Y26-118 - As a TL (Tom) I would like to check SequenceScape and Limber against the new MySQL 8.4 UAT databases so that we can detect any issues prior to the production upgrade.

[TWJW-SANGER]

Describe the Housekeeping
As a TL (Tom) I would like to check SequenceScape and Limber against the new MySQL 8.4 UAT databases so that we can detect any issues prior to the production upgrade.

Acceptance criteria

• Local unit tests passing against a local MySQL 8.4 installation.
• Tests pass on CI
• Applications pass Integration Test Suite in UAT environment.

Additional context
EOL of the current version is the end of May.

See the private PSD confluence page MySQL v8.4 Test Databases for database details.

[andrewsparkes]

Had some flakiness testing locally (rspec feature tests mainly). But integration suite tests were running fine so judged ok.

Uploaded SS branch to CI to run tests there, all passed. Branch #5702

Deployed above branch to UAT, also creating a specific deployment branch with vault changes to include UAT testing database details from confluence page. Deployment branch https://github.com/sanger/deployment/tree/y26-118-mysql-8-4-testing
Ran integration suite against this version, passed.
Checked by connecting MySQL workbench to 8.4 database and running queries to see that it had run against this database, saw labwares with recent timestamps in that database.

Reverted SS and Limber back to latest develop in UAT using master branch of deployment project, so using v8.0 DB again.

[andrewsparkes]

MySQL testing 8.4.7

Notes about setup of 8.4 in local using homebrew in case useful to someone

current local version:

mysql Ver 8.0.44 for macos15.4 on arm64 (Homebrew)

drop the current 8.0 database

In MySQL workbench:
drop schemas sequencescape_development and sequencescape_test_cuke

uninstall current version

brew services stop mysql@8.0
brew uninstall mysql@8.0
[
Error: mysql@8.0 is pinned. You must unpin it to uninstall.
brew unpin mysql@8.0
brew uninstall mysql@8.0
]

install 8.4.7

brew install mysql@8.4
NB. this installs 8.4.8 rather than 8.4.7, don't see how to install a minor version

brew link --force mysql@8.4
[
Warning: Already linked: /opt/homebrew/Cellar/mysql@8.4/8.4.8_2
To relink, run:
brew unlink mysql@8.4 && brew link mysql@8.4
]

start service

brew services start mysql@8.4

delete SS directories

delete vendors directory
delete node_modules directory (probably not necessary)

bundle install
(or instead of deleting vendor directory can do bundle install --redownload)
yarn install --dev

setup the database

bundle exec rake db:setup
bundle exec rake application:post_deploy

start the server

bundle exec rails s

start the jobs worker

bundle exec rake jobs:work

run config generate in Limber

bundle exec rake config:generate

start Limber server

bundle exec rails s

run integration suite

in latest integration suite repo:
ENVIRONMENT=local DEBUG_ON_FAIL=true bundle exec rspec