NaccessTask

Naccesstask is an instance of taskobject (Git repo, NPM package), used to process a simple Naccess job (Naccess website).

Installation

In your project repository :

npm install naccesstask

Tests

You can either make a test in your proper JS file or use the test file we provide.

Your proper test

In your JS script, import the test file :

var nacTest = require('./node_modules/naccesstask/test/test');

Then you have to start and set up a JM (= Job Manager, more info in the More section). We provide a method that takes care of that :

nacTest.JMsetup();

JMsetup returns an object instance of EventEmitter. It emits "ready" when the JM is ready to receive jobs, and provide the JM object. Then, you can run the naccessTest method :

nacTest.JMsetup().on('ready', function (JMobject) {
	nacTest.naccessTest(pdbFile, management);
});

• pdbFile is the absolute path to your PDB file.
• management is a literal like :

let management = {
	'jobManager' : JMobject // provided by the JMsetup method
}

The naccessTest method :

1. creates a stream (Readable) containing a JSON with your pdbFile content,
2. instantiates a naccesstask (more info on the Naccess website),
3. pipes the stream on the naccesstask, also piped on process.stdout, so you can watch the results in your console.

The test file

The previous test is already implemented in the ./node_modules/naccesstask/test/ directory. To use it :

node ./node_modules/naccesstask/test.js

This script needs some command line options. You can use option -u to display the documentation.

Usage

Creating an instance of naccesstask - not updated !!!!

In your JavaScript module :

var nac = require('naccesstask');
var n = new nac.Naccess (management);

Note that you need a job manager to use naccesstask, like nslurm (GitHub repo, NPM package) adapted to SLURM manager.

Using in a pipeline - not updated !!!!

In your JavaScript module :

readableStream
	.pipe(n)
	.pipe(writableStream);

Setting the naccesstask - not updated !!!!

You can modify the parameters in the ./data/settings.json file :

{
	"coreScript": "./data/run_naccess.sh",
	"automaticClosure": false,
	"settings": {} // proper naccesstask parameters
}

Proper naccesstask parameters must be defined in the "settings" part of the JSON.

More

Job Manager

Coming soon...
A Job Manager (JM) is necessary to run a Task. In our case, we use the nslurm package (GitHub repo, NPM package), adapted for SLURM.