SystemTest is not a JUnit test. It is something I rolled myself. It is
a business layer test that just parses this file that gives terse
commands to the system and then calls the appropriate API to drive the
basic functionality of the system. Here is the source below:

package pizza;
import java.io.FileReader;

import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;

public class SystemTest
{

    public static void readFile(String fileName)
   {
       FileReader theFile;
       BufferedReader fileIn = null;
       String oneLine;
       String whichDatabase="oracle";
       System.out.println( "FILE: " + fileName );
       try
       {
           theFile = new FileReader( fileName );
           fileIn  = new BufferedReader( theFile );
           while( ( oneLine = fileIn.readLine( ) ) != null )
           {
               //admin initializes system

    if(oneLine.substring(0,1).equals("a")&&oneLine.substring(1,2).equals("i"))
               {
                   System.out.println("admin initializes system");
                   DAOAdmin daoAdmin = new DAOAdmin("1",whichDatabase);
                   daoAdmin.setupShop();
                   //Initialize toppings table
                   daoAdmin = new DAOAdmin("2",whichDatabase);
                   daoAdmin.addTopping("pepperoni");
                   daoAdmin = new DAOAdmin("2",whichDatabase);
                   daoAdmin.addTopping("onions");
                   daoAdmin = new DAOAdmin("2",whichDatabase);
                   daoAdmin.addTopping("mushroom");
                   daoAdmin = new DAOAdmin("2",whichDatabase);
                   daoAdmin.addTopping("hot peppers");
                   daoAdmin = new DAOAdmin("2",whichDatabase);
                   daoAdmin.addTopping("extra cheese");
                   //Initialize sizes table
                   daoAdmin = new DAOAdmin("4",whichDatabase);
                   daoAdmin.addSize("small");
                   daoAdmin = new DAOAdmin("4",whichDatabase);
                   daoAdmin.addSize("medium");
                   daoAdmin = new DAOAdmin("4",whichDatabase);
                   daoAdmin.addSize("large");
               }
               //student order from room n
               else
if(oneLine.substring(0,1).equals("s")&&oneLine.substring(1,2).equals("o"))
               {
                   int roomno=Integer.parseInt(oneLine.substring(2,3));
                   System.out.println("student order from room "+roomno);
                   ArrayList toppings = new ArrayList();
                   //Pepperoni
                   toppings.add("1");
                   //Mushrooms
                   toppings.add("3");
                   //Order large pizza
                   String size = "3";
                   OrderTO orderTO=new OrderTO(100,1,roomno,new
Pizza(size,toppings),false);
                   DAOOrder daoOrder = new DAOOrder(orderTO,whichDatabase);
                   daoOrder.sendOrder(whichDatabase);
               }
               //status of orders from room n
               else
if(oneLine.substring(0,1).equals("s")&&oneLine.substring(1,2).equals("s"))
               {
                   System.out.println("status of orders from room n");
                   int roomno=Integer.parseInt(oneLine.substring(2,3));
                   DAOOrder daoOrder = new DAOOrder(whichDatabase);
                   if(daoOrder.isOrderDone(Integer.toString(roomno)))
                   {
                       System.out.println("Your order is completed");
                   }
                   else
                   {
                       System.out.println("Your order is not completed");
                   }
               }
               //baker reports pizza done
               else
if(oneLine.substring(0,1).equals("b")&&oneLine.substring(1,2).equals("p")&&
                       oneLine.substring(2,3).equals("d"))
               {
                   System.out.println("baker reports pizza done");
                   DAOBaker daoBaker = new DAOBaker("1",whichDatabase);
                   daoBaker.cookOrders();
               }
               //admin status report for today
               else
if(oneLine.substring(0,1).equals("a")&&oneLine.substring(1,2).equals("s")&&
                       oneLine.substring(2,3).equals("t"))
               {
                   System.out.println("admin status report for today");
               }
               //baker reports day is done
               else
if(oneLine.substring(0,1).equals("b")&&oneLine.substring(1,2).equals("d")&&
                       oneLine.substring(2,3).equals("d"))
               {
                   System.out.println("baker reports day is done");
                   DAOBaker daoBaker = new DAOBaker("2",whichDatabase);
                   daoBaker.endDay();
               }
               //generate admin college report on completed days since
last such report
               else
if(oneLine.substring(0,1).equals("a")&&oneLine.substring(1,2).equals("c")&&
                       oneLine.substring(2,3).equals("r"))
               {
                   System.out.println("generate admin college report on
completed days since last such report");
               }
           }
       }
       catch( IOException e )
       {
           System.out.println( e );
       }
       finally
       {
           // Close the stream
           try
           {
               if(fileIn != null )
                   fileIn.close( );
           }
           catch( IOException e )
           { }
       }
   }
    public static void main( String [ ] args )
    {
        String fileName="c:\\Documents and Settings\\"+
            "Scott Spiegler\\workspace\\PizzaShop\\business layer test.txt";
       readFile( fileName );
    }  
}

Weird, I did what you suggested by creating a new configuration rather
than just updating an existing one. And, it worked! :-0 I used all the
same settings as the one that didn't work, but this new one works and
the old one doesn't.

Any idea why?