You'll get this during Mission 2 (Follow the Ink). I believe this is story related/unmissable.
The first key is in the safe on the third floor of Shan Yun's mansion. To open the safe, you'll need to have collected an audiograph recording of him singing to activate the safe lock. Next to the safe, there is a desk with a journal and an audiograph player next to it. The journal will tell you which audiograph card is needed. Use the audiograph player to open the safe and collect the first key along with the other contents of the safe.
The second key is hidden in Ivan Jacobi's apartment. You'll need to deal with him to get his apartment key. Once inside, head into his office and it's located on his desk. There is also a painting behind his desk you can interact with to reveal a safe.