Hi Manjula, Jack Hsu is the BioMart API expert. I cc'ed him on this email in case he wants to comment
a On Thu, Oct 27, 2011 at 2:24 AM, Manjula Dharmawardhana < [email protected]> wrote: > 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.* > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
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