Limber Pipeline Application

Description

A flexible front end to plate bases pipelines in Sequencescape.

Initial Setup (using Docker)

Docker provides all the dependencies needed by Limber, so there is less to install on your machine. It can make development harder though, so it might be preferable to use a native installation (see below) if that is possible on your machine. The only dependency that isn't provided is Sequencescape, so please ensure you have that running on port 3000 on your localhost before attempting to run Limber in Docker.

You must have Docker Desktop installed on your machine. Then the only command you should need to run is:

docker-compose up

Variations on this command include:

• docker-compose up -d which starts the container as a background task (freeing up the terminal). You can then use docker-compose down to turn it off again.
• GENERATE_CONFIG=false docker-compose up which will avoid running the config:generate rake task as Limber is started.
• docker-compose up --build which forces a rebuild of the Docker image if your changes to the Dockerfile or related scripts don't seem to be taking effect.

Limber should be accessible via http://localhost:3001.

Initial Setup (using native installation)

Steps must be followed in either the Sequencescape repository or this Limber repository, as indicated:

1. In Limber, ensure the appropriate version of Ruby is installed. The command here is for rbenv but you may want to use a different Ruby version manager:

   rbenv install

2. In Limber, make the Bundler gem install the dependencies for this project:

   bundle install

3. In Limber, install the yarn dependencies:

   yarn install

4. In Sequencescape, perform the post deploy actions:

   bundle exec rake application:post_deploy

5. In Sequencescape, start the local server (will start on port 3000):

   bundle exec rails s

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

   bundle exec rake config:generate

7. In Sequencescape, configure all Limber required data:

   bundle exec rake limber:setup

8. In Sequencescape, start the delayed job processor

   bundle exec rake jobs:work

9. In Limber, start the local server (will start on port 3001):

   bundle exec rails s

Linting and formatting

Linting and formatting are provided by rubocop, prettier and Eslint. I strongly recommend checking out editor integrations. Also, using lefthook will help ensure that only valid files are committed.

# Run rubocop
bundle exec rubocop
# Run rubocop with safe autofixes
bundle exec rubocop -a
# ESlint
yarn lint
# Check prettier formatting
yarn prettier --check .
# Fix prettier formatting
yarn prettier --write .

Troubleshooting

If during development changes do not seem to be taking effect, try:

• Restart the application:
• Destroy and recreate the Docker container docker-compose down && GENERATE_CONFIG=false docker-compose up -d
• Rebuild the Docker image, particularly useful for changing dependencies
• Clobber local resources rails assets:clobber

Note about the remainder of this document

The rest of the sections shown here were written for and apply to the native installation, but can also be used in the Docker container if required. In order to use Docker, it's probably best to create a shell in the running container. Assuming you started the container via docker-compose you can access the shell using:

docker exec -ti limber_limber_1 bash

If the container isn't recognised, check the container name (right hand column) using docker ps --all, ensure it's up/running and substitute the name into the above command in place of limber_limber_1.

Docs

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

{file:docs/configuring_new_pipelines.md Configuring new pipelines}

Running Specs

RSpec

Ruby unit and feature tests:

bundle exec rspec

Jest

JavaScript unit tests:

yarn test
yarn test "path/to/file" -t "name of the test"

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:

yarn
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

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.