From 3cb42868ce14f5a5de962b09c6b86ea47a488a4b Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 12 Feb 2026 15:20:00 +0000
Subject: [PATCH 1/6] build: install rails 7.1

---
 Gemfile      |   2 +-
 Gemfile.lock | 174 +++++++++++++++++++++++++++++++--------------------
 2 files changed, 107 insertions(+), 69 deletions(-)

diff --git a/Gemfile b/Gemfile
index c4661e77..a8352f83 100644
--- a/Gemfile
+++ b/Gemfile
@@ -17,7 +17,7 @@ gem 'mutex_m'
 gem 'oj', '~> 3.13'
 gem 'pmb-client', '0.1.0', github: 'sanger/pmb-client'
 gem 'puma'
-gem 'rails', '~> 7.0.8', '>= 7.0.8.7'
+gem 'rails', '~> 7.1.0'
 gem 'roo', '~> 2.8.0'
 gem 'sanger_barcode_format', github: 'sanger/sanger_barcode_format', branch: 'development'
 gem 'sassc-rails'
diff --git a/Gemfile.lock b/Gemfile.lock
index 1a039c70..c805e3dd 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -15,72 +15,78 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (7.0.10)
-      actionpack (= 7.0.10)
-      activesupport (= 7.0.10)
+    actioncable (7.1.6)
+      actionpack (= 7.1.6)
+      activesupport (= 7.1.6)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (7.0.10)
-      actionpack (= 7.0.10)
-      activejob (= 7.0.10)
-      activerecord (= 7.0.10)
-      activestorage (= 7.0.10)
-      activesupport (= 7.0.10)
+      zeitwerk (~> 2.6)
+    actionmailbox (7.1.6)
+      actionpack (= 7.1.6)
+      activejob (= 7.1.6)
+      activerecord (= 7.1.6)
+      activestorage (= 7.1.6)
+      activesupport (= 7.1.6)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.0.10)
-      actionpack (= 7.0.10)
-      actionview (= 7.0.10)
-      activejob (= 7.0.10)
-      activesupport (= 7.0.10)
+    actionmailer (7.1.6)
+      actionpack (= 7.1.6)
+      actionview (= 7.1.6)
+      activejob (= 7.1.6)
+      activesupport (= 7.1.6)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
-      rails-dom-testing (~> 2.0)
-    actionpack (7.0.10)
-      actionview (= 7.0.10)
-      activesupport (= 7.0.10)
+      rails-dom-testing (~> 2.2)
+    actionpack (7.1.6)
+      actionview (= 7.1.6)
+      activesupport (= 7.1.6)
+      cgi
+      nokogiri (>= 1.8.5)
       racc
-      rack (~> 2.0, >= 2.2.4)
+      rack (>= 2.2.4)
+      rack-session (>= 1.0.1)
       rack-test (>= 0.6.3)
-      rails-dom-testing (~> 2.0)
-      rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (7.0.10)
-      actionpack (= 7.0.10)
-      activerecord (= 7.0.10)
-      activestorage (= 7.0.10)
-      activesupport (= 7.0.10)
+      rails-dom-testing (~> 2.2)
+      rails-html-sanitizer (~> 1.6)
+    actiontext (7.1.6)
+      actionpack (= 7.1.6)
+      activerecord (= 7.1.6)
+      activestorage (= 7.1.6)
+      activesupport (= 7.1.6)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.0.10)
-      activesupport (= 7.0.10)
+    actionview (7.1.6)
+      activesupport (= 7.1.6)
       builder (~> 3.1)
-      erubi (~> 1.4)
-      rails-dom-testing (~> 2.0)
-      rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (7.0.10)
-      activesupport (= 7.0.10)
+      cgi
+      erubi (~> 1.11)
+      rails-dom-testing (~> 2.2)
+      rails-html-sanitizer (~> 1.6)
+    activejob (7.1.6)
+      activesupport (= 7.1.6)
       globalid (>= 0.3.6)
-    activemodel (7.0.10)
-      activesupport (= 7.0.10)
-    activerecord (7.0.10)
-      activemodel (= 7.0.10)
-      activesupport (= 7.0.10)
-    activestorage (7.0.10)
-      actionpack (= 7.0.10)
-      activejob (= 7.0.10)
-      activerecord (= 7.0.10)
-      activesupport (= 7.0.10)
+    activemodel (7.1.6)
+      activesupport (= 7.1.6)
+    activerecord (7.1.6)
+      activemodel (= 7.1.6)
+      activesupport (= 7.1.6)
+      timeout (>= 0.4.0)
+    activestorage (7.1.6)
+      actionpack (= 7.1.6)
+      activejob (= 7.1.6)
+      activerecord (= 7.1.6)
+      activesupport (= 7.1.6)
       marcel (~> 1.0)
-      mini_mime (>= 1.1.0)
-    activesupport (7.0.10)
+    activesupport (7.1.6)
       base64
       benchmark (>= 0.3)
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.0.2)
+      connection_pool (>= 2.2.5)
       drb
       i18n (>= 1.6, < 2)
       logger (>= 1.4.2)
@@ -116,15 +122,18 @@ GEM
     capybara-selenium (0.0.6)
       capybara
       selenium-webdriver
+    cgi (0.5.1)
     childprocess (5.1.0)
       logger (~> 1.5)
     coderay (1.1.3)
     concurrent-ruby (1.3.4)
+    connection_pool (3.0.2)
     crass (1.0.6)
     csv (3.3.5)
     date (3.5.0)
     docile (1.4.0)
     drb (2.2.3)
+    erb (6.0.1)
     erubi (1.13.1)
     exception_notification (4.6.0)
       actionmailer (>= 5.2, < 9)
@@ -164,6 +173,12 @@ GEM
       logger
     i18n (1.14.8)
       concurrent-ruby (~> 1.0)
+    io-console (0.8.2)
+    irb (1.17.0)
+      pp (>= 0.6.0)
+      prism (>= 1.3.0)
+      rdoc (>= 4.0.0)
+      reline (>= 0.4.2)
     jquery-rails (4.6.1)
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
@@ -201,9 +216,9 @@ GEM
     method_source (1.1.0)
     mini_mime (1.1.5)
     minitest (5.27.0)
-    minitest-rails (7.0.1)
-      minitest (~> 5.10)
-      railties (~> 7.0.0)
+    minitest-rails (7.1.1)
+      minitest (~> 5.20)
+      railties (>= 7.1.0, < 8.0.0)
     minitest-rails-capybara (0.0.2)
       capybara
       minitest-rails
@@ -237,33 +252,44 @@ GEM
     parser (3.3.10.1)
       ast (~> 2.4.1)
       racc
+    pp (0.6.3)
+      prettyprint
+    prettyprint (0.2.0)
     prism (1.9.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     pry-rails (0.3.11)
       pry (>= 0.13.0)
+    psych (5.3.1)
+      date
+      stringio
     public_suffix (6.0.1)
     puma (7.2.0)
       nio4r (~> 2.0)
     racc (1.8.1)
     rack (2.2.21)
+    rack-session (1.0.2)
+      rack (< 3)
     rack-test (2.2.0)
       rack (>= 1.3)
-    rails (7.0.10)
-      actioncable (= 7.0.10)
-      actionmailbox (= 7.0.10)
-      actionmailer (= 7.0.10)
-      actionpack (= 7.0.10)
-      actiontext (= 7.0.10)
-      actionview (= 7.0.10)
-      activejob (= 7.0.10)
-      activemodel (= 7.0.10)
-      activerecord (= 7.0.10)
-      activestorage (= 7.0.10)
-      activesupport (= 7.0.10)
+    rackup (1.0.1)
+      rack (< 3)
+      webrick
+    rails (7.1.6)
+      actioncable (= 7.1.6)
+      actionmailbox (= 7.1.6)
+      actionmailer (= 7.1.6)
+      actionpack (= 7.1.6)
+      actiontext (= 7.1.6)
+      actionview (= 7.1.6)
+      activejob (= 7.1.6)
+      activemodel (= 7.1.6)
+      activerecord (= 7.1.6)
+      activestorage (= 7.1.6)
+      activesupport (= 7.1.6)
       bundler (>= 1.15.0)
-      railties (= 7.0.10)
+      railties (= 7.1.6)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -275,19 +301,28 @@ GEM
     rails-html-sanitizer (1.6.2)
       loofah (~> 2.21)
       nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
-    railties (7.0.10)
-      actionpack (= 7.0.10)
-      activesupport (= 7.0.10)
-      method_source
+    railties (7.1.6)
+      actionpack (= 7.1.6)
+      activesupport (= 7.1.6)
+      cgi
+      irb
+      rackup (>= 1.0.0)
       rake (>= 12.2)
-      thor (~> 1.0)
-      zeitwerk (~> 2.5)
+      thor (~> 1.0, >= 1.2.2)
+      tsort (>= 0.2)
+      zeitwerk (~> 2.6)
     rainbow (3.1.1)
     rake (13.3.1)
     rb-fsevent (0.11.2)
     rb-inotify (0.11.1)
       ffi (~> 1.0)
+    rdoc (7.2.0)
+      erb
+      psych (>= 4.0.0)
+      tsort
     regexp_parser (2.11.3)
+    reline (0.6.3)
+      io-console (~> 0.5)
     rexml (3.4.4)
     roo (2.8.3)
       nokogiri (~> 1)
@@ -350,12 +385,14 @@ GEM
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       sprockets (>= 3.0.0)
+    stringio (3.2.0)
     syslog (0.4.0)
       logger
     thor (1.4.0)
     tilt (2.1.0)
     timecop (0.9.10)
     timeout (0.4.4)
+    tsort (0.2.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uglifier (4.2.1)
@@ -363,6 +400,7 @@ GEM
     unicode-display_width (3.2.0)
       unicode-emoji (~> 4.1)
     unicode-emoji (4.2.0)
+    webrick (1.9.2)
     websocket (1.2.11)
     websocket-driver (0.8.0)
       base64
@@ -405,7 +443,7 @@ DEPENDENCIES
   pmb-client (= 0.1.0)!
   pry-rails
   puma
-  rails (~> 7.0.8, >= 7.0.8.7)
+  rails (~> 7.1.0)
   rails-controller-testing
   roo (~> 2.8.0)
   rubocop

From 0cd6aec9f7a0e2ede8baa46e9d4a0b83cde5a04f Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 12 Feb 2026 15:20:26 +0000
Subject: [PATCH 2/6] build: remove old framework files

---
 .../new_framework_defaults_5_2.rb             |  40 -----
 .../new_framework_defaults_7_0.rb             | 144 ------------------
 2 files changed, 184 deletions(-)
 delete mode 100644 config/initializers/new_framework_defaults_5_2.rb
 delete mode 100644 config/initializers/new_framework_defaults_7_0.rb

diff --git a/config/initializers/new_framework_defaults_5_2.rb b/config/initializers/new_framework_defaults_5_2.rb
deleted file mode 100644
index c300f213..00000000
--- a/config/initializers/new_framework_defaults_5_2.rb
+++ /dev/null
@@ -1,40 +0,0 @@
-# frozen_string_literal: true
-
-# Be sure to restart your server when you modify this file.
-#
-# This file contains migration options to ease your Rails 5.2 upgrade.
-#
-# Once upgraded flip defaults one by one to migrate to the new default.
-#
-# Read the Guide for Upgrading Ruby on Rails for more info on each option.
-
-# Make Active Record use stable #cache_key alongside new #cache_version method.
-# This is needed for recyclable cache keys.
-# Rails.application.config.active_record.cache_versioning = true
-
-# Use AES-256-GCM authenticated encryption for encrypted cookies.
-# Also, embed cookie expiry in signed or encrypted cookies for increased security.
-#
-# This option is not backwards compatible with earlier Rails versions.
-# It's best enabled when your entire app is migrated and stable on 5.2.
-#
-# Existing cookies will be converted on read then written with the new scheme.
-# Rails.application.config.action_dispatch.use_authenticated_cookie_encryption = true
-
-# Use AES-256-GCM authenticated encryption as default cipher for encrypting messages
-# instead of AES-256-CBC, when use_authenticated_message_encryption is set to true.
-# Rails.application.config.active_support.use_authenticated_message_encryption = true
-
-# Add default protection from forgery to ActionController::Base instead of in
-# ApplicationController.
-# Rails.application.config.action_controller.default_protect_from_forgery = true
-
-# Store boolean values are in sqlite3 databases as 1 and 0 instead of 't' and
-# 'f' after migrating old data.
-# Rails.application.config.active_record.sqlite3.represent_boolean_as_integer = true
-
-# Use SHA-1 instead of MD5 to generate non-sensitive digests, such as the ETag header.
-# Rails.application.config.active_support.use_sha1_digests = true
-
-# Make `form_with` generate id attributes for any generated HTML tags.
-# Rails.application.config.action_view.form_with_generates_ids = true
diff --git a/config/initializers/new_framework_defaults_7_0.rb b/config/initializers/new_framework_defaults_7_0.rb
deleted file mode 100644
index ce2d234f..00000000
--- a/config/initializers/new_framework_defaults_7_0.rb
+++ /dev/null
@@ -1,144 +0,0 @@
-# frozen_string_literal: true
-
-# Be sure to restart your server when you modify this file.
-#
-# This file eases your Rails 7.0 framework defaults upgrade.
-#
-# Uncomment each configuration one by one to switch to the new default.
-# Once your application is ready to run with all new defaults, you can remove
-# this file and set the `config.load_defaults` to `7.0`.
-#
-# Read the Guide for Upgrading Ruby on Rails for more info on each option.
-# https://guides.rubyonrails.org/upgrading_ruby_on_rails.html
-
-# `button_to` view helper will render `<button>` element, regardless of whether
-# or not the content is passed as the first argument or as a block.
-# Rails.application.config.action_view.button_to_generates_button_tag = true
-
-# `stylesheet_link_tag` view helper will not render the media attribute by default.
-# Rails.application.config.action_view.apply_stylesheet_media_default = false
-
-# Change the digest class for the key generators to `OpenSSL::Digest::SHA256`.
-# Changing this default means invalidate all encrypted messages generated by
-# your application and, all the encrypted cookies. Only change this after you
-# rotated all the messages using the key rotator.
-#
-# See upgrading guide for more information on how to build a rotator.
-# https://guides.rubyonrails.org/v7.0/upgrading_ruby_on_rails.html
-# Rails.application.config.active_support.key_generator_hash_digest_class = OpenSSL::Digest::SHA256
-
-# Change the digest class for ActiveSupport::Digest.
-# Changing this default means that for example Etags change and
-# various cache keys leading to cache invalidation.
-# Rails.application.config.active_support.hash_digest_class = OpenSSL::Digest::SHA256
-
-# Don't override ActiveSupport::TimeWithZone.name and use the default Ruby
-# implementation.
-# Rails.application.config.active_support.remove_deprecated_time_with_zone_name = true
-
-# Calls `Rails.application.executor.wrap` around test cases.
-# This makes test cases behave closer to an actual request or job.
-# Several features that are normally disabled in test, such as Active Record query cache
-# and asynchronous queries will then be enabled.
-# Rails.application.config.active_support.executor_around_test_case = true
-
-# Set both the `:open_timeout` and `:read_timeout` values for `:smtp` delivery method.
-# Rails.application.config.action_mailer.smtp_timeout = 5
-
-# The ActiveStorage video previewer will now use scene change detection to generate
-# better preview images (rather than the previous default of using the first frame
-# of the video).
-# Rails.application.config.active_storage.video_preview_arguments =
-#   "-vf 'select=eq(n\\,0)+eq(key\\,1)+gt(scene\\,0.015),loop=loop=-1:size=2,trim=start_frame=1' -frames:v 1 -f image2"
-
-# Automatically infer `inverse_of` for associations with a scope.
-# Rails.application.config.active_record.automatic_scope_inversing = true
-
-# Raise when running tests if fixtures contained foreign key violations
-# Rails.application.config.active_record.verify_foreign_keys_for_fixtures = true
-
-# Disable partial inserts.
-# This default means that all columns will be referenced in INSERT queries
-# regardless of whether they have a default or not.
-# Rails.application.config.active_record.partial_inserts = false
-
-# Protect from open redirect attacks in `redirect_back_or_to` and `redirect_to`.
-# Rails.application.config.action_controller.raise_on_open_redirects = true
-
-# Change the variant processor for Active Storage.
-# Changing this default means updating all places in your code that
-# generate variants to use image processing macros and ruby-vips
-# operations. See the upgrading guide for detail on the changes required.
-# The `:mini_magick` option is not deprecated; it's fine to keep using it.
-# Rails.application.config.active_storage.variant_processor = :vips
-
-# Enable parameter wrapping for JSON.
-# Previously this was set in an initializer. It's fine to keep using that initializer if you've customized it.
-# To disable parameter wrapping entirely, set this config to `false`.
-# Rails.application.config.action_controller.wrap_parameters_by_default = true
-
-# Specifies whether generated namespaced UUIDs follow the RFC 4122 standard for namespace IDs provided as a
-# `String` to `Digest::UUID.uuid_v3` or `Digest::UUID.uuid_v5` method calls.
-#
-# See https://guides.rubyonrails.org/configuring.html#config-active-support-use-rfc4122-namespaced-uuids for
-# more information.
-# Rails.application.config.active_support.use_rfc4122_namespaced_uuids = true
-
-# Change the default headers to disable browsers' flawed legacy XSS protection.
-# Rails.application.config.action_dispatch.default_headers = {
-#   "X-Frame-Options" => "SAMEORIGIN",
-#   "X-XSS-Protection" => "0",
-#   "X-Content-Type-Options" => "nosniff",
-#   "X-Download-Options" => "noopen",
-#   "X-Permitted-Cross-Domain-Policies" => "none",
-#   "Referrer-Policy" => "strict-origin-when-cross-origin"
-# }
-
-# ** Please read carefully, this must be configured in config/application.rb **
-# Change the format of the cache entry.
-# Changing this default means that all new cache entries added to the cache
-# will have a different format that is not supported by Rails 6.1 applications.
-# Only change this value after your application is fully deployed to Rails 7.0
-# and you have no plans to rollback.
-# When you're ready to change format, add this to `config/application.rb` (NOT this file):
-#  config.active_support.cache_format_version = 7.0
-
-# Cookie serializer: 2 options
-#
-# If you're upgrading and haven't set `cookies_serializer` previously, your cookie serializer
-# is `:marshal`. The default for new apps is `:json`.
-#
-# Rails.application.config.action_dispatch.cookies_serializer = :json
-#
-#
-# To migrate an existing application to the `:json` serializer, use the `:hybrid` option.
-#
-# Rails transparently deserializes existing (Marshal-serialized) cookies on read and
-# re-writes them in the JSON format.
-#
-# It is fine to use `:hybrid` long term; you should do that until you're confident *all* your cookies
-# have been converted to JSON. To keep using `:hybrid` long term, move this config to its own
-# initializer or to `config/application.rb`.
-#
-# Rails.application.config.action_dispatch.cookies_serializer = :hybrid
-#
-#
-# If your cookies can't yet be serialized to JSON, keep using `:marshal` for backward-compatibility.
-#
-# If you have configured the serializer elsewhere, you can remove this section of the file.
-#
-# See https://guides.rubyonrails.org/action_controller_overview.html#cookies for more information.
-
-# Change the return value of `ActionDispatch::Request#content_type` to the Content-Type header without modification.
-# Rails.application.config.action_dispatch.return_only_request_media_type_on_content_type = false
-
-# Active Storage `has_many_attached` relationships will default to replacing the current collection instead of appending to it.
-# Thus, to support submitting an empty collection, the `file_field` helper will render an hidden field `include_hidden` by default
-# when `multiple_file_field_include_hidden` is set to `true`.
-# See https://guides.rubyonrails.org/configuring.html#config-active-storage-multiple-file-field-include-hidden for more information.
-# Rails.application.config.active_storage.multiple_file_field_include_hidden = true
-
-# ** Please read carefully, this must be configured in config/application.rb (NOT this file) **
-# Disables the deprecated #to_s override in some Ruby core classes
-# See https://guides.rubyonrails.org/configuring.html#config-active-support-disable-to-s-conversion for more information.
-# config.active_support.disable_to_s_conversion = true

From 941591cbe81e0514e773cddd369d587999b67c2d Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 12 Feb 2026 15:35:47 +0000
Subject: [PATCH 3/6] build: Rails 7.1 app:update and rubocop

---
 bin/setup                                     |  25 +-
 config/application.rb                         |  19 +-
 config/environments/development.rb            |  34 ++-
 config/environments/test.rb                   |  55 +++-
 .../initializers/content_security_policy.rb   |   4 +-
 .../initializers/filter_parameter_logging.rb  |   6 +-
 .../new_framework_defaults_7_1.rb             | 282 ++++++++++++++++++
 config/initializers/permissions_policy.rb     |  20 +-
 8 files changed, 396 insertions(+), 49 deletions(-)
 create mode 100644 config/initializers/new_framework_defaults_7_1.rb

diff --git a/bin/setup b/bin/setup
index aacb6b9c..cf2acd18 100755
--- a/bin/setup
+++ b/bin/setup
@@ -1,28 +1,25 @@
 #!/usr/bin/env ruby
-require 'fileutils'
-include FileUtils
+require "fileutils"
 
 # path to your application root.
-APP_ROOT = File.expand_path('..', __dir__)
+APP_ROOT = File.expand_path("..", __dir__)
 
 def system!(*args)
-  system(*args) || abort("\n== Command #{args} failed ==")
+  system(*args, exception: true)
 end
 
-chdir APP_ROOT do
-  # This script is a starting point to setup your application.
+FileUtils.chdir APP_ROOT do
+  # This script is a way to set up or update your development environment automatically.
+  # This script is idempotent, so that you can run it at any time and get an expectable outcome.
   # Add necessary setup steps to this file.
 
-  puts '== Installing dependencies =='
-  system! 'gem install bundler --conservative'
-  system('bundle check') || system!('bundle install')
-
-  # Install JavaScript dependencies if using Yarn
-  # system('bin/yarn')
+  puts "== Installing dependencies =="
+  system! "gem install bundler --conservative"
+  system("bundle check") || system!("bundle install")
 
   puts "\n== Removing old logs and tempfiles =="
-  system! 'bin/rails log:clear tmp:clear'
+  system! "bin/rails log:clear tmp:clear"
 
   puts "\n== Restarting application server =="
-  system! 'bin/rails restart'
+  system! "bin/rails restart"
 end
diff --git a/config/application.rb b/config/application.rb
index b987323b..1f4dcb43 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -3,9 +3,13 @@
 require_relative 'boot'
 
 # We don't want ActiveRecord
+require 'rails'
+# Pick the frameworks you want:
+require 'active_model/railtie'
+require 'active_job/railtie'
 require 'action_controller/railtie'
 require 'action_mailer/railtie'
-require 'sprockets/railtie'
+require 'action_view/railtie'
 require 'rails/test_unit/railtie'
 require './lib/gatekeeper/version'
 
@@ -27,6 +31,19 @@ class Application < Rails::Application
     # Run "rake -D time" for a list of tasks for finding time zone names. Default is UTC.
     # config.time_zone = 'Central Time (US & Canada)'
 
+    # Please, add to the `ignore` list any other `lib` subdirectories that do
+    # not contain `.rb` files, or that should not be reloaded or eager loaded.
+    # Common ones are `templates`, `generators`, or `middleware`, for example.
+    config.autoload_lib(ignore: %w[assets tasks])
+
+    # Configuration for the application, engines, and railties goes here.
+    #
+    # These settings can be overridden in specific environments using the files
+    # in config/environments, which are processed later.
+    #
+    # config.time_zone = "Central Time (US & Canada)"
+    # config.eager_load_paths << Rails.root.join("extras")
+
     # The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
     # config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
     config.i18n.enforce_available_locales = false
diff --git a/config/environments/development.rb b/config/environments/development.rb
index 236f3675..f778f5c0 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -1,26 +1,32 @@
 # frozen_string_literal: true
 
+require 'active_support/core_ext/integer/time'
+
 require 'pry'
 
 Rails.application.configure do
   # Settings specified here will take precedence over those in config/application.rb.
 
   config.secret_key_base = 'example_dev_environment_key'
-  # In the development environment your application's code is reloaded on
-  # every request. This slows down response time but is perfect for development
+  # In the development environment your application's code is reloaded any time
+  # it changes. This slows down response time but is perfect for development
   # since you don't have to restart the web server when you make code changes.
-  config.cache_classes = false
+  config.enable_reloading = true
 
   # Do not eager load code on boot.
   config.eager_load = false
 
-  # Show full error reports and disable caching.
+  # Show full error reports.
   config.consider_all_requests_local = true
 
+  # Enable server timing
+  config.server_timing = true
+
   # Enable/disable caching. By default caching is disabled.
   # Run rails dev:cache to toggle caching.
-  if Rails.root.join('tmp', 'caching-dev.txt').exist? # rubocop:todo Rails/FilePath
+  if Rails.root.join('tmp/caching-dev.txt').exist?
     config.action_controller.perform_caching = true
+    config.action_controller.enable_fragment_cache_logging = true
 
     config.cache_store = :memory_store
     config.public_file_server.headers = {
@@ -40,9 +46,27 @@
   # Print deprecation notices to the Rails logger.
   config.active_support.deprecation = :log
 
+  # Raise exceptions for disallowed deprecations.
+  config.active_support.disallowed_deprecation = :raise
+
+  # Tell Active Support which deprecation messages to disallow.
+  config.active_support.disallowed_deprecation_warnings = []
+
+  # Highlight code that enqueued background job in logs.
+  config.active_job.verbose_enqueue_logs = true
+
   # Suppress logger output for asset requests.
   config.assets.quiet = true
 
+  # Raises error for missing translations.
+  # config.i18n.raise_on_missing_translations = true
+
+  # Annotate rendered view with file names.
+  # config.action_view.annotate_rendered_view_with_filenames = true
+
+  # Raise error when a before_action's only/except options reference missing actions
+  config.action_controller.raise_on_missing_callback_actions = true
+
   # Use an evented file watcher to asynchronously detect changes in source code,
   # routes, locales, etc. This feature depends on the listen gem.
   config.file_watcher = ActiveSupport::EventedFileUpdateChecker
diff --git a/config/environments/test.rb b/config/environments/test.rb
index 85703975..e3dc4f28 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -1,33 +1,43 @@
 # frozen_string_literal: true
 
+require 'active_support/core_ext/integer/time'
+
+# The test environment is used exclusively to run your application's
+# test suite. You never need to work with it otherwise. Remember that
+# your test database is "scratch space" for the test suite and is wiped
+# and recreated between test runs. Don't rely on the data there!
+
 Rails.application.configure do
   # Settings specified here will take precedence over those in config/application.rb.
 
-  # The test environment is used exclusively to run your application's
-  # test suite. You never need to work with it otherwise. Remember that
-  # your test database is "scratch space" for the test suite and is wiped
-  # and recreated between test runs. Don't rely on the data there!
-  config.cache_classes = true
+  # While tests run files are not watched, reloading is not necessary.
+  config.enable_reloading = false
 
-  # Do not eager load code on boot. This avoids loading your whole application
-  # just for the purpose of running a single test. If you are using a tool that
-  # preloads Rails for running tests, you may have to set it to true.
-  config.eager_load = false
+  # Eager loading loads your entire application. When running a single test locally,
+  # this is usually not necessary, and can slow down your test suite. However, it's
+  # recommended that you enable it in continuous integration systems to ensure eager
+  # loading is working properly before deploying your code.
+  config.eager_load = ENV['CI'].present?
 
-  # Configure static asset server for tests with Cache-Control for performance.
-  config.serve_static_assets  = true
-  config.static_cache_control = 'public, max-age=3600'
+  # Configure public file server for tests with Cache-Control for performance.
+  config.public_file_server.enabled = true
+  config.public_file_server.headers = {
+    'Cache-Control' => "public, max-age=#{1.hour.to_i}"
+  }
 
   # Show full error reports and disable caching.
-  config.consider_all_requests_local       = true
+  config.consider_all_requests_local = true
   config.action_controller.perform_caching = false
+  config.cache_store = :null_store
 
-  # Raise exceptions instead of rendering exception templates.
-  config.action_dispatch.show_exceptions = false
+  # Render exception templates for rescuable exceptions and raise for other exceptions.
+  config.action_dispatch.show_exceptions = :rescuable
 
   # Disable request forgery protection in test environment.
   config.action_controller.allow_forgery_protection = false
 
+  config.action_mailer.perform_caching = false
+
   # Tell Action Mailer not to deliver emails to the real world.
   # The :test delivery method accumulates sent emails in the
   # ActionMailer::Base.deliveries array.
@@ -36,6 +46,21 @@
   # Print deprecation notices to the stderr.
   config.active_support.deprecation = :stderr
 
+  # Raise exceptions for disallowed deprecations.
+  config.active_support.disallowed_deprecation = :raise
+
+  # Tell Active Support which deprecation messages to disallow.
+  config.active_support.disallowed_deprecation_warnings = []
+
+  # Raises error for missing translations.
+  # config.i18n.raise_on_missing_translations = true
+
+  # Annotate rendered view with file names.
+  # config.action_view.annotate_rendered_view_with_filenames = true
+
+  # Raise error when a before_action's only/except options reference missing actions
+  config.action_controller.raise_on_missing_callback_actions = true
+
   # Set up the API connection options
   config.api_connection_options               = ActiveSupport::OrderedOptions.new
   config.api_connection_options.namespace     = 'Gatekeeper'
diff --git a/config/initializers/content_security_policy.rb b/config/initializers/content_security_policy.rb
index 53538c14..35ab3fd6 100644
--- a/config/initializers/content_security_policy.rb
+++ b/config/initializers/content_security_policy.rb
@@ -18,9 +18,9 @@
 #     # policy.report_uri "/csp-violation-report-endpoint"
 #   end
 #
-#   # Generate session nonces for permitted importmap and inline scripts
+#   # Generate session nonces for permitted importmap, inline scripts, and inline styles.
 #   config.content_security_policy_nonce_generator = ->(request) { request.session.id.to_s }
-#   config.content_security_policy_nonce_directives = %w(script-src)
+#   config.content_security_policy_nonce_directives = %w(script-src style-src)
 #
 #   # Report violations without enforcing the policy.
 #   # config.content_security_policy_report_only = true
diff --git a/config/initializers/filter_parameter_logging.rb b/config/initializers/filter_parameter_logging.rb
index 3df77c5b..c416e6a6 100644
--- a/config/initializers/filter_parameter_logging.rb
+++ b/config/initializers/filter_parameter_logging.rb
@@ -2,9 +2,9 @@
 
 # Be sure to restart your server when you modify this file.
 
-# Configure parameters to be filtered from the log file. Use this to limit dissemination of
-# sensitive information. See the ActiveSupport::ParameterFilter documentation for supported
-# notations and behaviors.
+# Configure parameters to be partially matched (e.g. passw matches password) and filtered from the log file.
+# Use this to limit dissemination of sensitive information.
+# See the ActiveSupport::ParameterFilter documentation for supported notations and behaviors.
 Rails.application.config.filter_parameters += %i[
   passw secret token _key crypt salt certificate otp ssn
 ]
diff --git a/config/initializers/new_framework_defaults_7_1.rb b/config/initializers/new_framework_defaults_7_1.rb
new file mode 100644
index 00000000..ebedc26c
--- /dev/null
+++ b/config/initializers/new_framework_defaults_7_1.rb
@@ -0,0 +1,282 @@
+# frozen_string_literal: true
+
+# Be sure to restart your server when you modify this file.
+#
+# This file eases your Rails 7.1 framework defaults upgrade.
+#
+# Uncomment each configuration one by one to switch to the new default.
+# Once your application is ready to run with all new defaults, you can remove
+# this file and set the `config.load_defaults` to `7.1`.
+#
+# Read the Guide for Upgrading Ruby on Rails for more info on each option.
+# https://guides.rubyonrails.org/upgrading_ruby_on_rails.html
+
+###
+# No longer add autoloaded paths into `$LOAD_PATH`. This means that you won't be able
+# to manually require files that are managed by the autoloader, which you shouldn't do anyway.
+#
+# This will reduce the size of the load path, making `require` faster if you don't use bootsnap, or reduce the size
+# of the bootsnap cache if you use it.
+#
+# To set this configuration, add the following line to `config/application.rb` (NOT this file):
+#   config.add_autoload_paths_to_load_path = false
+
+###
+# Remove the default X-Download-Options headers since it is used only by Internet Explorer.
+# If you need to support Internet Explorer, add back `"X-Download-Options" => "noopen"`.
+#++
+# Rails.application.config.action_dispatch.default_headers = {
+#   "X-Frame-Options" => "SAMEORIGIN",
+#   "X-XSS-Protection" => "0",
+#   "X-Content-Type-Options" => "nosniff",
+#   "X-Permitted-Cross-Domain-Policies" => "none",
+#   "Referrer-Policy" => "strict-origin-when-cross-origin"
+# }
+
+###
+# Do not treat an `ActionController::Parameters` instance
+# as equal to an equivalent `Hash` by default.
+#++
+# Rails.application.config.action_controller.allow_deprecated_parameters_hash_equality = false
+
+###
+# Active Record Encryption now uses SHA-256 as its hash digest algorithm.
+#
+# There are 3 scenarios to consider.
+#
+# 1. If you have data encrypted with previous Rails versions, and you have
+# +config.active_support.key_generator_hash_digest_class+ configured as SHA1 (the default
+# before Rails 7.0), you need to configure SHA-1 for Active Record Encryption too:
+#++
+# Rails.application.config.active_record.encryption.hash_digest_class = OpenSSL::Digest::SHA1
+#
+# 2. If you have +config.active_support.key_generator_hash_digest_class+ configured as SHA256 (the new default
+# in 7.0), then you need to configure SHA-256 for Active Record Encryption:
+#++
+# Rails.application.config.active_record.encryption.hash_digest_class = OpenSSL::Digest::SHA256
+#
+# 3. If you don't currently have data encrypted with Active Record encryption, you can disable this setting to
+# configure the default behavior starting 7.1+:
+#++
+# Rails.application.config.active_record.encryption.support_sha1_for_non_deterministic_encryption = false
+
+###
+# No longer run after_commit callbacks on the first of multiple Active Record
+# instances to save changes to the same database row within a transaction.
+# Instead, run these callbacks on the instance most likely to have internal
+# state which matches what was committed to the database, typically the last
+# instance to save.
+#++
+# Rails.application.config.active_record.run_commit_callbacks_on_first_saved_instances_in_transaction = false
+
+###
+# Configures SQLite with a strict strings mode, which disables double-quoted string literals.
+#
+# SQLite has some quirks around double-quoted string literals.
+# It first tries to consider double-quoted strings as identifier names, but if they don't exist
+# it then considers them as string literals. Because of this, typos can silently go unnoticed.
+# For example, it is possible to create an index for a non existing column.
+# See https://www.sqlite.org/quirks.html#double_quoted_string_literals_are_accepted for more details.
+#++
+# Rails.application.config.active_record.sqlite3_adapter_strict_strings_by_default = true
+
+###
+# Disable deprecated singular associations names.
+#++
+# Rails.application.config.active_record.allow_deprecated_singular_associations_name = false
+
+###
+# Enable the Active Job `BigDecimal` argument serializer, which guarantees
+# roundtripping. Without this serializer, some queue adapters may serialize
+# `BigDecimal` arguments as simple (non-roundtrippable) strings.
+#
+# When deploying an application with multiple replicas, old (pre-Rails 7.1)
+# replicas will not be able to deserialize `BigDecimal` arguments from this
+# serializer. Therefore, this setting should only be enabled after all replicas
+# have been successfully upgraded to Rails 7.1.
+#++
+# Rails.application.config.active_job.use_big_decimal_serializer = true
+
+###
+# Specify if an `ArgumentError` should be raised if `Rails.cache` `fetch` or
+# `write` are given an invalid `expires_at` or `expires_in` time.
+# Options are `true`, and `false`. If `false`, the exception will be reported
+# as `handled` and logged instead.
+#++
+# Rails.application.config.active_support.raise_on_invalid_cache_expiration_time = true
+
+###
+# Specify whether Query Logs will format tags using the SQLCommenter format
+# (https://open-telemetry.github.io/opentelemetry-sqlcommenter/), or using the legacy format.
+# Options are `:legacy` and `:sqlcommenter`.
+#++
+# Rails.application.config.active_record.query_log_tags_format = :sqlcommenter
+
+###
+# Specify the default serializer used by `MessageEncryptor` and `MessageVerifier`
+# instances.
+#
+# The legacy default is `:marshal`, which is a potential vector for
+# deserialization attacks in cases where a message signing secret has been
+# leaked.
+#
+# In Rails 7.1, the new default is `:json_allow_marshal` which serializes and
+# deserializes with `ActiveSupport::JSON`, but can fall back to deserializing
+# with `Marshal` so that legacy messages can still be read.
+#
+# In Rails 7.2, the default will become `:json` which serializes and
+# deserializes with `ActiveSupport::JSON` only.
+#
+# Alternatively, you can choose `:message_pack` or `:message_pack_allow_marshal`,
+# which serialize with `ActiveSupport::MessagePack`. `ActiveSupport::MessagePack`
+# can roundtrip some Ruby types that are not supported by JSON, and may provide
+# improved performance, but it requires the `msgpack` gem.
+#
+# For more information, see
+# https://guides.rubyonrails.org/v7.1/configuring.html#config-active-support-message-serializer
+#
+# If you are performing a rolling deploy of a Rails 7.1 upgrade, wherein servers
+# that have not yet been upgraded must be able to read messages from upgraded
+# servers, first deploy without changing the serializer, then set the serializer
+# in a subsequent deploy.
+#++
+# Rails.application.config.active_support.message_serializer = :json_allow_marshal
+
+###
+# Enable a performance optimization that serializes message data and metadata
+# together. This changes the message format, so messages serialized this way
+# cannot be read by older versions of Rails. However, messages that use the old
+# format can still be read, regardless of whether this optimization is enabled.
+#
+# To perform a rolling deploy of a Rails 7.1 upgrade, wherein servers that have
+# not yet been upgraded must be able to read messages from upgraded servers,
+# leave this optimization off on the first deploy, then enable it on a
+# subsequent deploy.
+#++
+# Rails.application.config.active_support.use_message_serializer_for_metadata = true
+
+###
+# Set the maximum size for Rails log files.
+#
+# `config.load_defaults 7.1` does not set this value for environments other than
+# development and test.
+#++
+# if Rails.env.local?
+#   Rails.application.config.log_file_size = 100 * 1024 * 1024
+# end
+
+###
+# Enable raising on assignment to attr_readonly attributes. The previous
+# behavior would allow assignment but silently not persist changes to the
+# database.
+#++
+# Rails.application.config.active_record.raise_on_assign_to_attr_readonly = true
+
+###
+# Enable validating only parent-related columns for presence when the parent is mandatory.
+# The previous behavior was to validate the presence of the parent record, which performed an extra query
+# to get the parent every time the child record was updated, even when parent has not changed.
+#++
+# Rails.application.config.active_record.belongs_to_required_validates_foreign_key = false
+
+###
+# Enable precompilation of `config.filter_parameters`. Precompilation can
+# improve filtering performance, depending on the quantity and types of filters.
+#++
+# Rails.application.config.precompile_filter_parameters = true
+
+###
+# Enable before_committed! callbacks on all enrolled records in a transaction.
+# The previous behavior was to only run the callbacks on the first copy of a record
+# if there were multiple copies of the same record enrolled in the transaction.
+#++
+# Rails.application.config.active_record.before_committed_on_all_records = true
+
+###
+# Disable automatic column serialization into YAML.
+# To keep the historic behavior, you can set it to `YAML`, however it is
+# recommended to explicitly define the serialization method for each column
+# rather than to rely on a global default.
+#++
+# Rails.application.config.active_record.default_column_serializer = nil
+
+###
+# Enable a performance optimization that serializes Active Record models
+# in a faster and more compact way.
+#
+# To perform a rolling deploy of a Rails 7.1 upgrade, wherein servers that have
+# not yet been upgraded must be able to read caches from upgraded servers,
+# leave this optimization off on the first deploy, then enable it on a
+# subsequent deploy.
+#++
+# Rails.application.config.active_record.marshalling_format_version = 7.1
+
+###
+# Run `after_commit` and `after_*_commit` callbacks in the order they are defined in a model.
+# This matches the behaviour of all other callbacks.
+# In previous versions of Rails, they ran in the inverse order.
+#++
+# Rails.application.config.active_record.run_after_transaction_callbacks_in_order_defined = true
+
+###
+# Whether a `transaction` block is committed or rolled back when exited via `return`, `break` or `throw`.
+#++
+# Rails.application.config.active_record.commit_transaction_on_non_local_return = true
+
+###
+# Controls when to generate a value for <tt>has_secure_token</tt> declarations.
+#++
+# Rails.application.config.active_record.generate_secure_token_on = :initialize
+
+###
+# ** Please read carefully, this must be configured in config/application.rb **
+#
+# Change the format of the cache entry.
+#
+# Changing this default means that all new cache entries added to the cache
+# will have a different format that is not supported by Rails 7.0
+# applications.
+#
+# Only change this value after your application is fully deployed to Rails 7.1
+# and you have no plans to rollback.
+# When you're ready to change format, add this to `config/application.rb` (NOT
+# this file):
+#   config.active_support.cache_format_version = 7.1
+
+###
+# Configure Action View to use HTML5 standards-compliant sanitizers when they are supported on your
+# platform.
+#
+# `Rails::HTML::Sanitizer.best_supported_vendor` will cause Action View to use HTML5-compliant
+# sanitizers if they are supported, else fall back to HTML4 sanitizers.
+#
+# In previous versions of Rails, Action View always used `Rails::HTML4::Sanitizer` as its vendor.
+#++
+# Rails.application.config.action_view.sanitizer_vendor = Rails::HTML::Sanitizer.best_supported_vendor
+
+###
+# Configure Action Text to use an HTML5 standards-compliant sanitizer when it is supported on your
+# platform.
+#
+# `Rails::HTML::Sanitizer.best_supported_vendor` will cause Action Text to use HTML5-compliant
+# sanitizers if they are supported, else fall back to HTML4 sanitizers.
+#
+# In previous versions of Rails, Action Text always used `Rails::HTML4::Sanitizer` as its vendor.
+#++
+# Rails.application.config.action_text.sanitizer_vendor = Rails::HTML::Sanitizer.best_supported_vendor
+
+###
+# Configure the log level used by the DebugExceptions middleware when logging
+# uncaught exceptions during requests.
+#++
+# Rails.application.config.action_dispatch.debug_exception_log_level = :error
+
+###
+# Configure the test helpers in Action View, Action Dispatch, and rails-dom-testing to use HTML5
+# parsers.
+#
+# Nokogiri::HTML5 isn't supported on JRuby, so JRuby applications must set this to :html4.
+#
+# In previous versions of Rails, these test helpers always used an HTML4 parser.
+#++
+# Rails.application.config.dom_testing_default_html_version = :html5
diff --git a/config/initializers/permissions_policy.rb b/config/initializers/permissions_policy.rb
index 810aadeb..e8d0b2ae 100644
--- a/config/initializers/permissions_policy.rb
+++ b/config/initializers/permissions_policy.rb
@@ -1,13 +1,15 @@
 # frozen_string_literal: true
 
+# Be sure to restart your server when you modify this file.
+
 # Define an application-wide HTTP permissions policy. For further
-# information see https://developers.google.com/web/updates/2018/06/feature-policy
-#
-# Rails.application.config.permissions_policy do |f|
-#   f.camera      :none
-#   f.gyroscope   :none
-#   f.microphone  :none
-#   f.usb         :none
-#   f.fullscreen  :self
-#   f.payment     :self, "https://secure.example.com"
+# information see: https://developers.google.com/web/updates/2018/06/feature-policy
+
+# Rails.application.config.permissions_policy do |policy|
+#   policy.camera      :none
+#   policy.gyroscope   :none
+#   policy.microphone  :none
+#   policy.usb         :none
+#   policy.fullscreen  :self
+#   policy.payment     :self, "https://secure.example.com"
 # end

From fcdeea782a0bcbc643df8e56ae11b4e3b6059330 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 12 Feb 2026 16:00:39 +0000
Subject: [PATCH 4/6] build: update initial framework defaults

---
 config/application.rb                         |  7 +++
 .../new_framework_defaults_7_1.rb             | 60 +++++++++----------
 2 files changed, 36 insertions(+), 31 deletions(-)

diff --git a/config/application.rb b/config/application.rb
index 1f4dcb43..9217bbd3 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -31,6 +31,13 @@ class Application < Rails::Application
     # Run "rake -D time" for a list of tasks for finding time zone names. Default is UTC.
     # config.time_zone = 'Central Time (US & Canada)'
 
+    # No longer add autoloaded paths into `$LOAD_PATH`. This means that you won't be able
+    # to manually require files that are managed by the autoloader, which you shouldn't do anyway.
+    #
+    # This will reduce the size of the load path, making `require` faster if you don't use bootsnap, or reduce the size
+    # of the bootsnap cache if you use it.
+    config.add_autoload_paths_to_load_path = false
+
     # Please, add to the `ignore` list any other `lib` subdirectories that do
     # not contain `.rb` files, or that should not be reloaded or eager loaded.
     # Common ones are `templates`, `generators`, or `middleware`, for example.
diff --git a/config/initializers/new_framework_defaults_7_1.rb b/config/initializers/new_framework_defaults_7_1.rb
index ebedc26c..1164342a 100644
--- a/config/initializers/new_framework_defaults_7_1.rb
+++ b/config/initializers/new_framework_defaults_7_1.rb
@@ -25,19 +25,19 @@
 # Remove the default X-Download-Options headers since it is used only by Internet Explorer.
 # If you need to support Internet Explorer, add back `"X-Download-Options" => "noopen"`.
 #++
-# Rails.application.config.action_dispatch.default_headers = {
-#   "X-Frame-Options" => "SAMEORIGIN",
-#   "X-XSS-Protection" => "0",
-#   "X-Content-Type-Options" => "nosniff",
-#   "X-Permitted-Cross-Domain-Policies" => "none",
-#   "Referrer-Policy" => "strict-origin-when-cross-origin"
-# }
+Rails.application.config.action_dispatch.default_headers = {
+  'X-Frame-Options' => 'SAMEORIGIN',
+  'X-XSS-Protection' => '0',
+  'X-Content-Type-Options' => 'nosniff',
+  'X-Permitted-Cross-Domain-Policies' => 'none',
+  'Referrer-Policy' => 'strict-origin-when-cross-origin'
+}
 
 ###
 # Do not treat an `ActionController::Parameters` instance
 # as equal to an equivalent `Hash` by default.
 #++
-# Rails.application.config.action_controller.allow_deprecated_parameters_hash_equality = false
+Rails.application.config.action_controller.allow_deprecated_parameters_hash_equality = true
 
 ###
 # Active Record Encryption now uses SHA-256 as its hash digest algorithm.
@@ -48,7 +48,7 @@
 # +config.active_support.key_generator_hash_digest_class+ configured as SHA1 (the default
 # before Rails 7.0), you need to configure SHA-1 for Active Record Encryption too:
 #++
-# Rails.application.config.active_record.encryption.hash_digest_class = OpenSSL::Digest::SHA1
+Rails.application.config.active_record.encryption.hash_digest_class = OpenSSL::Digest::SHA1
 #
 # 2. If you have +config.active_support.key_generator_hash_digest_class+ configured as SHA256 (the new default
 # in 7.0), then you need to configure SHA-256 for Active Record Encryption:
@@ -67,7 +67,7 @@
 # state which matches what was committed to the database, typically the last
 # instance to save.
 #++
-# Rails.application.config.active_record.run_commit_callbacks_on_first_saved_instances_in_transaction = false
+Rails.application.config.active_record.run_commit_callbacks_on_first_saved_instances_in_transaction = true
 
 ###
 # Configures SQLite with a strict strings mode, which disables double-quoted string literals.
@@ -83,7 +83,7 @@
 ###
 # Disable deprecated singular associations names.
 #++
-# Rails.application.config.active_record.allow_deprecated_singular_associations_name = false
+Rails.application.config.active_record.allow_deprecated_singular_associations_name = true
 
 ###
 # Enable the Active Job `BigDecimal` argument serializer, which guarantees
@@ -95,7 +95,7 @@
 # serializer. Therefore, this setting should only be enabled after all replicas
 # have been successfully upgraded to Rails 7.1.
 #++
-# Rails.application.config.active_job.use_big_decimal_serializer = true
+Rails.application.config.active_job.use_big_decimal_serializer = true
 
 ###
 # Specify if an `ArgumentError` should be raised if `Rails.cache` `fetch` or
@@ -103,7 +103,7 @@
 # Options are `true`, and `false`. If `false`, the exception will be reported
 # as `handled` and logged instead.
 #++
-# Rails.application.config.active_support.raise_on_invalid_cache_expiration_time = true
+Rails.application.config.active_support.raise_on_invalid_cache_expiration_time = false
 
 ###
 # Specify whether Query Logs will format tags using the SQLCommenter format
@@ -140,7 +140,7 @@
 # servers, first deploy without changing the serializer, then set the serializer
 # in a subsequent deploy.
 #++
-# Rails.application.config.active_support.message_serializer = :json_allow_marshal
+Rails.application.config.active_support.message_serializer = :json_allow_marshal
 
 ###
 # Enable a performance optimization that serializes message data and metadata
@@ -153,7 +153,7 @@
 # leave this optimization off on the first deploy, then enable it on a
 # subsequent deploy.
 #++
-# Rails.application.config.active_support.use_message_serializer_for_metadata = true
+Rails.application.config.active_support.use_message_serializer_for_metadata = true
 
 ###
 # Set the maximum size for Rails log files.
@@ -161,36 +161,34 @@
 # `config.load_defaults 7.1` does not set this value for environments other than
 # development and test.
 #++
-# if Rails.env.local?
-#   Rails.application.config.log_file_size = 100 * 1024 * 1024
-# end
+Rails.application.config.log_file_size = 100 * 1024 * 1024 if Rails.env.local?
 
 ###
 # Enable raising on assignment to attr_readonly attributes. The previous
 # behavior would allow assignment but silently not persist changes to the
 # database.
 #++
-# Rails.application.config.active_record.raise_on_assign_to_attr_readonly = true
+Rails.application.config.active_record.raise_on_assign_to_attr_readonly = false
 
 ###
 # Enable validating only parent-related columns for presence when the parent is mandatory.
 # The previous behavior was to validate the presence of the parent record, which performed an extra query
 # to get the parent every time the child record was updated, even when parent has not changed.
 #++
-# Rails.application.config.active_record.belongs_to_required_validates_foreign_key = false
+Rails.application.config.active_record.belongs_to_required_validates_foreign_key = true
 
 ###
 # Enable precompilation of `config.filter_parameters`. Precompilation can
 # improve filtering performance, depending on the quantity and types of filters.
 #++
-# Rails.application.config.precompile_filter_parameters = true
+Rails.application.config.precompile_filter_parameters = true
 
 ###
 # Enable before_committed! callbacks on all enrolled records in a transaction.
 # The previous behavior was to only run the callbacks on the first copy of a record
 # if there were multiple copies of the same record enrolled in the transaction.
 #++
-# Rails.application.config.active_record.before_committed_on_all_records = true
+Rails.application.config.active_record.before_committed_on_all_records = false
 
 ###
 # Disable automatic column serialization into YAML.
@@ -198,7 +196,7 @@
 # recommended to explicitly define the serialization method for each column
 # rather than to rely on a global default.
 #++
-# Rails.application.config.active_record.default_column_serializer = nil
+Rails.application.config.active_record.default_column_serializer = YAML
 
 ###
 # Enable a performance optimization that serializes Active Record models
@@ -209,24 +207,24 @@
 # leave this optimization off on the first deploy, then enable it on a
 # subsequent deploy.
 #++
-# Rails.application.config.active_record.marshalling_format_version = 7.1
+Rails.application.config.active_record.marshalling_format_version = 7.1
 
 ###
 # Run `after_commit` and `after_*_commit` callbacks in the order they are defined in a model.
 # This matches the behaviour of all other callbacks.
 # In previous versions of Rails, they ran in the inverse order.
 #++
-# Rails.application.config.active_record.run_after_transaction_callbacks_in_order_defined = true
+Rails.application.config.active_record.run_after_transaction_callbacks_in_order_defined = false
 
 ###
 # Whether a `transaction` block is committed or rolled back when exited via `return`, `break` or `throw`.
 #++
-# Rails.application.config.active_record.commit_transaction_on_non_local_return = true
+Rails.application.config.active_record.commit_transaction_on_non_local_return = false
 
 ###
 # Controls when to generate a value for <tt>has_secure_token</tt> declarations.
 #++
-# Rails.application.config.active_record.generate_secure_token_on = :initialize
+Rails.application.config.active_record.generate_secure_token_on = :initialize
 
 ###
 # ** Please read carefully, this must be configured in config/application.rb **
@@ -252,7 +250,7 @@
 #
 # In previous versions of Rails, Action View always used `Rails::HTML4::Sanitizer` as its vendor.
 #++
-# Rails.application.config.action_view.sanitizer_vendor = Rails::HTML::Sanitizer.best_supported_vendor
+Rails.application.config.action_view.sanitizer_vendor = Rails::HTML4::Sanitizer.best_supported_vendor
 
 ###
 # Configure Action Text to use an HTML5 standards-compliant sanitizer when it is supported on your
@@ -263,13 +261,13 @@
 #
 # In previous versions of Rails, Action Text always used `Rails::HTML4::Sanitizer` as its vendor.
 #++
-# Rails.application.config.action_text.sanitizer_vendor = Rails::HTML::Sanitizer.best_supported_vendor
+Rails.application.config.action_text.sanitizer_vendor = Rails::HTML4::Sanitizer.best_supported_vendor
 
 ###
 # Configure the log level used by the DebugExceptions middleware when logging
 # uncaught exceptions during requests.
 #++
-# Rails.application.config.action_dispatch.debug_exception_log_level = :error
+Rails.application.config.action_dispatch.debug_exception_log_level = :error
 
 ###
 # Configure the test helpers in Action View, Action Dispatch, and rails-dom-testing to use HTML5
@@ -279,4 +277,4 @@
 #
 # In previous versions of Rails, these test helpers always used an HTML4 parser.
 #++
-# Rails.application.config.dom_testing_default_html_version = :html5
+Rails.application.config.dom_testing_default_html_version = :html4

From 83db085b86718b0bca4a83c459fbd3a7a644266a Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 12 Feb 2026 16:28:22 +0000
Subject: [PATCH 5/6] build: adjust some framework defaults

---
 config/environments/development.rb            |  2 +-
 .../new_framework_defaults_7_1.rb             | 26 +++++++++----------
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/config/environments/development.rb b/config/environments/development.rb
index f778f5c0..0f205cdf 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -59,7 +59,7 @@
   config.assets.quiet = true
 
   # Raises error for missing translations.
-  # config.i18n.raise_on_missing_translations = true
+  config.i18n.raise_on_missing_translations = false
 
   # Annotate rendered view with file names.
   # config.action_view.annotate_rendered_view_with_filenames = true
diff --git a/config/initializers/new_framework_defaults_7_1.rb b/config/initializers/new_framework_defaults_7_1.rb
index 1164342a..acc35196 100644
--- a/config/initializers/new_framework_defaults_7_1.rb
+++ b/config/initializers/new_framework_defaults_7_1.rb
@@ -48,7 +48,7 @@
 # +config.active_support.key_generator_hash_digest_class+ configured as SHA1 (the default
 # before Rails 7.0), you need to configure SHA-1 for Active Record Encryption too:
 #++
-Rails.application.config.active_record.encryption.hash_digest_class = OpenSSL::Digest::SHA1
+# Rails.application.config.active_record.encryption.hash_digest_class = OpenSSL::Digest::SHA1
 #
 # 2. If you have +config.active_support.key_generator_hash_digest_class+ configured as SHA256 (the new default
 # in 7.0), then you need to configure SHA-256 for Active Record Encryption:
@@ -67,7 +67,7 @@
 # state which matches what was committed to the database, typically the last
 # instance to save.
 #++
-Rails.application.config.active_record.run_commit_callbacks_on_first_saved_instances_in_transaction = true
+# Rails.application.config.active_record.run_commit_callbacks_on_first_saved_instances_in_transaction = true
 
 ###
 # Configures SQLite with a strict strings mode, which disables double-quoted string literals.
@@ -83,7 +83,7 @@
 ###
 # Disable deprecated singular associations names.
 #++
-Rails.application.config.active_record.allow_deprecated_singular_associations_name = true
+# Rails.application.config.active_record.allow_deprecated_singular_associations_name = true
 
 ###
 # Enable the Active Job `BigDecimal` argument serializer, which guarantees
@@ -168,14 +168,14 @@
 # behavior would allow assignment but silently not persist changes to the
 # database.
 #++
-Rails.application.config.active_record.raise_on_assign_to_attr_readonly = false
+# Rails.application.config.active_record.raise_on_assign_to_attr_readonly = false
 
 ###
 # Enable validating only parent-related columns for presence when the parent is mandatory.
 # The previous behavior was to validate the presence of the parent record, which performed an extra query
 # to get the parent every time the child record was updated, even when parent has not changed.
 #++
-Rails.application.config.active_record.belongs_to_required_validates_foreign_key = true
+# Rails.application.config.active_record.belongs_to_required_validates_foreign_key = true
 
 ###
 # Enable precompilation of `config.filter_parameters`. Precompilation can
@@ -188,7 +188,7 @@
 # The previous behavior was to only run the callbacks on the first copy of a record
 # if there were multiple copies of the same record enrolled in the transaction.
 #++
-Rails.application.config.active_record.before_committed_on_all_records = false
+# Rails.application.config.active_record.before_committed_on_all_records = false
 
 ###
 # Disable automatic column serialization into YAML.
@@ -196,7 +196,7 @@
 # recommended to explicitly define the serialization method for each column
 # rather than to rely on a global default.
 #++
-Rails.application.config.active_record.default_column_serializer = YAML
+# Rails.application.config.active_record.default_column_serializer = YAML
 
 ###
 # Enable a performance optimization that serializes Active Record models
@@ -207,24 +207,24 @@
 # leave this optimization off on the first deploy, then enable it on a
 # subsequent deploy.
 #++
-Rails.application.config.active_record.marshalling_format_version = 7.1
+# Rails.application.config.active_record.marshalling_format_version = 7.1
 
 ###
 # Run `after_commit` and `after_*_commit` callbacks in the order they are defined in a model.
 # This matches the behaviour of all other callbacks.
 # In previous versions of Rails, they ran in the inverse order.
 #++
-Rails.application.config.active_record.run_after_transaction_callbacks_in_order_defined = false
+# Rails.application.config.active_record.run_after_transaction_callbacks_in_order_defined = false
 
 ###
 # Whether a `transaction` block is committed or rolled back when exited via `return`, `break` or `throw`.
 #++
-Rails.application.config.active_record.commit_transaction_on_non_local_return = false
+# Rails.application.config.active_record.commit_transaction_on_non_local_return = false
 
 ###
 # Controls when to generate a value for <tt>has_secure_token</tt> declarations.
 #++
-Rails.application.config.active_record.generate_secure_token_on = :initialize
+# Rails.application.config.active_record.generate_secure_token_on = :initialize
 
 ###
 # ** Please read carefully, this must be configured in config/application.rb **
@@ -250,7 +250,7 @@
 #
 # In previous versions of Rails, Action View always used `Rails::HTML4::Sanitizer` as its vendor.
 #++
-Rails.application.config.action_view.sanitizer_vendor = Rails::HTML4::Sanitizer.best_supported_vendor
+Rails.application.config.action_view.sanitizer_vendor = Rails::HTML4::Sanitizer
 
 ###
 # Configure Action Text to use an HTML5 standards-compliant sanitizer when it is supported on your
@@ -261,7 +261,7 @@
 #
 # In previous versions of Rails, Action Text always used `Rails::HTML4::Sanitizer` as its vendor.
 #++
-Rails.application.config.action_text.sanitizer_vendor = Rails::HTML4::Sanitizer.best_supported_vendor
+# Rails.application.config.action_text.sanitizer_vendor = Rails::HTML4::Sanitizer
 
 ###
 # Configure the log level used by the DebugExceptions middleware when logging

From eba6d45013b6fe49e368a85eca129cb23bf9bb42 Mon Sep 17 00:00:00 2001
From: Stephen Hulme <sh51@sanger.ac.uk>
Date: Thu, 12 Feb 2026 15:18:24 +0000
Subject: [PATCH 6/6] feat: add default health controller

TODO: upgrade to rails 7.1
---
 config/routes.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/config/routes.rb b/config/routes.rb
index 8d11834b..ad820b97 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -7,6 +7,8 @@
   # You can have the root of your site routed with "root"
   root 'pages#index'
 
+  get 'health' => 'rails/health#show', :as => :rails_health_check
+
   resources :lots, only: %i[create show new], constraints: { id: /[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}/ } do
     collection do
       get :search