API

Namespace: AuthController

Description

Authentication Controller.

See also Passport model.

Function: login

Render the login page

The login form itself is just a simple HTML form:

<form role="form" action="/auth/local" method="post">
  <input type="text" name="identifier" placeholder="Username or Email">
  <input type="password" name="password" placeholder="Password">
  <button type="submit">Sign in</button>
</form>

You could optionally add CSRF-protection as outlined in the documentation: http://sailsjs.org/#!documentation/config.csrf

A simple example of automatically listing all available providers in a Handlebars template would look like this:

{{#each providers}}
  <a href="/auth/{{slug}}" role="button">{{name}}</a>
{{/each}}

The next parameter can specify the target URL upon successful login.

Example: GET http://localhost:1337/login?next=http://localhost:1337/jbrowse?data=sample_data/json/volvox

login(req, res)
Arguments:
  • req (Object) – request
  • res (Object) – response

Function: logout

Log out a user and return them to the homepage

Passport exposes a logout() function on req (also aliased as logOut()) that can be called from any route handler which needs to terminate a login session. Invoking logout() will remove the req.user property and clear the login session (if any).

For more information on logging out users in Passport.js, check out: http://passportjs.org/guide/logout/

Example: GET http://localhost:1337/logout

logout(req, res)
Arguments:
  • req (Object) – request
  • res (Object) – response

Function: loginstate

get login state

GET http://localhost:1337/loginstate

Example Result:

{
    "loginstate": true,
    "user": {
        "username": "juser",
        "email": "juser@jbrowse.org"
    }
}
loginstate(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Function: provider

Create a third-party authentication endpoint

provider(req, res)
Arguments:
  • req (Object) – request
  • res (Object) – response

Function: callback

Create a authentication callback endpoint

This endpoint handles everything related to creating and verifying Pass- ports and users, both locally and from third-aprty providers.

Passport exposes a login() function on req (also aliased as logIn()) that can be used to establish a login session. When the login operation completes, user will be assigned to req.user.

For more information on logging in users in Passport.js, check out: http://passportjs.org/guide/login/

callback(req, res)
Arguments:
  • req (Object) – request
  • res (Object) – response

Module: controllers/DatasetController

Local Navigation

Description

REST Interfaces for Dataset model

Datasets are configure in config/globals.js file.

See Dataset Model

Subscribe to Dataset events:

io.socket.get('/dataset', function(resData, jwres) {console.log(resData);});
io.socket.on('dataset', function(event){
   consol.log(event);
}

Function: get

Enumerate or search datasets

GET /dataset/get

get(req, res)
Arguments:
  • req (object) – request data
  • res (object) – response data

Module: controllers/JobActiveController

Local Navigation

Description

REST interfaces for JobActive model.

See: JobActive model.

Subscribe to JobActive events:

io.socket.get('/jobactive', function(resData, jwres) {console.log(resData);});
io.socket.on('jobactive', function(event){
   consol.log(event);
}

Function: get

Read job active record

GET /jobactive/get

get(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Module: controllers/JobController

Description

REST interfaces for Job model

See Job model.

Subscribe to Job events:

io.socket.get('/job', function(resData, jwres) {console.log(resData);});
io.socket.on('job', function(event){
   consol.log(event);
}

Function: get

Enumerate or search job list.

GET /job/get

Example usage (jQuery):

$.ajax({
    url: "/job/get",
    dataType: "text",
    success: function (data) {
       console.log(data)
    }
});

The returned data is a JSON array of job objects.

Example Job object:

{
    "id": 113,
    "type": "workflow",
    "progress": "100",
    "priority": 0,
    "data": {
      "service": "serverSearchService",
      "dataset": "sample_data/json/volvox",
      "searchParams": {
        "expr": "ttt",
        "regex": "false",
        "caseIgnore": "true",
        "translate": "false",
        "fwdStrand": "true",
        "revStrand": "true",
        "maxLen": "100"
      },
      "name": "ttt search",
      "asset": "113_search_1513478281528",
      "path": "/var/www/html/jbconnect/node_modules/jbrowse/sample_data/json/volvox/ServerSearch",
      "outfile": "113_search_1513478281528.gff",
      "track": {
        "maxFeatureScreenDensity": 16,
        "style": {
          "showLabels": false
        },
        "displayMode": "normal",
        "storeClass": "JBrowse/Store/SeqFeature/GFF3",
        "type": "JBrowse/View/Track/HTMLFeatures",
        "metadata": {
          "description": "Search result job: 113"
        },
        "category": "Search Results",
        "key": "113 ttt results",
        "label": "113_search_1513478281528",
        "urlTemplate": "ServerSearch/113_search_1513478281528.gff",
        "sequenceSearch": true
      }
    },
    "state": "complete",
    "promote_at": "1513478280038",
    "created_at": "1513478280038",
    "updated_at": "1513478292634",
    "createdAt": "2018-02-01T05:38:27.371Z",
    "updatedAt": "2018-02-01T05:38:27.371Z"
  }
get(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Function: submit

Submit a job.

Example - submit sequence search:

var postData = {
    service: "serverSearchService",
    dataset: "sample_data/json/volvox,
    searchParams: searchParams
};
$.post("/job/submit, postData, function(retdata) {
   console.log(retdata)
},'json');

Returned data from job submit: { status: "success", jobId: 152 }, where jobId is the id of the created job in the job queue.

submit(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Module: controllers/ServiceController

Local Navigation

Description

REST interfaces for Service model.

See Service model

Subscribe to Service events:

io.socket.get('/service', function(resData, jwres) {console.log(resData);});
io.socket.on('service', function(event){
   consol.log(event);
}

Function: get

Enumerate job services (jservices)

GET /service/get

get(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

GET or POST /service/exec/

This example calls set_filter, a JBlast operation:

var postData = {
      filterParams: data,
      asset: "jblast_sample",
      dataset: "sample_data/json/volvox"
}
$.post( "/service/exec/set_filter", postData , function( data) {
    console.log( data );
}, "json");

The returned data depends on the service function that is called.

Module: controllers/TrackController

Description

REST interfaces for TrackController

Subscribe to Track events:

io.socket.get('/track', function(resData, jwres) {console.log(resData);});
io.socket.on('track', function(event){
   consol.log(event);
}

Function: get

enumerate tracks or search track list.

Get all tracks GET /track/get

Get filtered tracks by dataset:

GET /track/get?id=1 where id is the dataset id

GET /track/get?path=sample_data/json/volvox where path is the dataset path

get(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Function: get_tracklist

get JBrowse tracklist

GET /track/get_tracklist

get_tracklist(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Function: add

add a new track

POST /track/add

Must include “dataset” in the fields, which can be the path (string) or id (int)

Calling example:

let newTrack = {
    "dataset":"sample_data/json/volvox",
    "autocomplete": "all",
    "track": "EST",
    "style": {
        "className": "est"
    },
    "key": "HTMLFeatures - ESTs",
    "feature": [
        "EST_match:est"
    ],
    "storeClass": "JBrowse/Store/SeqFeature/NCList",
    "urlTemplate": "tracks/EST/{refseq}/trackData.json",
    "compress": 0,
    "label": "EST",
    "type": "FeatureTrack",
    "category": "Miscellaneous"
};
$.post( "/track/add", newTrack, function( data ) {
  console.log( "result", data );
}, "json");
add(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Function: modify

modify an existing track

POST /track/modify

Calling example:

let modifyTrack = {
    "autocomplete": "all",
    "track": "EST",
    "style": {
        "className": "est"
    },
    "key": "HTMLFeatures - ESTs",
    "feature": [
        "EST_match:est"
    ],
    "storeClass": "JBrowse/Store/SeqFeature/NCList",
    "urlTemplate": "tracks/EST/{refseq}/trackData.json",
    "compress": 0,
    "label": "EST",
    "type": "FeatureTrack",
    "category": "Miscellaneous"
};
$.post( "/track/modify", modifyTrack, function( data ) {
  console.log( "result", data );
}, "json");
modify(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Function: remove

remove an existing track

POST /track/remove

Calling example:

$.post( "/track/remove", { id: 23 }, function( data ) {
  console.log( "result", data );
}, "json");
remove(req, res)
Arguments:
  • req (object) – request
  • res (object) – response

Module: controllers/UserController

Local Navigation

Description

REST interfaces for UserController

Subscribe to User events:

io.socket.get('/user', function(resData, jwres) {console.log(resData);});
io.socket.on('user', function(event){
   consol.log(event);
}

Function: get

Enumerate or search users

GET /user/get

get(req, res)
Arguments:
  • req (object) – Enumerate or search users

GET /user/get :param object res: Enumerate or search users

GET /user/get

Module: models/Dataset

Description

Dataset is a model that represents the JBrowse dataset. Generally, this includes path to the dataset and some of the data contained in trackList.json.

Datasets known to JBConnect are defined in config/globals.js (see: Configuration)

Dataset object:

{
  "name": "Volvox",
  "path": "sample_data/json/volvox",
  "createdAt": "2018-02-01T05:38:26.320Z",
  "updatedAt": "2018-02-01T05:38:26.320Z",
  "id": 1
}

Ref: Sails Models and ORM

Function: Init

Initializes datasets as defined in config/globals.js. (see: Configuration)

Init(params, cb)
Arguments:
  • params (object) – callback function
  • cb (function) – callback function
Return undefined:
 

Initializes datasets as defined in config/globals.js.

(see: Configuration)

Function: Get

Get list of tracks based on critera in params

Get(params, cb)
Arguments:
  • params (object) – search critera (i.e. {id: 1,user:'jimmy'} )
  • cb (function) – callback function(err,array)

Function: Resolve

Given either a dataset string (ie. “sample_data/json/volvox” or the database id of a dataset, it returns a dataset object in the form:

{
    path: "sample_data/json/volvox",
    id: 3
}
Resolve(dval)
Arguments:
  • dval (val) – dataset string (ie. “sample_data/json/volvox”) or id (int)

Code Example

{
    path: "sample_data/json/volvox",
    id: 3
}
Return object:
  • dataset object

dataset (string - i.e. “sample_data/json/volvox” if input was an id returns null if not found

Function: Sync

Sync datasets, defined in globals with database.

todo: need to improve, perhaps use async?

Sync()
Arguments:
  • Sync() – cb - callback function

Module: models/Job

Description

Job model is an encapsulation of the Kue job framework.

Kue uses redis database. This model synchronizes the Job database with the redis data through the use of Kue’s API.

Kue event messages are stuffed into a FIFO _eventList and dequeued with _processNextEvent to ensure order.
  • Example Job object:
{
    "id": 113,
    "type": "workflow",
    "progress": "100",
    "priority": 0,
    "data": {
      "service": "serverSearchService",
      "dataset": "sample_data/json/volvox",
      "searchParams": {
        "expr": "ttt",
        "regex": "false",
        "caseIgnore": "true",
        "translate": "false",
        "fwdStrand": "true",
        "revStrand": "true",
        "maxLen": "100"
      },
      "name": "ttt search",
      "asset": "113_search_1513478281528",
      "path": "/var/www/html/jbconnect/node_modules/jbrowse/sample_data/json/volvox/ServerSearch",
      "outfile": "113_search_1513478281528.gff",
      "track": {
        "maxFeatureScreenDensity": 16,
        "style": {
          "showLabels": false
        },
        "displayMode": "normal",
        "storeClass": "JBrowse/Store/SeqFeature/GFF3",
        "type": "JBrowse/View/Track/HTMLFeatures",
        "metadata": {
          "description": "Search result job: 113"
        },
        "category": "Search Results",
        "key": "113 ttt results",
        "label": "113_search_1513478281528",
        "urlTemplate": "ServerSearch/113_search_1513478281528.gff",
        "sequenceSearch": true
      }
    },
    "state": "complete",
    "promote_at": "1513478280038",
    "created_at": "1513478280038",
    "updated_at": "1513478292634",
    "createdAt": "2018-02-01T05:38:27.371Z",
    "updatedAt": "2018-02-01T05:38:27.371Z"
  }

Event Mappings:

Kue Events Job Events
  • queue-enqueue
 create
  • queue-start
 update
  • queue-failed
 update
  • queue-failed-attempt
 update
  • queue-progress
 update
  • queue-complete
 update
  • queue-remove
 remove
  • queue-promotion
 unused

Ref: Sails Models and ORM

Function: Init

start the monitor

Init()

Function: Get

Get list of tracks based on critera in params

Get(params, cb)
Arguments:
  • params (object) – search critera (i.e. {id: 1,user:'jimmy'} )
  • cb (function) – callback function(err,array)

Function: Remove

Remove(id)
Arguments:
  • id (int) – id of the item to be removed
  • Remove(id) – cb - callback function(err,

Function: _kueEventMonitor

_kueEventMonitor()

Function: _processNextEvent

_processNextEvent()

Function: _syncJobs

Synchronize all kue jobs (kJobs) and sails db jobs (sJobs) Called upon initialization of the Job model

if the kJob exists but sJob does not, then create the sJob from kJob. If the sJob exists but not kJob, then delete the sJob

_syncJobs()

Function: sJobs

sJobs()

Constant: async:

Constant: _:

Constant: fetch:

Module: models/JobActive

Description

JobActive holds a count of the number of active jobs. It only contains one record that gets updated when the number of active jobs changes. A timer thread monitors the job queue for active jobs and updates the JobActive record with any changes to the number of active jobs. Subscribers to the record (clients) will get notification. JBClient plugin uses this to determine if a job is active and changes the activity icon of the job queue panel.

JobActive object example:

{
  "active": 0,
  "createdAt": "2017-11-23T00:53:41.864Z",
  "updatedAt": "2018-02-07T07:59:32.471Z",
  "id": 1
}

Function: Init

initialize starts the job active monitor

Init(params, cb)
Arguments:
  • params (object) – value is ignored
  • cb (type) – callback function cb(err)

Function: Get

Get list of tracks based on critera in params

Get(params, cb)
Arguments:
  • params (object) – search critera (i.e. {id: 1,user:'jimmy'} )
  • cb (function) – callback function(err,array)

Function: _activeMonitor

_activeMonitor()

Module: models/Passport

Description

The Passport model handles associating authenticators with users. An authen- ticator can be either local (password) or third-party (provider). A single user can have multiple passports, allowing them to connect and use several third-party strategies in optional conjunction with a password.

Since an application will only need to authenticate a user once per session, it makes sense to encapsulate the data specific to the authentication process in a model of its own. This allows us to keep the session itself as light- weight as possible as the application only needs to serialize and deserialize the user, but not the authentication data, to and from the session.

Function: hashPassword

Hash a passport password.

hashPassword(password, next)
Arguments:
  • password (Object) – password
  • next (function) – next policy

Module: models/Service

Local Navigation

Description

The service module implements the job service frameowrk which are installable modules that can host web services and be a job execution processing for a particular type of job.

Installable services are generally named <servicename>Service.js and reside in the api/services directory. For example: a job service built into this project is serverSearchService.js

api/services/serviceProc.js is the bettr part of the implementation of service

Job services are defined in config/globals.js in the jbrowse/services section.

Example job service object:

{
  "name": "serverSearchService",
  "type": "service",
  "module": "search",
  "createdAt": "2018-02-01T05:38:26.289Z",
  "updatedAt": "2018-02-07T07:59:31.430Z",
  "id": 1
}

Module: models/Track

Description

Track is a model for a list of tracks that are in the trackList.json’s [tracks] section.

Ref: Sails Models and ORM

Track object example:

{
  "dataset": 1,
  "path": "sample_data/json/volvox",
  "lkey": "DNA",
  "trackData": {
    "seqType": "dna",
    "key": "Reference sequence",
    "storeClass": "JBrowse/Store/Sequence/StaticChunked",
    "chunkSize": 20000,
    "urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
    "label": "DNA",
    "type": "SequenceTrack",
    "category": "Reference sequence"
  },
  "createdAt": "2018-02-01T05:38:26.339Z",
  "updatedAt": "2018-02-01T05:38:26.339Z",
  "id": 1
}

Function: Init

Init(params, cb)
Arguments:
  • params (type) – parameters
  • cb (type) – callback function

Function: Get

Get list of tracks based on critera in params

Get(params, cb)
Arguments:
  • params (object) – search critera
  • cb (function) – callback function(err,array)

Function: GetTrackList

Get JBrowse tracklist in JSON format of tracks based on critera in params

GetTrackList(params, cb)
Arguments:
  • params (object) – search critera
  • cb (function) – callback function(err,json)

Function: Remove

Remove(dataset, id)
Arguments:
  • dataset (string) – (eg: “sample_data/json/volvox”)
  • id (int) – id of the item to be removed
  • id) (Remove(dataset,) – cb - callback function(err,

Function: Sync

Sync tracklist.json tracks with Track model (promises version)

Sync(dataset)
Arguments:
  • dataset (string) – ie. (“sample_data/json/volvox”)

Function: cleanTracks

remove all tracks for a given user. if params.session does not exist or user not logged in, returns false.

cleanTracks(params)
Arguments:
  • params (object) – remove all tracks for a given user.

if params.session does not exist or user not logged in, returns false. :return int: returns true if successful, false if nothing done

Constant: Promise:

Constant: fs:

Constant: path:

Constant: deferred:

Constant: deepmerge:

Constant: _:

Module: models/User

Local Navigation

Description

User is the data model for a user.

Example User object:

{
  "username": "juser",
  "email": "juser@jbrowse.org",
  "admin": true,
  "createdAt": "2017-11-29T21:00:56.726Z",
  "updatedAt": "2017-11-29T21:00:56.726Z",
  "id": 2
}

Module: policies/bearerAuth

Local Navigation

Description

bearerAuth Policy

Policy for authorizing API requests. The request is authenticated if the it contains the accessToken in header, body or as a query param. Unlike other strategies bearer doesn’t require a session. Add this policy (in config/policies.js) to controller actions which are not accessed through a session. For example: API request from another client

Module: policies/isAdmin

Description

isAdmin policy provides passage if the user contains the property admin: true.

req.session looks something like this: req.session Session {

cookie: { path: ‘/’,
_expires: null, originalMaxAge: null, httpOnly: true

}, passport: { user: 2 }, authenticated: true, (true if logged in, user: { username: ‘juser’, email: ‘juser@jbrowse.org’ }

}

Function: nonAdminAction

nonAdminAction()

Module: policies/passport

Local Navigation

Description

Passport Middleware

Policy for Sails that initializes Passport.js and as well as its built-in session support.

In a typical web application, the credentials used to authenticate a user will only be transmitted during the login request. If authentication succeeds, a session will be established and maintained via a cookie set in the user’s browser.

Each subsequent request will not contain credentials, but rather the unique cookie that identifies the session. In order to support login sessions, Passport will serialize and deserialize user instances to and from the session.

For more information on the Passport.js middleware, check out: http://passportjs.org/guide/configure/

Module: policies/sessionAuth

Local Navigation

Description

Simple policy to allow any authenticated user. Assumes that your login action in one of your controllers sets req.session.authenticated = true;

Ref: Sails Policies Concepts

Module: services/jbutillib

Description

Support library for jbutil command

Function: doExtScripts

Traverse jbutils-ext.js of submodules (*-jbconnect-hook)

doExtScripts(cb)
Arguments:
  • cb (function) – callback

Function: getMergedConfig

Returned merged jbrowse config. Merged from *-jbconnect-hook config/globals.js, local config/globals.js

getMergedConfig()

Function: mergeConfigJs

mergeConfigJs()

Function: getClientDependencies

getClientDependencies(filter)
Arguments:
  • filter (string) – (ie. “.css” or “.js”)
Return Array:

the aggregated client dependencies from webIncludes.

Function: injectIncludesIntoHtml

Inject css/js into JBrowse index.html

injectIncludesIntoHtml()

Function: setupPlugins

add plugins to trackList.json.

setupPlugins()

Function: removeIncludesFromHtml

remove css/js from JBrowse index.html

removeIncludesFromHtml()

Function: unsetupPlugins

remove plugins from trackList.json.

unsetupPlugins()

Function: safeCopy

copy src to targ, but if targ exists, it will backup the target by appending a number

safeCopy(src, origTarg)
Arguments:
  • src (string) – source
  • origTarg (string) – target
Return string:

final target filename

Function: safeWriteFile

if content is the same as target, do nothing. if content is different than target, write new content to target file.

safeWriteFile(content, origTarg)
Arguments:
  • content (type) – content to write
  • origTarg (type) – target file
Return string:

backuped up filename

Function: install_database

Install the sails database from ./bin.

install_database(overwrite)
Arguments:
  • overwrite (int) – 0, do not overwrite db. 1, overwrite db.

Function: zapRedis

cleanout redis database

zapRedis()

Function: injectPlugins

Inject client-side plugins into the JBrowse plugins dir

Note: as of JBrowse 1.13.0, you must run npm run build after this function, webpack build. called in sails lift /tasks/register .. jb-inject-plugins to function properly

if env E2E_COVERAGE is defined, it will instrument the plugins before installing.

Example: // injects plugins and instruments JBClient plugin and builds webpack in JBrowse ./jbutil –pushplugins –coverage JBClient –buildwebpack

injectPlugins(plugin)
Arguments:
  • plugin (string) – if defined (ie. “JBClient”), it will instrument the given plugin
Return injectPlugins(plugin):
 

(int) count - count of plugins injected.

Function: injectTracklist

injectTracklist()

Function: removePlugins

remove client side plugins from JBrowse index.html

removePlugins()

Function: getPlugins

get the list of plugins. This includes JBConnect plugins as well as plugins of JBConnect hook modules that are loaded.

getPlugins()
Return object:array of plugin objects

Function: addRoute

Add a route

addRoute(params, module, route, target)
Arguments:
  • params (object) – eg. {app: <app-object>,express: <express-object>}
  • module (string) – the module name (ie. "jquery")
  • route (string) – the route (ie. "/jblib/jquery")
  • target (string) – the target (ie "/var/www/html/jbconnect/node_modules/jquery")

Function: addPluginRoute

Add a plugin route

addPluginRoute(params, module, route, target)
Arguments:
  • params (object) – eg. {app: <app-object>,express: <express-object>}
  • module (string) – the module name (ie. "jblast")
  • route (string) – the route (ie. "/jbrowse/plugins/JBlast")
  • target (string) – the target (ie "/var/www/html/jbconnect/node_modules/jblast-jbconnect-hook/plugins/JBlast")

Constant: fs:

Constant: path:

Constant: approot:

Constant: glob:

Constant: sh:

Constant: merge:

Constant: config:

Constant: html2json:

Constant: json2html:

Constant: _:

Constant: async:

Module: services/passport

Local Navigation

Description

Passport Service

A painless Passport.js service for your Sails app that is guaranteed to Rock Your Socks™. It takes all the hassle out of setting up Passport.js by encapsulating all the boring stuff in two functions:

passport.endpoint() passport.callback()

The former sets up an endpoint (/auth/:provider) for redirecting a user to a third-party provider for authentication, while the latter sets up a callback endpoint (/auth/:provider/callback) for receiving the response from the third-party provider. All you have to do is define in the configuration which third-party providers you’d like to support. It’s that easy!

Behind the scenes, the service stores all the data it needs within “Pass- ports”. These contain all the information required to associate a local user with a profile from a third-party provider. This even holds true for the good ol’ password authentication scheme – the Authentication Service takes care of encrypting passwords and storing them in Passports, allowing you to keep your User model free of bloat.

Module: services/postAction

Description

Used by hooks to add a track and announce to subscribers.

Function: addToTrackList

Add track to track list and notify.

addToTrackList(kJob, newTrackJson)
Arguments:
  • kJob (object) – kue job reference
  • newTrackJson (JSON) – new track JSON

Module: services/serviceProc

Description

Support functions for Service model.

Function: init

initialize the job service framework

init(params, cb2)
Arguments:
  • params (type) – parameters
  • cb2 (type) – callback

Function: addService

add a service

addService(service, cb)
Arguments:
  • service (object) – service
  • cb (function) – callback

Function: execute

execute()

Constant: async:

Constant: fs: