Mixtio

Reagent creation and barcoding service for DNA Pipeline.

Prerequisites

• Ruby 2.7.2
• MySQL 8.0
• Chrome (for testing)

Installation

1. The gems in the gemfile are separated into groups. When running bundle install, you will not need the gems in the deployment group for working locally. In order to ignore the deployment group on install, run:

bundle config set without 'deployment'

2. bundle install

Testing

1. Check the details in database.yml are correct for your local setup. By default the configuration expects a user root with no password on the default MySQL port (3306).

2. Initialise the test database:

RAILS_ENV=test rails db:create
RAILS_ENV=test rails db:schema:load

3. Run the tests

bundle exec rspec

Running Locally

1. Initialise the development database:

RAILS_ENV=development rails db:create
RAILS_ENV=development rails db:schema:load

2. Add the seed data

RAILS_ENV=development rails db:seed

3. Create a new team and add yourself as a user:

rails console
> team = Team.create(name: "Team Name")
> user = User.create(username: "YOUR_SANGER_USERNAME", team: team)

4. Run rails server and navigate to http://localhost:3000

5. Log in with your username and no password.

Mixtio in production uses the Sanger LDAP server to authenticate users. In development, this is stubbed out and any password for a valid user will successfully authenticate them.

To turn this feature off, set stub_ldap to false in development.rb.

Misc

• Trouble with libv8 and therubyracer? Check out https://stackoverflow.com/a/55645176

Gems used

• Testing: RSpec Rails
• Pagination: Kaminari
• Creating test data: Factory Girl
• For testing web interactions: Capybara