After reading through the documentation it doesn't seem like passing an array to a stored procedure is possible:

Java stored procedure:

package com.test.annotation;

public class UpdateData
{
   public static void NewDataAdded(List newIds, long speciesId) throws SQLException
    {
        Connection conn = null;
        try
        {
                etc….

Derby Stored Procedure….

CREATE PROCEDURE gt.newdataadded(IN newIds ??????, IN speciesid BIGINT)
PARAMETER STYLE JAVA MODIFIES SQL DATA LANGUAGE JAVA EXTERNAL NAME
'com.test.annotation.UpdateData.NewDataAdded';

There doesn't seem to be a datatype to support this.  I tried setting the datatype to BIGINT but when I called the procedure it would throw an error 'ERROR 42X50: No method was found that matched the method call….' 

Is there a way to do this?

- Andrew