IRIDA Next

IRIDA Next is an open source bioinformatics platform for the storage, management, and analysis of genomic sequences and metadata.

Contributing

devenv is used to provide a reproducible development environment for this project. Follow the getting started instructions (note: I recommend going with single-user mode for nix which can be found under the WSL2 tab, and then installing deven under the Nix profiles (requires experimental flags)).

Note: to use Nix profiles you will need to create the following file with the following content

~/.config/nix/nix.conf:

experimental-features = nix-command flakes

Note: If using a linux system with ldap auth via sssd, then install the following with nix.

nix profile install nixpkgs#sssd

To automatically load the environment you should install direnv and then load the direnv.

# The security mechanism didn't allow to load the `.envrc`.
# Since we trust it, let's allow it execution.
direnv allow .

At this point you should see the nix commands available in your terminal.

Startup the services

$ devenv up

Run the setup script (which will by default startup the application)

$ bin/setup

Navigate in your browser to http://localhost:3000

Test

bin/rails test:all

Running tests headful

HEADLESS=false bin/rails test:system

View Coverage:

Open coverage/index.html

Documentation

See docs.

Pre-commit Hooks & Formatting

This project uses Lefthook (via Bundler) to automatically format and lint code before each commit. The following tools run on staged files:

• RuboCop: Ruby files (.rb) are auto-corrected and linted
• Prettier: JavaScript, TypeScript, CSS, JSON, and Markdown files are formatted
• ESLint: JavaScript files are auto-fixed
• Herb: HTML+ERB templates (.erb) are formatted and linted
• i18n-tasks: Locale files are normalized (i18n-tasks normalize) when locale YAML changes are staged

How it works

• Hooks are configured in lefthook.yml
• Install hooks with bundle exec lefthook install --reset-hooks-path (also run automatically by bin/setup)
• On commit, staged files matching configured patterns are checked and auto-fixed
• You can bypass hooks with git commit --no-verify (not recommended)

Manual formatting

• Run all formatters manually:

  bin/rubocop -a
  pnpm run format

Manual linting (ERB)

pnpm run herb:lint

Ignore files

• .prettierignore excludes build outputs, dependencies, and generated files from Prettier formatting