Limber Pipeline Application

Linting Ruby RSpec Tests Javascript testing Yard Docs


A flexible front end to plate bases pipelines in Sequencescape

Initial Setup

  1. In Limber, connect to Sequencescape to configure required data:

    bundle exec rake config:generate
  2. In Sequencescape, configure all Limber required data:

    bundle exec rake limber:setup
  3. Start Sequencescape (will start in 3000):

    bundle exec rails s
  4. Start the delayed job processor

    bundle exec rake jobs:work
  5. In Limber, start Limber (will start in 3001):

    bundle exec rails s


In addition to the externally hosted YARD docs, you can also run a local server:

yard server -r --gems -m limber

You can then access the Limber documentation through: http://localhost:8808/docs/limber Yard will also try and document the installed gems: http://localhost:8808/docs

Configuring pipelines

Configuring new pipelines

Running Specs


Ruby unit and feature tests:

    bundle exec rspec


JavaScript unit tests:

    yarn karma start --single-run

If you get '[Webpacker] Compilation Failed' when trying to run specs, you might need to get yarn to install its dependencies properly. One way of doing this is by precompiling the assets:

    rake assets:precompile

This has the added benefit that it reduces the risk of timeouts when the tests are running, as assets will not get compiled on the fly.

Writing specs

There are a few tools available to assist with writing specs:

Factory Bot

  • Strategies: You can use json :factory_name to generate the json that the API is expected to receive. This is very useful for mocking web responses. The association strategy is used for building nested json, it will usually only be used as part of other factories.

  • Traits:

    • api_object: Ensures that lots of the shared behaviour, like actions and uuids are generated automatically barcoded: Automatically ensures that barcode is populated with the correct hash, and calculates human and machine barcodes
    • build: Returns an actual object, as though already found via the api. Useful for unit tests
  • Helpers: with_has_many_associations and with_belongs_to_associations can be used in factories to set up the relevant json. They won't actually mock up the relevant requests, but ensure that things like actions are defined so that the api knows where to find them.

Request stubbing

Request stubs are provided by webmock. Two helper methods will assist with the majority of mocking requests to the api, stub_api_get and stub_api_post. See spec/support/api_url_helper.rb for details.

Note: Due to the way the api functions, the factories don't yet support nested associations.


Lefthook is a git-hook manager that will ensure staged files are linted before committing.

You can install it either via homebrew brew install Arkweid/lefthook/lefthook or rubygems gem install lefthook

You'll then need to initialize it for each repository you wish to track lefthook install

Hooks will run automatically on commit, but you can test them with: lefthook run pre-commit

In addition you can also run lefthook run fix to run the auto-fixers on staged files only. Note that after doing this you will still need to stage the fixes before committing. I'd love to be able to automate this, but haven't discovered a solution that maintains the ability to partially stage a file, and doesn't involve running the linters directly on files in the .git folder.