There are several ways to allow users to move data into or out of a web app. Assuming users are not running your app on the desktop but rather are creating the data themselves in a common format (like CSV), you can use a file sharing service like Dropbox or Google Drive to meet your needs.
Using Dropbox as an example, the user saves his/her data file to their own Dropbox, then has interactivity with the data via the Dropbox Dropins API (Chooser and Saver) which you previously have built into your web app.
You would also need to create some code that imports external data in the format required by the web app, and then code that exports app data into CSV format back to Dropbox so that the user can pull it again back onto the desktop for use in a spreadsheet app…
Google Drive and some other services likely have similar APIs available. You could even support multiple APIs to give the user more flexibility in case they prefer one over the other.