Hi Manjula,

It is expected to use a 0.8 version registry xml file, not the 0.7 one. You will need to add the COSMIC data mart in 0.8 MartConfigurator, then save the registry file, and this will be the file to be used.

Hope this helps,

Junjun

From: Manjula Dharmawardhana <manjulapra <at> gmail.com>
Date: Thu, 27 Oct 2011 02:24:03 -0400

To: "users <at> biomart.org" <users <at> biomart.org>

Subject: [BioMart Users] Error using Java API

Hi All,

Thank you very much for all the help for the previous questions. Sadly I am stuck again. 

Here is my code (Same code given at Biomart Central)

package cosmicAccess;

import org.biomart.api.factory.*;

import org.biomart.api.Portal;

import org.biomart.api.Query;

/*

 * This is a runnable Java class that executes the query.

 * Please adapt this code as needed, and DON'T forget to change the xmlPath.

 */

public class accessCosmic {

    public static void main(String[] args) throws Exception {

        String xmlPath = "C:/cosmicRegistry.xml"; // Needs to be changed

        MartRegistryFactory factory = new XmlMartRegistryFactory(xmlPath, null);

        Portal portal = new Portal(factory, null);

        Query query = new Query(portal);

        query.setProcessor("TSV");

        query.setClient("biomartclient");

        query.setLimit(-1);

        query.setHeader(true);

        Query.Dataset ds = query.addDataset("COSMIC54", "COSMIC54_config");

        ds.addFilter("sample_source", "primary");

        ds.addFilter("tumour_source", "primary");

        ds.addFilter("site_primary", "cervix");

        ds.addAttribute("id_sample");

        ds.addAttribute("tumour_source");

        ds.addAttribute("id_gene");

        ds.addAttribute("accession_number");

        ds.addAttribute("pubmed_pmid");

        // Print to System.out, but you can pass in any java.io.OutputStream

        query.getResults(System.out);

        System.exit(0);

    }

}

Here is the Registry file in C:/cosmicRegistry.xml

<?xml version="1.0" encoding="UTF-8"?>

<!-- <!DOCTYPE MartRegistry> -->

<MartRegistry>

  <MartURLLocation 

  database="cosp" 

  default="1" 

  displayName="COSMIC (SANGER UK)" 

  host="www.sanger.ac.uk" 

  includeDatasets="" 

  martUser="" 

  name="CosmicMart" 

  path="/genetics/CGP/cosmic/biomart/martservice" 

port="80" 

  redirect="1" 

  serverVirtualSchema="default" 

  visible="1"

  />

 </MartRegistry>

When I run this I get this error.

Exception in thread "main" java.lang.NoClassDefFoundError: net/infonode/docking/View

        at java.lang.ClassLoader.defineClass1(Native Method)

        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)

        at java.lang.ClassLoader.defineClass(ClassLoader.java:616)

        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)

        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)

        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)

        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)

        at java.security.AccessController.doPrivileged(Native Method)

        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)

        at org.biomart.api.factory.XmlMartRegistryFactory.<init>(XmlMartRegistryFactory.java:23)

        at cosmicAccess.accessCosmic.main(accessCosmic.java:21)

        at owlextract.Main.main(Main.java:26)

Caused by: java.lang.ClassNotFoundException: net.infonode.docking.View

        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)

        at java.security.AccessController.doPrivileged(Native Method)

        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)

        ... 15 more

Java Result: 1

BUILD SUCCESSFUL (total time: 2 seconds)

I am running this in windows 7 environment. I have added the biomart0.8.jre as a lib to my Netbeans project. I compiled it using Ant.

I will be grateful if anyone can point me to the error. Thank you very much for all the support and the great tool.

Regards,

Manjula

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