One way to handle this is to use an HTML redirect. This has the added benefit of freeing memory in use by mod_perl processes that would otherwise be used for each waiting client connection.

An outline of how I've planned to handle it (note: I haven't implemented it yet, but plan to soon):

receive request;
if (request has no job_id) {
  create new job_id;
  start processing external commands (providing job_id);
  return an HTTP redirect with a 10 second pause, such as:
    <meta http-equiv="REFRESH" content="10;URL=http://sample.com/?id=j
+ob_id">
} else {
  if (external commands have completed) {
    return results;
  } else {
    return the HTTP redirect again;
  }
}
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