Migrate to using native SQLAlchemy for all interactions with DB

[visch]

To address #58 (comment)

We want to switch at least how we're calculating the table names in our sql queries. If we can't get this to work with SQLAlchemy relatively easily we'll make a class representing the Database and add seperate getters for sqlalchemy and direct database pulls to help with quotation (ie compiling sql)

Once we fix this we need to remove the xfail from the tests that are currently failing due to this

[visch]

#138 closes this