Biomart Team,

We are attempted to use the Java API from Biomart 0.8 candidate 6 by writing a very simple Java client.  We used the MartConfigurator tool to create a registry XML file and to start the server on port 9000.  We successfully executed a query through the webapp GUI and then grabbed the java code snippet from the query results page.  The java code is shown below:

public class QueryTest {

    public static void main(String[] args) throws Exception {

        String xmlPath = "registry/snp.xml";

        //String keyPath = "registry/.snp";

        String keyPath = null;

        MartRegistryFactory factory = new XmlMartRegistryFactory(xmlPath, keyPath);

        Portal portal = new Portal(factory, null);

        Query query = new Query(portal);

        query.setProcessor("TSV");

        query.setClient("biomartclient");

        query.setLimit(10);

        query.setHeader(true);

        Query.Dataset ds = query.addDataset("hsapiens_snp", "hsapiens_snp_config");

        ds.addFilter("chr_name", "1");

        ds.addAttribute("refsnp_id");

        // Print to System.out, but you can pass in any java.io.OutputStream

        query.getResults(System.out);

        System.exit(0);

    }

}

When we execute this java application (with all the dist/lib JAR files on the classpath), we can a NullPointerException as shown from the STDOUT trace below:

2012-06-06 10:25:00,739 INFO  [main:Log.java:164]: Loading resources from org/biomart/configurator/resources/messages

2012-06-06 10:25:00,750 INFO  [main:Log.java:164]: Done loading resources

2012-06-06 10:25:01,249 INFO  [main:Log.java:164]: Loading resources from org/biomart/configurator/resources/messages

2012-06-06 10:25:01,250 INFO  [main:Log.java:164]: Done loading resources

2012-06-06 10:25:01,643 INFO  [main:Log.java:164]: Incoming XML query: <?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

<Query client="biomartclient" processor="TSV" limit="10" header="1"><Dataset name="hsapiens_snp" config="hsapiens_snp_config"><Filter name="chr_name" value="1" /><Attribute name="refsnp_id" /></Dataset></Query>

2012-06-06 10:25:01,660 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 QueryTest.main(QueryTest.java:31)

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 QueryTest.main(QueryTest.java:31)

I stepped through the Biomart code and traced the cause of the NullPointerException we were seeing.  It ends up being a HashMap named “lookup” in the ProcessorRegistry class not being initialized properly.  It’s completely empty and returns a null when ProcessorRegistry.get(“TSV”) is called.  There’s a static method named ProcessorRegistry.install() that does initialize the “lookup” hashmap properly so that the “TSV” key is present and a proper value is returned rather than null.

If I add ProcessRegistry.install(); to the start of my Java main method, the query runs perfectly.  Is there something wrong with our installation/approach?

Thank you,

-Patrick Duffy