Hi, Thank you very much for your answer.
I am using: Opensuse Linux 12.2 with kernel 3.4.28-2.20-desktop Oracle Java version "1.7.0_17" Apache Ant(TM) version 1.8.2 BioMart release 0.8 candidate 6 I tried from a local Biomart and from the live server and I have the same exception. I am thinking that the error should be a problem with the libraries included into the BioMart's dist folder and my Java version. If this is true it can be solved if the BioMart use Maven instead of Ant. Are you planning to move BioMart from Ant to Maven? Maven is a better option for the distribution of java software. Regards, Roberto On Thursday, March 07, 2013 06:51:10 PM you wrote: > 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(QueryControlle > > r.java:256)> > > at > > > > org.biomart.queryEngine.QueryController.<init>(QueryController.java:86) > > > > ... 4 more > > > > Caused by: java.lang.NullPointerException > > > > at > > > > org.biomart.queryEngine.QueryController.initializeProcessor(QueryControlle > > r.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
