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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