Removing Direct DB Calls from CLI

[djfinn14]

There are a decent amount (~15) of CLI commands that make direct DB calls or direct calls to operations. Is this something that we want to move away from? If so, there needs to be a discussion about the best way to do it because currently project name is an implicit requirement for every API call and I don't think we want that as a required argument for all of these commands.

[apoorvemohan]

@chemistry-sourabh @naved001 can we close this?