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Can some tell me if I'm wrong, but it doesn't look like I can create a variable to store a query result into it where I leveraged EE's native {exp:query} functionality?

I want to use PHP native json_encode functionality to output the contents of a complex query(some of the data I'm querying cannot be displayed using the Channel entries tag) to JSON. So either I have to create a pure PHP file outside of EE or "allow php" in my EE template.

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Create a plugin - don't do this in the template. Then you can do whatever you like in pure PHP (with access to all of EE's helper functions, libraries, etc), create a variables array, and then return it for use as template tags.

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