Update index creation before upgrading to Mongo 4.2

Mongo 4.2 change how indexes are built and it appears as though the default behavior is background creation. It's not clear if the client blocks while the index is created. If not, the service could start while the necessary indexes aren't in place which could cause corrupt data and index build fails.

Equivalent of https://github.com/kbase/workspace_deluxe/issues/472