I'm not familiar enough with your workflow to say whether Java, JavaScript, or some combination of the two is best here. Definitely review the JavaScript API, https://www.labkey.org/download/clientapi_docs/javascript-api -- building a JavaScript workflow that leverages the public API is very powerful and relatively easy. Of course, the functions you need must be exposed and keep in mind that the user doing the uploading will need all the necessary permissions. (I.e., looks like the user must have folder create permissions, study admin permissions, etc.)

Adam