Fresh install of Jabref not seeing largest database, only 3 smaller to open in Pop! 21.04?


I was running Jabref in a linux laptop that was running Pop! 20.10, but that system got corrupted and I had to wipe it and start fresh with Pop 21.04. I again installed Jabref and tried to “open” one of the xml libraries and Jabref only “saw” three of the smaller libraries, not the largest and main library??

I thought that the system Backup didn’t move the library over to the new system, but it did, I can see it in the file manager, but Jabref isn’t listing it to open??

I want the main library up front in the Jabref window, so I didn’t try to open any of the others. The only operator error that I can think of was that I “restored” two files “.org.jabref.-gui.JabrefMain” and “.org.jabref.JabRefMain” BEFORE I did the first install of Jabref 5.2, but after I “uninstalled” Jabref I couldn’t get the computer search function to find those files.

I then did another fresh install of Jabref 5.2 from the Pop!_shop application, which I guess they use “flatpak” or “flathub” to install it, and I again tried to use the “open” function, but the largest library still isn’t listed???

Anything else to try?? It doesn’t seem like the Backup app backed up applications from the previous system . . . so I can’t just bring that old app back.

I am now recalling that I did have some problems with Jabref when I first installed it in the older Pop! system and possibly ???Chris Siedlerchr??? provided me with some Beta option that did in fact work quite well . . . and that might have been either focal or groovy based Pop! and now the machine is up to “hirsute” . . . would “hirsute” be messing with Jabref 5.2 standard edition or any other thoughts on why the main database isn’t even listed as an option, but it finds the other three???

Hoping for a little help on this issue . . . I found my way to the development version for 5.3 from 6/28 . . . got it installed, but same situation where using the “open library” only shows the smaller three databases, not the main one.

I selected one of those three and it opens . . . . In the directory where all of the libraries are stored the file names all end in.xml . . . but the three libraries that show up in the open dialogue all show .bib as the file name.

I just tried to right-click on the main database and select “open with” . . . a number of applications are showing, but Jabref isn’t one of them??? When I right-click on one of the libraries that Jabref is showing to open, Jabref also isn’t showing as an optional application to open the library??


I think it was an issue with the 5.2 version which got fixed in the meantime in the dev version:
You can get the latest version always here index - powered by h5ai v0.29.0 (


Thanks for the reply, using my own history against me . . . I’ll check that out in a bit when I get back to the laptop.

I did upgrade to the latest development version, but these databases were all created by and are from the previous install of Jabref, so they should be “ready to rock” . . . in . . . Jabref?? Three of the four databases show up and I opened one of them, only one, the main one, isn’t opening?? Doesn’t make “sense” in that the formatting should be from the previous iteration of Jabref, either they all should open or none of them???

All of the databases in the directory have “.xml” extension, but the three showing in open dialogue appear there as “.bib” . . . .

If I do this “import to new” move, will that then make another “file” for the database? So there would be two of them in the directory??? Trying to keep it simple and tidy . . . .


So, I “understand” now, the xml file was the old export from Bookends . . . so it looks like the Back up app didn’t make a copy of the old .bib file for the main database, but it did for the smaller ones, because I see the .bib and .bib.bak files for the other three databases, but not for the large one . . . only the .xml file. : - ((

So, that is part of the pain of having a corrupt system and the fresh install . . . stuff gets lost . . . like all of my sub-groups and such . . . .

Anyway, thanks for the assistance on it . . . I just saw the .xml files for all of the databases and didn’t see that the other ones had .bib files nearby . . . .

Good news . . . I looked through the Backup files and saw that there was a library file in there that didn’t have a file name suffix. So I looked over in the internal files and found that file was there, so I simply “renamed” it with .bib at the end and voila, the Jabref open library dialogue found it and it opened, and all of the sub-groups appear to be intact!!!

Should be back in business for the new months Pubmed search digests . . . .

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