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sbgnml-to-cytoscape

An npm module that converts xml based Systems Biology Graphical Notation(SBGN) files to cytoscape.js graph JSON.

Requirements

sbgnml-to-cytoscape also expects that it will be receiving sbgnml files. You can see some example sbgnml files here, and their corresponding output here.

It would also be helpful to understand the SBGN language spec.

Installation

Instal with npm:

npm install sbgnml-to-cytoscape

Usage

let convert = require('sbgnml-to-cytoscape');

fetch('some-sbgnml-file.xml').then( fileString => {
  let cyGraph = convert( fileString );
} );

For a holistic view on how to use this module, take a look at the example folder.

Errors

Feeding invalid sbgnml text to the converter will result in an error being thrown.

let convert = require('sbgnml-to-cytoscape')

let graph = convert(null);  //  error:  Could not convert the following text to xml: null

Commands

Development

Run the following commands to spin up a test server:

gulp

Tests

Run the tests with:

npm test

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An npm module that converts xml based SBGN files to JSON for Cytoscape.js

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