Dear Junjun, Thank you very much. But I am sorry I am a bit confused. Can you please be a bit clearer as to from where should I get the MartConfigurator and what to add. Thank you Regards, Manjula
On Tue, Nov 1, 2011 at 11:55 PM, Junjun Zhang <[email protected]>wrote: > 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]> > Date: Thu, 27 Oct 2011 02:24:03 -0400 > To: "[email protected]" <[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" > 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://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] by return e-mail message and delete all copies of > the original communication. Thank you for your cooperation.* > > -- * <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] by return e-mail message and delete all copies of the original communication. Thank you for your cooperation.*
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