Within my web application I want to access my database in two different ways. One using Java and another using PHP are there any issues with this? Would it be bad practice to do it this way?
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No, it happens all the time.
However, if you are constantly repeating the same queries and data access on both platforms, you might want to think about creating an API layer to communicate with your database in either Java or PHP and then using that layer to communicate with your DB.