Messed up my PDFs, need to restart. Some guidance requested

Hello, I am having a very frustrating time setting up zotero. I am sure I am doing something dumb and it is my fault but I am generally pretty tech savy, and this is confusing the hell out of me. I have installed a new desktop environment and had to reinstall all my apps. I will lay out some details below of my systems and what i want to achieve.

I have a desktop (linux) that has a large hard disk for storage, I would prefer to keep my PDFs there. I would also like to have a symlink to all of the pdf's in my home folder (~/pdfs/) for easier access. I have a laptop as well (macOS) in which I would like to have the pdfs linked in the same way to my home folder (~/pdfs/) but if possible store the hard copies on a box.com server. If the box.com cloud storage is not feasible then that is fine for now, I just want to be able to go to zotero and find my pdfs.

Right now, my library is all messed up. None of the pdfs link to the correct location and I am not sure where to find them. This is the case for my desktop and laptop. I would like to save my library but remove all the information about where PDF's are located. Is this doable?
  • edited 14 days ago
    The way to have this just work is to use stored files and file syncing with either Zotero Storage or WebDAV. Zotero manages everything for you.

    If you want to use linked files, it's certainly possible to set that up — many people do that — but you're going to be more on your own, and it's fundamentally more error-prone. If you're talking about symlinks, you're well beyond a standard setup, and you'll need to debug this yourself.
  • @dstillman Ok, I can set up a webdav on my home server with nextcloud pretty easily, so I guess I will do that. Do you know how I remove all the PDFs from my library, set up the webdav server, then re-download them?
  • You can search for Attachment item type -- is -- PDF, create a saved search, select all, move to trash, empty the trash. While this will delete the attachments in Zotero, it will only attach stored files that are still properly linked on your disk. You'd need to clean up the others.

    You can then use "Find available PDF" in the context menu though
    1) Do it in small increments so your institution doesn't lock you out
    2) Ideally do it on campus or connected via VPN for file access
    3) You'll still likely not get all PDFs back that way

    Given that, I'd probably try to fix your files first and then switch to webDAV, but it's unclear what you did to unlink them in the first place.
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