Lighthouse UI

A Nuxt JS application that provides SSRs the ability to interact with the lighthouse service and other LIMS. Some of the features include:

• Create and download reports which contain the fit to pick samples and their locations.

• The ability to scan the barcode of a box or plate and get information about it, such as:

  • whether there is plate map data for the barcode(s).
  • the number of fit to pick samples.
  • the number of 'must_sequence' samples.
  • the number of 'preferentially_sequence' samples.

• Create samples in Sequencescape when scanning in a box - it retrieves the plates from LabWhere, then inserts the fit to pick samples into Sequencescape.

• Create a cherrypick batch from Sentinel - on scaning a box barcode, it retrieves the plates from LabWhere, then creates a cherrypick submission in Sequencescsape. It assumes that the samples are already in Sequencescape and also gives you an opportunity to deselect samples that you do not want to include.

• View the status of the CSV imports from the lighthouse service.

• Print labels.

• Create and fail plates in the Beckman pipeline.

Table of Contents

• Requirements for development
• Getting started
  • Configuring environment
  • Setup steps
• Running
• Linting
• Testing
  • Running tests
• Deployment
• Miscellaneous
  • Updating the Table of Contents

Requirements for development

The following tools are required for development:

• node (the version used is found in .nvmrc)

Getting started

The following services are not required but can be beneficial during development:

• lighthouse service
• Sequencescape

Configuring environment

Create a .env file, or copy the .env.example, and update the values to meet your setup.

Setup steps

Install the require packages:

npm install

Running

To serve the application with hot reloading:

npm run dev

Linting

This project is linted using ESLint. To lint the code, run:

npm run lint .

Testing

Running tests

To run the Jest test suite:

npm test

There are also some cypress tests which can be run as follows:

npx cypress run

Deployment

This project uses a Docker image as the unit of deployment. To create a release for deployment, create a release in GitHub and wait for the GitHub action to create the Docker image.

The release version should align with the standards.

Miscellaneous

Updating the Table of Contents

To update the table of contents after adding things to this README you can use the markdown-toc node module. To run:

npx markdown-toc -i --bullets="-" -- README.md