Features¶

JBConnect is a Sails.js application¶

JBConnect utilizes Sails.js, provideing the following features:

Javascript (NODE-based)

Blueprints Auto-generate CRUD APIs, ESTful APIs, Socket.io (events)

Waterline ORM, Any Database, MySql, PostgreSQL Mongo, Redis, local

Express-based Compatible routes & Middleware

Socket.io sub/pub, WebSockets, Auto Integrate Models

Passport.js role-based security, access control, OAuth

Installable Hooks (jbh-*), Extensible plugin framework

Grunt Customizable asset workflow, LESS, SASS, Stylus

Front-End Agnostic Angular, backbone, bootstrap, ember, …

Directory Layout¶

JBConnect project
├── api                             Standard sails API layout
├── assets                          contains client accessible assets
├── bin                             Utilities
├── config                          Configuration files.
│   ├── globals.js                  Config file for module
│   └── libroutes.js                Library Routes
├── data                            Contains the local database file
│   └── localDiskDb.db              Local database file
├── docs                            Documentation
│   └── genapi-rst                  jsdoc generated rst files
├── plugins                         Client-side Plugins
│   └── JBClient                    Client plugin
├── test                            Test
├── views                           View pages
├── Gruntfile.js                    Grunt config
├── jbutil                          JBServer Utility
└── package.json

jbutil Command¶

jbutil is a setup/configuration utility for JBConnect. jbh-hook can extend jbutil command options. (see: jbs-hooks-extend)

This example shows that jbh-jblast adds a number of commands to jbutil

$ ./jbutil --help
Usage: jbutil [OPTION]
      --config            display merged config
      --blastdbpath=PATH  (jblast) existing database path
      --setupworkflows    (jblast) [install|<path>] "install" project wf, or specify .ga file
      --setuptools        (jblast) setup jblast tools for galaxy
      --setupdata         (jblast) setup data and samples
      --setupindex        (jblast) setup index.html in the jbrowse directory
      --setuphistory      setup history
  -h, --help              display this help

Queue Framework¶

JBConnect uses Kue as the basis for the queue framework. However, Kue is encapsulated in the Job model/controller. Since Kue requires redis database, redis server must be running. An integrated job panel is available when the JBClient plugin is active. (see: JBClient Plugin)

For diagnostic purposes, a Kue utility can be used to view/manage the Kue database content: http://localhost:1337/kue

This route can be disabled with in config/http.js.

Configuration¶

JBrowse configurations are in config/globals.js

jbrowse: {
    jbrowseRest: "http://localhost:1337",       // path accessible by web browser
    jbrowsePath: jbPath,                        // or point to jbrowse directory (ie. "/var/www/jbrowse/")
    routePrefix: "jbrowse",                     // jbrowse is accessed with http://<addr>/jbrowse
    dataSet: [
        {
            dataPath: "sample_data/json/volvox" // registered datasets.
        }
    ]
}

Client-Side Plugins¶

Client-side plugins are defined in the plugins directory. Plugins will automatically be accessible by the client side. However, they need to be configured in the plugins: section of the particular dataset in JBrowse trackList.json.

Plugin routes are virtual routes With respect to the client side, they appear in the client-side’s plugin directory only when the server is lifted.

Library Routes¶

libroutes maps dependancy routes for client-side access. These provide access to modules that are required for use by the client-side plugins or other client-side code. The framework looks for libroutes.js in jbh- (hook modules), in their respective config directories

For example: for the module jquery, The module is installed with ‘npm install jquery’ The mapping the mapping ‘jquery’: ‘/jblib/jquery’ makes the jquery directory accessible as /jblib/jquery from the client side.

Library Routes are virtual routes, in that they only exist when the server is lifted. They are virtually mapped to their respective locations in the node_modules directory.

config/libroutes.js:

module.exports = {
    lib: {
            'jquery.mb.extruder':       '/jblib/mb.extruder',
            'jQuery-ui-Slider-Pips':    '/jblib/slider-pips',
            'jquery-ui-dist':           '/jblib/jquery-ui'
    }
};

Standalone Register / Login / Logout Routes¶

Stand-alone routes allow for basic register/login/logout functionality free from the JBrowse interface.

Stand-alone interfaces use bootstrap

Register: http://<address>:1337/register

Login: http://<address>:1337/login

Logout: http://<address>:1337/logout

Get Login State: http://<address>:1337/loginstate

The routes are defined in config/routes.js.

Job Queue Panel¶

JBConnect uses Kue as the queue framework. Since Kue requires redis database, redis server must be running. An integrated job panel is available when the JBClient plugin is active. (see: JBClient Plugin)

Integrated Job Panel:

Jservice Framework¶

todo

Test Framework¶

Test framework uses

Mocha for unit test
Nightwatch for end-to-end, supporting phantomjs, selenium and online service such as browserstack.
Istanbul for coverage

To execute

npm test

by default nightwatch is setup for phantomjs. Selenium requires running an additional selenium server

package.json:

"scripts": {
  "test": "nyc node ./node_modules/mocha/bin/mocha test/bootstrap.test.js test/integration/**/*.test.js test/e2e/**/*.test.js --nightwatch-test phantomjs",
},

The option --nightwatch-test can be:

phantomjs - runs client tests with phantomjs
selenium - runs client tests with selenium
browserstack - runs client test with selenium through remote browserstack account.

Documentation Framework¶

For integrated documentation, JSdoc3 is used to generate API docs from code with jsdoc-sphinx, a jsdoc template that generates RestructuredText (RST) and Sphinx. This enables support for readthedocs.

See: RST/Sphinx Cheatsheet

npm run gendocs