As we don't want to allow working directly with EntityManager in
the Db level migrations this commit replaces direct access with helper
methods from the parent class.
We don't want to allow working with EntityManager since it is considered
high level service and causes errors when DB structure is not up to date.
[MAILPOET-5416]
All these extracted methods contain DB version check so for existing
sites the migration will be just added as completed to the migrations table.
[MAILPOET-5416]
