Yes, my concern was that QiiTa-pet have the three layers: presentation (web), logic and storage (SQL queries). I am working in a refactor that unifies the three repos into one, but I'll keep the three layer separation (QiiTa-pet, QiiTa-ware and QiiTa-db) within that repository.

QiiTa-pet will consist only on web front-end. Anything that it needs, will be a python function call to QiiTa-ware.
QiiTa-ware will contain all the logic. It will fire IPython parallel jobs when necessary and it will make any necessary computation. If it needs some data, it will ask QiiTa-db for it.
QiiTa-db will manage all the storage. It will provide different back-ends: one of them will be all the DB development that we are currently doing. Another one will be to just serve the data from files. Since QiiTa will the recommended way of running QIIME 2.0.0 I think that it makes sense to not to force the user to install a DB backend, only for those users that are managing huge amount of data, as we are doing.

I'm planning to get the project structure ready for next week meeting. Feel free to ping me with any question!