At my previous company we also resorted to using dotdefender after we came under a serious sql injection attack. The product worked very well and we were able to get it up and running very fast. It...

Here is a link to an article on creating an event schedule in mysql, unfortunately I don't use mysql so it is the best I can do for you.
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I don't know mysql very much but if you schedule a job it should not care if a file is open or not.

Schedule a job to run the script at whatever interval you want.