Close Protoype modal window on div refresh

We have a backend process that takes up to 10 seconds to run and when it's complete we change the content in a div to display new info.

The idea is to open a modal window until the new content loads in the div so people know something is happening and don't click on other things. The modal just has an animated processing gif on it.

I've got the modal coming up and the div changing however I can't figure out how to remove the modal without interaction from user. Thought about simulating a click on a button but could not get that to work.