Store bitcoin transactions in mysql
You can't use jsonRPC to do this, because jsonRPC commands like gettransaction only work for wallet addresses you have in your wallet.  They don't work for arbitrary addresses.

Sites like blockchain.info basically read the physical blockchain files, not using jsonRPC.  You could do something similar.  I've heard that bitcoinj may do what you want, but I've never used that library.  You also want to check into Bitcore from BitPay.