Creating folder or label for a collection of PDFs

I’m just migrating from Papers, where I had accumulated ~3000 PDFs organized into >40 collections. I’ve managed to import the PDFs into Paperpile, but I’ve lost all the “collections” metadata. It’s a bit overwhelming to think about reconstructing that info reference-by-reference, using either Folders or Labels. Is there a workaround? For example, I just tried making a folder of PDFs from one of my Papers collections, and attempted to drag them into a “Folder” or “Label” in Paperpile. But no joy, as PP said the PDFs weren’t imported because they were already in library (which, of course, I knew). It’s too bad that Papers couldn’t recognize that by dragging an external PDF into a Folder/`Label, my goal was to add the Folder/Label association even if the ref was already in the Library. Is this a feature that could be added? Or is there another workaround?

In general we could do better when importing from non zotero/mendeley libraries. At the moment, we do not add any collection data which may be in the file because RIS and Bib files can get passed around a lot and are the standard way to transmit metadata. We do not want random imports to create new folders and labels in your library. In theory, we could make it an option to use such data when available, as this could improve imports from less common reference managers. This would require a fair bit of rewiring under the hood, so I do not know when we could get around to it.

Here is what i suggest for your case. It is a bit drastic, but it could be easier than manually organizing everything.

  1. Trash all your papers with PDFs attached. This can be done by clicking the “Has PDF” filter to the right of your list of references, selecting them, and sending them to the trash. You should also empty the trash.
  2. Import the PDFs folder-by-folder as you were planning to. In most cases, we will get the right metadata based on the DOI we find in the PDF file. The upload box lets you specify a folder to import to, so you will be able to create a folder for each set of uploaded PDFs.

Note that this could leave you with a fair amount of papers with bad metadata (particularly book chapters or any scanned document), so it may not be the best idea for your particular library.