Moving from Bibdesk with many, many PDFs

Greetings. I’m moving from Bibdesk to Jabref and hope for a little help. I apologize if these questions seem very basic, but I’m still struggling to shift my mind-set from how BD does things.

  1. Along with the .bib file, I have about 6000 associated PDFs (I know…). They are all in subfolders of the folder holding the .bib file and named according to the Bibtexkey. When I open the .bib file, some of the entires are linked to their PDFs, but most aren’t. What is the best way to mass associate the remaining PDFs with their entries? I’m thrown by the range of options in the Quality menu that refer to file links.

  2. Once I’ve solved point 1, I will change the bibtexkey for all of the articles (JR can’t automatically create keys using the scheme I used in BD). Is it possible to have JR change the name of the associated files to reflect the new key? I understand how to make it name files for NEW entries according to the bibtexkey, but not if I can rename files when the bibtexkey changes.

I really appreciate any help. Also, it’s been a few years since I last looked at Jabref and it’s really impressive how much it’s advanced. Thank you to all involved with it!


thanks for using JabRef!

There are multiple possible solutions:

  1. In the settings you should configure a file directory pattern with the value [bibtexkey] and your file name pattern according similar
    And you should tick the check mark “Bibtex file as main file directory”

A File directory pattern will move your file to subfolders according to the specific pattern (e.g. if you use entrytype, all files would be grouped by type: e,g. article, incollection etc)

Associate pdfs: I think the correct one is here “Automatically set File links”

2.) Regarding the pattern: Have you checked the help page ? You can customize your bibtexkey:

Renaming of Files : Quality -> Cleanup -> Rename PDFs


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Thank you for the quick answer. Worked great. Here are two notes that future users may find useful if they search the group for the same issue. They may be specific to how I had BibDesk set up.

  1. Given the bibtex key “Smith-1990-The-title”, Bibdesk will name the associated pdf “Smith-1990-The title.pdf”. Note the space therein. It will prevent Jabref from matching the file.

  2. Bibdesk sometimes seemed to catch a comma from the title of an article. So, “Dogs, cats and birds” generated the bibtex key “Smith-2012-Dogs”, but the PDF was renamed “Smith-2012-Dogs,.pdf” Again, it won’t match.

On the Mac, it is trivial to fix this using the “Rename files” option, replace " " with “-” and “,” with “”. I assume something similar can be done in other operating systems. After that, Jabref was able to match the files.

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Thanks for the explaination!

You can also set up regex matching instead of exact maching. So you could tweak the regex tto match with optional dash/comma for title etc.