void processTask(ETask task, ObjectMessage msg, EntityManager em) {
EMethod method;
EModel model;
Collection<EBounds> bounds;
TaskMessage tm;
System.out.println("Processing task [id=" + String.valueOf(task.getId()) + "]...");
method = task.getMethod();
model = task.getModel();
bounds = getBoundsForModel(model, em);
try {
tm = (TaskMessage) msg.getObject();
if (method.getIdent().equals(EMethod.fba)) {
FbaMethod.run(task, model, bounds);
} else if (method.getIdent().equals(EMethod.fva)) {
FvaMethod.run(task, model, bounds, (MultipleReactionsTaskMessage) tm);
} else if (method.getIdent().equals(EMethod.rscan)) {
RscanMethod.run(task, model, bounds, (MultipleReactionsTaskMessage) tm);
} else if (method.getIdent().equals(EMethod.kgene)) {
KgeneMethod.run(task, model, bounds);
}
msg.acknowledge();
} catch (AmkfbaException e) {
AcornLogger.logError("AmkfbaException: " + e.getMessage());
markAsBroken(task, em);
} catch (JMSException e) {
e.printStackTrace(System.err);
throw new Error("JMSException, aborting...");
}
}
void markAsBroken(ETask task, EntityManager em) {
EntityTransaction et = em.getTransaction();
et.begin();
task.setStatus(ETask.statusSysError);
et.commit();
}
public void run() throws Exception {
EntityManagerFactory emf = PersistenceManager.getInstance().getEntityManagerFactory();
EntityManager em = emf.createEntityManager();
setupMessageListener();
ETask task;
try {
while (true) {
ObjectMessage msg;
TaskMessage tm;
Message mm;
System.out.println("Waiting for message...");
mm = receiver.receive();
System.out.println("Message received");
if (mm instanceof ObjectMessage) {
msg = (ObjectMessage) mm;
tm = (TaskMessage) msg.getObject();
try {
task =
(ETask)
em.createNamedQuery("ETask.findById")
.setParameter("id", tm.getTaskId())
.setHint("toplink.refresh", true)
.getSingleResult();
if (!task.getStatus().equals(ETask.statusSysError)) {
processTask(task, msg, em);
} else {
System.out.println("Task marked as broken, omitting.");
}
} catch (NoResultException e) {
System.out.println("Task has been deleted");
}
}
mm.acknowledge();
}
} finally {
closeReceiver();
PersistenceManager.getInstance().closeEntityManagerFactory();
}
}