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 <[email protected]<mailto:[email protected]>> Date: Thu, 27 Oct 2011 02:24:03 -0400 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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<http://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 -- [http://www.linkedin.com/img/webpromo/btn_myprofile_160x33.png]<http://lk.linkedin.com/in/manjulapra> This communication (including any attachments) is intended for the use of the intended recipient only and may contain information that is confidential, privileged or legally protected. Any unauthorized use or dissemination of this communication is strictly prohibited. If you have received this communication in error, please immediately notify [email protected]<mailto:[email protected]> by return e-mail message and delete all copies of the original communication. Thank you for your cooperation.
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