PEPPER-1413 delay the shutdown to give the db more time (#2876)

PEPPER-1413 delay the shutdown to give the db more time to clear connections ahead of starting up replacement instance.

pepper-apis/ddp-common/src/main/java/org/broadinstitute/ddp/appengine/spark/SparkBootUtil.java

@@ -78,7 +78,7 @@ public static void startSparkServer(AppEngineShutdown stopRouteCallback, Config
                 // as a failure
                 if (numShutdownAttempts == 0) {
                     final ScheduledThreadPoolExecutor executor = new ScheduledThreadPoolExecutor(1);
-                    executor.schedule(() -> stopRouteCallback.onAhStop(), 500, TimeUnit.MILLISECONDS);
+                    executor.schedule(() -> stopRouteCallback.onAhStop(), 5, TimeUnit.SECONDS);
                 } else {
                     log.info("Ignoring shutdown attempt {}", numShutdownAttempts);
                 }