Today, I decided to go and restructure my webapp into a package as recommended by the Flask "Larger Applications" pattern. Thanks to my existing test suite, the move was quick and pain-free. I had to fix imports in one of the tests, but apart from that, the only thing I had to do was splitting up the webapp.py file correctly into webapp/__init__.py, webapp/views.py and webapp/models.py.
I then started playing with implementing the actual functionality for uploading files and creating database entries for the jobs submitted. Took a while to get this right, never done database stuff with Flask before. But again, pretty easy to set up tests for all this. Also, I discovered Flask-Testing, making flask unit testing even more comfy. Just had to fix up the Twill module Flask-Testing comes with to not use the md5 and sha modules, triggering deprecation warnings. Will continue to write the last tests for the job submission form tomorrow, and then see how to deal with making the web app download data from elsewhere for the user.