This sounds like a horribly bloated stack. Might it be possible to compile the Python part into a lib that the Java app can access? And then package the Java app as a distributable, maybe with a JRE bundled?
If your audience is developers (or similarly tech-savvy), that's probably enough to package it up as `brew install my_pdf_parser` for Macs (and Chocolatey for Windows) and have them take care of the Python deps.
If you're going for a mainstream desktop app though, that's a bit harder, but there's stuff like https://pyinstaller.org/en/stable/ (edit: as you already mentioned in another comment, lol)