I'm using flask-whooshalchemy on sqlite, and mannually imported a lot of data, now whoosh can search none of it. I think it's because whoosh haven't indexed any of the data, right? How could I add whoosh index on those data manually?
Have a look at https://gist.github.com/davb5/21fbffd7a7990f5e066c
I've just written this to solve the same issue - rebuild search indices after a bulk data import.
It won't work out of the box for anyone else (my "lib" import contains all of my third party libraries, and you'll need to specify your Flask-SQLAlchemy models in the if name=="main" block), but it should be enough to get you started.
As stated in the file comments, you should consider deleting your search.db folder (WHOOSH_BASE) as this script doesn't remove deleted data, only re-indexes the current data set.
I've found it to be much quicker importing all of my data using SQLAlchemy core then running this script compared to importing my data via SQLAlchemy ORM with on-the-fly Whoosh index updates (44s vs 48m for my data set).