Don't use ModelBase.save() inside of transaction

Don't use ModelBase.save() inside of transaction

'with session.begin()' makes some operations in one transaction.
session.begin() returns a transaction instance, then does some operations,
and will commit or rollback automatically before leaving the block.
ModelBase.save() always submit a commit, and that is not expected.
When we get a persistent object from database, we just modify the
object inside of block 'with session.begin()' and sqlalchemy will
update it, don't need method session.add() or ModelBase.save().

Closes-Bug: #1224429
Change-Id: I4af58e98b2783d3945d92e57680d58e7ae356a67