Way to execute scripts in MongoDB 4.2+ using mongodb java driver

Some of my automated tests use real MongoDB database connection, and prior to version 4.2, they had applied initialization script (which contains some indexes and constraints) using db.eval() command, but with the release of 4.2 eval got removed.

Is there another way to repeatedly setup MongoDB environment for auto tests?

(Using embedded Mongo is a undesirable, because I need replica set for several operations, and embedded replica set startup/initialization takes about thirty seconds for each set of tests.)