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There are several libraries for creating/verifying TOTP secrets and tokens. It would be trivial to make such a library. QR codes can be created by a few PHP libraries or even by requiring a linux package named "qrencode" and use a shell_exec to generate the image. The secret should be encrypted in the database and decrypted when the user enters the correct password. Or a site secret could be used so the TOTP secret could be used as verification at other times without asking for a password again. Ideally the secret isn't in plaintext.