Roberto. couple of questions:
1- which release version of biomart v0.8 are you using ? try release candidate 6 in case you are using release candidate 7. 2- Since you installed Biomart locally and accessing Zebra fish from local instance, can you not access the same data from Biomart or Ensembl's live server ? Syed On 5 March 2013 11:20, Roberto Vera <[email protected]> wrote: > Dear Sr. > > I am trying to use the BioMart from java. > > I made a simple test but it doesn't run. > > This is the steps that I followed: > > 1- Download and compile the BioMart > 2- Run the ./scripts/martconfigurator.sh > 3- Add the default source http://www.biomart.org/biomart/martservice > 4- Add an access point for the Danio Rerio genes (Zv9) > 5- Start the server and save the register.xml file. > 6- From the web site all runs well. So I receive the result list. > 7- Copy the java code from the web site and set the register XML previously > saved. > 8- Add all lib to my CLASSPATH > 9- Run the java code: > > ProteinCUDA1:biomartExamples> java -cp $CLASSPATH:dist/biomartExamples.jar > biomartexamples.BiomartExamples /home/roberto/biomart/register.xml > 2013-03-05 12:01:36,248 INFO [main:Log.java:164]: Loading resources from > org/biomart/configurator/resources/messages > 2013-03-05 12:01:36,269 INFO [main:Log.java:164]: Done loading resources > 2013-03-05 12:01:44,062 INFO [main:Log.java:164]: Loading resources from > org/biomart/configurator/resources/messages > 2013-03-05 12:01:44,063 INFO [main:Log.java:164]: Done loading resources > 2013-03-05 12:01:56,783 INFO [main:Log.java:164]: Incoming XML query: <?xml > version="1.0" encoding="UTF-8"?> > <!DOCTYPE Query> > <Query client="biomartclient" processor="TSV" limit="-1" header="1"><Dataset > name="drerio_gene_ensembl" config="drerio_gene_ensembl_config"><Filter > name="with_uniprotsptrembl" value="only" /><Attribute name="entrezgene" > /><Attribute name="uniprot_swissprot" /></Dataset></Query> > > 2013-03-05 12:01:56,800 ERROR [main:Log.java:220]: Error during querying > org.biomart.common.exceptions.ValidationException > at > org.biomart.queryEngine.QueryController.<init>(QueryController.java:113) > at > org.biomart.queryEngine.QueryController.<init>(QueryController.java:118) > at org.biomart.api.Portal.executeQuery(Portal.java:218) > at org.biomart.api.Query.getResults(Query.java:108) > at biomartexamples.BiomartExamples.main(BiomartExamples.java:38) > Caused by: org.biomart.common.exceptions.ValidationException > at > org.biomart.queryEngine.QueryController.initializeProcessor(QueryController.java:256) > at > org.biomart.queryEngine.QueryController.<init>(QueryController.java:86) > ... 4 more > Caused by: java.lang.NullPointerException > at > org.biomart.queryEngine.QueryController.initializeProcessor(QueryController.java:229) > ... 5 more > Exception in thread "main" org.biomart.api.BioMartApiException > at org.biomart.api.Portal.executeQuery(Portal.java:222) > at org.biomart.api.Query.getResults(Query.java:108) > at biomartexamples.BiomartExamples.main(BiomartExamples.java:38) > ProteinCUDA1:biomartExamples> > > > What is wrong on this workflow? > > Thanking in advanced and best regards, > Roberto Vera > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
