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This is a daily occurrence at some companies

Surely by the time you're programmatically generating SQL queries you should be using either an ORM or some other kind of SQL expression language embedded in a more expressive language (such as SQLAlchemy or the myriad lisp DSPs for relational databases)?

I am not sure of its origin. But these days you'll find good ORMs that would craft the query for you. My point is, the Mongo API seems to be more of a machine readable API with the $ keys used somewhat in a hacky way.