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
