + '-' + crypto.randomUUID();
+        const extraClass = '';
+        const titleText = '';
+        const allowNewItems = column.cv_allows_free_text;
+        setTimeout(ObjectsInput.init);
 
     return objectInputTemp
     .replace(/_NAME_/g, objectInputName)
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index b9c458fc5c..6d98f1920e 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -578,9 +578,11 @@ def get_parent_resource
     parent_id_param = request.path_parameters.keys.detect { |k| k.to_s.end_with?('_id') }
     if parent_id_param
       parent_type = parent_id_param.to_s.chomp('_id')
-      parent_class = safe_class_lookup(parent_type.camelize)
+      parent_class = safe_class_lookup(parent_type.camelize, raise: false)
       if parent_class
         @parent_resource = parent_class.find(params[parent_id_param])
+      else
+        error('Parent resource not recognized','Parent resource not recognized')
       end
     end
   end
diff --git a/app/controllers/extended_metadata_types_controller.rb b/app/controllers/extended_metadata_types_controller.rb
index e775bd424c..1e9547a5a0 100644
--- a/app/controllers/extended_metadata_types_controller.rb
+++ b/app/controllers/extended_metadata_types_controller.rb
@@ -1,9 +1,8 @@
 class ExtendedMetadataTypesController < ApplicationController
-
-
-  before_action :is_user_admin_auth, except: [:form_fields, :show]
+  respond_to :json
+  before_action :is_user_admin_auth, except: [:form_fields, :show, :index]
   before_action :find_requested_item, only: [:administer_update, :show]
-
+  include Seek::IndexPager
 
   # generated for form, to display fields for selected metadata type
   def form_fields
@@ -30,6 +29,21 @@ def show
       end
   end
 
+  def index
+    @extended_metadata_types = ExtendedMetadataType.all.reject { |type| type.supported_type == 'ExtendedMetadata' }
+    respond_to do |format|
+       format.json do
+         render json:  @extended_metadata_types,
+                each_serializer: SkeletonSerializer,
+                links: json_api_links,
+                meta: {
+                  base_url: Seek::Config.site_base_host,
+                  api_version: ActiveModel::Serializer.config.api_version
+                }
+       end
+     end
+  end
+
   def administer_update
     @extended_metadata_type.update(extended_metadata_type_params)
     unless @extended_metadata_type.save
diff --git a/app/controllers/git_controller.rb b/app/controllers/git_controller.rb
index bbcce46bbd..d3f39f5963 100644
--- a/app/controllers/git_controller.rb
+++ b/app/controllers/git_controller.rb
@@ -8,6 +8,7 @@ class GitController < ApplicationController
   before_action :fetch_git_version
   before_action :get_tree, only: [:tree]
   before_action :get_blob, only: [:blob, :download, :raw]
+  before_action :check_fetched, only: [:download, :raw]
 
   user_content_actions :raw
 
@@ -257,6 +258,12 @@ def log_event
     end
   end
 
+  def check_fetched
+    if @blob.remote? && !@blob.fetched?
+      render_git_error('This file is held externally.', status: 404)
+    end
+  end
+
   # # Rugged does not allow streaming blobs
   # def stream_blob(blob, filename)
   #   response.headers['Content-Disposition'] = "attachment; filename=#{filename}"
diff --git a/app/controllers/presentations_controller.rb b/app/controllers/presentations_controller.rb
index f643e170ff..5938f8946f 100644
--- a/app/controllers/presentations_controller.rb
+++ b/app/controllers/presentations_controller.rb
@@ -8,7 +8,7 @@ class PresentationsController < ApplicationController
   before_action :presentations_enabled?
   before_action :find_assets, :only => [ :index ]
   before_action :find_and_authorize_requested_item, :except => [ :index, :new, :create, :preview,:update_annotations_ajax]
-  before_action :find_display_asset, :only=>[:show, :download]
+  before_action :find_display_asset, :only=>[:show, :explore, :download]
 
   include Seek::Publishing::PublishingCommon
 
diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb
index c63bc2197c..73864029d0 100644
--- a/app/controllers/projects_controller.rb
+++ b/app/controllers/projects_controller.rb
@@ -8,6 +8,7 @@ class ProjectsController < ApplicationController
   include CommonSweepers
   include Seek::DestroyHandling
   include Seek::Projects::Population
+  include Seek::AnnotationCommon
 
   before_action :login_required, only: [:guided_join, :guided_create, :guided_import, :request_join, :request_create, :request_import,
                                         :administer_join_request, :respond_join_request,
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index 2b100795cb..5ad9e952df 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -54,7 +54,7 @@ def determine_query
     @search_query = ActionController::Base.helpers.sanitize(search_params[:q] || search_params[:search_query])
     @search = @search_query # used for logging, and logs the origin search query - see ApplicationController#log_event
     @search_query ||= ''
-    @search_query = Seek::Search::SearchTermFilter.filter @search_query
+    @search_query.strip!
     raise InvalidSearchException, 'Query string is empty or blank' if @search_query.blank?
   end
 
diff --git a/app/controllers/studies_controller.rb b/app/controllers/studies_controller.rb
index 642494ae57..51460ca610 100644
--- a/app/controllers/studies_controller.rb
+++ b/app/controllers/studies_controller.rb
@@ -202,7 +202,7 @@ def batch_create
     # e.g: Study.new(title: 'title', investigation: investigations(:metabolomics_investigation), policy: FactoryBot.create(:private_policy))
     # study.policy = Policy.create(name: 'default policy', access_type: 1)
     # render plain: params[:studies].inspect
-    metadata_types = ExtendedMetadataType.where(title: 'MIAPPE metadata', supported_type: 'Study').last
+    metadata_types = ExtendedMetadataType.where(title: ExtendedMetadataType::MIAPPE_TITLE, supported_type: 'Study').last
     studies_length = params[:studies][:title].length
     studies_uploaded = false
     data_file_uploaded = false
diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb
index 1704c8ba86..1489a3370f 100644
--- a/app/controllers/workflows_controller.rb
+++ b/app/controllers/workflows_controller.rb
@@ -1,3 +1,5 @@
+require 'ro_crate'
+
 class WorkflowsController < ApplicationController
   include Seek::IndexPager
   include Seek::AssetsCommon
@@ -5,7 +7,7 @@ class WorkflowsController < ApplicationController
   before_action :workflows_enabled?
   before_action :find_assets, only: [:index]
   before_action :find_and_authorize_requested_item, except: [:index, :new, :create, :preview, :update_annotations_ajax]
-  before_action :find_display_asset, only: [:show, :download, :diagram, :ro_crate, :edit_paths, :update_paths]
+  before_action :find_display_asset, only: [:show, :download, :diagram, :ro_crate, :ro_crate_metadata, :edit_paths, :update_paths]
   before_action :login_required, only: [:create, :create_version, :new_version,
                                         :create_from_files, :create_from_ro_crate,
                                         :create_metadata, :provide_metadata, :create_from_git, :create_version_from_git]
@@ -17,11 +19,11 @@ class WorkflowsController < ApplicationController
   include RoCrateHandling
   include Legacy::WorkflowSupport
 
-  api_actions :index, :show, :create, :update, :destroy, :ro_crate, :create_version
+  api_actions :index, :show, :create, :update, :destroy, :ro_crate, :ro_crate_metadata, :create_version
 
   rescue_from ROCrate::ReadException do |e|
-    logger.error("Error whilst attempting to read RO-Crate metadata for #{@workflow&.id}.")
-    message = "Couldn't read RO-Crate metadata. Check the file is valid."
+    logger.error("Error whilst attempting to read RO-Crate metadata for Workflow #{@workflow&.id}: #{e.exception.class.name} #{e.message}")
+    message = "Couldn't read RO-Crate metadata - check the RO-Crate is valid: #{e.message}"
     respond_to do |format|
       format.html do
         flash[:error] = message
@@ -31,18 +33,6 @@ class WorkflowsController < ApplicationController
     end
   end
 
-  rescue_from ROCrate::WriteException do |e|
-    exception_notification(500, e) unless Rails.application.config.consider_all_requests_local
-    message = "Couldn't generate RO-Crate. Check the ro-crate-metadata.json file is valid."
-    respond_to do |format|
-      format.html do
-        flash[:error] = message
-        redirect_to workflow_path(@workflow)
-      end
-      format.json { render json: { title: 'RO-Crate Write Error', detail: message }, status: :internal_server_error }
-    end
-  end
-
   def new_git_version
     @git_version = @workflow.latest_git_version.next_version(mutable: !@git_repository&.remote?)
 
@@ -268,6 +258,13 @@ def ro_crate
                   "workflow-#{@workflow.id}-#{@display_workflow.version}.crate.zip")
   end
 
+  def ro_crate_metadata
+    metadata = @display_workflow.ro_crate.metadata
+    json = metadata.generate
+    response.headers['Content-Length'] = json.length.to_s
+    send_data(json, filename: metadata.id, type: 'application/json', disposition: 'inline')
+  end
+
   def edit_paths
 
   end
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 6cb40302d7..327ecc6b9f 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -273,22 +273,6 @@ def contributor(contributor, _avatar = false, _size = 100, _you_text = false)
     contributor_name_link.html_safe
   end
 
-  # this helper is to be extended to include many more types of objects that can belong to the
-  # user - for example, SOPs and others
-  def mine?(thing)
-    return false if thing.nil?
-    return false unless logged_in?
-
-    c_id = current_user.id.to_i
-
-    case thing.class.name
-    when 'Person'
-      return (current_user.person.id == thing.id)
-    else
-      return false
-    end
-  end
-
   def link_to_draggable(link_name, url, link_options = {})
     link_to(link_name, url, link_options)
   end
diff --git a/app/helpers/dynamic_table_helper.rb b/app/helpers/dynamic_table_helper.rb
index a698f5f7cb..47ec75dc4a 100644
--- a/app/helpers/dynamic_table_helper.rb
+++ b/app/helpers/dynamic_table_helper.rb
@@ -101,13 +101,13 @@ def dt_cols(sample_type)
       attribute = { title: a.title, name: sample_type.id.to_s, required: a.required, description: a.description,
                     is_title: a.is_title }
       attribute.merge!({ cv_id: a.sample_controlled_vocab_id }) unless a.sample_controlled_vocab_id.blank?
-      is_seek_sample = a.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE
-      is_seek_multi_sample = a.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE_MULTI
-      is_cv_list = a.sample_attribute_type.base_type == Seek::Samples::BaseType::CV_LIST
+      is_seek_sample = a.sample_attribute_type.seek_sample?
+      is_seek_multi_sample = a.sample_attribute_type.seek_sample_multi?
+      is_cv_list = a.sample_attribute_type.seek_cv_list?
       cv_allows_free_text =  a.allow_cv_free_text
       attribute.merge!({ multi_link: true, linked_sample_type: a.linked_sample_type_id }) if is_seek_multi_sample
       attribute.merge!({ multi_link: false, linked_sample_type: a.linked_sample_type_id }) if is_seek_sample
-      attribute.merge!({is_cv_list: , cv_allows_free_text:}) if is_cv_list
+      attribute.merge!({ is_cv_list: true, cv_allows_free_text:}) if is_cv_list
       attribute
     end
     (dt_default_cols(sample_type.id.to_s) + attribs).flatten
@@ -158,10 +158,14 @@ def dt_cumulative_cols(sample_types)
       s.sample_attributes.map do |a|
         attribute = { title: a.title, name: s.id.to_s, required: a.required, description: a.description,
                       is_title: a.is_title }
-        condition = a.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE_MULTI
-        attribute.merge!({ multi_link: true, linked_sample_type: a.linked_sample_type.id }) if condition
+        is_seek_sample_multi = a.sample_attribute_type.seek_sample_multi?
+        is_seek_sample = a.sample_attribute_type.seek_sample?
+        is_cv_list = a.sample_attribute_type.seek_cv_list?
+        attribute.merge!({ multi_link: true, linked_sample_type: a.linked_sample_type.id }) if is_seek_sample_multi
+        attribute.merge!({ multi_link: false, linked_sample_type: a.linked_sample_type.id }) if is_seek_sample
+        attribute.merge!({ is_cv_list: true }) if is_cv_list
         attribute
-      end.unshift({ title: 'id' }, {title: 'uuid'})
+      end.unshift({ title: 'id' }, { title: 'uuid' })
     end
   end
 end
diff --git a/app/helpers/policy_helper.rb b/app/helpers/policy_helper.rb
index 7c431caa93..63c456a03c 100644
--- a/app/helpers/policy_helper.rb
+++ b/app/helpers/policy_helper.rb
@@ -169,23 +169,28 @@ def permission_title(permission, member_prefix: false, icon: false, link: false)
     end
 
     option = { target: :_blank }
+    text = ''.html_safe # Open safe buffer
     case type
     when 'Person'
-      text = "#{contributor.first_name} #{contributor.last_name}"
-      text = link_to(h(text), contributor, option).html_safe if link
+      text += "#{contributor.first_name} #{contributor.last_name}"
+      text += link_to(text, contributor, option).html_safe if link
     when 'WorkGroup'
       institution = contributor.institution
       project = contributor.project
       if link
-        text = "#{member_prefix ? 'Members of ' : ''}#{link_to(h(project.title), project, option)} @ #{link_to(h(institution.title), institution, option)}".html_safe
+        text += 'Members of ' if member_prefix
+        text += link_to(project.title, project, option)
+        text += ' @ '
+        text += link_to(institution.title, institution, option)
       else
-        text = "#{member_prefix ? 'Members of ' : ''}#{project.title} @ #{institution.title}"
+        text += "#{member_prefix ? 'Members of ' : ''}#{project.title} @ #{institution.title}"
       end
     else
       if link
-        text = "#{member_prefix ? 'Members of ' : ''}#{link_to(h(contributor.title), contributor, option)}".html_safe
+        text += 'Members of' if member_prefix
+        text += link_to(contributor.title, project, option)
       else
-        text = "#{member_prefix ? 'Members of ' : ''}#{contributor.title}"
+        text += "#{member_prefix ? 'Members of ' : ''}#{contributor.title}"
       end
     end
 
diff --git a/app/helpers/search_helper.rb b/app/helpers/search_helper.rb
index 1960662ebf..39824e8ed8 100644
--- a/app/helpers/search_helper.rb
+++ b/app/helpers/search_helper.rb
@@ -3,7 +3,7 @@
 module SearchHelper
 
   def search_type_options
-    [['All', '']] | Seek::Util.searchable_types.collect { |c| [(c.name.underscore.humanize == 'Sop' ? t('sop') : c.name.underscore.humanize.pluralize), c.name.underscore.pluralize] }
+    [['All', '']] | Seek::Util.searchable_types.collect { |c| [(c.name.underscore.humanize == 'Sop' ? t('sop') : t(c.name.underscore).humanize.pluralize), c.name.underscore.pluralize] }
   end
 
   def external_search_tooltip_text
diff --git a/app/helpers/studies_helper.rb b/app/helpers/studies_helper.rb
index 1e95a3b95c..fa7ea53613 100644
--- a/app/helpers/studies_helper.rb
+++ b/app/helpers/studies_helper.rb
@@ -24,6 +24,6 @@ def authorised_studies(projects = nil)
   end
 
   def show_batch_miappe_button?
-    ExtendedMetadataType.where(supported_type: 'Study', title: 'MIAPPE metadata v1.1').any?
+    ExtendedMetadataType.where(supported_type: 'Study', title: ExtendedMetadataType::MIAPPE_TITLE, enabled: true).any?
   end
 end
diff --git a/app/helpers/tags_helper.rb b/app/helpers/tags_helper.rb
index a4d1eaa17c..01593e4a39 100644
--- a/app/helpers/tags_helper.rb
+++ b/app/helpers/tags_helper.rb
@@ -20,6 +20,10 @@ def fetch_tags_for_item(object, attribute = 'tag')
     [all_tags, item_tags]
   end
 
+  def fetch_tags_for_item_owned_by_current_user (object)
+    current_user ? object.annotations.with_attribute_name("tag").by_source("User", User.current_user.id).collect { |a| a.value }.uniq : []
+  end
+
   def link_for_ann(tag, options = {})
     length = options[:truncate_length]
     length ||= 150
diff --git a/app/jobs/application_job.rb b/app/jobs/application_job.rb
index 055321c02d..703b72c9fc 100644
--- a/app/jobs/application_job.rb
+++ b/app/jobs/application_job.rb
@@ -59,6 +59,7 @@ def queue_job(priority = nil, delay = default_delay)
   end
 
   def report_exception(exception, message = nil, data = {})
+    data.merge!({job_class: self.class.name})
     message ||= "Error executing job for #{self.class.name}"
     Seek::Errors::ExceptionForwarder.send_notification(exception, data: data)
     Rails.logger.error(message)
diff --git a/app/jobs/auth_lookup_maintenance_job.rb b/app/jobs/auth_lookup_maintenance_job.rb
new file mode 100644
index 0000000000..14c4d73fcd
--- /dev/null
+++ b/app/jobs/auth_lookup_maintenance_job.rb
@@ -0,0 +1,39 @@
+class AuthLookupMaintenanceJob < ApplicationJob
+  RUN_PERIOD = 8.hours.freeze
+
+  queue_as QueueNames::AUTH_LOOKUP
+  queue_with_priority  3
+
+  def perform
+    check_authlookup_consistency
+  end
+
+  # checks lookup_table_consistent? on each type for each user, and if not triggers a job to repopulate for that user
+  def check_authlookup_consistency
+    found_types = [].to_set
+
+    Seek::Util.authorized_types.each do |type|
+      #skip if there are any items of this type queued
+      next if AuthLookupUpdateQueue.where(item_type: type.name).any?
+
+      items_for_queue = [].to_set
+
+      User.where.not(person_id: nil).to_a.push(nil).each do |user|
+
+        # skip if this user or person is queued up
+        next if user && AuthLookupUpdateQueue.where(item: user).or(AuthLookupUpdateQueue.where(item: user.person)).any?
+
+        next if type.lookup_table_consistent?(user)
+
+        items_for_queue.merge(type.items_missing_from_authlookup(user))
+        found_types << type
+      end
+      AuthLookupUpdateQueue.enqueue(items_for_queue.to_a) unless items_for_queue.empty?
+    end
+
+    found_types.each(&:remove_invalid_auth_lookup_entries)
+  end
+
+
+
+end
\ No newline at end of file
diff --git a/app/jobs/regular_maintenance_job.rb b/app/jobs/regular_maintenance_job.rb
index f5ef49efa1..d42afdf85e 100644
--- a/app/jobs/regular_maintenance_job.rb
+++ b/app/jobs/regular_maintenance_job.rb
@@ -20,8 +20,6 @@ def perform
     clean_git_repositories
     resend_activation_emails
     remove_unregistered_users
-    trim_session
-    check_authlookup_consistency
   end
 
   private
@@ -58,12 +56,6 @@ def remove_unregistered_users
     User.where(person: nil).where('created_at < ?', USER_GRACE_PERIOD.ago).destroy_all
   end
 
-  # trims old sessions, using the db:sessions:trim task
-  def trim_session
-    Rails.application.load_tasks
-    Rake::Task['db:sessions:trim'].invoke
-  end
-
   # resends an activation email, for unactivated users that haven't received an email since RESEND_ACTIVATION_EMAIL_DELAY
   # and a total maximum of MAX_ACTIVATION_EMAILS (which will include the first one)
   def resend_activation_emails
@@ -80,26 +72,4 @@ def resend_activation_emails
     end
   end
 
-  # checks lookup_table_consistent? on each type for each user, and if not triggers a job to repopulate for that user
-  # if not already queued
-  def check_authlookup_consistency
-    found_types = [].to_set
-    items_for_queue = [].to_set
-    User.where.not(person_id: nil).to_a.push(nil).each do |user|
-
-      # will only deal with 1 type per user per run
-      found = Seek::Util.authorized_types.find do |type|
-        !type.lookup_table_consistent?(user)
-      end
-
-      next unless found.present?
-
-      found_types << found
-      missing = found.items_missing_from_authlookup(user)
-      items_for_queue.merge(missing)
-    end
-
-    found_types.each(&:remove_invalid_auth_lookup_entries)
-    AuthLookupUpdateQueue.enqueue(items_for_queue.to_a) unless items_for_queue.empty?
-  end
 end
diff --git a/app/jobs/reindexing_job.rb b/app/jobs/reindexing_job.rb
index ff45e69e65..a19281775e 100644
--- a/app/jobs/reindexing_job.rb
+++ b/app/jobs/reindexing_job.rb
@@ -25,7 +25,7 @@ def gather_items
   end
 
   def follow_on_job?
-    ReindexingQueue.any?
+    Seek::Config.solr_enabled && ReindexingQueue.any?
   end
 
   def timelimit
diff --git a/app/jobs/user_auth_lookup_update_job.rb b/app/jobs/user_auth_lookup_update_job.rb
index 957c9320f0..6ea614771d 100644
--- a/app/jobs/user_auth_lookup_update_job.rb
+++ b/app/jobs/user_auth_lookup_update_job.rb
@@ -2,11 +2,21 @@
 class UserAuthLookupUpdateJob < ApplicationJob
   queue_as QueueNames::AUTH_LOOKUP
   queue_with_priority 0
+  BATCH_SIZE = 8000
 
-  def perform(user, type)
-    type.constantize.includes(policy: :permissions).find_each do |item|
+  # needs longer, otherwise the samples can time out
+  def timelimit
+    30.minutes
+  end
+
+  def perform(user, type, offset = 0)
+    type.constantize.offset(offset).limit(BATCH_SIZE).includes(policy: :permissions).each do |item|
       item.update_lookup_table(user)
     end
+
+    offset += BATCH_SIZE
+
+    self.class.perform_later(user, type, offset) if offset < type.constantize.count
   end
 end
 
diff --git a/app/models/concerns/has_extended_metadata.rb b/app/models/concerns/has_extended_metadata.rb
index c99293ab19..48782aedbc 100644
--- a/app/models/concerns/has_extended_metadata.rb
+++ b/app/models/concerns/has_extended_metadata.rb
@@ -3,8 +3,10 @@ module HasExtendedMetadata
 
   included do
     def extended_metadata_attribute_values_for_search
-      extended_metadata ? extended_metadata.data.values.reject(&:blank?).uniq : []
+      return [] unless extended_metadata
+      extended_metadata.data.extract_all_values.uniq.compact
     end
+
   end
 
   class_methods do
diff --git a/app/models/concerns/workflow_extraction.rb b/app/models/concerns/workflow_extraction.rb
index a9cf9ed027..6df16675e3 100644
--- a/app/models/concerns/workflow_extraction.rb
+++ b/app/models/concerns/workflow_extraction.rb
@@ -226,17 +226,13 @@ def ro_crate
   end
 
   def ro_crate_zip
-    begin
-      ro_crate do |crate|
-        path = ro_crate_path
-        File.delete(path) if File.exist?(path)
-        ROCrate::Writer.new(crate).write_zip(path)
-      end
-
-      ro_crate_path
-    rescue StandardError => e
-      raise ::ROCrate::WriteException.new("Couldn't generate RO-Crate metadata.", e)
+    ro_crate do |crate|
+      path = ro_crate_path
+      File.delete(path) if File.exist?(path)
+      ROCrate::Writer.new(crate).write_zip(path)
     end
+
+    ro_crate_path
   end
 
   def ro_crate_identifier
diff --git a/app/models/extended_metadata.rb b/app/models/extended_metadata.rb
index 05ffa2c5e5..d657987f95 100644
--- a/app/models/extended_metadata.rb
+++ b/app/models/extended_metadata.rb
@@ -22,4 +22,5 @@ def extended_metadata_type=(type)
   def attribute_class
     ExtendedMetadataAttribute
   end
+
 end
diff --git a/app/models/extended_metadata_type.rb b/app/models/extended_metadata_type.rb
index 8ea439518e..4fbb9293c0 100644
--- a/app/models/extended_metadata_type.rb
+++ b/app/models/extended_metadata_type.rb
@@ -13,6 +13,9 @@ class ExtendedMetadataType < ApplicationRecord
   scope :enabled, ->{ where(enabled: true) }
   scope :disabled, ->{ where(enabled: false) }
 
+  # built in type
+  MIAPPE_TITLE = 'MIAPPE metadata v1.1'.freeze
+
   def attribute_by_title(title)
     extended_metadata_attributes.where(title: title).first
   end
diff --git a/app/models/presentation.rb b/app/models/presentation.rb
index c2cd8f7c6e..267c350b76 100644
--- a/app/models/presentation.rb
+++ b/app/models/presentation.rb
@@ -35,4 +35,8 @@ def use_mime_type_for_avatar?
   def is_in_isa_publishable?
     true
   end
+
+  def supports_spreadsheet_explore?
+    true
+  end
 end
diff --git a/app/models/project.rb b/app/models/project.rb
index 4431d7c9ae..2aa17d69fc 100644
--- a/app/models/project.rb
+++ b/app/models/project.rb
@@ -2,6 +2,7 @@ class Project < ApplicationRecord
   include Seek::Annotatable
   include HasSettings
   include Seek::Roles::Scope
+  include Seek::Taggable
 
   acts_as_yellow_pages
   title_trimmer
diff --git a/app/models/reindexing_queue.rb b/app/models/reindexing_queue.rb
index e01186c0cd..40a988713c 100644
--- a/app/models/reindexing_queue.rb
+++ b/app/models/reindexing_queue.rb
@@ -1,7 +1,13 @@
 class ReindexingQueue < ApplicationRecord
   include ResourceQueue
 
+  def self.enqueue(*items, priority: DEFAULT_PRIORITY, queue_job: true)
+    return unless Seek::Config.solr_enabled
+    super(items, priority: priority, queue_job: queue_job)
+  end
+
   def self.job_class
     ReindexingJob
   end
+
 end
diff --git a/app/models/sample.rb b/app/models/sample.rb
index d731bcac4c..c68ec6eb0f 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -145,8 +145,12 @@ def refresh_linking_samples
           sample['title'] = title if sample['id'] == id
         end
         metadata.values[p - 1] = item_linked_samples
-        s.json_metadata = metadata.to_json
-        s.save
+
+        # only update if changed, to prevent triggered jobs that could potentially create an infinate loop
+        if s.json_metadata != metadata.to_json
+          s.json_metadata = metadata.to_json
+          s.save
+        end
       end
     end
   end
diff --git a/app/models/study_batch_upload.rb b/app/models/study_batch_upload.rb
index 6a85f47c88..90cb4b789e 100644
--- a/app/models/study_batch_upload.rb
+++ b/app/models/study_batch_upload.rb
@@ -29,7 +29,7 @@ def self.extract_study_data_from_file(studies_file)
   def self.extract_studies_from_file(studies_file)
     studies = []
     parsed_sheet = Seek::Templates::StudiesReader.new(studies_file)
-    metadata_type = ExtendedMetadataType.where(title: 'MIAPPE metadata', supported_type: 'Study').last
+    metadata_type = ExtendedMetadataType.where(title: ExtendedMetadataType::MIAPPE_TITLE, supported_type: 'Study').last
     columns = [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
     study_start_row_index = 4
     parsed_sheet.each_record(3, columns) do |index, data|
diff --git a/app/models/template_attribute.rb b/app/models/template_attribute.rb
index 3e12de3e88..74af563484 100644
--- a/app/models/template_attribute.rb
+++ b/app/models/template_attribute.rb
@@ -15,7 +15,7 @@ class TemplateAttribute < ApplicationRecord
   before_save :default_pos
 
   def controlled_vocab?
-    sample_attribute_type.base_type == Seek::Samples::BaseType::CV
+    sample_attribute_type&.base_type == Seek::Samples::BaseType::CV
   end
 
   def allow_isa_tag_change?
diff --git a/app/models/user.rb b/app/models/user.rb
index ed0e487e03..6d0f25e762 100644
--- a/app/models/user.rb
+++ b/app/models/user.rb
@@ -67,7 +67,7 @@ class User < ApplicationRecord
   delegate :is_admin_or_project_administrator?, to: :person, allow_nil: true
   delegate :is_programme_administrator?, to: :person, allow_nil: true
 
-  after_commit :queue_update_auth_table, on: :create
+  after_save_commit :queue_update_auth_table
 
   after_destroy :queue_auth_lookup_delete_job
 
@@ -336,7 +336,9 @@ def email_available?
   end
 
   def queue_update_auth_table
-    AuthLookupUpdateQueue.enqueue(self)
+    if saved_changes.keys.include?("person_id")
+      AuthLookupUpdateQueue.enqueue(self, priority: 1)
+    end
   end
 
   def queue_auth_lookup_delete_job
diff --git a/app/serializers/extended_metadata_type_serializer.rb b/app/serializers/extended_metadata_type_serializer.rb
index 36b251edba..dbce96999b 100644
--- a/app/serializers/extended_metadata_type_serializer.rb
+++ b/app/serializers/extended_metadata_type_serializer.rb
@@ -1,5 +1,5 @@
 class ExtendedMetadataTypeSerializer < BaseSerializer
-  attributes :title, :supported_type
+  attributes :title, :supported_type,:enabled
   attribute :extended_metadata_attributes
 
   def extended_metadata_attributes
@@ -17,7 +17,8 @@ def get_extended_metadata_attribute(attribute)
       "sample_attribute_type": get_sample_attribute_type(attribute),
       "required": attribute.required,
       "pos": attribute.pos,
-      "sample_controlled_vocab_id": attribute.sample_controlled_vocab_id.nil? ? nil : attribute.sample_controlled_vocab_id.to_s
+      "sample_controlled_vocab_id": attribute.sample_controlled_vocab_id&.to_s,
+      "linked_extended_metadata_type_id": attribute.linked_extended_metadata_type_id&.to_s
     }
   end
 
diff --git a/app/views/admin/stats/_job_queue.html.erb b/app/views/admin/stats/_job_queue.html.erb
index e026c48c78..9c5ad64cc4 100644
--- a/app/views/admin/stats/_job_queue.html.erb
+++ b/app/views/admin/stats/_job_queue.html.erb
@@ -1,5 +1,5 @@
 <%
-   queue = AuthLookupUpdateQueue.all.to_a | ReindexingQueue.all.to_a
+   queue = AuthLookupUpdateQueue.all.to_a | ReindexingQueue.all.to_a | RdfGenerationQueue.all.to_a
    queue = queue.sort_by(&:created_at)
    delayed_jobs = Delayed::Job.order(locked_at: :desc, created_at: :asc)
 %>
diff --git a/app/views/assays/show.html.erb b/app/views/assays/show.html.erb
index fabd8c63f9..e0c12ee449 100644
--- a/app/views/assays/show.html.erb
+++ b/app/views/assays/show.html.erb
@@ -160,7 +160,7 @@
   <%= tab_pane('related-items') do %>
     <%= render partial: 'general/items_related_to', object: @assay %>
   <% end %>
-	<% if Seek::Config.isa_json_compliance_enabled && @assay.is_isa_json_compliant? %>
+	<% if Seek::Config.isa_json_compliance_enabled && @assay.is_isa_json_compliant? && !@assay.is_assay_stream? %>
 		<%= tab_pane('assay_design') do %>
 			<%= render :partial=>"isa_assays/assay_design", locals: { assay: @assay} -%>
       <%= render partial: 'single_pages/change_batch_persmission_modal' %>
diff --git a/app/views/assets/_resource_main_content_right.html.erb b/app/views/assets/_resource_main_content_right.html.erb
index 3490041283..910babeb86 100644
--- a/app/views/assets/_resource_main_content_right.html.erb
+++ b/app/views/assets/_resource_main_content_right.html.erb
@@ -21,26 +21,26 @@
 
 <% if resource.respond_to?(:snapshots)  %>
   <% if resource.latest_citable_resource %>
-    <%= render :partial => "assets/citation_box", locals: { doi: resource.latest_citable_resource.doi,
-                                                            snapshot: resource.latest_citable_resource }  %>
+    <%= render partial: "assets/citation_box", locals: { doi: resource.latest_citable_resource.doi,
+                                                         snapshot: resource.latest_citable_resource } %>
   <% elsif resource.can_manage? && Seek::Config.doi_minting_enabled %>
-    <%= render :partial => "assets/isa_citation_instructions", locals: { resource: resource } %>
+    <%= render partial: "assets/isa_citation_instructions", locals: { resource: resource } %>
   <% end %>
   <% if resource.snapshots.any? %>
-    <%= render :partial => "snapshots/snapshots", locals: { snapshots: resource.snapshots, resource: resource } %>
+    <%= render partial: "snapshots/snapshots", locals: { snapshots: resource.snapshots, resource: resource } %>
   <% end %>
 <% elsif versioned_resource.respond_to?(:doi) %>
   <% if versioned_resource.doi.present? %>
-    <%= render :partial => "assets/citation_box", locals: { doi: versioned_resource.doi } %>
+    <%= render partial: "assets/citation_box", locals: { doi: versioned_resource.doi } %>
   <% elsif versioned_resource.is_git_versioned? && versioned_resource.file_exists?(Seek::WorkflowExtractors::CFF::FILENAME) %>
-    <%= render :partial => "assets/citation_box", locals: { blob: versioned_resource.get_blob(Seek::WorkflowExtractors::CFF::FILENAME) } %>
+    <%= render partial: "assets/citation_box", locals: { blob: versioned_resource.get_blob(Seek::WorkflowExtractors::CFF::FILENAME) } %>
   <% elsif resource.can_manage? && Seek::Config.doi_minting_enabled && resource.supports_doi? %>
-    <%= render :partial => "assets/citation_instructions", locals: { resource: resource, versioned_resource: versioned_resource } %>
+    <%= render partial: "assets/citation_instructions", locals: { resource: resource, versioned_resource: versioned_resource } %>
   <% end %>
 <% end %>
 
 <% if Seek::Config.file_templates_enabled && resource.respond_to?(:file_template) && !resource.file_template.nil? %>
-  <%= render :partial => "assets/file_template_box", :locals => { :resource => resource } -%>
+  <%= render partial: "assets/file_template_box", locals: { resource: resource } %>
 <% end %>
 
 <% suffix = 'the Data file'
@@ -52,23 +52,23 @@
    %>
 
 <% if resource.respond_to?(:license) && !hide_license %>
-  <%= render :partial => "assets/license_box", :locals => { :resource => resource, :versioned_resource=> versioned_resource } -%>
+  <%= render partial: "assets/license_box", locals: { resource: resource, versioned_resource: versioned_resource } %>
 <% end %>
 
-<%= render :partial => "assets/usage_info_box",:locals => { :resource => resource } -%>
+<%= render partial: "assets/usage_info_box", locals: { resource: resource } %>
 
 <% if resource.controlled_vocab_annotations? %>
   <%= render partial:'assets/controlled_vocab_annotations_properties_box', :locals => { :resource => resource } -%>
 <% end %>
 
 <% if resource.class.is_taggable? %>
-    <%= render :partial=>"assets/tags_box", :no_tags_message=>"Add tags (comma separated) ..." -%>
+  <%= render partial: "assets/tags_box", locals: { resource: resource }, no_tags_message: "Add tags (comma separated) ..." %>
 <% end -%>
 
 <% if resource.respond_to? :attributions_objects -%>
-  <%= render :partial => "assets/resource_attributions_box",
-             :locals => { :resource => resource, :attributed_to => resource.attributions_objects,
-                          :truncate_to => truncate_length_for_boxes } -%>
+  <%= render partial: "assets/resource_attributions_box",
+             locals: { resource: resource, attributed_to: resource.attributions_objects,
+                       truncate_to: truncate_length_for_boxes } %>
 <% end -%>
 
 <% if resource.respond_to?(:collections) && resource.collections.any? -%>
diff --git a/app/views/assets/_tags_box.html.erb b/app/views/assets/_tags_box.html.erb
index cc1d43b6c6..48850ca3b4 100644
--- a/app/views/assets/_tags_box.html.erb
+++ b/app/views/assets/_tags_box.html.erb
@@ -1,11 +1,10 @@
 <%
-   entity=controller_name.singularize
-   object=instance_variable_get("@#{entity}")
-   title||="Tags"
-   all_tags,all_item_tags = fetch_tags_for_item object
-   owner_item_tags = current_user ? object.annotations.with_attribute_name("tag").by_source("User",User.current_user.id).collect{|a| a.value}.uniq : []
-   create_tag_link_text = ((owner_item_tags.empty? ? "Add your tags" : "Update your tags") + ' <span class="caret"></span>').html_safe
-   existing_tags = owner_item_tags.map(&:text).uniq
+  title||="Tags"
+  all_tags,all_item_tags = fetch_tags_for_item resource
+  owner_item_tags = fetch_tags_for_item_owned_by_current_user resource
+
+  create_tag_link_text = ((owner_item_tags.empty? ? "Add your tags" : "Update your tags") + ' <span class="caret"></span>').html_safe
+  existing_tags = owner_item_tags.map(&:text).uniq
 %>
 <%= panel(title, :id => "tags_box", :help_text => "Tagging an item helps describe it and other people find it. You can contribute by applying your own tags to this item. The weight of a tag indicates how often it has been used.") do %>
   <div id='tag_cloud' class='tags_smaller'>
diff --git a/app/views/assets/_view_content.html.erb b/app/views/assets/_view_content.html.erb
index a6c807019e..a1d6657bad 100644
--- a/app/views/assets/_view_content.html.erb
+++ b/app/views/assets/_view_content.html.erb
@@ -18,7 +18,7 @@
       <% url = polymorphic_path([asset, content_blob], action: 'view_content', code: params[:code]) %>
       <% options = { title: 'View contents of this file' } %>
     <% end %>
-  <% elsif !asset.is_a?(Model) && content_blob.is_supported_spreadsheet_format? %>
+  <% elsif asset.supports_spreadsheet_explore? && content_blob.is_supported_spreadsheet_format? %>
     <% if content_blob.is_extractable_spreadsheet? %>
       <% url = polymorphic_path([asset], action: 'explore', code: params[:code], version: asset_version) %>
       <% options = { title: 'Explore the contents of this file' } %>
diff --git a/app/views/avatars/index.html.erb b/app/views/avatars/index.html.erb
index e3dbb250ce..0120c20cba 100644
--- a/app/views/avatars/index.html.erb
+++ b/app/views/avatars/index.html.erb
@@ -1,4 +1,4 @@
-<% editable = mine?(@avatar_owner_instance) || @avatar_owner_instance.can_edit?(current_user) -%>
+<% editable = @avatar_owner_instance.can_edit?(current_user) -%>
 
 <%
     item = @avatar_owner_instance.class.name.downcase
diff --git a/app/views/general/_item_title.html.erb b/app/views/general/_item_title.html.erb
index 9807954105..9d17f3335a 100644
--- a/app/views/general/_item_title.html.erb
+++ b/app/views/general/_item_title.html.erb
@@ -37,7 +37,7 @@ gatekeeper_status_bar = item.is_asset? && item.can_manage? && (item.is_waiting_a
                 </ul>
               </div>
           <% else %>
-              <div class="version">Version <%= version -%></div>
+              <div class="version"><%= visible_versions.first&.name -%></div>
           <% end %>
       <% end %>
     </h1>
@@ -72,4 +72,4 @@ gatekeeper_status_bar = item.is_asset? && item.can_manage? && (item.is_waiting_a
     <% end %>
     </div>
   </div>
-<% end %>
\ No newline at end of file
+<% end %>
diff --git a/app/views/general/_show_page_tab_definitions.html.erb b/app/views/general/_show_page_tab_definitions.html.erb
index 5ea7c76dc3..612f1fecfe 100644
--- a/app/views/general/_show_page_tab_definitions.html.erb
+++ b/app/views/general/_show_page_tab_definitions.html.erb
@@ -18,7 +18,8 @@
   <% end %>
 
 	<% if resource %>
-		<% if Seek::Config.isa_json_compliance_enabled && resource.is_isa_json_compliant? %>
+		<% resource_is_assay_stream = resource_name == 'Assay' ? resource.is_assay_stream? : false %>
+		<% if Seek::Config.isa_json_compliance_enabled && resource.is_isa_json_compliant? && !resource_is_assay_stream %>
 			<%= tab(resource_name&.downcase + "_design") do %>
 				<span class="glyphicon glyphicon-th-list"></span> <%= resource.model_name.human %> design
 			<% end %>
diff --git a/app/views/git/_blob.html.erb b/app/views/git/_blob.html.erb
index d89bb8f8c0..8bbf2d40dd 100644
--- a/app/views/git/_blob.html.erb
+++ b/app/views/git/_blob.html.erb
@@ -8,8 +8,13 @@
 
 <div>
   <div class="pull-right">
-    <%= button_link_to('Download', 'download', polymorphic_path([@parent_resource, :git_download], version: @git_version.version, path: @blob.path)) %>
-    <%= button_link_to('Raw', 'markup', polymorphic_path([@parent_resource, :git_raw], version: @git_version.version, path: @blob.path)) %>
+    <% if @blob.fetched? %>
+      <%= button_link_to('Download', 'download', polymorphic_path([@parent_resource, :git_download], version: @git_version.version, path: @blob.path)) %>
+      <%= button_link_to('Raw', 'markup', polymorphic_path([@parent_resource, :git_raw], version: @git_version.version, path: @blob.path)) %>
+    <% end %>
+    <% if @blob.remote? %>
+      <%= button_link_to('External Link', 'external_link', @blob.url, target: :_blank) %>
+    <% end %>
     <% if @git_version.can_edit? %>
       <% if @git_version.mutable? %>
         <%= button_link_to('Move/rename', 'move', '#', { 'data-toggle' => 'modal', 'data-target' => '#git-move-modal' }) %>
@@ -25,7 +30,9 @@
   </div>
 
   <strong>Path: </strong> <%= @blob.path -%><br/>
-  <strong>Size: </strong> <%= number_to_human_size @blob.size -%><br/>
+  <% if @blob.fetched? %>
+    <strong>Size: </strong> <%= number_to_human_size @blob.size -%><br/>
+  <% end %>
   <div class="hidden">
     <strong>SHA: </strong> <code><%= @blob.oid %></code><br/>
   </div>
diff --git a/app/views/institutions/_buttons.html.erb b/app/views/institutions/_buttons.html.erb
index 36740072fa..a7ae775b07 100644
--- a/app/views/institutions/_buttons.html.erb
+++ b/app/views/institutions/_buttons.html.erb
@@ -1,5 +1,5 @@
 <%= item_actions_dropdown do %>
-    <% if mine?(item) || item.can_edit? -%>
+    <% if item.can_edit? -%>
           <li><%= icon_link_to("Edit #{t('institution')} Details", 'edit', edit_institution_path(item)) -%></li>
           <% if admin_logged_in? -%>
               <li><%= delete_icon(item,current_user) %></li>
diff --git a/app/views/isa_assays/_assay_table.html.erb b/app/views/isa_assays/_assay_table.html.erb
index 267cc8536a..266503a1c7 100644
--- a/app/views/isa_assays/_assay_table.html.erb
+++ b/app/views/isa_assays/_assay_table.html.erb
@@ -16,11 +16,10 @@
 
 <% if valid_assay %>
     <script>
-        var assayDynamicTable
         let assayOverviewInitialLoad = true;
         $j(document).ready(function () {
             const dt = <%= sanitize(dt_aggregated(assay.study, assay).to_json) %>
-            assayDynamicTable = new $j.dynamicTable('#assay-table')
+            window.assayDynamicTable = new $j.dynamicTable('#assay-table')
             const ajax = {
                 url: dynamicTableDataPath,
                 data: function(d) {
diff --git a/app/views/isa_assays/_form.html.erb b/app/views/isa_assays/_form.html.erb
index 20fe51faaf..899e57ad4f 100644
--- a/app/views/isa_assays/_form.html.erb
+++ b/app/views/isa_assays/_form.html.erb
@@ -80,7 +80,11 @@
   <%= assay_fields.hidden_field :assay_stream_id, value: assay_stream_id -%>
   <%= assay_fields.hidden_field :assay_class_id, value: assay_class_id -%>
 
-  <% unless is_assay_stream %>
+  <% if is_assay_stream %>
+    <% if User.current_user  -%>
+      <%= render partial: 'assets/manage_specific_attributes', locals:{f:assay_fields} if show_form_manage_specific_attributes? %>
+    <% end %>
+  <% else %>
     <% if User.current_user  -%>
       <%= render partial: 'assets/manage_specific_attributes', locals:{f:assay_fields} if show_form_manage_specific_attributes? %>
       <%= assay_fields.fancy_multiselect(:sops, other_projects_checkbox: true, name: "isa_assay[assay][sop_ids]")%>
diff --git a/app/views/people/_batch_permission_changes_buttons.html.erb b/app/views/people/_batch_permission_changes_buttons.html.erb
new file mode 100644
index 0000000000..fddb1d6502
--- /dev/null
+++ b/app/views/people/_batch_permission_changes_buttons.html.erb
@@ -0,0 +1,2 @@
+<%= button_link_to "Batch permission changes", "publish", batch_sharing_permission_preview_person_path(@person), 'data-tooltip': tooltip(t('tooltips.batch_permission_changes_button')) -%>
+<%= button_link_to "Publish your items", "publish", batch_publishing_preview_person_path(@person), 'data-tooltip': tooltip(t('tooltips.publish_your_items_button')) -%>
\ No newline at end of file
diff --git a/app/views/people/_buttons.html.erb b/app/views/people/_buttons.html.erb
index bd48f3beff..590e0e578c 100644
--- a/app/views/people/_buttons.html.erb
+++ b/app/views/people/_buttons.html.erb
@@ -1,8 +1,5 @@
-<% if mine?(@person) -%>
-    <% tooltip_text_sharing = "You can change the sharing policy and permissions for your items in batch. A preview of selected items will be given before you choose new permissions for them." %>
-    <% tooltip_text_publishing = "Publish your owned items in one click. A preview will be given before publishing" %>
-    <%= button_link_to "Batch permission changes", "publish", batch_sharing_permission_preview_person_path(@person), 'data-tooltip': tooltip(tooltip_text_sharing) -%>
-    <%= button_link_to "Publish your items", "publish", batch_publishing_preview_person_path(@person), 'data-tooltip': tooltip(tooltip_text_publishing) -%>
+<% if @person.me? -%>
+  <%= render partial:'batch_permission_changes_buttons' %>
   <% if @person.is_in_any_gatekept_projects? %>
     <%= button_link_to "Assets awaiting approval", "waiting", waiting_approval_assets_person_path(@person),
                        'data-tooltip': tooltip("The assets you have requested to publish, but are awaiting the #{t('asset_gatekeeper').downcase} approval") -%>
@@ -14,11 +11,11 @@
 <% end %>
 
 <%= item_actions_dropdown do %>
-  <% if (mine?(@person) || @person.can_edit?(current_user)) -%>
+  <% if @person.me? || @person.can_edit?(current_user) -%>
       <li>
         <%= image_tag_for_key('edit', edit_person_path(@person), "Edit Person Profile", nil, 'Edit Profile') -%>
       </li>
-      <% if mine?(@person) -%>
+      <% if @person.me? -%>
           <li>
             <%= image_tag_for_key "lock", url_for({controller: :users, action: :edit, id: @person.user}), "Manage Account", nil, "Manage Account" -%>
           </li>
diff --git a/app/views/people/items.html.erb b/app/views/people/items.html.erb
index f657873357..a54fe905ce 100644
--- a/app/views/people/items.html.erb
+++ b/app/views/people/items.html.erb
@@ -1,4 +1,8 @@
+
 <div id="my-items">
+  <div class='pull-right' id='buttons'>
+    <%= render partial:'batch_permission_changes_buttons' %>
+  </div>
   <%= render partial: "general/items_related_to", object: @person,
              locals: { limit: 50, title: "Items related to #{link_to(h(@person.name),@person)}".html_safe } %>
 </div>
diff --git a/app/views/people/show.html.erb b/app/views/people/show.html.erb
index 08b248ebc2..fa91fe73ab 100644
--- a/app/views/people/show.html.erb
+++ b/app/views/people/show.html.erb
@@ -70,7 +70,7 @@
         </div>
       <% end %>
     </div>
-    <%= render :partial => "people/project_subscriptions", :locals => { :person => @person } if (mine?(@person) || current_user.try(:person).try(:is_admin?)) %>
+    <%= render :partial => "people/project_subscriptions", :locals => { :person => @person } if @person.me? || current_user.try(:person).try(:is_admin?) %>
 
   <% end %>
 
diff --git a/app/views/presentations/explore.html.erb b/app/views/presentations/explore.html.erb
new file mode 100644
index 0000000000..8ec5595981
--- /dev/null
+++ b/app/views/presentations/explore.html.erb
@@ -0,0 +1 @@
+<%= render partial: "spreadsheets/explore", locals: { resource: @display_presentation } -%>
diff --git a/app/views/projects/show.html.erb b/app/views/projects/show.html.erb
index 53591297cd..7b0259fda1 100644
--- a/app/views/projects/show.html.erb
+++ b/app/views/projects/show.html.erb
@@ -105,23 +105,23 @@
       </div>
 
       <div class="col-md-3 col-sm-4">
-        <%= render :partial => "layouts/contribution_section_box_avatar", :locals => { :object => @project } -%>
+        <%= render partial: "layouts/contribution_section_box_avatar", locals: { object: @project } %>
 
-        <% if @project.is_discussable? -%>
-          <% if @project.discussion_links.select{|link| link.url.present?}.any?  %>
-            <%= render partial: 'assets/discussion_links_box', locals: {resource: @project } -%>
-          <% end -%>
-        <% end -%>
+        <% if @project.is_discussable? && @project.discussion_links.any? { |link| link.url.present? } %>
+          <%= render partial: "assets/discussion_links_box", locals: { resource: @project } %>
+        <% end %>
 
         <% if @project.controlled_vocab_annotations? %>
-          <%= render partial:'assets/controlled_vocab_annotations_properties_box', :locals => { :resource => @project } %>
+          <%= render partial: "assets/controlled_vocab_annotations_properties_box", locals: { resource: @project } %>
         <% end %>
 
         <% if @project.can_manage? %>
-          <%= render :partial => 'general/storage_usage_box', locals: { programme: @project,
-                                                                        url: storage_report_project_path(@project)} %>
+          <%= render partial: "general/storage_usage_box", locals: { programme: @project, url: storage_report_project_path(@project) } %>
         <% end %>
 
+        <% if @project.is_taggable? %>
+          <%= render partial: "assets/tags_box", locals: { resource: @project }, no_tags_message: "Add tags (comma separated) ..." %>
+        <% end %>
       </div>
     </div>
 
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 41ddb55a0e..31a337630a 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -336,3 +336,7 @@ you can choose to have a %{project} linked to a site managed %{programme} instea
       all: Allow all cookies
       embedding: Allow necessary cookies and embedded content
       necessary: Allow only necessary cookies
+
+  tooltips:
+    batch_permission_changes_button: "You can change the sharing policy and permissions for your items as a batch. A preview of selected items will be given before you choose new permissions for them."
+    publish_your_items_button: "Publish your owned items as a batch. A preview will be given before publishing"
diff --git a/config/routes.rb b/config/routes.rb
index 016f0963ae..8261d3f63a 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -349,6 +349,7 @@
       get :administer_join_request
       post :respond_join_request
       get :guided_join
+      post :update_annotations_ajax
     end
     resources :programmes, :people, :institutions, :assays, :studies, :investigations, :models, :sops, :workflows, :data_files, :presentations,
               :publications, :events, :sample_types, :samples, :specimens, :strains, :search, :organisms, :human_diseases, :documents, :file_templates, :placeholders, :collections, :templates, only: [:index]
@@ -501,7 +502,7 @@
     resources :people, :programmes, :projects, :investigations, :assays, :samples, :studies, :publications, :events, :collections, :workflows, :file_templates, :placeholders, only: [:index]
   end
 
-  resources :presentations, concerns: [:has_content_blobs, :publishable, :has_versions, :asset] do
+  resources :presentations, concerns: [:has_content_blobs, :publishable, :has_versions, :asset, :explorable_spreadsheet] do
     resources :people, :programmes, :projects, :publications, :events, :collections, :workflows, :investigations, :studies, :assays, only: [:index]
   end
 
@@ -537,6 +538,7 @@
     member do
       get :diagram
       get :ro_crate
+      get :ro_crate_metadata
       get :new_version
       get :new_git_version
       post :create_version_metadata
@@ -761,6 +763,7 @@
   resources :single_pages do
     member do
       get :dynamic_table_data
+      post :update_annotations_ajax
     end
     collection do
       get :batch_sharing_permission_preview
diff --git a/config/schedule.rb b/config/schedule.rb
index 743d0d60ed..ba8c045099 100644
--- a/config/schedule.rb
+++ b/config/schedule.rb
@@ -47,6 +47,10 @@ def offset(off_hours)
   runner "RegularMaintenanceJob.perform_later"
 end
 
+every AuthLookupMaintenanceJob::RUN_PERIOD, at: offset(1) do
+  runner "AuthLookupMaintenanceJob.perform_later"
+end
+
 every LifeMonitorStatusJob::PERIOD, at: offset(2) do
   runner "LifeMonitorStatusJob.perform_later"
 end
@@ -82,3 +86,8 @@ def offset(off_hours)
     command "sh /seek/script/kill-long-running-soffice.sh"
   end
 end
+
+# trim sessions
+every 1.day, at: '1:15 am' do
+  rake 'db:sessions:trim'
+end
diff --git a/config/version.yml b/config/version.yml
index 3bc73edb05..df417d0345 100644
--- a/config/version.yml
+++ b/config/version.yml
@@ -8,5 +8,5 @@
 # patch:        sprint-555
 
 major:        1
-minor:        15
+minor:        16
 patch:        0-main 
diff --git a/db/seeds/017_minimal_starter_isa_templates.seeds.rb b/db/seeds/017_minimal_starter_isa_templates.seeds.rb
index e78e477916..8413acf657 100644
--- a/db/seeds/017_minimal_starter_isa_templates.seeds.rb
+++ b/db/seeds/017_minimal_starter_isa_templates.seeds.rb
@@ -1,21 +1,38 @@
+# This code seeds the starter templates in the database.
+# To keep the link between parent and child template attributes, do not change the attribute titles !!!
+# Changing the titles will replace the existing attributes with new ones instead of updating them.
+
+# Custom upsert function for template attributes
+# This will create a new template attribute if it does not exist, or update the existing one.
+# This also assumes that a template_attribute is considered unique by its title and template_id.
+# All other fields can be updated.
+def upsert_template_attribute(title, template_id, **fields)
+  template_attribute = TemplateAttribute.find_or_create_by(title:, template_id:)
+  template_attribute.update(fields)
+  template_attribute
+end
+
 # Source - ISA minimal starter template
 source_template = Template.find_or_initialize_by(title: 'Source - ISA minimal starter template', level: 'study source',
                                                  group: 'ISA minimal starter')
 
 source_temp_attributes = []
-source_temp_attributes << TemplateAttribute.new(title: 'Source Name',
-                                                description: 'Sources are considered as the starting biological material used in a study.',
-                                                sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                is_title: true,
-                                                required: true,
-                                                isa_tag: IsaTag.find_by(title: 'source'))
-
-source_temp_attributes << TemplateAttribute.new(title: 'Source Characteristic 1',
-                                                description: 'A characteristic of the source.',
-                                                sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                is_title: false,
-                                                required: true,
-                                                isa_tag: IsaTag.find_by(title: 'source_characteristic'))
+source_temp_attributes << upsert_template_attribute('Source Name',
+                                                    source_template.id,
+                                                    description: 'Sources are considered as the starting biological material used in a study.',
+                                                    sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                    is_title: true,
+                                                    required: true,
+                                                    isa_tag: IsaTag.find_by(title: 'source')
+)
+
+source_temp_attributes << upsert_template_attribute('Source Characteristic 1',
+                                                    source_template.id,
+                                                    description: 'A characteristic of the source.',
+                                                    sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                    is_title: false,
+                                                    required: true,
+                                                    isa_tag: IsaTag.find_by(title: 'source_characteristic'))
 
 disable_authorization_checks do
   source_template.update(group_order: 1,
@@ -36,40 +53,45 @@
                                                  group: 'ISA minimal starter')
 
 sample_temp_attributes = []
-sample_temp_attributes << TemplateAttribute.new(title: 'Input',
-                                                description: 'Registered Samples in the platform used as input for this protocol.',
-                                                sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'),
-                                                is_title: false,
-                                                required: true)
-
-sample_temp_attributes << TemplateAttribute.new(title: 'Name of a protocol with samples as outputs',
-                                                description: 'Type of experimental step that generates samples as outputs from the study sources.',
-                                                sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                is_title: false,
-                                                required: true,
-                                                isa_tag: IsaTag.find_by(title: 'protocol'))
-
-sample_temp_attributes << TemplateAttribute.new(title: 'Name of protocol parameter 1',
-                                                description: 'A parameter for the protocol.',
-                                                sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                is_title: false,
-                                                required: true,
-                                                isa_tag: IsaTag.find_by(title: 'parameter_value'))
-
-sample_temp_attributes << TemplateAttribute.new(title: 'Sample Name',
-                                                description: 'Samples are considered as biological material sampled from sources and used in the study.',
-                                                sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                is_title: true,
-                                                required: true,
-                                                isa_tag: IsaTag.find_by(title: 'sample'))
-
-sample_temp_attributes << TemplateAttribute.new(title: 'Sample Characteristic 1',
-                                                description: 'A characteristic of the sample.',
-                                                sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                is_title: false,
-                                                required: true,
-                                                sample_controlled_vocab: nil,
-                                                isa_tag: IsaTag.find_by(title: 'sample_characteristic'))
+sample_temp_attributes << upsert_template_attribute('Input',
+                                                    sample_template.id,
+                                                    description: 'Registered Samples in the platform used as input for this protocol.',
+                                                    sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'),
+                                                    is_title: false,
+                                                    required: true)
+
+sample_temp_attributes << upsert_template_attribute('Name of a protocol with samples as outputs',
+                                                    sample_template.id,
+                                                    description: 'Type of experimental step that generates samples as outputs from the study sources.',
+                                                    sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                    is_title: false,
+                                                    required: true,
+                                                    isa_tag: IsaTag.find_by(title: 'protocol'))
+
+sample_temp_attributes << upsert_template_attribute('Name of protocol parameter 1',
+                                                    sample_template.id,
+                                                    description: 'A parameter for the protocol.',
+                                                    sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                    is_title: false,
+                                                    required: true,
+                                                    isa_tag: IsaTag.find_by(title: 'parameter_value'))
+
+sample_temp_attributes << upsert_template_attribute('Sample Name',
+                                                    sample_template.id,
+                                                    description: 'Samples are considered as biological material sampled from sources and used in the study.',
+                                                    sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                    is_title: true,
+                                                    required: true,
+                                                    isa_tag: IsaTag.find_by(title: 'sample'))
+
+sample_temp_attributes << upsert_template_attribute('Sample Characteristic 1',
+                                                    sample_template.id,
+                                                    description: 'A characteristic of the sample.',
+                                                    sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                    is_title: false,
+                                                    required: true,
+                                                    sample_controlled_vocab: nil,
+                                                    isa_tag: IsaTag.find_by(title: 'sample_characteristic'))
 
 disable_authorization_checks do
   sample_template.update(group_order: 2,
@@ -92,39 +114,44 @@
                                                    level: 'assay - material', group: 'ISA minimal starter')
 
 material_temp_attributes = []
-material_temp_attributes << TemplateAttribute.new(title: 'Input',
-                                                  description: 'Registered Samples in the platform used as input for this protocol.',
-                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'),
-                                                  is_title: false,
-                                                  required: true)
-
-material_temp_attributes << TemplateAttribute.new(title: 'Name of a protocol with material output',
-                                                  description: 'Type of assay or experimental step performed that generates a material output.',
-                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                  is_title: false,
-                                                  required: true,
-                                                  isa_tag: IsaTag.find_by(title: 'protocol'))
-
-material_temp_attributes << TemplateAttribute.new(title: 'Name of protocol parameter 1',
-                                                  description: 'A parameter for the protocol.',
-                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                  is_title: false,
-                                                  required: true,
-                                                  isa_tag: IsaTag.find_by(title: 'parameter_value'))
-
-material_temp_attributes << TemplateAttribute.new(title: 'Output material Name',
-                                                  description: 'Name of the major material output resulting from the application of the protocol.',
-                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                  is_title: true,
-                                                  required: true,
-                                                  isa_tag: IsaTag.find_by(title: 'other_material'))
-
-material_temp_attributes << TemplateAttribute.new(title: 'Output material characteristic 1',
-                                                  description: 'Characteristic 1 of the output material.',
-                                                  sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                  is_title: false,
-                                                  required: true,
-                                                  isa_tag: IsaTag.find_by(title: 'other_material_characteristic'))
+material_temp_attributes << upsert_template_attribute('Input',
+                                                      material_template.id,
+                                                      description: 'Registered Samples in the platform used as input for this protocol.',
+                                                      sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'),
+                                                      is_title: false,
+                                                      required: true)
+
+material_temp_attributes << upsert_template_attribute('Name of a protocol with material output',
+                                                      material_template.id,
+                                                      description: 'Type of assay or experimental step performed that generates a material output.',
+                                                      sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                      is_title: false,
+                                                      required: true,
+                                                      isa_tag: IsaTag.find_by(title: 'protocol'))
+
+material_temp_attributes << upsert_template_attribute('Name of protocol parameter 1',
+                                                      material_template.id,
+                                                      description: 'A parameter for the protocol.',
+                                                      sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                      is_title: false,
+                                                      required: true,
+                                                      isa_tag: IsaTag.find_by(title: 'parameter_value'))
+
+material_temp_attributes << upsert_template_attribute('Output material Name',
+                                                      material_template.id,
+                                                      description: 'Name of the major material output resulting from the application of the protocol.',
+                                                      sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                      is_title: true,
+                                                      required: true,
+                                                      isa_tag: IsaTag.find_by(title: 'other_material'))
+
+material_temp_attributes << upsert_template_attribute('Output material characteristic 1',
+                                                      material_template.id,
+                                                      description: 'Characteristic 1 of the output material.',
+                                                      sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                      is_title: false,
+                                                      required: true,
+                                                      isa_tag: IsaTag.find_by(title: 'other_material_characteristic'))
 
 disable_authorization_checks do
   material_template.update(group_order: 3,
@@ -148,39 +175,44 @@
                                                     level: 'assay - data file', group: 'ISA minimal starter')
 
 data_file_temp_attributes = []
-data_file_temp_attributes << TemplateAttribute.new(title: 'Input',
-                                                   description: 'Registered Samples in the platform used as input for this protocol.',
-                                                   sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'),
-                                                   is_title: false,
-                                                   required: true)
-
-data_file_temp_attributes << TemplateAttribute.new(title: 'Name of a protocol with data file output',
-                                                   description: 'Type of assay or experimental step performed that generates a data file output.',
-                                                   sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                   is_title: false,
-                                                   required: true,
-                                                   isa_tag: IsaTag.find_by(title: 'protocol'))
-
-data_file_temp_attributes << TemplateAttribute.new(title: 'Name of protocol parameter 1',
-                                                   description: 'A parameter for the protocol.',
-                                                   sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                   is_title: false,
-                                                   required: true,
-                                                   isa_tag: IsaTag.find_by(title: 'data_file_comment'))
-
-data_file_temp_attributes << TemplateAttribute.new(title: 'Data file Name',
-                                                   description: 'Name of the major data file output resulting from the application of the protocol.',
-                                                   sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                   is_title: true,
-                                                   required: true,
-                                                   isa_tag: IsaTag.find_by(title: 'data_file'))
-
-data_file_temp_attributes << TemplateAttribute.new(title: 'Data file characteristic 1',
-                                                   description: 'Characteristic 1 of the data file output.',
-                                                   sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
-                                                   is_title: false,
-                                                   required: true,
-                                                   isa_tag: IsaTag.find_by(title: 'data_file_comment'))
+data_file_temp_attributes << upsert_template_attribute('Input',
+                                                       data_file_template.id,
+                                                       description: 'Registered Samples in the platform used as input for this protocol.',
+                                                       sample_attribute_type: SampleAttributeType.find_by(title: 'Registered Sample List'),
+                                                       is_title: false,
+                                                       required: true)
+
+data_file_temp_attributes << upsert_template_attribute('Name of a protocol with data file output',
+                                                       data_file_template.id,
+                                                       description: 'Type of assay or experimental step performed that generates a data file output.',
+                                                       sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                       is_title: false,
+                                                       required: true,
+                                                       isa_tag: IsaTag.find_by(title: 'protocol'))
+
+data_file_temp_attributes << upsert_template_attribute('Name of protocol parameter 1',
+                                                       data_file_template.id,
+                                                       description: 'A parameter for the protocol.',
+                                                       sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                       is_title: false,
+                                                       required: true,
+                                                       isa_tag: IsaTag.find_by(title: 'data_file_comment'))
+
+data_file_temp_attributes << upsert_template_attribute('Data file Name',
+                                                       data_file_template.id,
+                                                       description: 'Name of the major data file output resulting from the application of the protocol.',
+                                                       sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                       is_title: true,
+                                                       required: true,
+                                                       isa_tag: IsaTag.find_by(title: 'data_file'))
+
+data_file_temp_attributes << upsert_template_attribute('Data file characteristic 1',
+                                                       data_file_template.id,
+                                                       description: 'Characteristic 1 of the data file output.',
+                                                       sample_attribute_type: SampleAttributeType.find_by(title: 'String'),
+                                                       is_title: false,
+                                                       required: true,
+                                                       isa_tag: IsaTag.find_by(title: 'data_file_comment'))
 
 disable_authorization_checks do
   data_file_template.update(group_order: 4,
diff --git a/lib/ro_crate/exception.rb b/lib/ro_crate/exception.rb
deleted file mode 100644
index df4517b6e8..0000000000
--- a/lib/ro_crate/exception.rb
+++ /dev/null
@@ -1,11 +0,0 @@
-module ROCrate
-  class Exception < RuntimeError
-    attr_reader :cause
-
-    def initialize(message, original_exception)
-      @cause = original_exception
-      super("#{self.class.name} - #{message}\n#{@cause.class.name} - #{@cause.message}")
-      set_backtrace(@cause.backtrace)
-    end
-  end
-end
diff --git a/lib/ro_crate/read_exception.rb b/lib/ro_crate/read_exception.rb
deleted file mode 100644
index 0aa8488921..0000000000
--- a/lib/ro_crate/read_exception.rb
+++ /dev/null
@@ -1,3 +0,0 @@
-module ROCrate
-  class ReadException < ROCrate::Exception; end
-end
diff --git a/lib/ro_crate/write_exception.rb b/lib/ro_crate/write_exception.rb
deleted file mode 100644
index f25c7663a6..0000000000
--- a/lib/ro_crate/write_exception.rb
+++ /dev/null
@@ -1,3 +0,0 @@
-module ROCrate
-  class WriteException < ROCrate::Exception; end
-end
diff --git a/lib/scrapers/github_scraper.rb b/lib/scrapers/github_scraper.rb
index 7ed04da4c5..4b8e6c42eb 100644
--- a/lib/scrapers/github_scraper.rb
+++ b/lib/scrapers/github_scraper.rb
@@ -105,6 +105,7 @@ def create_resource(repo, tag)
       workflow.policy = Policy.projects_policy(workflow.projects)
       workflow.policy.access_type = Policy::ACCESSIBLE
       workflow.source_link_url = repo.remote.chomp('.git')
+      workflow.tags = topics(repo)
       if wiz.next_step == :provide_metadata
         unless @debug
           if new_version
@@ -153,6 +154,21 @@ def github
       RestClient::Resource.new('https://api.github.com', {})
     end
 
+    def topics(repo)
+      remote = repo.remote
+      @_topics_cache ||= {}
+      return @_topics_cache[remote] if @_topics_cache[remote]
+      remote_uri = URI(remote)
+      if remote_uri.hostname.include?('github.com')
+        user, repo, *_ = remote_uri.path.split('/')[1..-1]
+        repo = repo.split('.').first
+
+        @_topics_cache[remote] = JSON.parse(github["repos/#{user}/#{repo}/topics"].get(accept: 'application/vnd.github.mercy-preview+json').body)&.dig('names') || []
+      else
+        @_topics_cache[remote] = []
+      end
+    end
+
     def latest_tag(repo)
       tag = `cd #{repo.git_base.path}/.. && git describe --tags --abbrev=0 remotes/origin/#{main_branch(repo)}`.chomp
       return nil unless $?.success?
diff --git a/lib/scrapers/nfcore_scraper.rb b/lib/scrapers/nfcore_scraper.rb
index abadedf0cb..a85ba76619 100644
--- a/lib/scrapers/nfcore_scraper.rb
+++ b/lib/scrapers/nfcore_scraper.rb
@@ -5,7 +5,7 @@ class NfcoreScraper < GithubScraper
 
     def list_repositories
       repos = JSON.parse(RestClient.get('https://nf-co.re/pipelines.json'))['remote_workflows']
-      @nfcore_pipelines = {} # Store repo metadata from pipelines.json to fetch main branch name later
+      @nfcore_pipelines = {} # Store repo metadata from pipelines.json to fetch main branch name and topics later
       repos.each do |r|
         r['clone_url'] = "https://github.com/#{r['full_name']}.git"
         @nfcore_pipelines[r['clone_url']] = r
@@ -18,6 +18,10 @@ def main_branch(repo)
       @nfcore_pipelines.dig(repo.remote, 'default_branch') || super
     end
 
+    def topics(repo)
+      @nfcore_pipelines.dig(repo.remote, 'topics') || []
+    end
+
     def workflow_wizard(repo, tag)
       GitWorkflowWizard.new(workflow_class: WorkflowClass.find_by_key('nextflow'),
         params: {
diff --git a/lib/scrapers/util.rb b/lib/scrapers/util.rb
index 4bd505a8b8..55f251f587 100644
--- a/lib/scrapers/util.rb
+++ b/lib/scrapers/util.rb
@@ -30,7 +30,9 @@ def self.bot_project(attributes)
       unless project
         project = Project.new(attributes)
         disable_authorization_checks { project.save! }
-        bot = bot_account
+      end
+      bot = bot_account
+      unless project.has_member?(bot)
         bot.add_to_project_and_institution(project, bot_institution)
         bot.is_project_administrator = true, project
         disable_authorization_checks { bot.save! }
diff --git a/lib/seek/config.rb b/lib/seek/config.rb
index 0f3350d932..a363d1986e 100644
--- a/lib/seek/config.rb
+++ b/lib/seek/config.rb
@@ -332,6 +332,14 @@ def assays_enabled
       isa_enabled
     end
 
+    def templates_enabled
+      isa_json_compliance_enabled
+    end
+
+    def strains_enabled
+      organisms_enabled
+    end
+
     def omniauth_elixir_aai_config
       if omniauth_elixir_aai_legacy_mode
         {
@@ -365,7 +373,7 @@ def omniauth_elixir_aai_config
           name: :elixir_aai,
           scope: [:openid, :email],
           response_type: 'code',
-          issuer: 'https://proxy.aai.lifescience-ri.eu/',
+          issuer: 'https://login.aai.lifescience-ri.eu/oidc/',
           discovery: true,
           client_options: {
             identifier: omniauth_elixir_aai_client_id,
diff --git a/lib/seek/content_extraction.rb b/lib/seek/content_extraction.rb
index b5e4190731..5168e878d8 100644
--- a/lib/seek/content_extraction.rb
+++ b/lib/seek/content_extraction.rb
@@ -69,7 +69,6 @@ def extract_text_from_pdf
         Docsplit.extract_text(pdf_filepath, output: converted_storage_directory) unless File.exist?(txt_filepath)
         File.read(txt_filepath)
       rescue Docsplit::ExtractionFailed => e
-        extract_text_from_pdf if double_check_mime_type
         Rails.logger.error("Problem with extracting text from pdf #{id} #{e}")
         ''
       end
@@ -78,11 +77,7 @@ def extract_text_from_pdf
 
     def to_csv(sheet = 1, trim = false)
       return '' unless is_excel?
-      begin
-        spreadsheet_to_csv(filepath, sheet, trim, Seek::Config.jvm_memory_allocation)
-      rescue SysMODB::SpreadsheetExtractionException
-        to_csv(sheet, trim) if double_check_mime_type
-      end
+      spreadsheet_to_csv(filepath, sheet, trim, Seek::Config.jvm_memory_allocation)
     end
 
     def extract_csv()
@@ -90,34 +85,11 @@ def extract_csv()
     end
 
     def to_spreadsheet_xml
-      begin
-        spreadsheet_to_xml(filepath, Seek::Config.jvm_memory_allocation)
-      rescue SysMODB::SpreadsheetExtractionException=>e
-        if double_check_mime_type
-          to_spreadsheet_xml
-        else
-          raise e
-        end
-      end
+      spreadsheet_to_xml(filepath, Seek::Config.jvm_memory_allocation)
     end
 
     private
 
-    # checks the type using mime magic, and updates if found to be different. This is to help cases where extraction
-    # fails due to the mime type being incorrectly set
-    #
-    # @return boolean - the mime type was changed
-    def double_check_mime_type
-      suggested_type = mime_magic_content_type
-      if suggested_type && suggested_type != content_type
-        update_column(:content_type, suggested_type)
-        true
-      else
-        false
-      end
-    end
-
-
     # filters special characters, keeping alphanumeric characters, hyphen ('-'), underscore('_') and newlines
     def filter_text_content(content)
       content.gsub(/[^-_0-9a-z \n]/i, ' ')
diff --git a/lib/seek/filtering/search_filter.rb b/lib/seek/filtering/search_filter.rb
index 8b3dbeb017..9d0c62b45c 100644
--- a/lib/seek/filtering/search_filter.rb
+++ b/lib/seek/filtering/search_filter.rb
@@ -5,8 +5,7 @@ def apply(collection, query)
         q = query.join(' ')
         q = ActionController::Base.helpers.sanitize(q)
         q ||= ''
-        q = Seek::Search::SearchTermFilter.filter(q)
-        q = q.downcase
+        q = q.downcase.strip
         collection.with_search_query(q)
       end
 
diff --git a/lib/seek/index_table_columns.yml b/lib/seek/index_table_columns.yml
index a718883713..87bfa3d624 100644
--- a/lib/seek/index_table_columns.yml
+++ b/lib/seek/index_table_columns.yml
@@ -88,6 +88,7 @@ columns:
     required: [ ]
     default: [ published_date, journal ]
     additional_allowed: [ abstract, citation, bookmark, publisher, editor, url ]
+    blocked: [ license ]
 
   sample_type:
     required: [ ]
diff --git a/lib/seek/json_metadata/data.rb b/lib/seek/json_metadata/data.rb
index 05aadae6f7..51760ad4b3 100644
--- a/lib/seek/json_metadata/data.rb
+++ b/lib/seek/json_metadata/data.rb
@@ -34,6 +34,17 @@ def mass_assign(hash, pre_process: true)
         end
       end
 
+      # extracts all values from the data as a list, including from within nested structures
+      def extract_all_values(data = self)
+        data.values.collect do |value|
+          if value.is_a?(Seek::JSONMetadata::Data)
+            extract_all_values(value)
+          else
+            value
+          end
+        end.flatten
+      end
+
       private
 
       def validate_hash(hash)
diff --git a/lib/seek/permissions/translator.rb b/lib/seek/permissions/translator.rb
index 08dc1511eb..6bb9dec5ff 100644
--- a/lib/seek/permissions/translator.rb
+++ b/lib/seek/permissions/translator.rb
@@ -12,7 +12,7 @@ class Translator
         download: Set.new(%i[
                             download named_download launch submit_job data execute plot explore
                             download_log download_results input output download_output download_input
-                            view_result compare_versions simulate diagram ro_crate
+                            view_result compare_versions simulate diagram ro_crate ro_crate_metadata
                           ]).freeze,
 
         edit: Set.new(%i[
diff --git a/lib/seek/renderers/text_renderer.rb b/lib/seek/renderers/text_renderer.rb
index 62d013ee61..b6ca7797c2 100644
--- a/lib/seek/renderers/text_renderer.rb
+++ b/lib/seek/renderers/text_renderer.rb
@@ -6,7 +6,13 @@ def can_render?
       end
 
       def render_content
-        "<pre>#{h(blob.read)}</pre>"
+        content = blob.read
+        if content.empty?
+          '<span class="subtle">No content to display</span>'
+        else
+          "<pre>#{h(content)}</pre>"
+        end
+
       end
 
       def render_standalone
diff --git a/lib/seek/search/search_term_filter.rb b/lib/seek/search/search_term_filter.rb
deleted file mode 100644
index f806eaae16..0000000000
--- a/lib/seek/search/search_term_filter.rb
+++ /dev/null
@@ -1,17 +0,0 @@
-module Seek
-  module Search
-    class SearchTermFilter
-      def self.filter(query)
-        query = query.strip
-        query = query.delete('*')
-        query = query.delete('?')
-        query = query.chop if query.end_with?(':')
-
-        query = query.strip
-        query = '' if query == '-'
-
-        query
-      end
-    end
-  end
-end
diff --git a/lib/seek/workflow_extractors/ro_crate.rb b/lib/seek/workflow_extractors/ro_crate.rb
index 33fbde69d4..116ccd66ed 100644
--- a/lib/seek/workflow_extractors/ro_crate.rb
+++ b/lib/seek/workflow_extractors/ro_crate.rb
@@ -54,8 +54,6 @@ def open_crate
         @opened_crate = nil
 
         v
-      rescue StandardError => e
-        raise ::ROCrate::ReadException.new("Couldn't read RO-Crate metadata.", e)
       end
 
       def diagram_extension
diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake
index 5f06c3b5ab..769e95aed1 100644
--- a/lib/tasks/seek_upgrades.rake
+++ b/lib/tasks/seek_upgrades.rake
@@ -11,9 +11,6 @@ namespace :seek do
     decouple_extracted_samples_policies
     decouple_extracted_samples_projects
     link_sample_datafile_attributes
-    strip_sample_attribute_pids
-    rename_registered_sample_multiple_attribute_type
-    remove_ontology_attribute_type
     db:seed:007_sample_attribute_types
     db:seed:001_create_controlled_vocabs
     db:seed:017_minimal_starter_isa_templates
@@ -32,8 +29,6 @@ namespace :seek do
   desc('upgrades SEEK from the last released version to the latest released version')
   task(upgrade: [:environment]) do
     puts 'Starting upgrade ...'
-    puts '... trimming old session data ...'
-    Rake::Task['db:sessions:trim'].invoke
     puts '... migrating database ...'
     Rake::Task['db:migrate'].invoke
     Rake::Task['tmp:clear'].invoke
@@ -57,93 +52,60 @@ namespace :seek do
     end
   end
 
-  task(rename_registered_sample_multiple_attribute_type: [:environment]) do
-    attr = SampleAttributeType.find_by(title:'Registered Sample (multiple)')
-    if attr
-      puts "..... Renaming sample attribute type 'Registered Sample (multiple)' to 'Registered Sample List'."
-      attr.update_column(:title, 'Registered Sample List')
-    end
-  end
-
-  task(strip_sample_attribute_pids: [:environment]) do
-    puts '..... Stripping Sample Attribute PIds ...'
-    n = 0
-    SampleAttribute.where('pid is NOT NULL AND pid !=?','').each do |attribute|
-      new_pid = attribute.pid.strip
-      if attribute.pid != new_pid
-        attribute.update_column(:pid, new_pid)
-        n += 1
-      end
-    end
-    puts "..... Finished stripping #{n} Sample Attribute PIds."
-  end
-
-  task(remove_ontology_attribute_type: [:environment]) do
-    ontology_attr_type = SampleAttributeType.find_by(title:'Ontology')
-    cv_attr_type = SampleAttributeType.find_by(title:'Controlled Vocabulary')
-    if ontology_attr_type
-      puts '..... Removing the Ontology sample attribute type ...'
-      if cv_attr_type
-        if ontology_attr_type.sample_attributes.any?
-          puts "..... Moving #{ontology_attr_type.sample_attributes.count} sample attributes to Controlled Vocabulary"
-          ontology_attr_type.sample_attributes.each do |attr_type|
-            attr_type.update_column(:sample_attribute_type_id, cv_attr_type.id)
-          end
-        end
-        if ontology_attr_type.isa_template_attributes.any?
-          puts "..... Moving #{ontology_attr_type.isa_template_attributes.count} template attributes to Controlled Vocabulary"
-          ontology_attr_type.isa_template_attributes.each do |attr_type|
-            attr_type.update_column(:sample_attribute_type_id, cv_attr_type.id)
-          end
-        end
-
-        ontology_attr_type.destroy
-      else
-        puts '..... Target Controlled Vocabulary attribute type not found'
-      end
-    end
-  end
-
   task(decouple_extracted_samples_policies: [:environment]) do
     puts '..... creating independent policies for extracted samples (this can take a while if there are many samples) ...'
     affected_samples = []
+
+    Policy.skip_callback :commit, :after, :queue_update_auth_table
+    Policy.skip_callback :commit, :after, :queue_rdf_generation_job
+    Permission.skip_callback :commit, :after, :queue_update_auth_table
+    Permission.skip_callback :commit, :after, :queue_rdf_generation_job
+
     disable_authorization_checks do
-      Sample.includes(:originating_data_file).find_each do |sample|
-        # check if the sample was extracted from a datafile and their policies are linked
-        if sample.extracted? && sample.policy_id == sample.originating_data_file&.policy_id
-          policy = sample.policy.deep_copy
-          policy.save
-          sample.update_column(:policy_id, policy.id)
-          putc('.')
-          affected_samples << sample
+      Sample.includes(:originating_data_file).in_batches(of: 250) do |batch|
+        batch.each do |sample|
+          # check if the sample was extracted from a datafile and their policies are linked
+          if sample.extracted? && sample.policy_id == sample.originating_data_file&.policy_id
+            policy = sample.policy.deep_copy
+            policy.save
+            sample.update_column(:policy_id, policy.id)
+            affected_samples << sample
+          end
         end
+        putc('.')
       end
-      #won't have been queued, as the policy has no associated assets yet when saved
-      AuthLookupUpdateQueue.enqueue(affected_samples) if affected_samples.any?
     end
     puts "..... finished creating independent policies of #{affected_samples.count} extracted samples"
+  ensure
+    Policy.set_callback :commit, :after, :queue_update_auth_table
+    Policy.set_callback :commit, :after, :queue_rdf_generation_job
+    Permission.set_callback :commit, :after, :queue_update_auth_table
+    Permission.set_callback :commit, :after, :queue_rdf_generation_job
   end
 
   task(decouple_extracted_samples_projects: [:environment]) do
     puts '..... copying project ids for extracted samples...'
-    decoupled = 0
+    decoupled_count = 0
     hash_array = []
     disable_authorization_checks do
-      Sample.find_each do |sample|
-        # check if the sample was extracted from a datafile and their projects are linked
-        if sample.extracted? && sample.project_ids.empty?
-          sample.originating_data_file.project_ids.each do |project_id|
-            hash_array << { project_id: project_id, sample_id: sample.id }
+      Sample.includes(:originating_data_file).where.missing(:projects).in_batches(of: 250) do |batch|
+        batch.each do |sample|
+          # check if the sample was extracted from a datafile and their projects are linked
+          if sample.extracted? && sample.project_ids.empty?
+            sample.originating_data_file.project_ids.each do |project_id|
+              hash_array << { project_id: project_id, sample_id: sample.id }
+            end
+            decoupled_count += 1
           end
-          decoupled += 1
         end
+        putc('.')
       end
       unless hash_array.empty?
         class ProjectsSample < ActiveRecord::Base; end;
         ProjectsSample.insert_all(hash_array)
       end
     end
-    puts " ... finished copying project ids of #{decoupled.to_s} extracted samples"
+    puts " ... finished copying project ids of #{decoupled_count.to_s} extracted samples"
   end
 
   task(link_sample_datafile_attributes: [:environment]) do
diff --git a/public/api/definitions/_paths.yml b/public/api/definitions/_paths.yml
index dcde4f6fd1..d1cf992c96 100644
--- a/public/api/definitions/_paths.yml
+++ b/public/api/definitions/_paths.yml
@@ -1100,6 +1100,61 @@
         $ref: "#/components/responses/forbidden"
       "404":
         $ref: "#/components/responses/notFound"
+/extended_metadata_types:
+  get:
+    operationId: listExtendedMetadataTypes
+    summary: List extended metadata types
+    description:
+      $ref: ../descriptions/listExtendedMetadataTypes.md
+    tags:
+      - list
+      - extendedMetadataTypes
+    responses:
+      "200":
+        description: OK
+        content:
+          application/json:
+            schema:
+              $ref: "#/components/schemas/indexResponse"
+            examples:
+              response:
+                value:
+                  $ref: ../examples/extendedMetadataTypesResponse.json
+      "501":
+        $ref: "#/components/responses/notImplemented"
+
+"/extended_metadata_types/{id}":
+  parameters:
+    - name: id
+      in: path
+      required: true
+      description: The extended metadata type to fetch
+      schema:
+        type: integer
+      example: 1152
+  get:
+    operationId: readExtendedMetadataType
+    summary: Fetch an extended metadata type
+    description:
+      $ref: ../descriptions/readExtendedMetadataType.md
+    tags:
+      - read
+      - extendedMetadataTypes
+    responses:
+      "200":
+        description: OK
+        content:
+          application/json:
+            schema:
+              $ref: "#/components/schemas/extendedMetadataTypeResponse"
+            examples:
+              response:
+                value:
+                  $ref: ../examples/extendedMetadataTypeResponse.json
+      "403":
+        $ref: "#/components/responses/forbidden"
+      "404":
+        $ref: "#/components/responses/notFound"
 /institutions:
   get:
     operationId: listInstitutions
diff --git a/public/api/definitions/_schemas.yml b/public/api/definitions/_schemas.yml
index 74b9601ee9..2b1bcffcdb 100644
--- a/public/api/definitions/_schemas.yml
+++ b/public/api/definitions/_schemas.yml
@@ -473,6 +473,8 @@ collectionAttributes:
       $ref: "#/components/schemas/assetsCreatorsList"
     discussion_links:
       $ref: "#/components/schemas/assetLinkList"
+    extended_attributes:
+      $ref: "#/components/schemas/extendedMetadata"
   required:
     - title
     - license
@@ -867,6 +869,7 @@ anyType:
     - sops
     - studies
     - workflows
+    - extended_metadata_types
 assetType:
   type: string
   minLength: 1
@@ -1128,6 +1131,8 @@ assayPost:
               $ref: "#/components/schemas/policy"
             discussion_links:
               $ref: "#/components/schemas/assetLinkPostList"
+            extended_attributes:
+              $ref: "#/components/schemas/extendedMetadata"
           required:
             - title
             - assay_class
@@ -1218,6 +1223,8 @@ assayPatch:
               $ref: "#/components/schemas/policy"
             discussion_links:
               $ref: "#/components/schemas/assetLinkPatchList"
+            extended_attributes:
+              $ref: "#/components/schemas/extendedMetadata"
           additionalProperties: false
         relationships:
           type: object
@@ -1868,6 +1875,8 @@ investigationPost:
               $ref: "#/components/schemas/policy"
             discussion_links:
               $ref: "#/components/schemas/assetLinkPostList"
+            extended_attributes:
+              $ref: "#/components/schemas/extendedMetadata"
           required:
             - title
           additionalProperties: false
@@ -1918,6 +1927,8 @@ investigationPatch:
               $ref: "#/components/schemas/policy"
             discussion_links:
               $ref: "#/components/schemas/assetLinkPatchList"
+            extended_attributes:
+              $ref: "#/components/schemas/extendedMetadata"
           additionalProperties: false
         relationships:
           type: object
@@ -3230,6 +3241,8 @@ assayResponse:
               $ref: "#/components/schemas/assetLinkList"
             position:
               $ref: "#/components/schemas/nullableInteger"
+            extended_attributes:
+              $ref: "#/components/schemas/extendedMetadata"
           required:
             - title
             - assay_class
@@ -3330,8 +3343,6 @@ collectionResponse:
               $ref: "#/components/schemas/multipleReferences"
             items:
               $ref: "#/components/schemas/multipleReferences"
-            extended_attributes:
-              $ref: "#/components/schemas/extendedMetadata"
           required:
             - creators
             - submitter
@@ -3810,6 +3821,8 @@ investigationResponse:
               $ref: "#/components/schemas/assetLinkList"
             position:
               $ref: "#/components/schemas/nullableInteger"
+            extended_attributes:
+              $ref: "#/components/schemas/extendedMetadata"
           required:
             - title
           additionalProperties: false
@@ -4720,6 +4733,100 @@ sampleTypeSampleAttributeResponse:
     - title
     - sample_attribute_type
   additionalProperties: false
+extendedMetadataTypeResponse:
+  type: object
+  properties:
+    data:
+      type: object
+      properties:
+        id:
+          $ref: "#/components/schemas/nonEmptyString"
+        type:
+          $ref: "#/components/schemas/nonEmptyString"
+        attributes:
+          type: object
+          properties:
+            title:
+              $ref: "#/components/schemas/nonEmptyString"
+            supported_type:
+              $ref: "#/components/schemas/nonEmptyString"
+            enabled:
+              type: boolean
+            extended_metadata_attributes:
+              $ref: "#/components/schemas/extendedMetadataTypeExtendedMetadataAttributesResponse"
+          required:
+            - title
+            - supported_type
+            - enabled
+            - extended_metadata_attributes
+        links:
+          $ref: "#/components/schemas/links"
+        meta:
+          type: object
+          properties:
+            base_url:
+              $ref: "#/components/schemas/uriString"
+            api_version:
+              $ref: "#/components/schemas/nonEmptyString"
+          required:
+            - base_url
+            - api_version
+          additionalProperties: false
+      required:
+        - id
+        - type
+        - attributes
+        - links
+        - meta
+      additionalProperties: false
+    jsonapi:
+      $ref: "#/components/schemas/JsonApiVersion"
+  required:
+      - data
+      - jsonapi
+  additionalProperties: false
+extendedMetadataTypeExtendedMetadataAttributesResponse:
+  type: array
+  minItems: 1
+  uniqueItems: true
+  items:
+    $ref: "#/components/schemas/extendedMetadataTypeExtendedMetadataAttributeResponse"
+extendedMetadataTypeExtendedMetadataAttributeResponse:
+  type: object
+  properties:
+    id:
+      $ref: "#/components/schemas/nonEmptyString"
+    title:
+      $ref: "#/components/schemas/nonEmptyString"
+    label:
+      $ref: "#/components/schemas/nonEmptyString"
+    description:
+      $ref: "#/components/schemas/nullableNonEmptyString"
+    sample_attribute_type:
+      type: object
+      properties:
+        id:
+          $ref: "#/components/schemas/nonEmptyString"
+        title:
+          $ref: "#/components/schemas/nonEmptyString"
+        base_type:
+          $ref: "#/components/schemas/sampleAttributeBaseType"
+        regexp:
+          $ref: "#/components/schemas/nonEmptyString"
+    required:
+      type: boolean
+    pos:
+      $ref: "#/components/schemas/nullableInteger"
+    sample_controlled_vocab_id:
+      $ref: "#/components/schemas/nullableNonEmptyString"
+    linked_extended_metadata_type_id:
+      $ref: "#/components/schemas/nullableNonEmptyString"
+  required:
+    - id
+    - title
+    - sample_attribute_type
+    - required
+  additionalProperties: false
 searchResponse:
   type: object
   properties:
diff --git a/public/api/definitions/openapi-v3.yml b/public/api/definitions/openapi-v3.yml
index 8eb1eb492e..b9024f98a8 100644
--- a/public/api/definitions/openapi-v3.yml
+++ b/public/api/definitions/openapi-v3.yml
@@ -87,6 +87,9 @@ tags:
   - name: documents
     description:
       $ref: ../descriptions/documents.md
+  - name: extendedMetadataTypes
+    description:
+      $ref: ../descriptions/extendedMetadataTypes.md
   - name: models
     description:
       $ref: ../descriptions/models.md
@@ -158,6 +161,9 @@ x-tagGroups:
       - sampleTypes
       - samples
       - sampleAttributeTypes
+  - name: Extended Metadata Types
+    tags:
+      - extendedMetadataTypes
 components:
   securitySchemes:
     OAuth2:
diff --git a/public/api/descriptions/api.md b/public/api/descriptions/api.md
index 0138724b85..797774f3d5 100644
--- a/public/api/descriptions/api.md
+++ b/public/api/descriptions/api.md
@@ -90,3 +90,37 @@ A placeholder can then be satisfied by uploading a file to the location URI. For
 may be satisfied by uploading a file to http://fairdomhub.org/data_files/57/content_blobs/313 using the <a href="#uploadAssetContent">uploadAssetContent</a> operation
 
 The content of a resource may be downloaded by first *reading* the resource and then *downloading* the ContentBlobs from their URI.
+
+## Extended Metadata
+
+Some types support [Extended Metadata](https://docs.seek4science.org/tech/extended-metadata), which allows additional attributes to be defined according to an Extended Metadata Type.
+
+Types currently supported are <a href="#investigations">**Investigation**</a>, <a href="#studies">**Study**</a>, <a href="#assays">**Assay**</a>, 
+<a href="#dataFiles">**DataFile**</a>, <a href="#sops">**SOP**</a>, <a href="#presentations">**Presentation**</a>,
+<a href="#documents">**Document**</a>, <a href="#models">**Model**</a>,
+<a href="#events">**Event**</a>, <a href="#collections">**Collection**</a>, <a href="#projects">**Project**</a>
+
+The responses and requests for each of these types include an additional optional attribute _extended_attributes_ which describes
+
+* _extended_metadata_type_id_ - the id of the extended metadata type which can be used to find more details about what its attributes are.
+* _attribute_map_ - which is a map of key / value pairs where the key is the attribute name
+
+
+For example, a Study may have extended metadata, defined by an Extended Metadata Type with id 12, that has attributes for
+age, name, and date_of_birth. These could be shown, within its attributes, as:
+
+```
+"extended_attributes": {
+  "extended_metadata_type_id": "12",
+  "attribute_map": {
+    "age": 44,
+    "name": "Fred Bloggs",
+    "date_of_birth": "2024-01-01"
+  }
+}
+```
+
+If you wish to create or update a study to make use of this extended metadata, the request payload would be described the same. 
+Upon creation or update there would be a validation check that the attributes are valid.
+
+The API supports listing all available Extended Metadata Types, and inspecting an individual type by its id. For more information see the [Extended Metadata Type definitions](api#tag/extendedMetadataTypes).
\ No newline at end of file
diff --git a/public/api/descriptions/assays.md b/public/api/descriptions/assays.md
index f1e1ae40df..6847eb61a2 100644
--- a/public/api/descriptions/assays.md
+++ b/public/api/descriptions/assays.md
@@ -23,7 +23,7 @@ A response for an **Assay** such as that for a <a href="#create">**Create**</a>,
 * A singleton reference to the <a href="#investigations">**Investigation**</a> which the **Assay** is part of
 * References to the <a href="#projects">**Projects**</a> that indirectly contain the **Assay**
 
-
+**Assays** have support for [Extended Metadata](/api#section/Extended-Metadata)
 
 
 
diff --git a/public/api/descriptions/collections.md b/public/api/descriptions/collections.md
index c6b8dde8ca..f40482c29f 100644
--- a/public/api/descriptions/collections.md
+++ b/public/api/descriptions/collections.md
@@ -5,3 +5,5 @@ The collections API can be used to create an empty collections, and add metadata
 Assets can be added, removed, re-ordered and annotated (in the context of the collection) via the <a href="#collection_items">**Collection Items**</a> API.
 
 <a name="collection_items"></a>A **Collection Item** is a resource that links an asset to a collection.
+
+**Collections** have support for [Extended Metadata](/api#section/Extended-Metadata)
\ No newline at end of file
diff --git a/public/api/descriptions/dataFiles.md b/public/api/descriptions/dataFiles.md
index 2771eabab4..fb2dcb08af 100644
--- a/public/api/descriptions/dataFiles.md
+++ b/public/api/descriptions/dataFiles.md
@@ -27,5 +27,5 @@ A response for a **DataFile** such as that for a <a href="#create">**Create**</a
 * References to the <a href="#investigations">**Investigations**</a> associated with the **DataFile**
 * References to the <a href="#studies">**Studies**</a> associated with the **DataFile**
 
-
+**DataFiles** have support for [Extended Metadata](/api#section/Extended-Metadata)
 
diff --git a/public/api/descriptions/documents.md b/public/api/descriptions/documents.md
index 64cf82b519..34cd23c2e4 100644
--- a/public/api/descriptions/documents.md
+++ b/public/api/descriptions/documents.md
@@ -26,6 +26,7 @@ A response for a **Document** such as that for a <a href="#create">**Create**</a
 * References to the <a href="#studies">**Studies**</a> associated with the **Document**
 * References to the <a href="#publications">**Publications**</a> associated with the **Document**
 
+**Documents** have support for [Extended Metadata](/api#section/Extended-Metadata)
 
 
 
diff --git a/public/api/descriptions/events.md b/public/api/descriptions/events.md
index f252713489..e321ebd421 100644
--- a/public/api/descriptions/events.md
+++ b/public/api/descriptions/events.md
@@ -18,4 +18,6 @@ An **Event** has the following associated information:
 
 A response for an **Event** such as that for a <a href="#create">**Create**</a>, <a href="#read">**Read**</a> or <a href="#update">**Update**</a> includes the additional information
 
-* Reference to the <a href="#people">**Person**</a> who submitted the **Event**
\ No newline at end of file
+* Reference to the <a href="#people">**Person**</a> who submitted the **Event**
+
+**Events** have support for [Extended Metadata](/api#section/Extended-Metadata)
\ No newline at end of file
diff --git a/public/api/descriptions/extendedMetadataTypes.md b/public/api/descriptions/extendedMetadataTypes.md
new file mode 100644
index 0000000000..37bfe777c8
--- /dev/null
+++ b/public/api/descriptions/extendedMetadataTypes.md
@@ -0,0 +1,7 @@
+<a name="extendedMetadataTypes"></a>
+**Extended Metadata Types** define additional attributes that can be embedded within a number of different assets and items, which extends the metadata. An
+**Extended Metadata Type** is tied to a particular supported type (such as Investigation, Study, Assay, DataFile) and is only available for that type.
+
+Only the READ operations [List](/api#operation/listExtendedMetadataTypes) and [Fetch](/api#operation/readExtendedMetadataType) are currently supported.
+
+For more details please visit [Extended Metadata](/api#section/Extended-Metadata)
\ No newline at end of file
diff --git a/public/api/descriptions/investigations.md b/public/api/descriptions/investigations.md
index ea1df6dcb0..6cb157cf36 100644
--- a/public/api/descriptions/investigations.md
+++ b/public/api/descriptions/investigations.md
@@ -21,4 +21,4 @@ A response for an **Investigation** such as that for a <a href="#create">**Creat
 * References to <a href="#sops">**Sops**</a> that belong to the **Investigation**
 * References to <a href="#publications">**Publications**</a> that belong to the **Investigation**
 
-
+**Investigations** have support for [Extended Metadata](/api#section/Extended-Metadata)
diff --git a/public/api/descriptions/listExtendedMetadataTypes.md b/public/api/descriptions/listExtendedMetadataTypes.md
new file mode 100644
index 0000000000..8aeaaaf499
--- /dev/null
+++ b/public/api/descriptions/listExtendedMetadataTypes.md
@@ -0,0 +1,2 @@
+<a name="listExtendedMetadataTypes"></a>The **listExtendedMetadataTypes** operation returns a JSON object containing a list of all the
+<a href="#extendedMetadataTypes">**Extended Metadata Types**</a> to which the authenticated user has access.
\ No newline at end of file
diff --git a/public/api/descriptions/models.md b/public/api/descriptions/models.md
index 0c743885f4..e25bdb9b41 100644
--- a/public/api/descriptions/models.md
+++ b/public/api/descriptions/models.md
@@ -28,3 +28,5 @@ A response for a **Model** such as that for a <a href="#create">**Create**</a>,
 * A reference to the <a href="#people">**Person**</a> who submitted the **Model**
 * References to the <a href="#investigations">**Investigations**</a> associated with the **Model**
 * References to the <a href="#studies">**Studies**</a> associated with the **Model**
+
+**Models** have support for [Extended Metadata](/api#section/Extended-Metadata)
\ No newline at end of file
diff --git a/public/api/descriptions/presentations.md b/public/api/descriptions/presentations.md
index e6babfddb6..1b25ef58d4 100644
--- a/public/api/descriptions/presentations.md
+++ b/public/api/descriptions/presentations.md
@@ -25,4 +25,6 @@ A response for a **Presentation** such as that for a <a href="#create">**Create*
 * ** The last time the Presentation was updated**
 * A reference to the <a href="#people">**Person**</a> who submitted the **Presentation**
 * References to the <a href="#investigations">**Investigations**</a> associated with the **Presentation**
-* References to the <a href="#studies">**Studies**</a> associated with the **Presentation**
\ No newline at end of file
+* References to the <a href="#studies">**Studies**</a> associated with the **Presentation**
+
+**Presentations** have support for [Extended Metadata](/api#section/Extended-Metadata)
\ No newline at end of file
diff --git a/public/api/descriptions/projects.md b/public/api/descriptions/projects.md
index 1ebf4984af..777c0b0581 100644
--- a/public/api/descriptions/projects.md
+++ b/public/api/descriptions/projects.md
@@ -30,4 +30,5 @@ A response for a **Project** such as that for a <a href="#create">**Create**</a>
 * References to <a href="#presentations">**Presentations**</a> that belong to the <a href="#projects">**Project**</a>
 * References to <a href="#events">**Events**</a> that are held by or attended by the <a href="#projects">**Project**</a>
 
+**Projects** have support for [Extended Metadata](/api#section/Extended-Metadata)
 
diff --git a/public/api/descriptions/readExtendedMetadataType.md b/public/api/descriptions/readExtendedMetadataType.md
new file mode 100644
index 0000000000..cec5828fe2
--- /dev/null
+++ b/public/api/descriptions/readExtendedMetadataType.md
@@ -0,0 +1,3 @@
+<a name="readExtendedMetadataType"></a>A **readExtendedMetadataType** operation will return information about the <a href="#extendedMetadataTypes">Extended Metadata Type</a> identified, provided the authenticated user has access to it.
+
+The **readExtendedMetadataType** operation returns a JSON object representing the <a href="#extendedMetadataTypes">**Extended Metadata Type**</a>.
\ No newline at end of file
diff --git a/public/api/descriptions/sops.md b/public/api/descriptions/sops.md
index cfd2b0454e..2f7c94156d 100644
--- a/public/api/descriptions/sops.md
+++ b/public/api/descriptions/sops.md
@@ -26,3 +26,4 @@ A response for a **SOP** such as that for a <a href="#create">**Create**</a>, <a
 * References to the <a href="#studies">**Studies**</a> associated with the **SOP**
 * References to the <a href="#publications">**Publications**</a> associated with the **SOP**
 
+**SOPs** have support for [Extended Metadata](/api#section/Extended-Metadata)
diff --git a/public/api/descriptions/studies.md b/public/api/descriptions/studies.md
index 75858c3697..aebb436ab3 100644
--- a/public/api/descriptions/studies.md
+++ b/public/api/descriptions/studies.md
@@ -23,7 +23,7 @@ A response for a **Study** such as that for a <a href="#create">**Create**</a>,
 * References to <a href="#sops">**Sops**</a> that belong to the **Study**
 * References to <a href="#publications">**Publications**</a> that belong to the **Study**
 
-
+**Studies** have support for [Extended Metadata](/api#section/Extended-Metadata)
 
 
 
diff --git a/public/api/examples/extendedMetadataTypeResponse.json b/public/api/examples/extendedMetadataTypeResponse.json
new file mode 100644
index 0000000000..23f238bd37
--- /dev/null
+++ b/public/api/examples/extendedMetadataTypeResponse.json
@@ -0,0 +1,71 @@
+{
+  "data": {
+    "id": "233",
+    "type": "extended_metadata_types",
+    "attributes": {
+      "title": "A Max Extended Metadata Type",
+      "supported_type": "Investigation",
+      "enabled": true,
+      "extended_metadata_attributes": [
+        {
+          "id": "502",
+          "title": "age",
+          "label": "Age",
+          "description": null,
+          "sample_attribute_type": {
+            "id": "539",
+            "title": "Integer attribute type 4",
+            "base_type": "Integer",
+            "regexp": ".*"
+          },
+          "required": false,
+          "pos": null,
+          "sample_controlled_vocab_id": null,
+          "linked_extended_metadata_type_id": null
+        },
+        {
+          "id": "503",
+          "title": "name",
+          "label": "Name",
+          "description": null,
+          "sample_attribute_type": {
+            "id": "540",
+            "title": "String attribute type 7",
+            "base_type": "String",
+            "regexp": ".*"
+          },
+          "required": true,
+          "pos": null,
+          "sample_controlled_vocab_id": null,
+          "linked_extended_metadata_type_id": null
+        },
+        {
+          "id": "504",
+          "title": "date",
+          "label": "Date",
+          "description": null,
+          "sample_attribute_type": {
+            "id": "541",
+            "title": "DateTime attribute type 4",
+            "base_type": "DateTime",
+            "regexp": ".*"
+          },
+          "required": false,
+          "pos": null,
+          "sample_controlled_vocab_id": null,
+          "linked_extended_metadata_type_id": null
+        }
+      ]
+    },
+    "links": {
+      "self": "/extended_metadata_types/233"
+    },
+    "meta": {
+      "api_version": "0.3",
+      "base_url": "http://localhost:3000"
+    }
+  },
+  "jsonapi": {
+    "version": "1.0"
+  }
+}
\ No newline at end of file
diff --git a/public/api/examples/extendedMetadataTypesResponse.json b/public/api/examples/extendedMetadataTypesResponse.json
new file mode 100644
index 0000000000..08b883ad75
--- /dev/null
+++ b/public/api/examples/extendedMetadataTypesResponse.json
@@ -0,0 +1,34 @@
+{
+  "data": [
+    {
+      "id": "231",
+      "type": "extended_metadata_types",
+      "attributes": {
+        "title": "A Min Extended Metadata Type"
+      },
+      "links": {
+        "self": "/extended_metadata_types/231"
+      }
+    },
+    {
+      "id": "232",
+      "type": "extended_metadata_types",
+      "attributes": {
+        "title": "A Max Extended Metadata Type"
+      },
+      "links": {
+        "self": "/extended_metadata_types/232"
+      }
+    }
+  ],
+  "jsonapi": {
+    "version": "1.0"
+  },
+  "links": {
+    "self": "/extended_metadata_types"
+  },
+  "meta": {
+    "base_url": "http://localhost:3000",
+    "api_version": "0.3"
+  }
+}
\ No newline at end of file
diff --git a/test/factories/extended_metadata_types.rb b/test/factories/extended_metadata_types.rb
index 9cd6bf75a3..9118877bdb 100644
--- a/test/factories/extended_metadata_types.rb
+++ b/test/factories/extended_metadata_types.rb
@@ -21,6 +21,24 @@
     association :sample_attribute_type, factory: :datetime_sample_attribute_type
   end
 
+  factory(:min_extended_metadata_type,class: ExtendedMetadataType) do
+    title { 'A Min Extended Metadata Type' }
+    supported_type { 'Investigation' }
+    after(:build) do |a|
+      a.extended_metadata_attributes << FactoryBot.create(:name_extended_metadata_attribute, required: true)
+    end
+  end
+
+  factory(:max_extended_metadata_type,class: ExtendedMetadataType) do
+    title { 'A Max Extended Metadata Type' }
+    supported_type { 'Investigation' }
+    after(:build) do |a|
+      a.extended_metadata_attributes << FactoryBot.create(:age_extended_metadata_attribute)
+      a.extended_metadata_attributes << FactoryBot.create(:name_extended_metadata_attribute, required: true)
+      a.extended_metadata_attributes << FactoryBot.create(:datetime_extended_metadata_attribute)
+    end
+  end
+
   factory(:study_extended_metadata_type_with_cv_and_cv_list_type, class: ExtendedMetadataType) do
     title { 'study extended metadata type with and list attributes' }
     supported_type { 'Study' }
@@ -142,7 +160,7 @@
   end
 
   factory(:study_extended_metadata_type_for_MIAPPE, class: ExtendedMetadataType) do
-    title { 'MIAPPE metadata' }
+    title { ExtendedMetadataType::MIAPPE_TITLE }
     supported_type { 'Study' }
     after(:build) do |a|
       a.extended_metadata_attributes << FactoryBot.create(:name_extended_metadata_attribute, title:'id')
diff --git a/test/factories/presentations.rb b/test/factories/presentations.rb
index 3a10559a13..7aff9f9477 100644
--- a/test/factories/presentations.rb
+++ b/test/factories/presentations.rb
@@ -104,4 +104,8 @@
       end
     end
   end
+
+  factory(:small_test_spreadsheet_presentation, parent: :presentation) do
+    association :content_blob, factory: :small_test_spreadsheet_content_blob
+  end
 end
diff --git a/test/fixtures/files/workflows/ro-crate-metadata-missing-file.json b/test/fixtures/files/workflows/ro-crate-metadata-missing-file.json
new file mode 100644
index 0000000000..4ce5414aaa
--- /dev/null
+++ b/test/fixtures/files/workflows/ro-crate-metadata-missing-file.json
@@ -0,0 +1,63 @@
+{
+  "@context": [
+    "https://w3id.org/ro/crate/1.1/context"
+  ],
+  "@graph": [
+    {
+      "@id": "ro-crate-metadata.json",
+      "@type": "CreativeWork",
+      "about": {
+        "@id": "./"
+      },
+      "conformsTo": {
+        "@id": "https://w3id.org/ro/crate/1.1"
+      }
+    },
+    {
+      "@id": "./",
+      "@type": "Dataset",
+      "name": "Concat two files",
+      "description": "Concats two files",
+      "license": "https://opensource.org/licenses/MIT",
+      "mainEntity": {
+        "@id": "concat_two_files.ga"
+      },
+      "hasPart": [
+        {
+          "@id": "concat_two_files.ga"
+        },
+        {
+          "@id": "this-file-does-not-exist"
+        }
+
+      ]
+    },
+    {
+      "@id": "concat_two_files.ga",
+      "@type": [
+        "File",
+        "SoftwareSourceCode",
+        "ComputationalWorkflow"
+      ],
+      "programmingLanguage": {
+        "@id": "#galaxy"
+      },
+      "name": "concat_two_files"
+    },
+    {
+      "@id": "this-file-does-not-exist",
+      "@type": "File"
+    },
+    {
+      "@id": "#galaxy",
+      "@type": "ComputerLanguage",
+      "name": "Galaxy",
+      "identifier": {
+        "@id": "https://galaxyproject.org/"
+      },
+      "url": {
+        "@id": "https://galaxyproject.org/"
+      }
+    }
+  ]
+}
diff --git a/test/fixtures/json/responses/get_max_extended_metadata_type.json.erb b/test/fixtures/json/responses/get_max_extended_metadata_type.json.erb
new file mode 100644
index 0000000000..96dd2c483d
--- /dev/null
+++ b/test/fixtures/json/responses/get_max_extended_metadata_type.json.erb
@@ -0,0 +1,71 @@
+{
+  "data": {
+    "id": "<%= res.id %>",
+    "type": "extended_metadata_types",
+    "attributes": {
+      "title": "A Max Extended Metadata Type",
+      "supported_type": "Investigation",
+      "enabled": true,
+      "extended_metadata_attributes": [
+        {
+          "id": "<%= res.extended_metadata_attributes.first.id %>",
+          "title": "age",
+          "label": "Age",
+          "description": null,
+          "sample_attribute_type": {
+            "id": "<%= res.extended_metadata_attributes.first.sample_attribute_type_id %>",
+            "title": "<%= res.extended_metadata_attributes.first.sample_attribute_type.title %>",
+            "base_type": "Integer",
+            "regexp": ".*"
+          },
+          "required":false,
+          "pos":null,
+          "sample_controlled_vocab_id":null,
+          "linked_extended_metadata_type_id":null
+        },
+        {
+          "id": "<%= res.extended_metadata_attributes.second.id %>",
+          "title": "name",
+          "label": "Name",
+          "description": null,
+          "sample_attribute_type": {
+            "id": "<%= res.extended_metadata_attributes.second.sample_attribute_type_id %>",
+            "title": "<%= res.extended_metadata_attributes.second.sample_attribute_type.title %>",
+            "base_type": "String",
+            "regexp": ".*"
+          },
+          "required":true,
+          "pos":null,
+          "sample_controlled_vocab_id":null,
+          "linked_extended_metadata_type_id":null
+        },
+        {
+          "id": "<%= res.extended_metadata_attributes.last.id %>",
+          "title": "date",
+          "label": "Date",
+          "description": null,
+          "sample_attribute_type": {
+            "id": "<%= res.extended_metadata_attributes.last.sample_attribute_type_id %>",
+            "title": "<%= res.extended_metadata_attributes.last.sample_attribute_type.title %>",
+            "base_type": "DateTime",
+            "regexp": ".*"
+          },
+          "required":false,
+          "pos":null,
+          "sample_controlled_vocab_id":null,
+          "linked_extended_metadata_type_id":null
+        }
+      ]
+    },
+    "links": {
+      "self": "/extended_metadata_types/<%= res.id %>"
+    },
+    "meta": {
+      "api_version": "0.3",
+      "base_url": "http://localhost:3000"
+    }
+  },
+  "jsonapi": {
+    "version": "1.0"
+  }
+}
\ No newline at end of file
diff --git a/test/fixtures/json/responses/get_min_extended_metadata_type.json.erb b/test/fixtures/json/responses/get_min_extended_metadata_type.json.erb
new file mode 100644
index 0000000000..730941160c
--- /dev/null
+++ b/test/fixtures/json/responses/get_min_extended_metadata_type.json.erb
@@ -0,0 +1,39 @@
+{
+  "data": {
+    "id": "<%= res.id %>",
+    "type": "extended_metadata_types",
+    "attributes": {
+      "title": "A Min Extended Metadata Type",
+      "supported_type": "Investigation",
+      "enabled": true,
+      "extended_metadata_attributes": [
+        {
+          "id": "<%= res.extended_metadata_attributes.first.id %>",
+          "title": "name",
+          "label": "Name",
+          "description": null,
+          "sample_attribute_type": {
+            "id": "<%= res.extended_metadata_attributes.first.sample_attribute_type_id %>",
+            "title": "<%= res.extended_metadata_attributes.first.sample_attribute_type.title %>",
+            "base_type": "String",
+            "regexp": ".*"
+          },
+          "required":true,
+          "pos":null,
+          "sample_controlled_vocab_id":null,
+          "linked_extended_metadata_type_id":null
+        }
+      ]
+    },
+    "links": {
+      "self": "/extended_metadata_types/<%= res.id %>"
+    },
+    "meta": {
+      "api_version": "0.3",
+      "base_url": "http://localhost:3000"
+    }
+  },
+  "jsonapi": {
+    "version": "1.0"
+  }
+}
\ No newline at end of file
diff --git a/test/functional/admin_controller_test.rb b/test/functional/admin_controller_test.rb
index de9227fc5c..e28453ef84 100644
--- a/test/functional/admin_controller_test.rb
+++ b/test/functional/admin_controller_test.rb
@@ -236,6 +236,36 @@ def setup
     end
   end
 
+  test 'job queue table' do
+    sop = FactoryBot.create(:sop)
+    admin = FactoryBot.create(:admin)
+    login_as(admin)
+    RdfGenerationQueue.destroy_all
+    ReindexingQueue.destroy_all
+    AuthLookupUpdateQueue.destroy_all
+
+    with_config_value(:auth_lookup_enabled, true) do
+
+      assert RdfGenerationQueue.queue_enabled?
+      assert ReindexingQueue.queue_enabled?
+      assert AuthLookupUpdateQueue.queue_enabled?
+
+      RdfGenerationQueue.enqueue(sop)
+      ReindexingQueue.enqueue(sop)
+      AuthLookupUpdateQueue.enqueue(sop)
+    end
+
+    get :get_stats, xhr: true, params: { page: 'job_queue' }
+    assert_response :success
+
+    assert_select 'div.job-queue-table table' do
+      assert_select 'tbody > tr', count: 3
+      assert_select 'tbody > tr > td', text: 'RdfGenerationQueue'
+      assert_select 'tbody > tr > td', text: 'ReindexingQueue'
+      assert_select 'tbody > tr > td', text: 'AuthLookupUpdateQueue'
+    end
+  end
+
   test 'storage usage stats' do
     FactoryBot.create(:rightfield_datafile)
     FactoryBot.create(:rightfield_annotated_datafile)
diff --git a/test/functional/documents_controller_test.rb b/test/functional/documents_controller_test.rb
index f83fd9f291..219e484cec 100644
--- a/test/functional/documents_controller_test.rb
+++ b/test/functional/documents_controller_test.rb
@@ -302,7 +302,7 @@ class DocumentsControllerTest < ActionController::TestCase
     get :show, params: { id: doc }
     assert_response :success
     assert_select '#buttons' do
-      assert_select 'a[href=?]', explore_document_path(doc, version: doc.version), count: 1
+      assert_select 'a[href=?]', explore_document_path(doc, version: doc.version), text:'Explore', count: 1
       assert_select 'a.disabled', text: 'Explore', count: 0
     end
   end
@@ -1460,6 +1460,28 @@ class DocumentsControllerTest < ActionController::TestCase
     end
   end
 
+  test 'get index filtered by parent' do
+    programme = FactoryBot.create(:programme)
+    project = FactoryBot.create(:project, programme: programme)
+    document = FactoryBot.create(:public_document, projects: [project])
+    with_config_value(:programmes_enabled, true) do
+      get :index, params: { programme_id: programme.id }
+      assert_response :success
+      assert_includes assigns(:documents), document
+    end
+  end
+
+  test 'do not get index filtered by parent if parent feature disabled' do
+    programme = FactoryBot.create(:programme)
+    project = FactoryBot.create(:project, programme: programme)
+    document = FactoryBot.create(:public_document, projects: [project])
+    with_config_value(:programmes_enabled, false) do
+      get :index, params: { programme_id: programme.id }
+      assert_redirected_to root_path
+      assert flash[:error].include?('Parent resource not recognized')
+    end
+  end
+
   private
 
   def valid_document
diff --git a/test/functional/git_controller_test.rb b/test/functional/git_controller_test.rb
index 5a43c947ee..5223dcb68f 100644
--- a/test/functional/git_controller_test.rb
+++ b/test/functional/git_controller_test.rb
@@ -210,6 +210,17 @@ def setup
     assert_select 'img.git-image-preview[src=?]', workflow_git_raw_path(@workflow, version: @git_version.version, path: 'test.svg')
   end
 
+  test 'get remote blob' do
+    @git_version.add_remote_file('something', 'https://example.com/something', fetch: false)
+    @git_version.save!
+    get :blob, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'something' }
+
+    assert_response :success
+    assert_select 'a.btn[href=?]', workflow_git_remove_file_path(@workflow, version: @git_version.version, path: 'something')
+    assert_select 'a.btn[href=?]', 'https://example.com/something'
+    assert_select 'img.git-image-preview[src=?]', workflow_git_raw_path(@workflow, version: @git_version.version, path: 'something'), count: 0
+  end
+
   test 'get raw binary file' do
     get :raw, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'diagram.png' }
 
@@ -224,6 +235,24 @@ def setup
     assert @response.header['Content-Disposition'].include?('attachment')
   end
 
+  test 'attempting to download remote blob throws error' do
+    @git_version.add_remote_file('something', 'https://example.com/something', fetch: false)
+    @git_version.save!
+    get :download, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'something' }
+
+    assert_redirected_to workflow_path(@workflow, tab: 'files')
+    assert flash[:error].include?('held externally')
+  end
+
+  test 'attempting to get raw remote blob throws error' do
+    @git_version.add_remote_file('something', 'https://example.com/something', fetch: false)
+    @git_version.save!
+    get :raw, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'something' }
+
+    assert_redirected_to workflow_path(@workflow, tab: 'files')
+    assert flash[:error].include?('held externally')
+  end
+
   test 'getting non-existent blob throws error' do
     get :blob, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'doesnotexist' }
 
diff --git a/test/functional/homes_controller_test.rb b/test/functional/homes_controller_test.rb
index 51a9d86bc2..a8bbc1c54f 100644
--- a/test/functional/homes_controller_test.rb
+++ b/test/functional/homes_controller_test.rb
@@ -726,6 +726,54 @@ class HomesControllerTest < ActionController::TestCase
 
   end
 
+  test 'Show aliases in search options' do
+    original_load_path = I18n.load_path
+    I18n.load_path += Dir[Rails.root.join('test', 'config', 'translation_override.en.yml')]
+    I18n.backend.load_translations
+    with_config_values({ isa_json_compliance_enabled: true, solr_enabled: true }) do
+      get :index
+      assert_response :success
+      assert_select 'select#search_type' do
+        assert_select 'option', text: 'Investigation tests', count: 1
+        assert_select 'option', text: 'Study tests', count: 1
+        assert_select 'option', text: 'Assay tests', count: 1
+        assert_select 'option', text: 'Data file tests', count: 1
+        assert_select 'option', text: 'Document tests', count: 1
+        assert_select 'option', text: 'SOP_test', count: 1 # this is an exception, the alias is not in the translation file
+        assert_select 'option', text: 'Presentation tests', count: 1
+        assert_select 'option', text: 'Event tests', count: 1
+        assert_select 'option', text: 'Collection tests', count: 1
+        assert_select 'option', text: 'Sample tests', count: 1
+        assert_select 'option', text: 'Sample type tests', count: 1
+        assert_select 'option', text: 'Template tests', count: 1
+        assert_select 'option', text: 'Person tests', count: 1
+        assert_select 'option', text: 'Project tests', count: 1
+        assert_select 'option', text: 'Institution tests', count: 1
+        assert_select 'option', text: 'Programme tests', count: 1
+
+        # Making sure the default values are not shown
+        assert_select 'option', text: 'Investigations', count: 0
+        assert_select 'option', text: 'Studies', count: 0
+        assert_select 'option', text: 'Assays', count: 0
+        assert_select 'option', text: 'Data files', count: 0
+        assert_select 'option', text: 'Documents', count: 0
+        assert_select 'option', text: 'SOP', count: 0
+        assert_select 'option', text: 'Presentations', count: 0
+        assert_select 'option', text: 'Events', count: 0
+        assert_select 'option', text: 'Collections', count: 0
+        assert_select 'option', text: 'Samples', count: 0
+        assert_select 'option', text: 'Sample types', count: 0
+        assert_select 'option', text: 'Templates', count: 0
+        assert_select 'option', text: 'People', count: 0
+        assert_select 'option', text: 'Projects', count: 0
+        assert_select 'option', text: 'Institutions', count: 0
+        assert_select 'option', text: 'Programmes', count: 0
+      end
+    end
+    I18n.load_path = original_load_path
+    I18n.backend.load_translations
+  end
+
   test 'get dataset jsonld from index' do
     get :index, format: :jsonld
     assert_response :success
diff --git a/test/functional/people_controller_test.rb b/test/functional/people_controller_test.rb
index f00b35eafc..9894c34658 100644
--- a/test/functional/people_controller_test.rb
+++ b/test/functional/people_controller_test.rb
@@ -1039,6 +1039,12 @@ def test_should_add_nofollow_to_links_in_show_page
       assert_select 'div.list_item_title  a[href=?]', data_file_path(other_data_file), text: /#{other_data_file.title}/, count: 0
       assert_select 'div.list_item_title  a[href=?]', project_path(other_project), text: /#{other_project.title}/, count: 0
     end
+
+    assert_select 'div#buttons' do
+      assert_select 'a[href=?]', batch_sharing_permission_preview_person_path(me),text: /Batch permission changes/
+      assert_select 'a[href=?]', batch_publishing_preview_person_path(me),text: /Publish your items/
+    end
+
   end
 
   test 'my items permissions' do
diff --git a/test/functional/presentations_controller_test.rb b/test/functional/presentations_controller_test.rb
index 253e2a1be5..676b523998 100644
--- a/test/functional/presentations_controller_test.rb
+++ b/test/functional/presentations_controller_test.rb
@@ -656,4 +656,21 @@ def setup
       assert flash[:error].include?('disabled')
     end
   end
+
+  test 'show explore button' do
+    presentation = FactoryBot.create(:small_test_spreadsheet_presentation)
+    login_as(presentation.contributor.user)
+    get :show, params: { id: presentation }
+    assert_response :success
+    assert_select '#buttons' do
+      assert_select 'a[href=?]', explore_presentation_path(presentation, version: presentation.version), text:'Explore', count: 1
+      assert_select 'a.disabled', text: 'Explore', count: 0
+    end
+  end
+
+  test 'explore latest version' do
+    presentation = FactoryBot.create :small_test_spreadsheet_presentation, policy: FactoryBot.create(:public_policy)
+    get :explore, params: { id: presentation }
+    assert_response :success
+  end
 end
diff --git a/test/functional/projects_controller_test.rb b/test/functional/projects_controller_test.rb
index 21a8552a8c..5a551924ef 100644
--- a/test/functional/projects_controller_test.rb
+++ b/test/functional/projects_controller_test.rb
@@ -154,8 +154,8 @@ def test_avatar_show_in_list
     assert_no_difference('Project.count') do
       assert_no_difference('ExtendedMetadata.count') do
         put :update, params: { id: project.id, project: { title: "new title",
-                                                      extended_metadata_attributes: { extended_metadata_type_id: cmt.id, id: cm.id,
-                                                                                      data: {
+                                                          extended_metadata_attributes: { extended_metadata_type_id: cmt.id, id: cm.id,
+                                                                                          data: {
                                                                                         "age": 20,
                                                                                         "name": 'max'
                                                                                       } }
@@ -209,6 +209,21 @@ def test_avatar_show_in_list
     assert_empty project.programmes
   end
 
+  test 'update project with tags' do
+    proj_admin = FactoryBot.create(:project_administrator)
+    login_as(proj_admin)
+    project = proj_admin.projects.first
+
+    post :update_annotations_ajax, xhr: true, params: { id: project, tag_list: %w[alice rabbit] }
+    project.reload
+    assert_equal %w[alice rabbit], project.tags
+
+    project.annotate_with('dodo', 'tag', proj_admin)
+    project.save!
+    assert_equal ['dodo'], project.tags
+  end
+
+
   test 'cannot create project with programme if not administrator of programme' do
     person = FactoryBot.create(:programme_administrator)
     login_as(person)
@@ -1207,7 +1222,7 @@ def test_admin_can_edit
     new_person2 = FactoryBot.create(:person)
     new_person3 = FactoryBot.create(:person)
 
-    put :update, params: { id:project.id, project: { members: [{ 'person_id' => "#{new_person.id}", 'institution_id' => "#{new_institution.id}" },
+    put :update, params: { id: project.id, project: { members: [{ 'person_id' => "#{new_person.id}", 'institution_id' => "#{new_institution.id}" },
                                                                           { 'person_id' => "#{new_person2.id}", 'institution_id' => "#{new_institution.id}" },
                                                                           { 'person_id' => "#{new_person3.id}", 'institution_id' => "#{new_institution.id}" }] } }
 
@@ -1287,7 +1302,7 @@ def test_admin_can_edit
     assert_no_enqueued_jobs only: ProjectLeavingJob do
       assert_no_difference('GroupMembership.count') do
         post :update_members, params: { id: project, memberships_to_flag: { group_membership.id.to_s => { time_left_at: 1.day.ago },
-                                    former_group_membership.id.to_s => { time_left_at: '' } } }
+                                                                            former_group_membership.id.to_s => { time_left_at: '' } } }
         assert_redirected_to project_path(project)
         assert_nil flash[:error]
         refute_nil flash[:notice]
@@ -1601,8 +1616,8 @@ def test_admin_can_edit
     person = FactoryBot.create(:person, group_memberships: [group_membership])
 
     data_file = FactoryBot.create(:data_file, projects: [project], contributor: person,
-                        policy: FactoryBot.create(:policy, access_type: Policy::NO_ACCESS,
-                                        permissions: [FactoryBot.create(:permission,
+                                              policy: FactoryBot.create(:policy, access_type: Policy::NO_ACCESS,
+                                                                                 permissions: [FactoryBot.create(:permission,
                                                               contributor: project,
                                                               access_type: Policy::VISIBLE)]))
     refute data_file.can_delete?(proj_admin)
@@ -1900,10 +1915,10 @@ def test_admin_can_edit
     login_as(person)
     params = {
       project_ids: ['', project.id],
-        institution:{
+      institution: {
             id: ['', institution.id]
         },
-        comments: 'some comments'
+      comments: 'some comments'
     }
     assert_enqueued_emails(1) do
       assert_difference('ProjectMembershipMessageLog.count') do
@@ -1928,10 +1943,10 @@ def test_admin_can_edit
 
     institution_params = {
         id: ['fish'],
-        title:'fish',
-        city:'Sheffield',
-        country:'GB',
-        web_page:'http://google.com'
+        title: 'fish',
+        city: 'Sheffield',
+        country: 'GB',
+        web_page: 'http://google.com'
     }
     params = {
         project_ids: [project.id],
@@ -1965,10 +1980,10 @@ def test_admin_can_edit
 
     institution_params = {
       id: ['fish'],
-      title:'fish',
-      city:'Sheffield',
-      country:'GB',
-      web_page:'http://google.com'
+      title: 'fish',
+      city: 'Sheffield',
+      country: 'GB',
+      web_page: 'http://google.com'
     }
     params = {
       project_ids: ['', project1.id, project2.id],
@@ -2503,9 +2518,9 @@ def test_admin_can_edit
     with_config_value(:managed_programme_id, programme.id) do
       params = {
         project: {dmp: fixture_file_upload('dmp.json', 'application/json')},
-          institution: {id: ['the inst'], title: 'the inst', web_page: 'the page', city: 'London', country: 'GB'},
-          programme_id: '',
-          programme: {title: 'the prog'}
+        institution: {id: ['the inst'], title: 'the inst', web_page: 'the page', city: 'London', country: 'GB'},
+        programme_id: '',
+        programme: {title: 'the prog'}
       }
       assert_enqueued_emails(1) do
         assert_difference('ProjectImportationMessageLog.count') do
@@ -2644,8 +2659,8 @@ def test_admin_can_edit
     params = {
         message_log_id: log.id,
         accept_request: '1',
-        institution:{id:institution.id},
-        id:project.id
+        institution: {id:institution.id},
+        id: project.id
     }
 
     assert_enqueued_emails(2) do
@@ -2679,8 +2694,8 @@ def test_admin_can_edit
     params = {
         message_log_id: log.id,
         accept_request: '1',
-        institution:{id:institution.id},
-        id:project.id
+        institution: {id:institution.id},
+        id: project.id
     }
 
     assert_enqueued_emails(0) do
@@ -2703,8 +2718,8 @@ def test_admin_can_edit
     project = person.projects.first
     sender = FactoryBot.create(:person)
     institution = Institution.new({
-                                      title:'institution',
-                                   country:'DE'
+                                      title: 'institution',
+                                      country: 'DE'
                                   })
     log = ProjectMembershipMessageLog.log_request(sender:sender, project:project, institution:institution, comments:'some comments')
     login_as(person)
@@ -2712,11 +2727,11 @@ def test_admin_can_edit
     params = {
         message_log_id: log.id,
         accept_request: '1',
-        institution:{
-                     title:'institution',
-                     country:'FR' # admin may have corrected this from DE
+        institution: {
+                     title: 'institution',
+                     country: 'FR' # admin may have corrected this from DE
         },
-        id:project.id
+        id: project.id
     }
 
     assert_enqueued_emails(2) do
@@ -2746,8 +2761,8 @@ def test_admin_can_edit
     project = person.projects.first
     sender = FactoryBot.create(:person)
     institution = Institution.new({
-                                      title:'institution',
-                                      country:'DE'
+                                      title: 'institution',
+                                      country: 'DE'
                                   })
     log = ProjectMembershipMessageLog.log_request(sender:sender, project:project, institution:institution, comments:'some comments')
     login_as(person)
@@ -2755,10 +2770,10 @@ def test_admin_can_edit
     params = {
         message_log_id: log.id,
         accept_request: '1',
-        institution:{
-            title:'',
+        institution: {
+            title: '',
         },
-        id:project.id
+        id: project.id
     }
 
     assert_enqueued_emails(0) do
@@ -2789,7 +2804,7 @@ def test_admin_can_edit
         message_log_id: log.id,
         reject_details: 'bad request',
         institution: { id:institution.id },
-        id:project.id
+        id: project.id
     }
 
     assert_enqueued_emails(2) do
@@ -2977,19 +2992,19 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'new project updated',
-            web_page:'http://proj.org'
+        project: {
+            title: 'new project updated',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            title:'new programme updated'
+        programme: {
+            title: 'new programme updated'
         },
-        institution:{
-            title:'new institution updated',
-            city:'Paris',
-            country:'FR'
+        institution: {
+            title: 'new institution updated',
+            city: 'Paris',
+            country: 'FR'
         }
     }
 
@@ -3044,19 +3059,19 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'new project updated',
-            web_page:'http://proj.org'
+        project: {
+            title: 'new project updated',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            title:'new programme updated'
+        programme: {
+            title: 'new programme updated'
         },
-        institution:{
-            title:'new institution updated',
-            city:'Paris',
-            country:'FR'
+        institution: {
+            title: 'new institution updated',
+            city: 'Paris',
+            country: 'FR'
         }
     }
 
@@ -3087,19 +3102,19 @@ def test_admin_can_edit
     institution = Institution.new({title:'institution', country:'DE'})
     log = ProjectCreationMessageLog.log_request(sender: person, programme:programme, project:project, institution:institution)
     params = {
-      message_log_id:log.id,
+      message_log_id: log.id,
       accept_request: '1',
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
+      programme: {
         id: programme.id
       },
-      institution:{
-        title:'new institution',
-        city:'Paris',
-        country:'FR'
+      institution: {
+        title: 'new institution',
+        city: 'Paris',
+        country: 'FR'
       }
     }
 
@@ -3148,19 +3163,19 @@ def test_admin_can_edit
     institution = Institution.new({title:'institution', country:'DE'})
     log = ProjectCreationMessageLog.log_request(sender: person, programme:programme, project:project, institution:institution)
     params = {
-      message_log_id:log.id,
+      message_log_id: log.id,
       accept_request: '1',
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
+      programme: {
         id: programme.id
       },
-      institution:{
-        title:'new institution',
-        city:'Paris',
-        country:'FR'
+      institution: {
+        title: 'new institution',
+        city: 'Paris',
+        country: 'FR'
       }
     }
 
@@ -3197,18 +3212,18 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:''
+        project: {
+            title: ''
         },
-        programme:{
-            title:'new programme updated'
+        programme: {
+            title: 'new programme updated'
         },
-        institution:{
-            title:'new institution updated',
-            city:'Paris',
-            country:'FR'
+        institution: {
+            title: 'new institution updated',
+            city: 'Paris',
+            country: 'FR'
         }
     }
 
@@ -3242,18 +3257,18 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'a valid project'
+        project: {
+            title: 'a valid project'
         },
-        programme:{
-            title:''
+        programme: {
+            title: ''
         },
-        institution:{
-            title:duplicate_institution.title,
-            city:'Paris',
-            country:'FR'
+        institution: {
+            title: duplicate_institution.title,
+            city: 'Paris',
+            country: 'FR'
         }
     }
 
@@ -3286,17 +3301,17 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'new project',
-            web_page:'http://proj.org'
+        project: {
+            title: 'new project',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            id:programme.id
+        programme: {
+            id: programme.id
         },
-        institution:{
-            id:institution.id
+        institution: {
+            id: institution.id
         }
     }
 
@@ -3340,17 +3355,17 @@ def test_admin_can_edit
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     assert log.sent_by_self?
     params = {
-      message_log_id:log.id,
+      message_log_id: log.id,
       accept_request: '1',
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
-        id:programme.id
+      programme: {
+        id: programme.id
       },
-      institution:{
-        id:institution.id
+      institution: {
+        id: institution.id
       }
     }
 
@@ -3391,16 +3406,16 @@ def test_admin_can_edit
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     assert log.sent_by_self?
     params = {
-      message_log_id:log.id,
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      message_log_id: log.id,
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
-        id:programme.id
+      programme: {
+        id: programme.id
       },
-      institution:{
-        id:institution.id
+      institution: {
+        id: institution.id
       }
     }
 
@@ -3432,16 +3447,16 @@ def test_admin_can_edit
     log = ProjectCreationMessageLog.log_request(sender: requester, programme: programme, project: project, institution: institution)
     refute log.sent_by_self?
     params = {
-      message_log_id:log.id,
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      message_log_id: log.id,
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
-        id:programme.id
+      programme: {
+        id: programme.id
       },
-      institution:{
-        id:institution.id
+      institution: {
+        id: institution.id
       },
       delete_request: '1'
     }
@@ -3475,16 +3490,16 @@ def test_admin_can_edit
     refute log.sent_by_self?
     refute programme.can_manage?
     params = {
-      message_log_id:log.id,
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      message_log_id: log.id,
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
-        id:programme.id
+      programme: {
+        id: programme.id
       },
-      institution:{
-        id:institution.id
+      institution: {
+        id: institution.id
       },
       delete_request: '1'
     }
@@ -3517,17 +3532,17 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'new project',
-            web_page:'http://proj.org'
+        project: {
+            title: 'new project',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            id:programme.id
+        programme: {
+            id: programme.id
         },
-        institution:{
-            id:institution.id
+        institution: {
+            id: institution.id
         }
     }
 
@@ -3561,17 +3576,17 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectCreationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution)
     params = {
-        message_log_id:log.id,
-        reject_details:'not very good',
-        project:{
-            title:'new project',
-            web_page:'http://proj.org'
+        message_log_id: log.id,
+        reject_details: 'not very good',
+        project: {
+            title: 'new project',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            id:programme.id
+        programme: {
+            id: programme.id
         },
-        institution:{
-            id:institution.id
+        institution: {
+            id: institution.id
         }
     }
 
@@ -3606,16 +3621,16 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectCreationMessageLog.log_request(sender:requester, project:project, institution:institution)
     params = {
-      message_log_id:log.id,
+      message_log_id: log.id,
       accept_request: '1',
-      project:{
-        title:'new project updated',
-        web_page:'http://proj.org'
+      project: {
+        title: 'new project updated',
+        web_page: 'http://proj.org'
       },
-      institution:{
-        title:'new institution updated',
-        city:'Paris',
-        country:'FR'
+      institution: {
+        title: 'new institution updated',
+        city: 'Paris',
+        country: 'FR'
       }
     }
 
@@ -3769,19 +3784,19 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'new project updated',
-            web_page:'http://proj.org'
+        project: {
+            title: 'new project updated',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            title:'new programme updated'
+        programme: {
+            title: 'new programme updated'
         },
-        institution:{
-            title:'new institution updated',
-            city:'Paris',
-            country:'FR'
+        institution: {
+            title: 'new institution updated',
+            city: 'Paris',
+            country: 'FR'
         },
         people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -3840,19 +3855,19 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'new project updated',
-            web_page:'http://proj.org'
+        project: {
+            title: 'new project updated',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            title:'new programme updated'
+        programme: {
+            title: 'new programme updated'
         },
-        institution:{
-            title:'new institution updated',
-            city:'Paris',
-            country:'FR'
+        institution: {
+            title: 'new institution updated',
+            city: 'Paris',
+            country: 'FR'
         },
         people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -3885,19 +3900,19 @@ def test_admin_can_edit
     people = FactoryBot.create_list(:person, 3)
     log = ProjectImportationMessageLog.log_request(sender: person, programme:programme, project:project, institution:institution, people:people)
     params = {
-      message_log_id:log.id,
+      message_log_id: log.id,
       accept_request: '1',
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
+      programme: {
         id: programme.id
       },
-      institution:{
-        title:'new institution',
-        city:'Paris',
-        country:'FR'
+      institution: {
+        title: 'new institution',
+        city: 'Paris',
+        country: 'FR'
       },
       people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -3936,18 +3951,18 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:''
+        project: {
+            title: ''
         },
-        programme:{
-            title:'new programme updated'
+        programme: {
+            title: 'new programme updated'
         },
-        institution:{
-            title:'new institution updated',
-            city:'Paris',
-            country:'FR'
+        institution: {
+            title: 'new institution updated',
+            city: 'Paris',
+            country: 'FR'
         },
         people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -3983,18 +3998,18 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'a valid project'
+        project: {
+            title: 'a valid project'
         },
-        programme:{
-            title:''
+        programme: {
+            title: ''
         },
-        institution:{
-            title:duplicate_institution.title,
-            city:'Paris',
-            country:'FR'
+        institution: {
+            title: duplicate_institution.title,
+            city: 'Paris',
+            country: 'FR'
         },
         people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -4029,17 +4044,17 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'new project',
-            web_page:'http://proj.org'
+        project: {
+            title: 'new project',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            id:programme.id
+        programme: {
+            id: programme.id
         },
-        institution:{
-            id:institution.id
+        institution: {
+            id: institution.id
         },
         people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -4087,17 +4102,17 @@ def test_admin_can_edit
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     assert log.sent_by_self?
     params = {
-      message_log_id:log.id,
+      message_log_id: log.id,
       accept_request: '1',
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
-        id:programme.id
+      programme: {
+        id: programme.id
       },
-      institution:{
-        id:institution.id
+      institution: {
+        id: institution.id
       },
       people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -4142,16 +4157,16 @@ def test_admin_can_edit
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     assert log.sent_by_self?
     params = {
-      message_log_id:log.id,
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      message_log_id: log.id,
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
-        id:programme.id
+      programme: {
+        id: programme.id
       },
-      institution:{
-        id:institution.id
+      institution: {
+        id: institution.id
       },
       people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -4185,16 +4200,16 @@ def test_admin_can_edit
     log = ProjectImportationMessageLog.log_request(sender: requester, programme: programme, project: project, institution: institution, people: people)
     refute log.sent_by_self?
     params = {
-      message_log_id:log.id,
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      message_log_id: log.id,
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
-        id:programme.id
+      programme: {
+        id: programme.id
       },
-      institution:{
-        id:institution.id
+      institution: {
+        id: institution.id
       },
       people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} },
       delete_request: '1'
@@ -4230,16 +4245,16 @@ def test_admin_can_edit
     refute log.sent_by_self?
     refute programme.can_manage?
     params = {
-      message_log_id:log.id,
-      project:{
-        title:'new project',
-        web_page:'http://proj.org'
+      message_log_id: log.id,
+      project: {
+        title: 'new project',
+        web_page: 'http://proj.org'
       },
-      programme:{
-        id:programme.id
+      programme: {
+        id: programme.id
       },
-      institution:{
-        id:institution.id
+      institution: {
+        id: institution.id
       },
       people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} },
       delete_request: '1'
@@ -4274,17 +4289,17 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     params = {
-        message_log_id:log.id,
+        message_log_id: log.id,
         accept_request: '1',
-        project:{
-            title:'new project',
-            web_page:'http://proj.org'
+        project: {
+            title: 'new project',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            id:programme.id
+        programme: {
+            id: programme.id
         },
-        institution:{
-            id:institution.id
+        institution: {
+            id: institution.id
         },
         people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -4320,17 +4335,17 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectImportationMessageLog.log_request(sender:requester, programme:programme, project:project, institution:institution, people:people)
     params = {
-        message_log_id:log.id,
-        reject_details:'not very good',
-        project:{
-            title:'new project',
-            web_page:'http://proj.org'
+        message_log_id: log.id,
+        reject_details: 'not very good',
+        project: {
+            title: 'new project',
+            web_page: 'http://proj.org'
         },
-        programme:{
-            id:programme.id
+        programme: {
+            id: programme.id
         },
-        institution:{
-            id:institution.id
+        institution: {
+            id: institution.id
         },
         people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -4367,16 +4382,16 @@ def test_admin_can_edit
     requester = FactoryBot.create(:person)
     log = ProjectImportationMessageLog.log_request(sender:requester, project:project, institution:institution, people:people)
     params = {
-      message_log_id:log.id,
+      message_log_id: log.id,
       accept_request: '1',
-      project:{
-        title:'new project updated',
-        web_page:'http://proj.org'
+      project: {
+        title: 'new project updated',
+        web_page: 'http://proj.org'
       },
-      institution:{
-        title:'new institution updated',
-        city:'Paris',
-        country:'FR'
+      institution: {
+        title: 'new institution updated',
+        city: 'Paris',
+        country: 'FR'
       },
       people: people.map { |p| {first_name: p.first_name, last_name: p.last_name, email: p.email} }
     }
@@ -4623,7 +4638,7 @@ def test_admin_can_edit
     assert_difference('AssetLink.discussion.count') do
       assert_difference('Project.count') do
         post :create, params: { project: { title: 'test',
-                                          discussion_links_attributes: [{url: "http://www.slack.com/"}]}}
+                                           discussion_links_attributes: [{url: "http://www.slack.com/"}]}}
       end
     end
     project = assigns(:project)
@@ -4973,7 +4988,11 @@ def test_admin_can_edit
     login_as(person)
     assert project.has_member?(person)
     assert project.can_edit?
-    get :show, params: { id: project.id }
+
+    with_config_value :isa_json_compliance_enabled, true do
+      get :show, params: { id: project.id }
+    end
+
     assert_response :success
     params = { project_ids: [project.id] }
     directly_linked_types = [
@@ -5002,6 +5021,27 @@ def test_admin_can_edit
     end
   end
 
+  test 'do not show related templates if isa_compliance disabled' do
+    template = FactoryBot.create(:template)
+    person = template.contributor
+    project = template.projects.first
+    login_as(person)
+    assert template.can_view?
+
+    with_config_value(:isa_json_compliance_enabled, true) do
+      get :show, params:{id: project.id}
+      assert_response :success
+      assert_select 'div#related-items li a[data-model-name=Template]', count: 1
+    end
+
+    with_config_value(:isa_json_compliance_enabled, false) do
+      get :show, params:{id: project.id}
+      assert_response :success
+      assert_select 'div#related-items li a[data-model-name=Template]', count: 0
+    end
+
+  end
+
   private
 
   def check_project(project)
diff --git a/test/functional/sample_types_controller_test.rb b/test/functional/sample_types_controller_test.rb
index 3490543460..914d05f659 100644
--- a/test/functional/sample_types_controller_test.rb
+++ b/test/functional/sample_types_controller_test.rb
@@ -696,28 +696,28 @@ class SampleTypesControllerTest < ActionController::TestCase
     assert_response :forbidden
   end
 
-  test 'display sample type with related templates' do
-    person = FactoryBot.create(:person)
-
-    template = FactoryBot.create(:min_template, contributor: person, title:'related template')
-    template2 = FactoryBot.create(:min_template, contributor: person, title:'unrelated template')
-
-    # must be associated with a spreadsheet template
-    sample_type = FactoryBot.create(:strain_sample_type, isa_template: template, contributor: person)
-
-    assert_equal template, sample_type.isa_template
-    refute_nil sample_type.template
-
-    login_as(person.user)
-
-    get :show, params: { id: sample_type.id }
-    assert_response :success
-
-    assert_select 'div.related-items div#templates' do
-      assert_select 'a[href=?]', template_path(template), text: template.title
-      assert_select 'a[href=?]', template_path(template2), text: template2.title, count: 0
-    end
-  end
+  # test 'display sample type with related templates' do
+  #   person = FactoryBot.create(:person)
+  #
+  #   template = FactoryBot.create(:min_template, contributor: person, title:'related template')
+  #   template2 = FactoryBot.create(:min_template, contributor: person, title:'unrelated template')
+  #
+  #   # must be associated with a spreadsheet template
+  #   sample_type = FactoryBot.create(:strain_sample_type, isa_template: template, contributor: person)
+  #
+  #   assert_equal template, sample_type.isa_template
+  #   refute_nil sample_type.template
+  #
+  #   login_as(person.user)
+  #
+  #   get :show, params: { id: sample_type.id }
+  #   assert_response :success
+  #
+  #   assert_select 'div.related-items div#templates' do
+  #     assert_select 'a[href=?]', template_path(template), text: template.title
+  #     assert_select 'a[href=?]', template_path(template2), text: template2.title, count: 0
+  #   end
+  # end
 
   test 'filter sample types with template when advanced single page is enabled' do
     project = FactoryBot.create(:project)
diff --git a/test/functional/templates_controller_test.rb b/test/functional/templates_controller_test.rb
index d9a47f6295..753d43a28c 100644
--- a/test/functional/templates_controller_test.rb
+++ b/test/functional/templates_controller_test.rb
@@ -1,12 +1,17 @@
 require 'test_helper'
 
 class TemplatesControllerTest < ActionController::TestCase
+  fixtures :isa_tags
+
   include AuthenticatedTestHelper
   include SharingFormTestHelper
   include GeneralAuthorizationTestCases
 
   setup do
-    Seek::Config.send('isa_json_compliance_enabled=', true)
+    @old_setting = Seek::Config.isa_json_compliance_enabled
+    Seek::Config.isa_json_compliance_enabled = true
+    Seek::Util.clear_cached
+
     FactoryBot.create(:person) # to prevent person being first person and therefore admin
     @person = FactoryBot.create(:project_administrator)
     @project = @person.projects.first
@@ -23,6 +28,11 @@ class TemplatesControllerTest < ActionController::TestCase
     @default_isa_tag = FactoryBot.create(:default_isa_tag)
   end
 
+  teardown do
+    Seek::Config.isa_json_compliance_enabled = @old_setting
+    Seek::Util.clear_cached
+  end
+
   test 'should get new' do
     get :new
     assert_response :success
diff --git a/test/functional/workflows_controller_test.rb b/test/functional/workflows_controller_test.rb
index 845f75d45e..7e23025b99 100644
--- a/test/functional/workflows_controller_test.rb
+++ b/test/functional/workflows_controller_test.rb
@@ -663,7 +663,7 @@ def bad_generator.write_graph(struct)
     get :ro_crate, params: { id: workflow.id }
 
     assert_redirected_to workflow
-    assert flash[:error].include?("Couldn't generate RO-Crate")
+    assert flash[:error].include?('No @graph found in metadata!')
   end
 
   test 'create RO-Crate even with with duplicated filenames' do
@@ -1799,4 +1799,101 @@ def bad_generator.write_graph(struct)
     assert_select 'a.btn[href=?]', "https://galaxygalaxy.org/mygalaxy/workflows/trs_import?trs_url=#{trs_url}&run_form=true",
                   { text: 'Run on Galaxy' }
   end
+
+  test 'throws error when downloading RO-Crate with missing file' do
+    workflow = FactoryBot.create(:local_git_workflow, policy: FactoryBot.create(:public_policy))
+    gv = workflow.latest_git_version
+    disable_authorization_checks do
+      gv.add_file('ro-crate-metadata.json', File.open(File.join("#{Rails.root}/test/fixtures/files", 'workflows/ro-crate-metadata-missing-file.json')))
+      gv.save!
+    end
+
+    get :ro_crate, params: { id: workflow.id }
+
+    assert_redirected_to workflow
+    assert flash[:error].include?("not found in crate: this-file-does-not-exist")
+  end
+
+  test 'gets generated RO-Crate metadata' do
+    workflow = FactoryBot.create(:local_git_workflow, policy: FactoryBot.create(:public_policy))
+    refute workflow.git_version.get_blob('ro-crate-metadata.json')
+    assert workflow.is_git_versioned?
+
+    get :ro_crate_metadata, params: { id: workflow.id }
+
+    assert_response :success
+    assert @response.header['Content-Length'].present?
+    assert @response.header['Content-Length'].to_i > 100
+    j = JSON.parse(@response.body)
+    assert(j['@graph'].any? { |n| n['@id'] == 'ro-crate-metadata.json' })
+  end
+
+  test 'gets stored RO-Crate metadata' do
+    workflow = FactoryBot.create(:ro_crate_git_workflow, policy: FactoryBot.create(:public_policy))
+    assert workflow.git_version.get_blob('ro-crate-metadata.json')
+    assert workflow.is_git_versioned?
+
+    get :ro_crate_metadata, params: { id: workflow.id }
+
+    assert_response :success
+    assert @response.header['Content-Length'].present?
+    assert @response.header['Content-Length'].to_i > 100
+    j = JSON.parse(@response.body)
+    assert(j['@graph'].any? { |n| n['@id'] == 'ro-crate-metadata.json' })
+  end
+
+  test 'gets generated RO-Crate metadata for non-git workflow' do
+    workflow = FactoryBot.create(:workflow, policy: FactoryBot.create(:public_policy))
+    refute workflow.is_git_versioned?
+
+    get :ro_crate_metadata, params: { id: workflow.id }
+
+    assert_response :success
+    assert @response.header['Content-Length'].present?
+    assert @response.header['Content-Length'].to_i > 100
+    j = JSON.parse(@response.body)
+    assert(j['@graph'].any? { |n| n['@id'] == 'ro-crate-metadata.json' })
+  end
+
+  test 'gets RO-Crate metadata for specific version' do
+    workflow = FactoryBot.create(:local_ro_crate_git_workflow, policy: FactoryBot.create(:public_policy))
+    md = workflow.git_version.get_blob('ro-crate-metadata.json')
+    assert md
+    assert workflow.is_git_versioned?
+    assert_equal 1, workflow.version
+    disable_authorization_checks do
+      workflow.git_version.next_version(mutable: true).save!
+      gv = workflow.reload.latest_git_version
+      assert_equal 2, gv.version
+      assert_equal 2, workflow.version
+      json = md.read
+      json.gsub!('test1_1', 'test9_9')
+      gv.add_file('ro-crate-metadata.json', StringIO.new(json))
+      gv.save!
+    end
+
+    get :ro_crate_metadata, params: { id: workflow.id, version: 1 }
+
+    assert_response :success
+    assert response.body.include?('test1_1')
+    refute response.body.include?('test9_9')
+
+    get :ro_crate_metadata, params: { id: workflow.id, version: 2 }
+
+    assert_response :success
+    refute response.body.include?('test1_1')
+    assert response.body.include?('test9_9')
+  end
+
+  test 'does not get RO-Crate metadata if no download permission' do
+    workflow = FactoryBot.create(:existing_galaxy_ro_crate_workflow, policy: FactoryBot.create(:publicly_viewable_policy))
+    assert workflow.can_view?
+    refute workflow.can_download?
+
+    get :ro_crate_metadata, params: { id: workflow.id }
+
+    assert_redirected_to workflow
+    assert_includes flash[:error], 'You are not authorized to download this Workflow'
+  end
 end
+
diff --git a/test/integration/api/extended_metadata_type_api_test.rb b/test/integration/api/extended_metadata_type_api_test.rb
new file mode 100644
index 0000000000..87877f16f2
--- /dev/null
+++ b/test/integration/api/extended_metadata_type_api_test.rb
@@ -0,0 +1,11 @@
+require 'test_helper'
+
+class ExtendedMetadataTypeApiTest < ActionDispatch::IntegrationTest
+  include ReadApiTestSuite
+
+  def setup
+    person = FactoryBot.create(:person)
+    refute person.is_admin?
+    user_login(person)
+  end
+end
diff --git a/test/integration/github_scraper_test.rb b/test/integration/github_scraper_test.rb
index 85aefb1b1f..2ce2da5892 100644
--- a/test/integration/github_scraper_test.rb
+++ b/test/integration/github_scraper_test.rb
@@ -7,23 +7,26 @@ class GithubScraperTest < ActionDispatch::IntegrationTest
     bot = Scrapers::Util.bot_account
     scraper = Scrapers::GithubScraper.new('test-123', project, bot, main_branch: 'master', output: StringIO.new)
 
-    repos = [FactoryBot.create(:remote_workflow_ro_crate_repository, remote: 'https://not.real.url/repo.git')]
+    repos = [FactoryBot.create(:remote_workflow_ro_crate_repository, remote: 'https://github.com/crs4/sort-and-change-case-workflow.git')]
 
-    scraper.stub(:list_repositories, -> () { repos.map { |r| { 'clone_url' => r.remote } } }) do
-      scraper.stub(:clone_repositories, -> (_) { repos }) do
-        assert_difference('Workflow.count', 1) do
-          assert_difference('Workflow::Git::Version.count', 1) do
-            assert_difference('Git::Annotation.count', 1) do
-              assert_no_difference('Git::Repository.count') do
-                scraped = scraper.scrape
-                wf = scraped.first
-                assert_equal bot, wf.contributor
-                assert_equal [project], wf.projects
-                assert_equal 'sort-and-change-case', wf.title
-                assert_equal 'sort lines and change text to upper case', wf.description
-                assert_equal 'Apache-2.0', wf.license
-                assert_equal 'sort-and-change-case.ga', wf.main_workflow_path
-                assert_equal 'v0.02', wf.git_version.name
+    VCR.use_cassette('github/fetch_topics') do
+      scraper.stub(:list_repositories, -> () { repos.map { |r| { 'clone_url' => r.remote } } }) do
+        scraper.stub(:clone_repositories, -> (_) { repos }) do
+          assert_difference('Workflow.count', 1) do
+            assert_difference('Workflow::Git::Version.count', 1) do
+              assert_difference('Git::Annotation.count', 1) do
+                assert_no_difference('Git::Repository.count') do
+                  scraped = scraper.scrape
+                  wf = scraped.first
+                  assert_equal bot, wf.contributor
+                  assert_equal [project], wf.projects
+                  assert_equal 'sort-and-change-case', wf.title
+                  assert_equal 'sort lines and change text to upper case', wf.description
+                  assert_equal 'Apache-2.0', wf.license
+                  assert_equal 'sort-and-change-case.ga', wf.main_workflow_path
+                  assert_equal 'v0.02', wf.git_version.name
+                  assert_equal ['case', 'sort'], wf.tags.sort
+                end
               end
             end
           end
@@ -37,36 +40,38 @@ class GithubScraperTest < ActionDispatch::IntegrationTest
     bot = Scrapers::Util.bot_account
     scraper = Scrapers::GithubScraper.new('test-123', project, bot, main_branch: 'master', output: StringIO.new)
 
-    repos = [FactoryBot.create(:remote_workflow_ro_crate_repository, remote: 'https://not.real.url/repo.git')]
+    repos = [FactoryBot.create(:remote_workflow_ro_crate_repository, remote: 'https://github.com/crs4/sort-and-change-case-workflow.git')]
 
     existing = FactoryBot.create(:ro_crate_git_workflow,
-                       contributor: bot,
-                       projects: [project],
-                       source_link_url: 'https://not.real.url/repo',
-                       git_version_attributes: { name: 'v0.01',
-                                                 git_repository_id: repos.first.id,
-                                                 ref: 'refs/tags/v0.01',
-                                                 commit: 'a321b6e',
-                                                 main_workflow_path: 'sort-and-change-case.ga',
-                                                 mutable: false })
+                                 contributor: bot,
+                                 projects: [project],
+                                 source_link_url: 'https://github.com/crs4/sort-and-change-case-workflow',
+                                 git_version_attributes: { name: 'v0.01',
+                                                           git_repository_id: repos.first.id,
+                                                           ref: 'refs/tags/v0.01',
+                                                           commit: 'a321b6e',
+                                                           main_workflow_path: 'sort-and-change-case.ga',
+                                                           mutable: false })
 
-    scraper.stub(:list_repositories, -> () { repos.map { |r| { 'clone_url' => r.remote } } }) do
-      scraper.stub(:clone_repositories, -> (_) { repos }) do
-        assert_no_difference('Workflow.count') do
-          assert_difference('Workflow::Git::Version.count', 1) do
-            assert_difference('Git::Annotation.count', 1) do
-              assert_no_difference('Git::Repository.count') do
-                scraped = scraper.scrape
-                wf = scraped.first
-                assert_equal 2, existing.reload.git_versions.count
-                assert_equal existing, wf
-                assert_equal bot, wf.contributor
-                assert_equal [project], wf.projects
-                assert_equal 'sort-and-change-case', wf.title
-                assert_equal 'sort lines and change text to upper case', wf.description
-                assert_equal 'Apache-2.0', wf.license
-                assert_equal 'sort-and-change-case.ga', wf.main_workflow_path
-                assert_equal 'v0.02', wf.git_version.name
+    VCR.use_cassette('github/fetch_topics') do
+      scraper.stub(:list_repositories, -> () { repos.map { |r| { 'clone_url' => r.remote } } }) do
+        scraper.stub(:clone_repositories, -> (_) { repos }) do
+          assert_no_difference('Workflow.count') do
+            assert_difference('Workflow::Git::Version.count', 1) do
+              assert_difference('Git::Annotation.count', 1) do
+                assert_no_difference('Git::Repository.count') do
+                  scraped = scraper.scrape
+                  wf = scraped.first
+                  assert_equal 2, existing.reload.git_versions.count
+                  assert_equal existing, wf
+                  assert_equal bot, wf.contributor
+                  assert_equal [project], wf.projects
+                  assert_equal 'sort-and-change-case', wf.title
+                  assert_equal 'sort lines and change text to upper case', wf.description
+                  assert_equal 'Apache-2.0', wf.license
+                  assert_equal 'sort-and-change-case.ga', wf.main_workflow_path
+                  assert_equal 'v0.02', wf.git_version.name
+                end
               end
             end
           end
@@ -80,27 +85,29 @@ class GithubScraperTest < ActionDispatch::IntegrationTest
     bot = Scrapers::Util.bot_account
     scraper = Scrapers::GithubScraper.new('test-123', project, bot, main_branch: 'master', output: StringIO.new)
 
-    repos = [FactoryBot.create(:remote_workflow_ro_crate_repository, remote: 'https://not.real.url/repo.git')]
+    repos = [FactoryBot.create(:remote_workflow_ro_crate_repository, remote: 'https://github.com/crs4/sort-and-change-case-workflow.git')]
 
     existing = FactoryBot.create(:ro_crate_git_workflow,
-                       contributor: bot,
-                       projects: [project],
-                       source_link_url: 'https://not.real.url/repo',
-                       git_version_attributes: { name: 'v0.02',
-                                                 git_repository_id: repos.first.id,
-                                                 ref: 'refs/tags/v0.02',
-                                                 commit: '20eabdc',
-                                                 main_workflow_path: 'sort-and-change-case.ga',
-                                                 mutable: false })
+                                 contributor: bot,
+                                 projects: [project],
+                                 source_link_url: 'https://github.com/crs4/sort-and-change-case-workflow',
+                                 git_version_attributes: { name: 'v0.02',
+                                                           git_repository_id: repos.first.id,
+                                                           ref: 'refs/tags/v0.02',
+                                                           commit: '20eabdc',
+                                                           main_workflow_path: 'sort-and-change-case.ga',
+                                                           mutable: false })
 
-    scraper.stub(:list_repositories, -> () { repos.map { |r| { 'clone_url' => r.remote } } }) do
-      scraper.stub(:clone_repositories, -> (_) { repos }) do
-        assert_no_difference('Workflow.count') do
-          assert_no_difference('Workflow::Git::Version.count') do
-            assert_no_difference('Git::Annotation.count') do
-              assert_no_difference('Git::Repository.count') do
-                scraped = scraper.scrape
-                assert scraped.empty?
+    VCR.use_cassette('github/fetch_topics') do
+      scraper.stub(:list_repositories, -> () { repos.map { |r| { 'clone_url' => r.remote } } }) do
+        scraper.stub(:clone_repositories, -> (_) { repos }) do
+          assert_no_difference('Workflow.count') do
+            assert_no_difference('Workflow::Git::Version.count') do
+              assert_no_difference('Git::Annotation.count') do
+                assert_no_difference('Git::Repository.count') do
+                  scraped = scraper.scrape
+                  assert scraped.empty?
+                end
               end
             end
           end
diff --git a/test/integration/nfcore_scraper_test.rb b/test/integration/nfcore_scraper_test.rb
index 1be7345e8c..5b5321aa73 100644
--- a/test/integration/nfcore_scraper_test.rb
+++ b/test/integration/nfcore_scraper_test.rb
@@ -29,6 +29,7 @@ class NfcoreScraperTest < ActionDispatch::IntegrationTest
               assert_equal 'MIT', wf.license
               assert_equal 'nextflow.config', wf.main_workflow_path
               assert_equal '3.0', wf.git_version.name
+              assert_equal %w[rna rna-seq], wf.tags.sort
             end
           end
         end
diff --git a/test/integration/schedule_test.rb b/test/integration/schedule_test.rb
index 54f930f38d..b7aa273ccb 100644
--- a/test/integration/schedule_test.rb
+++ b/test/integration/schedule_test.rb
@@ -24,6 +24,11 @@ class ScheduleTest < ActionDispatch::IntegrationTest
     assert regular
     assert_equal [RegularMaintenanceJob::RUN_PERIOD, { at: '1:00am' }], regular[:every]
 
+    # AuthLookupMaintenanceJob
+    auth = pop_task(runners, "AuthLookupMaintenanceJob.perform_later")
+    assert auth
+    assert_equal [AuthLookupMaintenanceJob::RUN_PERIOD, { at: '1:00am' }], auth[:every]
+
     # LifeMonitor status
     lm_status = pop_task(runners, "LifeMonitorStatusJob.perform_later")
     assert lm_status
diff --git a/test/unit/assay_test.rb b/test/unit/assay_test.rb
index f16c9a2509..da6bd75bc4 100644
--- a/test/unit/assay_test.rb
+++ b/test/unit/assay_test.rb
@@ -753,7 +753,7 @@ def new_valid_assay
 
   test 'isa json compliance' do
     investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true)
-    isa_json_compliant_study = FactoryBot.create(:isa_json_compliant_study, investigation: )
+    isa_json_compliant_study = FactoryBot.create(:isa_json_compliant_study, investigation: investigation)
     assert isa_json_compliant_study.is_isa_json_compliant?
 
     default_assay = FactoryBot.create(:assay, study: isa_json_compliant_study)
@@ -777,7 +777,7 @@ def new_valid_assay
 
   test 'previous linked sample type' do
     investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true)
-    isa_study = FactoryBot.create(:isa_json_compliant_study, investigation: )
+    isa_study = FactoryBot.create(:isa_json_compliant_study, investigation: investigation )
     def_study = FactoryBot.create(:study)
 
     assay_stream = FactoryBot.create(:assay_stream, study: isa_study)
@@ -789,7 +789,7 @@ def new_valid_assay
     assert_nil def_assay.previous_linked_sample_type
 
     first_isa_assay = FactoryBot.create(:isa_json_compliant_assay,
-                                         assay_stream: ,
+                                         assay_stream: assay_stream ,
                                          study: isa_study)
     assert_equal first_isa_assay.previous_linked_sample_type, isa_study.sample_types.second
 
@@ -797,7 +797,7 @@ def new_valid_assay
                                               linked_sample_type: first_isa_assay.sample_type)
     second_isa_assay = FactoryBot.create(:assay,
                                           study: isa_study,
-                                          assay_stream: ,
+                                          assay_stream: assay_stream ,
                                           sample_type: data_file_sample_type)
 
     assert_equal second_isa_assay.previous_linked_sample_type, first_isa_assay.sample_type
@@ -806,7 +806,7 @@ def new_valid_assay
 
   test 'has_linked_child_assay?' do
     investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true)
-    isa_study = FactoryBot.create(:isa_json_compliant_study, investigation: )
+    isa_study = FactoryBot.create(:isa_json_compliant_study, investigation: investigation )
     def_study = FactoryBot.create(:study)
     def_assay = FactoryBot.create(:assay, study:def_study)
 
@@ -816,7 +816,7 @@ def new_valid_assay
                                               linked_sample_type: first_isa_assay.sample_type)
     second_isa_assay = FactoryBot.create(:assay,
                                           study: isa_study,
-                                          assay_stream: ,
+                                          assay_stream: assay_stream ,
                                           sample_type: data_file_sample_type)
 
     assert assay_stream.has_linked_child_assay?
@@ -827,17 +827,17 @@ def new_valid_assay
 
   test 'next_linked_child_assay' do
     investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true)
-    isa_study = FactoryBot.create(:isa_json_compliant_study, investigation: )
+    isa_study = FactoryBot.create(:isa_json_compliant_study, investigation: investigation )
     def_study = FactoryBot.create(:study)
     def_assay = FactoryBot.create(:assay, study:def_study)
 
     assay_stream = FactoryBot.create(:assay_stream, study: isa_study)
-    first_isa_assay = FactoryBot.create(:isa_json_compliant_assay, study: isa_study, assay_stream: )
+    first_isa_assay = FactoryBot.create(:isa_json_compliant_assay, study: isa_study, assay_stream: assay_stream )
     data_file_sample_type = FactoryBot.create(:isa_assay_data_file_sample_type,
                                               linked_sample_type: first_isa_assay.sample_type)
     second_isa_assay = FactoryBot.create(:assay,
                                           study: isa_study,
-                                          assay_stream: ,
+                                          assay_stream: assay_stream ,
                                           sample_type: data_file_sample_type)
 
     assert_equal assay_stream.first_assay_in_stream, first_isa_assay
diff --git a/test/unit/asset_test.rb b/test/unit/asset_test.rb
index e00e1d0055..fc966488e5 100644
--- a/test/unit/asset_test.rb
+++ b/test/unit/asset_test.rb
@@ -121,7 +121,7 @@ class AssetTest < ActiveSupport::TestCase
     assert FactoryBot.create(:sop).supports_spreadsheet_explore?
     assert FactoryBot.create(:file_template).supports_spreadsheet_explore?
     refute FactoryBot.create(:model).supports_spreadsheet_explore?
-    refute FactoryBot.create(:presentation).supports_spreadsheet_explore?
+    assert FactoryBot.create(:presentation).supports_spreadsheet_explore?
     refute FactoryBot.create(:placeholder).supports_spreadsheet_explore?
     refute FactoryBot.create(:workflow).supports_spreadsheet_explore?
     refute FactoryBot.create(:publication).supports_spreadsheet_explore?
diff --git a/test/unit/bio_schema/schema_ld_generation_test.rb b/test/unit/bio_schema/schema_ld_generation_test.rb
index 6bd1eed726..795b243b2a 100644
--- a/test/unit/bio_schema/schema_ld_generation_test.rb
+++ b/test/unit/bio_schema/schema_ld_generation_test.rb
@@ -325,6 +325,7 @@ def setup
       'logo' => "http://localhost:3000/projects/#{@project.id}/avatars/#{@project.avatar.id}?size=250",
       'image' => "http://localhost:3000/projects/#{@project.id}/avatars/#{@project.avatar.id}?size=250",
       'url' => @project.web_page,
+      'keywords' => '',
       'member' => [
         { '@type' => 'Person', '@id' => "http://localhost:3000/people/#{@person.id}", 'name' => @person.name },
         { '@type' => 'ResearchOrganization', '@id' => "http://localhost:3000/institutions/#{institution.id}",
diff --git a/test/unit/config_test.rb b/test/unit/config_test.rb
index a1ae027845..e117342561 100644
--- a/test/unit/config_test.rb
+++ b/test/unit/config_test.rb
@@ -7,7 +7,7 @@ class ConfigTest < ActiveSupport::TestCase
     assert Seek::Config.events_enabled
   end
   test 'jerm_disabled' do
-    assert !Seek::Config.jerm_enabled
+    refute Seek::Config.jerm_enabled
   end
   test 'solr enabled' do
     assert Seek::Config.solr_enabled
@@ -619,7 +619,7 @@ class ConfigTest < ActiveSupport::TestCase
         refute Seek::Config.omniauth_elixir_aai_legacy_mode
         assert_equal '/seeks/seek1/auth/elixir_aai/callback', config[:callback_path]
         assert_equal 'http://localhost/seeks/seek1/auth/elixir_aai/callback', config[:client_options][:redirect_uri]
-        assert_equal 'https://proxy.aai.lifescience-ri.eu/',config[:issuer]
+        assert_equal 'https://login.aai.lifescience-ri.eu/oidc/',config[:issuer]
         with_config_value(:omniauth_elixir_aai_legacy_mode, true) do
           assert Seek::Config.omniauth_elixir_aai_legacy_mode
           config = Seek::Config.omniauth_elixir_aai_config
@@ -630,4 +630,14 @@ class ConfigTest < ActiveSupport::TestCase
       end
     end
   end
+
+  test 'templates enabled' do
+    with_config_value(:isa_json_compliance_enabled, false) do
+      refute Seek::Config.templates_enabled
+    end
+
+    with_config_value(:isa_json_compliance_enabled, true) do
+      assert Seek::Config.templates_enabled
+    end
+  end
 end
diff --git a/test/unit/content_blob_test.rb b/test/unit/content_blob_test.rb
index f92574fc13..111a1cafd7 100644
--- a/test/unit/content_blob_test.rb
+++ b/test/unit/content_blob_test.rb
@@ -900,61 +900,6 @@ def test_exception_when_both_data_and_io_object
     refute File.exist?(txt_path)
   end
 
-  test 'fix mime type after failed csv extraction' do
-    blob = FactoryBot.create(:image_content_blob, content_type:'application/excel', original_filename:'image.xls')
-    assert blob.is_excel?
-
-    text = blob.to_csv
-
-    assert text.blank?
-
-    blob.reload
-
-    refute blob.is_excel?
-    assert_equal 'image/png',blob.content_type
-  end
-
-  test 'fix mime type after failed pdf contents for search' do
-    blob = FactoryBot.create(:image_content_blob, content_type: 'application/msword', original_filename: 'image.doc')
-    assert blob.is_pdf_convertable?
-
-    assert_empty blob.pdf_contents_for_search
-
-    blob.reload
-
-    refute blob.is_pdf_convertable?
-    assert_equal 'image/png', blob.content_type
-
-    # incorrectly described as pdf
-    blob = FactoryBot.create(:image_content_blob, content_type: 'application/pdf', original_filename: 'image.pdf')
-
-    assert_empty blob.pdf_contents_for_search
-
-    blob.reload
-
-    refute blob.is_pdf_convertable?
-    assert_equal 'image/png', blob.content_type
-
-    # handles when the file is actually broken, rather than failing due to the mime type
-    blob = FactoryBot.create(:broken_pdf_content_blob)
-    assert_empty blob.pdf_contents_for_search
-    assert_equal 'application/pdf', blob.content_type
-  end
-
-  test 'fix mime type after spreadsheet xml fail' do
-    blob = FactoryBot.create(:image_content_blob, content_type:'application/msexcel', original_filename:'image.xls')
-    assert blob.is_extractable_spreadsheet?
-
-    assert_raises(SysMODB::SpreadsheetExtractionException) do
-      blob.to_spreadsheet_xml
-    end
-
-    blob.reload
-
-    refute blob.is_extractable_spreadsheet?
-    assert_equal 'image/png',blob.content_type
-  end
-
   test 'tmp_io_objects in tmp dir are deleted' do
     file = Tempfile.new('testing-content-blob')
     file.write('test test test')
diff --git a/test/unit/helpers/studies_helper_test.rb b/test/unit/helpers/studies_helper_test.rb
index 45083f7f00..20dcdf0029 100644
--- a/test/unit/helpers/studies_helper_test.rb
+++ b/test/unit/helpers/studies_helper_test.rb
@@ -10,7 +10,10 @@ class StudiesHelperTest < ActionView::TestCase
     FactoryBot.create(:study_extended_metadata_type_for_MIAPPE, title: 'Not MIAPPE')
     refute show_batch_miappe_button?
 
-    FactoryBot.create(:study_extended_metadata_type_for_MIAPPE, title: 'MIAPPE metadata v1.1')
+    type = FactoryBot.create(:study_extended_metadata_type_for_MIAPPE, title: 'MIAPPE metadata v1.1')
     assert show_batch_miappe_button?
+
+    type.update_column(:enabled, false)
+    refute show_batch_miappe_button?
   end
 end
diff --git a/test/unit/index_table_column_definitions_test.rb b/test/unit/index_table_column_definitions_test.rb
index d2e264667e..388ca901c3 100644
--- a/test/unit/index_table_column_definitions_test.rb
+++ b/test/unit/index_table_column_definitions_test.rb
@@ -6,6 +6,7 @@ def setup
     @data_file = FactoryBot.create(:data_file)
     @person = FactoryBot.create(:person)
     @project = FactoryBot.create(:project)
+    @publication = FactoryBot.create(:publication)
   end
 
   test 'required columns' do
@@ -30,10 +31,15 @@ def setup
                  Seek::IndexTableColumnDefinitions.allowed_columns(@data_file)
     assert_equal %w[title first_name last_name projects orcid description],
                  Seek::IndexTableColumnDefinitions.allowed_columns(@person)
-    assert_equal %w[title web_page start_date end_date topic_annotation_values description created_at updated_at],
+    assert_equal %w[title web_page start_date end_date topic_annotation_values description created_at updated_at tags],
                  Seek::IndexTableColumnDefinitions.allowed_columns(@project)
   end
 
+  test 'blocked_columns' do
+    assert_not_includes %w[license],
+                        Seek::IndexTableColumnDefinitions.default_columns(@publication)
+  end
+
   test 'sanity check and responds to' do
     [Assay, Study, Investigation, Model, Sop, DataFile, FileTemplate, Placeholder, Presentation, Document, Workflow,
      Event, Publication, Organism, SampleType, Institution, Person, Project].each do |type|
diff --git a/test/unit/investigation_test.rb b/test/unit/investigation_test.rb
index 6b850aa69d..07abe718f5 100644
--- a/test/unit/investigation_test.rb
+++ b/test/unit/investigation_test.rb
@@ -221,6 +221,10 @@ class InvestigationTest < ActiveSupport::TestCase
                    )
     )
     assert_equal ['James','25'].sort, item.extended_metadata_attribute_values_for_search.map(&:to_s).sort
+
+    #nested
+    item = FactoryBot.create(:investigation, extended_metadata: FactoryBot.create(:role_multiple_extended_metadata))
+    assert_equal ['alice@email.com','0012345','liddell','alice','wonder','land'].sort, item.extended_metadata_attribute_values_for_search.map(&:to_s).sort
   end
   
   test 'related sop ids' do
diff --git a/test/unit/jobs/auth_lookup_maintenance_job_test.rb b/test/unit/jobs/auth_lookup_maintenance_job_test.rb
new file mode 100644
index 0000000000..102aa8c5e2
--- /dev/null
+++ b/test/unit/jobs/auth_lookup_maintenance_job_test.rb
@@ -0,0 +1,236 @@
+require 'test_helper'
+
+class AuthLookupMaintenaceJobTest < ActiveSupport::TestCase
+
+  def setup
+    #ensure a consistent initial state
+    disable_authorization_checks do
+      Seek::Util.authorized_types.each(&:destroy_all)
+      Seek::Util.authorized_types.each(&:clear_lookup_table)
+    end
+
+    User.destroy_all
+    AuthLookupUpdateQueue.destroy_all
+  end
+
+  test 'run period' do
+    assert_equal 8.hours, AuthLookupMaintenanceJob::RUN_PERIOD
+  end
+
+  test 'priority' do
+    assert_equal 3, AuthLookupMaintenanceJob.priority
+  end
+
+  test 'queue name' do
+    assert_equal QueueNames::AUTH_LOOKUP, AuthLookupMaintenanceJob.queue_name
+  end
+
+
+  test 'check authlookup consistency' do
+
+    p = FactoryBot.create(:person)
+    p2 = FactoryBot.create(:person)
+    u = FactoryBot.create(:brand_new_user)
+
+    assert_nil u.person
+
+    with_config_value(:auth_lookup_enabled, true) do
+      assert AuthLookupUpdateQueue.queue_enabled?
+
+      doc1 = FactoryBot.create(:document)
+      doc2 = FactoryBot.create(:document)
+      AuthLookupUpdateJob.perform_now
+
+      assert Document.lookup_table_consistent?(p.user)
+      assert Document.lookup_table_consistent?(p2.user)
+      assert Document.lookup_table_consistent?(nil)
+
+      assert_no_enqueued_jobs do
+        assert_no_difference('AuthLookupUpdateQueue.count') do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+      # delete a record
+      Document.lookup_class.where(user_id:p.user.id,asset_id:doc1.id).last.delete
+
+      #duplicate a record
+      Document.lookup_class.where(user_id:p2.user.id, asset_id:doc2.id).last.dup.save!
+
+      refute Document.lookup_table_consistent?(p.user)
+      refute Document.lookup_table_consistent?(p2.user)
+
+      assert_enqueued_jobs(1) do
+        assert_difference('AuthLookupUpdateQueue.count',1) do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+      # double check it will be fixed when the job runs
+      AuthLookupUpdateJob.perform_now
+      assert Document.lookup_table_consistent?(p.user)
+      assert Document.lookup_table_consistent?(p2.user)
+      assert Document.lookup_table_consistent?(nil)
+    end
+
+  end
+
+  test 'test for anonymous user' do
+
+    with_config_value(:auth_lookup_enabled, true) do
+      assert AuthLookupUpdateQueue.queue_enabled?
+
+      doc = FactoryBot.create(:document)
+      AuthLookupUpdateJob.perform_now
+
+      assert Document.lookup_table_consistent?(nil)
+
+      # delete a record
+      Document.lookup_class.where(user_id:0,asset_id:doc.id).last.delete
+
+      refute Document.lookup_table_consistent?(nil)
+
+      # queued after the user has been removed
+      assert_enqueued_jobs(1) do
+        assert_difference('AuthLookupUpdateQueue.count',1) do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+    end
+  end
+
+  test 'skip if user or person in the queue' do
+
+    p = FactoryBot.create(:person)
+
+    with_config_value(:auth_lookup_enabled, true) do
+      assert AuthLookupUpdateQueue.queue_enabled?
+
+      doc1 = FactoryBot.create(:document)
+      AuthLookupUpdateJob.perform_now
+
+      assert Document.lookup_table_consistent?(p.user)
+
+      # delete a record
+      Document.lookup_class.where(user_id:p.user.id,asset_id:doc1.id).last.delete
+
+      refute Document.lookup_table_consistent?(p.user)
+
+      refute AuthLookupUpdateQueue.any?
+      AuthLookupUpdateQueue.create!(item: p.user)
+      assert AuthLookupUpdateQueue.any?
+
+      # nothing queued whilst user is queued
+      assert_no_enqueued_jobs do
+        assert_no_difference('AuthLookupUpdateQueue.count') do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+      AuthLookupUpdateQueue.destroy_all
+      AuthLookupUpdateQueue.create!(item: p)
+      assert AuthLookupUpdateQueue.any?
+
+      # nothing queued whilst person is queued
+      assert_no_enqueued_jobs do
+        assert_no_difference('AuthLookupUpdateQueue.count') do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+      AuthLookupUpdateQueue.destroy_all
+      refute AuthLookupUpdateQueue.any?
+      #add another item to make sure it's only checking for user/person
+      AuthLookupUpdateQueue.create!(item: FactoryBot.create(:sop))
+      assert AuthLookupUpdateQueue.any?
+
+      # queued after the user has been removed
+      assert_enqueued_jobs(1) do
+        assert_difference('AuthLookupUpdateQueue.count',1) do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+    end
+  end
+
+  test 'skip if particular type is on the queue' do
+    p = FactoryBot.create(:person)
+
+    with_config_value(:auth_lookup_enabled, true) do
+      assert AuthLookupUpdateQueue.queue_enabled?
+
+      doc1 = FactoryBot.create(:document)
+      AuthLookupUpdateJob.perform_now
+
+      assert Document.lookup_table_consistent?(p.user)
+
+      # delete a record
+      Document.lookup_class.where(user_id:p.user.id,asset_id:doc1.id).last.delete
+
+      refute Document.lookup_table_consistent?(p.user)
+
+      refute AuthLookupUpdateQueue.any?
+      AuthLookupUpdateQueue.create!(item: doc1)
+      assert AuthLookupUpdateQueue.any?
+
+      # nothing queued whilst doc1 is queued
+      assert_no_enqueued_jobs do
+        assert_no_difference('AuthLookupUpdateQueue.count') do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+      AuthLookupUpdateQueue.destroy_all
+      refute AuthLookupUpdateQueue.any?
+
+      # queued after the doc1 has been removed
+      assert_enqueued_jobs(1) do
+        assert_difference('AuthLookupUpdateQueue.count',1) do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+    end
+  end
+
+  test 'checks each type' do
+    p = FactoryBot.create(:person)
+
+    with_config_value(:auth_lookup_enabled, true) do
+      assert AuthLookupUpdateQueue.queue_enabled?
+
+      doc = FactoryBot.create(:document)
+      sample = FactoryBot.create(:sample)
+      sop = FactoryBot.create(:sop)
+      with_config_value(:auth_lookup_update_batch_size, 20) do
+        AuthLookupUpdateJob.perform_now
+      end
+
+      assert Document.lookup_table_consistent?(p.user)
+      assert Sample.lookup_table_consistent?(p.user)
+      assert Sop.lookup_table_consistent?(p.user)
+
+      # delete a record
+      Document.lookup_class.where(user_id:p.user.id,asset_id:doc.id).last.delete
+      Sample.lookup_class.where(user_id:p.user.id,asset_id:sample.id).last.delete
+      Sop.lookup_class.where(user_id:p.user.id,asset_id:sop.id).last.delete
+
+      refute Document.lookup_table_consistent?(p.user)
+      refute Sample.lookup_table_consistent?(p.user)
+      refute Sop.lookup_table_consistent?(p.user)
+
+      assert_enqueued_jobs(3) do
+        assert_difference('AuthLookupUpdateQueue.count',3) do
+          AuthLookupMaintenanceJob.perform_now
+        end
+      end
+
+      assert AuthLookupUpdateQueue.where(item: doc).any?
+      assert AuthLookupUpdateQueue.where(item: sample).any?
+      assert AuthLookupUpdateQueue.where(item: sop).any?
+    end
+  end
+
+end
\ No newline at end of file
diff --git a/test/unit/jobs/linking_samples_update_job_test.rb b/test/unit/jobs/linking_samples_update_job_test.rb
index 4f9f31c87c..c38d6b2b9a 100644
--- a/test/unit/jobs/linking_samples_update_job_test.rb
+++ b/test/unit/jobs/linking_samples_update_job_test.rb
@@ -2,6 +2,7 @@
 
 class LinkingSamplesUpdateJobTest < ActiveSupport::TestCase
   def setup
+    @person = FactoryBot.create(:person)
     create_linked_samples
   end
 
@@ -17,9 +18,31 @@ def setup
     end
   end
 
+  test 'only trigger further jobs if the metadata changes' do
+    sample = Sample.first
+    sample.set_attribute_value('full name', 'Ali Mohammadi')
+    disable_authorization_checks { sample.save! }
+    assert_enqueued_jobs 2, only: LinkingSamplesUpdateJob do
+      LinkingSamplesUpdateJob.perform_now(sample)
+    end
+
+    sample.set_attribute_value('full name', 'Ali Mohammadi')
+    disable_authorization_checks { sample.save! }
+    assert_enqueued_jobs 0, only: LinkingSamplesUpdateJob do
+      LinkingSamplesUpdateJob.perform_now(sample)
+    end
+
+    sample.set_attribute_value('full name', 'Fred Flintstone')
+    disable_authorization_checks { sample.save! }
+    assert_enqueued_jobs 2, only: LinkingSamplesUpdateJob do
+      LinkingSamplesUpdateJob.perform_now(sample)
+    end
+  end
+
+
   def create_linked_samples
-    person = FactoryBot.create(:person)
-    project = person.projects.first
+
+    project = @person.projects.first
 
     main_sample = FactoryBot.create(:patient_sample)
     sample_type = main_sample.sample_type
@@ -38,4 +61,5 @@ def create_linked_samples
     linked_sample2.set_attribute_value(:patient, [main_sample.id])
     disable_authorization_checks { linked_sample2.save! }
   end
+
 end
diff --git a/test/unit/jobs/regular_maintenace_job_test.rb b/test/unit/jobs/regular_maintenace_job_test.rb
index 0cff108369..7b627541b9 100644
--- a/test/unit/jobs/regular_maintenace_job_test.rb
+++ b/test/unit/jobs/regular_maintenace_job_test.rb
@@ -154,65 +154,6 @@ def setup
     assert_equal [person3, person4].sort, logs.collect(&:subject).sort
   end
 
-  test 'check authlookup consistency' do
-    #ensure a consistent initial state
-    disable_authorization_checks do
-      Seek::Util.authorized_types.each(&:destroy_all)
-      Seek::Util.authorized_types.each(&:clear_lookup_table)
-    end
-
-    User.destroy_all
-    p = FactoryBot.create(:person)
-    p2 = FactoryBot.create(:person)
-    u = FactoryBot.create(:brand_new_user)
-
-    assert_nil u.person
-
-    with_config_value(:auth_lookup_enabled, true) do
-      assert AuthLookupUpdateQueue.queue_enabled?
-
-      doc1 = FactoryBot.create(:document)
-      doc2 = FactoryBot.create(:document)
-      AuthLookupUpdateJob.perform_now
-
-      assert Document.lookup_table_consistent?(p.user)
-      assert Document.lookup_table_consistent?(p2.user)
-      assert Document.lookup_table_consistent?(nil)
-
-      assert_no_enqueued_jobs do
-        assert_no_difference('AuthLookupUpdateQueue.count') do
-          RegularMaintenanceJob.perform_now
-        end
-      end
-
-      # delete a record
-      Document.lookup_class.where(user_id:p.user.id,asset_id:doc1.id).last.delete
-
-      #duplicate a record
-      Document.lookup_class.where(user_id:p2.user.id, asset_id:doc2.id).last.dup.save!
-
-      refute Document.lookup_table_consistent?(p.user)
-      refute Document.lookup_table_consistent?(p2.user)
-
-      #gets immmediately updated for anonymous user
-      assert Document.lookup_table_consistent?(nil)
-
-      assert_enqueued_jobs(1) do
-        assert_difference('AuthLookupUpdateQueue.count',1) do
-          RegularMaintenanceJob.perform_now
-        end
-      end
-
-      # double check it will be fixed when the job runs
-      AuthLookupUpdateJob.perform_now
-      assert Document.lookup_table_consistent?(p.user)
-      assert Document.lookup_table_consistent?(p2.user)
-      assert Document.lookup_table_consistent?(nil)
-    end
-
-
-  end
-
   test 'cleans redundant repositories' do
     redundant = FactoryBot.create(:blank_repository, created_at: 5.years.ago)
     redundant_but_in_grace = FactoryBot.create(:blank_repository, created_at: 1.second.ago)
diff --git a/test/unit/jobs/reindexing_job_test.rb b/test/unit/jobs/reindexing_job_test.rb
index 7bc3f20324..78e8804b89 100644
--- a/test/unit/jobs/reindexing_job_test.rb
+++ b/test/unit/jobs/reindexing_job_test.rb
@@ -27,6 +27,20 @@ class ReindexingJobTest < ActiveSupport::TestCase
     end
   end
 
+  test 'dont add items if search disabled' do
+    p = FactoryBot.create :person
+    ReindexingQueue.delete_all
+
+    with_config_value(:solr_enabled, false) do
+      assert_no_enqueued_jobs(only: ReindexingJob) do
+        assert_no_difference('ReindexingQueue.count') do
+          ReindexingQueue.enqueue(p)
+          ReindexingQueue.enqueue(FactoryBot.create(:sop))
+        end
+      end
+    end
+  end
+
   test 'gather_items strips deleted (nil) items' do
     model1 = FactoryBot.create(:model)
     model2 = FactoryBot.create(:model)
@@ -44,4 +58,14 @@ class ReindexingJobTest < ActiveSupport::TestCase
     assert_includes items, model2
     assert_includes items, document
   end
+
+  test 'follow on job' do
+    ReindexingQueue.delete_all
+    refute ReindexingJob.new.follow_on_job?
+    ReindexingQueue.enqueue(FactoryBot.create(:sop))
+    assert ReindexingJob.new.follow_on_job?
+    with_config_value(:solr_enabled, false) do
+      refute ReindexingJob.new.follow_on_job?
+    end
+  end
 end
diff --git a/test/unit/permissions/auth_lookup_update_queue_test.rb b/test/unit/permissions/auth_lookup_update_queue_test.rb
index a1cc616690..95b07d9a8c 100644
--- a/test/unit/permissions/auth_lookup_update_queue_test.rb
+++ b/test/unit/permissions/auth_lookup_update_queue_test.rb
@@ -161,10 +161,17 @@ def teardown
     end
   end
 
-  test 'updates when a user registers' do
+  test 'updates when a user registers but not until associated with a person' do
+    person = FactoryBot.create(:person)
+    user = assert_no_difference('AuthLookupUpdateQueue.count') do
+      FactoryBot.create(:brand_new_user)
+    end
     assert_difference('AuthLookupUpdateQueue.count', 1) do
-      user = FactoryBot.create(:brand_new_user)
-      assert_equal user, AuthLookupUpdateQueue.order(:id).last.item
+      user.person = person
+      user.save!
+      q = AuthLookupUpdateQueue.order(:id).last
+      assert_equal user, q.item
+      assert_equal 1, q.priority
     end
   end
 
diff --git a/test/unit/renderers_test.rb b/test/unit/renderers_test.rb
index 0f80fc7f4d..32c42d06f2 100644
--- a/test/unit/renderers_test.rb
+++ b/test/unit/renderers_test.rb
@@ -363,6 +363,12 @@ class RenderersTest < ActiveSupport::TestCase
     blob = FactoryBot.create(:image_content_blob, asset: @asset)
     renderer = Seek::Renderers::TextRenderer.new(blob)
     refute renderer.can_render?
+
+    @git.add_remote_file('empty', 'https://example.com/file', fetch: false)
+    git_blob = @git.get_blob('empty')
+    renderer = Seek::Renderers::TextRenderer.new(git_blob)
+    assert renderer.can_render?
+    assert_equal '<span class="subtle">No content to display</span>', renderer.render
   end
 
   test 'image renderer' do
diff --git a/test/unit/scraper_test.rb b/test/unit/scraper_test.rb
index 98c18baede..262d8eb6d9 100644
--- a/test/unit/scraper_test.rb
+++ b/test/unit/scraper_test.rb
@@ -29,9 +29,11 @@ def setup
     assert_difference('Project.count', 1) do
       assert_difference('Person.count', 1) do
         assert_difference('Institution.count', 1) do
-          project = Scrapers::Util.bot_project(title: 'iwc')
-          assert_equal 'iwc', project.title
-          assert_includes project.people, Scrapers::Util.bot_account
+          assert_difference('GroupMembership.count', 1) do
+            project = Scrapers::Util.bot_project(title: 'iwc')
+            assert_equal 'iwc', project.title
+            assert_includes project.people, Scrapers::Util.bot_account
+          end
         end
       end
     end
@@ -39,8 +41,10 @@ def setup
     assert_no_difference('Project.count') do
       assert_no_difference('Person.count') do
         assert_no_difference('Institution.count') do
-          project = Scrapers::Util.bot_project(title: 'iwc')
-          assert_equal 'iwc', project.title
+          assert_no_difference('GroupMembership.count') do
+            project = Scrapers::Util.bot_project(title: 'iwc')
+            assert_equal 'iwc', project.title
+          end
         end
       end
     end
@@ -48,9 +52,25 @@ def setup
     assert_difference('Project.count', 1) do
       assert_no_difference('Person.count') do
         assert_no_difference('Institution.count') do
-          project = Scrapers::Util.bot_project(title: 'Another Project')
-          assert_equal 'Another Project', project.title
-          assert_includes project.people, Scrapers::Util.bot_account
+          assert_difference('GroupMembership.count', 1) do
+            project = Scrapers::Util.bot_project(title: 'Another Project')
+            assert_equal 'Another Project', project.title
+            assert_includes project.people, Scrapers::Util.bot_account
+          end
+        end
+      end
+    end
+
+    # Add to existing project
+    FactoryBot.create(:project, title: 'An existing project 123')
+    assert_no_difference('Project.count') do
+      assert_no_difference('Person.count') do
+        assert_no_difference('Institution.count') do
+          assert_difference('GroupMembership.count', 1) do
+            project = Scrapers::Util.bot_project(title: 'An existing project 123')
+            assert_equal 'An existing project 123', project.title
+            assert_includes project.people, Scrapers::Util.bot_account
+          end
         end
       end
     end
diff --git a/test/unit/search_term_filter_test.rb b/test/unit/search_term_filter_test.rb
deleted file mode 100644
index ebb7a773bd..0000000000
--- a/test/unit/search_term_filter_test.rb
+++ /dev/null
@@ -1,27 +0,0 @@
-require 'test_helper'
-
-class SearchTermFilterTest < ActiveSupport::TestCase
-  test 'filter asterix and question marks' do
-    assert_equal 'fish', Seek::Search::SearchTermFilter.filter('*fis*h*')
-    assert_equal 'fish', Seek::Search::SearchTermFilter.filter('?fis?h?')
-  end
-
-  test 'filter semi colon, but only from end' do
-    assert_equal 'fish', Seek::Search::SearchTermFilter.filter('fish:')
-    assert_equal 'fish', Seek::Search::SearchTermFilter.filter('fish:  ')
-    assert_equal 'fish', Seek::Search::SearchTermFilter.filter('fish  :  ')
-    assert_equal 'fish:2', Seek::Search::SearchTermFilter.filter('fish:2')
-  end
-
-  test 'filter out single hyphen' do
-    assert_equal '', Seek::Search::SearchTermFilter.filter('-')
-    assert_equal '', Seek::Search::SearchTermFilter.filter('  -   ')
-    assert_equal 'fish-soup', Seek::Search::SearchTermFilter.filter('fish-soup')
-  end
-
-  test 'trims trailing spaces' do
-    assert_equal 'fish', Seek::Search::SearchTermFilter.filter('   fish  ')
-    assert_equal 'fish', Seek::Search::SearchTermFilter.filter("\tfish\t")
-    assert_equal 'fish', Seek::Search::SearchTermFilter.filter("\nfish\n")
-  end
-end
diff --git a/test/unit/studies/studies_extractor_test.rb b/test/unit/studies/studies_extractor_test.rb
index 5912af0d55..7ec3494358 100644
--- a/test/unit/studies/studies_extractor_test.rb
+++ b/test/unit/studies/studies_extractor_test.rb
@@ -39,7 +39,8 @@ class StudiesExtractorTest < ActiveSupport::TestCase
 
   test 'extract study correctly' do
     user_uuid = 'user_uuid'
-    FactoryBot.create(:study_extended_metadata_type_for_MIAPPE)
+    extended_metadata_type = FactoryBot.create(:study_extended_metadata_type_for_MIAPPE)
+    assert_equal 'MIAPPE metadata v1.1', extended_metadata_type.title, 'must match the seed data title'
     studies_file = ContentBlob.new
     studies_file.tmp_io_object = File.open("#{Rails.root}/tmp/#{user_uuid}_studies_upload/#{@studies.first.name}")
     studies_file.original_filename = @studies.first.name.to_s
diff --git a/test/unit/util_test.rb b/test/unit/util_test.rb
index 67011263fe..85af79b83c 100644
--- a/test/unit/util_test.rb
+++ b/test/unit/util_test.rb
@@ -7,10 +7,12 @@ def teardown
   end
 
   test 'creatable types' do
-    types = Seek::Util.user_creatable_types
-    # How to enable Placeholder?
     expected = [Collection, DataFile, Document, FileTemplate, Model, Placeholder, Presentation, Publication, Sample, Sop, Assay, Investigation, Study, Event, SampleType, Strain, Workflow, Template]
 
+    types = with_config_value :isa_json_compliance_enabled, true do
+      Seek::Util.user_creatable_types
+    end
+
     # first as strings for more readable failed assertion message
     assert_equal expected.map(&:to_s).sort, types.map(&:to_s).sort
 
@@ -19,9 +21,12 @@ def teardown
   end
 
   test 'authorized types' do
-    # How to enable Placeholder?
     expected = [Assay, Collection, DataFile, Document, Event, FileTemplate, Investigation, Model, Placeholder, Presentation, Publication, Sample, Sop, Strain, Study, Workflow, Template].map(&:name).sort
-    actual = Seek::Util.authorized_types.map(&:name).sort
+
+    actual = with_config_value :isa_json_compliance_enabled, true do
+      Seek::Util.authorized_types.map(&:name).sort
+    end
+
     assert_equal expected, actual
   end
 
@@ -32,9 +37,12 @@ def teardown
   end
 
   test 'searchable types' do
-    types = Seek::Util.searchable_types
     expected = [Assay, Collection, DataFile, Document, Event, FileTemplate, HumanDisease, Institution, Investigation, Model, Organism, Person, Placeholder, Presentation, Programme, Project, Publication, Sample, SampleType, Sop, Strain, Study, Workflow, Template]
 
+    types = with_config_value :isa_json_compliance_enabled, true do
+      Seek::Util.searchable_types
+    end
+
     # first as strings for more readable failed assertion message
     assert_equal expected.map(&:to_s).sort, types.map(&:to_s).sort
 
@@ -42,16 +50,26 @@ def teardown
     assert_equal expected.sort_by(&:to_s), types.sort_by(&:to_s)
 
     with_config_value :events_enabled, false do
-      Seek::Util.clear_cached
-      types = Seek::Util.searchable_types
-      assert_equal (expected - [Event]).map(&:to_s).sort, types.map(&:to_s).sort
+      with_config_value :isa_json_compliance_enabled, true do
+        Seek::Util.clear_cached
+        types = Seek::Util.searchable_types
+        assert_equal (expected - [Event]).map(&:to_s).sort, types.map(&:to_s).sort
+      end
     end
 
     with_config_value :programmes_enabled, false do
-      Seek::Util.clear_cached
+      with_config_value :isa_json_compliance_enabled, true do
+        Seek::Util.clear_cached
+        types = Seek::Util.searchable_types
+        assert_equal (expected - [Programme]).map(&:to_s).sort, types.map(&:to_s).sort
+      end
+    end
+
+    with_config_value :isa_json_compliance_enabled, false do
       types = Seek::Util.searchable_types
-     assert_equal (expected - [Programme]).map(&:to_s).sort, types.map(&:to_s).sort
+      assert_equal (expected - [Template]).map(&:to_s).sort, types.map(&:to_s).sort
     end
+
   end
 
   test 'multi-file assets' do
diff --git a/test/vcr_cassettes/github/fetch_topics.yml b/test/vcr_cassettes/github/fetch_topics.yml
new file mode 100644
index 0000000000..2ee2a886db
--- /dev/null
+++ b/test/vcr_cassettes/github/fetch_topics.yml
@@ -0,0 +1,79 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://api.github.com/repos/crs4/sort-and-change-case-workflow/topics
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      Accept:
+      - application/vnd.github.mercy-preview+json
+      User-Agent:
+      - rest-client/2.1.0 (linux x86_64) ruby/3.1.4p223
+      Accept-Encoding:
+      - gzip;q=1.0,deflate;q=0.6,identity;q=0.3
+      Host:
+      - api.github.com
+  response:
+    status:
+      code: 200
+      message: OK
+    headers:
+      Server:
+      - GitHub.com
+      Date:
+      - Thu, 18 Apr 2024 12:11:53 GMT
+      Content-Type:
+      - application/json; charset=utf-8
+      Content-Length:
+      - '25'
+      Cache-Control:
+      - public, max-age=60, s-maxage=60
+      Vary:
+      - Accept, Accept-Encoding, Accept, X-Requested-With
+      Etag:
+      - '"4312be9f94d4167301a1aefc48875953a71d3a73d1f113765668ab9b0a8e962e"'
+      X-Github-Media-Type:
+      - github.mercy-preview; format=json
+      X-Github-Api-Version-Selected:
+      - '2022-11-28'
+      Access-Control-Expose-Headers:
+      - ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining,
+        X-RateLimit-Used, X-RateLimit-Resource, X-RateLimit-Reset, X-OAuth-Scopes,
+        X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type, X-GitHub-SSO,
+        X-GitHub-Request-Id, Deprecation, Sunset
+      Access-Control-Allow-Origin:
+      - "*"
+      Strict-Transport-Security:
+      - max-age=31536000; includeSubdomains; preload
+      X-Frame-Options:
+      - deny
+      X-Content-Type-Options:
+      - nosniff
+      X-Xss-Protection:
+      - '0'
+      Referrer-Policy:
+      - origin-when-cross-origin, strict-origin-when-cross-origin
+      Content-Security-Policy:
+      - default-src 'none'
+      X-Ratelimit-Limit:
+      - '60'
+      X-Ratelimit-Remaining:
+      - '48'
+      X-Ratelimit-Reset:
+      - '1713445012'
+      X-Ratelimit-Resource:
+      - core
+      X-Ratelimit-Used:
+      - '12'
+      Accept-Ranges:
+      - bytes
+      X-Github-Request-Id:
+      - 8624:33B0C5:33D1224:34EAAEF:66210E09
+    body:
+      encoding: UTF-8
+      string: '{"names":["sort","case"]}'
+    http_version: 
+  recorded_at: Thu, 18 Apr 2024 12:11:53 GMT
+recorded_with: VCR 2.9.3