The second week included a lot more application of the information gathered in the first week. I also experimented with the pre populated layouts on Cytoscape desktop application.

TODOs

  • Figure out how to add multiple entries in the application menu from a single plugin.
  • Figure out the Cytoscape.js JSON export handler in the cytoscape desktop application.
  • Find out a way to trigger the export from the plugin.
  • Figure out how to populate the layout settings menu with the new layouts from cytoscape.js.

Experiments with code

  • Tried to populate a submenu in the layout menu with multiple entries which will ultimately be used to populate the layouts from the cytoscape.js layouts. To do this i had to register multiple services from a single application.
Properties createNetworkViewTaskFactoryProps = new Properties();
createNetworkViewTaskFactoryProps.setProperty("preferredMenu","Layout.CytoJS Layouts");
createNetworkViewTaskFactoryProps.setProperty("title","Layout 1");
registerService(bc,createNetworkViewTaskFactory,TaskFactory.class, createNetworkViewTaskFactoryProps);

Properties createNetworkViewTaskFactoryProps1 = new Properties();
createNetworkViewTaskFactoryProps1.setProperty("preferredMenu","Layout.CytoJS Layouts");
createNetworkViewTaskFactoryProps1.setProperty("title","Layout 2");
registerService(bc,createNetworkViewTaskFactory,TaskFactory.class, createNetworkViewTaskFactoryProps1);

Learnings

  • The Cytoscape desktop application uses a plugin named JSON which is included as a core plugin. Thanks to my mentor1 for pointing me to the right direction.
  • Upon investigating the code and a little help from Cytoscape app developers’ google group2 i was able to figure out how to use the CytoscapeJS JSON export service in my plugin.

Milestones

Automation of JSON export

Figured out how to trigger the JSON export from the plugin.

  • Create a service reference to the CyNetworkViewWriterFactory which will be passed to the Task factory. 
    String filter = "("+ID+"=cytoscapejsNetworkWriterFactory)";
CyNetworkViewWriterFactory writeCyJs = serviceRegistrar.getService(CyNetworkViewWriterFactory.class, filter);
  • Following code snippet triggers the service to generate the JSON file from the task. 
    OutputStream outputStream = new FileOutputStream("cynetwork.json");
// Open your output stream
CyWriter jsonWriter = this.writeCyJs.createWriter(outputStream, myView);
jsonWriter.run(monitor);
  • The following dependency needs to be added to the pom.xml file.
<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>io-api</artifactId>
    <version>${cytoscape.api.version}</version>
    <scope>provided</scope>
</dependency>

  1. Hasan Balci ↩

  2. Cytoscape app developers’ google group ↩