"Automatically set file links" (F7): not working any more


Dear all,
I have following situation:
My bib file is in the folder …\Documents\Literature
A pdf to link is for example in …\Documents\Literature\pdf\pdf2017

In the JabRef Preferences -> File -> External file links, I put following Main file directory: …\Documents (one level “above” the bib file, because I have also other pdf files in “Documents” and further subfolders linked to that bib file)

Addtionally I have chosen the option “Autolink only files that match the BibTex key”

I have been using this constellation for years in JabRef and never experienced problems. However, since some months the automatic file link function (F7) doesn’t work any more for me. The search is started and I get the typical little “searching window”:
but the file is never found, even after 30 min or more.

I hoped that this would change with installing JabRef 4.0 but unfortunately it didn’t.

So at the moment I set the file link manually being not very practical.

Do you have any ideas, why have now this problem? Was there a change in the software? How can I solve this problem?

Best regards

PS: If I change the Main file directory to …\Documents\Literature (so where the bib file is) then it works, but then I can’t access any more the files that are in Documents and its other subfolders…

(Christoph) #2

first of all there are different concept of File structures.
The global main file directory is meant to be an absolute one.

In the library properties you can actually define a relative path. So I suggest adding the …\Documents there

Btw, you could also use the cleanup operations to move or rename your files

(Matthias) #3


I can confirm the issue Heiko reports. I analyzed the issue a little further (see below).

  • “Automatically set file links (F7)” does not work with Jabref 4.0x64 on Win10.
  • I store my files in a subfolder \[BibtexFilename] as [BixtexKey][+OptionalExtension].pdf. My setting is “Autolink files with names starting with the Bibtex key”. But these particular settings don’t seem to be the issue.

What is strange and what makes me think it is a bug:

  • (The following also holds for files having the same name as the bibtexfile and being in the same folder.)
  • In the entry tab, File, Icon “Get fulltext”: when I click on it, the “modern hourglass icon” appars. No entry is found.
  • That is, most of the time! However, for the very same entry and files, files are suddenly “somwhat” added when in Preferences I change the option from “Autolink files with names starting with the Bibtex key” to “Regular expression” or back.
  • They are “somewhat” added in a sense, that they now appear in the file field, but are not written to the bibtex file and in the entry table, the entry gets no file icon in the file column of the table.
  • Opening via context menu (General tab -> File -> Context menu “Open”) works. This file information is not stored in the bibtex file. It’s still there after restarting Jabref. Where is this information stored?

I checked:

  • Jabref 4.0-beta – 2017-04-17 works fine; just like the version before.
  • From Jabref 4.0-beta2 – 2017-07-18 the issue occurs.
  • I assume, it’s related to what the ChangeLog describes as “The entry editor got a fresh coat of paint: […] Completely new interface to add or modify linked files.”
  • I couldn’t find any information on whether the intended behavior has changed.

Kind regards and hoping it can be fixed


Hi Christoph,
I also tried to add the absolute folder path for …/Documents (C:\Users\Heiko\Documents) directly in the bib-file options, but after adding it automatic setting of file links still didn’t work.

However I’m not sure how to add a relative path in the bib-file!

Thanks, for the hint to also use a cleanup operation.

Kind regards

(Melanie) #5

Just to add my today’s experience to this post, since I was looking on forum for this issue. I didn’t touch my settings since a while, only upgraded to 4.0 recently.

  • F7 didn’t work also (a folder is specified, Autolink files with names starting with the Bibtex key option)
  • New to me : a correct file is automatically added (without pressing F7 or the search button), with a “suitcase checked” icon. However, this file is not added to bibtex and disappear each time you change to another entry. Morever, the uncorrect file is not replaced, so icon in the entry table couldn’t open file (and there no message saying path is wrong). It just happen nothing.
  • I don’t know if it’s related, but jabref is so slow after couple of minutes, and freeze.
  • Unrelated comment: I’m not sure I like the fact you remove the delete button for file link. Now I press on delete and 90% of time I deleted the file instead of the link…
  • Small glitch for entry editor. File link icon is not the same line than the link so the selection is shifted, making difficult to select a file when you have more than one. I wanted to screenshot, but Jabref has freezed again…
    PS Edit: just discovering than clicking this icon, add permanently to bibtex. And CTL+MAJ+F7 is working fine to remove all wrong links. Just F7 is problematic.
    PPS 2nd edit: precision concerning selection of file. The first file is selectable, however the second is always impossible. A third one is possible.

(dvbowen) #6

Confirmed on Mac Sierra 10.12.6. I have to go do something else, like click on a different entry, then go back to the new one, to find the “File” field has added the pdf file name. Also, why the suitcase icon to confirm that’s the file I want associated with the entry. Unnecessary?

Additional: pressing the “get fulltext” icon on the “file” field correctly follows the URL to the paper and downloads it. But it isn’t selectable for, e.g. deleting, once there’s already a file associated with it. Also, if there’s no file initially associated, and the paper is downloaded, the entry is selectable, but selecting “delete from disk” causes JabRef to hang.

(James Harland) #7

Confirmed on:

JabRef 4.0
Linux 4.4.0-72-generic amd64
Java 1.8.0_144

Neither F7 nor the corresponding button create the file link(s) they used to before updating.

(Christoph) #8


regarding slowliness and freezings, I would like you to test the current dev version from here:

Regarding the file section: You can right click on every file (although it is not getting that “blue selected” focus/highlighting.
Autolink still seems to be an issue.


(Christoph) #9

@melTr @harlandski @s-p-i-f-f @heiko
for those of you having problems witht he Automatic setting of file links (including the “automagic” in the entry editor), could you please test this version and report back if it works?

I reworked the code so that it directly works with the new file list editor and fixed a problem with the similarity detection.
Thanks in advance for testing.


(Matthias) #10

Hi Christoph,

thanks for you effort! Unfortunately, it hasn’t fixed the issue on my side.

  • Alt+F7: No notable action. No change of status bar message.
  • “Get fulltext” icon: “Status: Full text document download failed”.

A possible “deeper” issue in this regard:

  • I reported above that in the “General:File”-field in Jabref client, “orphan” file links would suddenly appears. Those aren’t written to the BibTeX file and don’t allow any acation.
  • Stranger though is that I have them appear in unrelated keys. E.g., when creating the article entry MyArticle it suddenly shows in the client an “orphan” file link to \TestLibrary\Testentry_subfolder.pdf which belongs to my original BibTeX key Testentry. Again, none of that is written to the BibTeX file.

Please let me know if you need further information or want me to test anything else in particular

P.S.: While testing the above, Jabref entry editor tabs would freeze, i.e., all tabs are plain white. Changing the to another open libary, the entry editor there works. Going back to the original library, the issure persists. Jabref festart required.

(Christoph) #11

I tested my changes on Windows. F7 triggered correctly the file search and when a file is found (which is not yet linked), it is added.
This also works in the entry editor itself when you have Automatically set file links activated.
This kicks in when you open the General tab for the entry.

So maybe you already have a linked file. To test this, I would suggest removing all linked files from the entry (only removing the link, not deleting the file itself)

The search icon in the entry editor is a different function, it corresponds to the get full text action in the menu F8. It does an online search for the full text, not local.

(Christoph) #12

Regarding the freeze, could you check the log messages or start JabRef from command line?
java -jar JabRef.jar when freezes happen?

(dvbowen) #13

I tried " java -jar JabRef-4.1-dev–snapshot–2017-10-29–autofilelink–19481127d.jar" from the command line. here are some results:

  1. With jdk 1.8.0_151 installed: JabRef finds the pdf file automatically (though there’s still the annoying ‘suitcase’ icon that still needs pressing for some reason); using F7 doesn’t seem necessary. I’ll see if this continues to work.

  2. With jdk 1.8.0_121 installed (before I upgraded): This version brought back the old freezing problem which I thought I’d cured by going back to java 1.8, namely that when I highlight text in the “{} biblatex source” field to edit, JabRef hangs. The final output says:

[AWT-EventQueue-0] WARN org.jabref.logic.l10n.Localization - Warning: could not get message translation for “ID-based_entry_generator” for locale en

So didn’t get as far as testing the use of F7.

[Mac Sierra 10.12.6]

(Christoph) #14

@dvbowen Thank you very much for your feedback.
I did not change the suitcase behavior.

The JabRef version is the actual dev version + the changes regarding the auto file link behavior. As soon the PR gets merged it will be in the latest master as well.


jdk 1.8.152 is the latest java 8 version. Just don’t update to Java 9 as JabRef does not yet work with it.

Best Regards

(dvbowen) #15

Understood. Thanks for all your hard work… :grinning:

(Dellu) #16

It is now working on the mac as well. But, is 100x slower than Jabref 3.8.
Jabref 3.8 took a few seconds to put the links; this one takes up to hours for a bigger library.
This seems a completely new code; or sth like that.

(Christoph) #17

Are you sure you are not confusing this with Look up full text documents? (Alt + F7)?

(Dellu) #18

The latest build actually has a bug. It is autolinking all the files in the folder into each of the reference entries. That is why it is so slow.

Here is what happened I clicked Autolink files on one of my references.

  author     = {Thoms, Gary},
  title      = {‘Verb floating’ and VP-ellipsis: Towards a movement account of ellipsis licensing},
  journal    = {Linguistic Variation Yearbook},
  year       = {2010},
  volume     = {10},
  pages      = {252–297},
  date-added = {27-11-2017},
  doi        = {10.1075/livy.10.07tho},
  file       = {:/Users/dwo000/Documents/@Ling/@mBuzz/Dehaene2006 - Core Knowledge of Geometry in an Amazonian Indigene Group.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Kim2017 - An Experimental Study of Phonological Variation and Variation in Scope Judgments in Korean.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Erlewine2016a - Focus association by movement _ Evidence from Tanglewood.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Messick2016 - Deep properties of a surface anaphor _ on the contextual restriction of sluicing sites.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Lasersohn2006 - Event-based semantics.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Hovav2012 - Denominal and Deadjectival Verbs are Compatible.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Kratzer1999 - Beyond ‘Ouch’ and ‘Oops’. How descriptive and expressive meaning interact.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Kilbourn-Ceron2017 - Boundary phenomena and variability in Japanese high vowel devoicing.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Homer2010 - Actuality entailments in French_ A case of aspectual coercion.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Goldberg2015 - A-adjectives, statistical preemption, and the evidence_ Reply to Yang (2015).pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Grillo2015 - Event Kinds and the Pseudo-Relative.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Martin2014 - Causation in Grammatical Structures.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Muller2017 - A Local Reformulation of the Williams Cycle.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Geurts2001 - Donkey Business.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Li2014a - Generalized focus intervention.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Watumull2013 - Biolinguistics and Platonism_ Contradictory or Consilient_.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Svenonius2004 - How Phonological is Object Shift_.pdf:PDF;:/Users/dwo000/Documents/@Ling/@mBuzz/Villiers2000 - From Evidence to Belief. 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  keywords   = {a; a -; copy theory of movement; ellipsis licensing; sluicing; vp-ellipsis},

(Tobias Diez) #19

Can you please open a bug report at github including the exact configuration of your system (especially, with the file-related settings in the “database properties”). Thanks.

(Brian Michael Napoletano) #20

Hello, I have a similar directory setup for my reference library, and have been encountering the same trouble with JabRef 4.2 on Debian Linux. I tried the development snapshot, JabRef-4.2-dev–snapshot–2018-01-03–master–193bbbca6.jar, and it found the PDF automatically when I opened my database, but then lagged when I attempted to set the file link (or possibly froze; my reference library contains just under 8,000 entries, so it may be that the program was reviewing the file links for each). Thank you for your help with this, and for working so hard to make JabRef such an excellent bibliography manager.