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Update raw SQL queries to use SQLAlchemy #1281

@dadmobile

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@dadmobile

This has bitten us now that we are trying to support both SQLite and Postgres. For example, we have a table called user which is a reserved keyword in Postgres and if you don't handle that properly it acts very surprisingly!

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    apiChanges to be made to the transformerlab-api repochoreRoutine maintenance or internal task that doesn't add features or fix bugs—e.g., refactoring code

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