Hi Andy, forgot to mention that you can of course create your own registry file to access your own database using MConfigurator tool included in the distribution
a On Tue, Dec 20, 2011 at 7:46 AM, Arek Kasprzyk <[email protected]>wrote: > Hi Andy, > all the documentation for the Java API is available from > http://www.biomart.org/other/rc6_documentation.pdf > (page 85, section 11.6). However you know this already because you are > using an example from there. You must however make sure that your registry > xml file is in the 0.8 format (you can pick up an example of such file from > the 'registry' directory). Pleae let me know if you have problems finding > it. The registry file in your email is in 0.7 version format so it is not > going to work with your code. > > a > > > > On Tue, Dec 20, 2011 at 4:15 AM, 石偉良 <[email protected]> wrote: > >> Thank you very much for the help for the previous questions. >> >> I want to add the java API to my java program to access MYSQL serve for >> query database. >> >> Can you refer the documentation more detail about the biomart java API? >> >> Regards >> >> Andy >> >> >> Here is my code (Same code given at BioMart 0.8 User Manual release >> candidate 6 May, 2011) >> >> import java.util.List; import org.biomart.api.Portal; import >> org.biomart.api.factory.MartRegistryFactory; import >> org.biomart.api.factory.XmlMartRegistryFactory; import >> org.biomart.api.lite.Attribute; import org.biomart.api.lite.Dataset; import >> org.biomart.api.lite.Filter; import org.biomart.api.lite.Mart; public class >> PortalExample { public static void main(String[] args) { >> MartRegistryFactory factory = new XmlMartRegistryFactory("C:/main.xml"); >> Portal portal = new Portal(factory); List<Mart> marts = >> portal.getMarts(null); System.out.println(String.format("Got %s marts", >> marts.size())); List<Dataset> datasets = >> portal.getDatasets(marts.get(0).getName()); >> System.out.println(String.format("Got %s datasets", datasets.size())); >> List<Filter> filters = portal.getFilters(datasets.get(0).getName(), >> marts.get(0).getConfigName(), null); System.out.println(String.format("Got >> %s filters", filters.size())); List<Attribute> attributes = >> portal.getAttributes(datasets.get(0).getName(), >> marts.get(0).getConfigName(), null); System.out.println(String.format("Got >> %s attributes", attributes.size())); System.exit(0); } } >> >> >> Here is the Registry file in C:/main.xml >> >> >> >> <?xml version="1.0" encoding="UTF-8"?> >> <!DOCTYPE MartRegistry> >> <MartRegistry> >> >> <RegistryDBPointer >> databaseType = "mysql" >> host = "ensembldb.ensembl.org" >> port = "3306" >> database = "central_registry" >> schema = "central_registry" >> user = "anonymous" >> password = "" >> /> >> >> >> </MartRegistry> >> >> >> >> my error message: >> >> Exception in thread "main" java.lang.UnsupportedClassVersionError: >> org/biomart/api/factory/XmlMartRegistryFactory : Unsupported major.minor >> version 51.0 >> at java.lang.ClassLoader.defineClass1(Native Method) >> at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631) >> at java.lang.ClassLoader.defineClass(ClassLoader.java:615) >> 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$1.run(URLClassLoader.java:197) >> at java.security.AccessController.doPrivileged(Native Method) >> at java.net.URLClassLoader.findClass(URLClassLoader.java:190) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:306) >> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:247) >> at test.biomart.PortalExample.main(PortalExample.java:22) >> >> >> >> >
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