I have been using Flyway with Node.js. Works all right and you write everything (migrations, schema, seeds) in SQL. It does make working with SQL quite straightforward and non-magical.

The thing is of course that with very complex queries you'll end up making quite intricate string building stuff which may not be very pretty. I myself am curious to find out if Prisma can make that part go away.

I'm wondering at the moment whether Knex (solid query builder and migration) and Objection.js would not do this trick. That combo seems to give me json validation which is nice and seemingly both a way to handle entities and graphs in an efficient way.

https://jawj.github.io/zapatos/ (no built-in migration support, though)

Try Knex!