linking existing pdfs automatically

Hello, I have just moved from Mendeley to Zotero and as I already had the new version of Mendeley, I needed to do the synching and then using the old Mendeley version. I have 6Go of pdfs and 5000 references, so uploading the pdfs was not an aoption.

Now I have a great Zotero database, including my folders and hierarchy (this is just magnificent, I have over 500 folders). But no pdfs linked. I have a pdf folder with an annual filed structure (one subfolder per year) and would like to keep it that way. As far as I understand this means that I need to rather link the pdf files than attach them.
Mendeley ca actually do this automatically : I drag an drop all pdfs from a folder and drop it anywhere in Mendeley, and it will try see if there is already an existing reference and then attach (or link) it. Either by the filename (mine is Author.year.pdf or Author.year.b.pdf) or by extracting information from the pdf.
Zotero seems only to create a new reference when I drop a pdf, not trying to check if this creates a duplicate. It also attaches, where I would like to link.
I have had a look at extensions : Zotfile seem to improve pdf management, but does not seem to propose what I'm looking for.
Does anybody know of other extentions or any tips and trick of how I could achive more easily an (semi) automatic linking of pdf files (while keeping my file structure) ?
Thanks very much in advance, I'm just discovering Zotero and already quite like what I can do.


  • You might have dealt with this by now, but to answer your question, no, there's no easy way to automate this.

    Whereas Mendeley seems fairly content to offer garbage data, show completely wrong data for PDFs, etc., Zotero takes a more precise and deliberate approach to metadata. One result of that is that there's no automatic deduplication of files in Zotero — if you drag a PDF in, Zotero will attempt to recognize the PDF and create an item with the metadata it retrieved at that moment. If you want to use the Duplicate Items feature to merge the items and choose the data to keep, that's under your control, but it's a separate step.
    It also attaches, where I would like to link.
    You can add linked files by holding down a modifier key while dragging or by using "Link to File…"/"Attach Link to File…".
    Zotfile seem to improve pdf management, but does not seem to propose what I'm looking for.
    ZotFile can help you create the end result you're looking for, but it doesn't deal with your current situation. ZotFile helps you use a linked-file workflow, creating linked files in a given directory with a folder and filename structure of your choosing, but it won't import an existing file hierarchy.

    Your main options are to 1) just manually link files to Zotero items as you need them or 2) add all files as linked files, let Zotero recognize them as best as it can, and then merge duplicates for files it recognized and manually drag PDFs to their appropriate parent items for files it didn't. This isn't ideal, obviously, but this is really the only situation where it comes into play — and it's only an issue because Mendeley encrypted their database and doesn't sync file path information separately from files. If either of those weren't the case, we could simply extract existing file path information from the database without your syncing all files to Mendeley servers.
  • Thanks very much for your detailed comment. I think I will have to link the files as and when I work on the references. Otherwise, Windows search is extremely rapid in finding my files.
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