JBConnect

Paper: JBrowse Connect: A server API to connect JBrowse instances and users, Yao, Buels, Stein, Sen, Holmes, et al. 2020; PLOS Computational Biology

JBConnect provides the following features:

Sails JS - NodeJS/Expressed-based

Tightly integrated with JBrowse

Track & Dataset Management with JBrowse integration RESTful track data access Track API (CRUD) Auth and Secure Tracks/Datasets/Assets Track/Asset SubPub events with Socket.io

Flexible Authentication – (Passport.js) supporting strategies, like OAuth2, OpenID, etc.

User management services

Policy Engine f0r managing access to Tracks, Datasets, Services, Assets

Extensible server-side analysis with workflow abstraction and job queue

Waterline ORM (MongoDB, MySQL, Postgres, Redis, etc.) with integrated Blueprint object models

npm installable hook model supporting both client-side (JBrowse plugins) and server-side extensions in a single package.

Grunt – task management (minification, watches, etc.)

Quick Start

The quick start instructions demonstrate installing JBConnect with JBrowse loaded as a an NPM module (since JBConnect is generally intended to be a companion of JBrowse. JBrowse may also be installed in a separate directory. (See JBrowse Installed In Separate Directory.)

Pre-Install

JBConnect requires sailsjs and redis . Redis is only used by the queue framework (kue)

yum install redis
redis-server
npm install -g sails@1.0.2

Install

Install the JBConnect and JBrowse. jb_setup.js ensures the sample data is loaded.

git clone http://github.com/gmod/jbconnect
cd jbconnect
npm install
npm install @gmod/jbrowse@1.15.1
patch node_modules/@gmod/jbrowse/setup.sh fix_jbrowse_setup.patch
./utils/jb_setup.js

The patch operation is needed to make JBrowse 1.15.1 setup.sh run properly. If JBrowse is installed in another location, the patch should be run before setup.sh.

Run

Launch the server.

sails lift

From a web browser, access the application.

http://localhost:1337/login

You will arrive at the following screen

The default username/password: juser/password

Vulnerabilty Warnings

npm currently reports a number of vulnerability warnings of various degrees of severity, most of which are coming from Sails. Many of these warnings are fixed in a later version of SailsJS. We hope in a future release of the software to correct more of these warnings.

Contents

• Features
  • Directory Layout
  • jbutil Command
  • Queue Framework
  • Configuration
  • Client-Side Plugins
  • Web Includes
  • Standalone Register / Login / Logout Routes
  • Test Framework
  • Documentation Framework
• Configuration Options
  • JBrowse Installed In Separate Directory
  • Configuration Files
  • Limiting Query Size
  • Installing JBConnect jbh-hooks
  • JBClient Plugin
  • Job Service Configuration
  • Extending jbutil
• JBConnect Hooks
  • Directory Layout
  • package.json
  • Configurations
  • Client-Side JBrowse Plugins
  • Extending Commands
  • Sails Module Layout
  • Job Service
• Tutorials
  • JBConnect Hook Tutorial
  • Creating a Stand-Alone Job Service for local workflow processing
• API
  • Namespace: AuthController
  • Module: controllers/DatasetController
  • Module: controllers/JobActiveController
  • Module: controllers/JobController
  • Module: controllers/ServiceController
  • Module: controllers/TrackController
  • Module: controllers/UserController
  • Module: models/Dataset
  • Module: models/Job
  • Module: models/JobActive
  • Module: models/Passport
  • Module: models/Service
  • Module: models/Track
  • Module: models/User
  • Module: policies/bearerAuth
  • Module: policies/isAdmin
  • Module: policies/passport
  • Module: policies/sessionAuth
  • Module: services/jbutillib
  • Module: services/passport
  • Module: services/postAction
  • Module: services/serviceProc