JabRef
Empty 'backup' wrote over database
JabRef version
Latest development branch build (please note build date below)
Operating system
GNU / Linux
Details on version and operating system
Ubuntu 22.04, Swaywm 17, JabRef 5.8--2022-08-15--f7648e8 via snap
Checked with the latest development build
- [X] I made a backup of my libraries before testing the latest development version.
- [X] I have tested the latest development version and the problem persists
Steps to reproduce the behaviour
1.Updated JR via snap CLI snap refresh
2. Open the JabRef GUI from CLI. Tried to 'parse metadata from pdf'.
3. Killed JabRef process because it froze.
4. Restart JabRef GUI from CLI.
I was greeted with a message that a backup was detected in the snap folder: /home/user/snap/jabref/1886/.local/share/JabRef/5.8--2022-08-15--f7648e8/backups/
I clicked 'restore from backup' without much thought.
My library database (in my home directory) was replaced with the empty 'backup' from the snap folder.
Appendix
The issue was caused by the latest development version.
Please go to the backup folder asap, before you continue to work with a library having the same name. There should be at most 10 backups in /home/user/snap/jabref/1886/.local/share/JabRef/5.8--2022-08-15--f7648e8/backups/. Please check if there are other (older) backup files that are still functional.
Thanks for the quick reply. I have a daily backintime snapshot that I used to recover the library - so nothing was lost. There are 11 backups of the library in the folder but they have already been replaced by my backintime-recovered version. Each backup was about 20s apart and I had been trying to recover the library for 10 mins, so my guess is that all the backups would have been of the empty library.
Perhaps it is a good idea to space out the backups a bit? like five that record every 30s and another five for every minute, 10 mins, hour etc?
Alright. Great that there was no loss of data!
About spreading out the times, yeah I was thinking of this too. Regardless of the timer, the fact that there are empty backup files and JabRef was freezing is a little concerning.
Do you have an idea, why JabRef was freezing? How did you know it was freezing? Is the freeze reproducible? (E.g. JabRef sometimes does some indexing, which can take a long time with huge libraries); Is JabRef running on a local or a remote device? Is the library stored purely locally or does it get synced to remote via dropbox / onedrive / syncthing etc.?
The backup issue is new for me. I don't recall ever needing to nor been prompted to restore from a backup so I can't really say anything about the empty backups.
The freezing happens occasionally and is probably related to JabRef using a lot of memory/resources at times. I saw other bug reports so I didn't add another.
On this occasion I was getting bib info from a pdf and a blank screen popped up and didn't go away after 5 mins. Jabref stopped responding. It's the first its ever happened but if it happens again, I'll file a separate bug.
I am running locally and the library is local only.
how did you "get bib info from a pdf"? You mean you were looking at the annotation tab? Also, I thought you were running JabRef from commandline only? You also use it with ui?
By 'get bib info', I meant the 'Parse metadata from pdf' button. Yes, sorry, I only started jabref from the CLI. I was using the GUI for everything else. That might have been unclear. I'll edit to make it clearer.
By 'get bib info', I meant the 'Parse metadata from pdf' button. Yes, sorry, I only started jabref from the CLI. I was using the GUI for everything else. That might have been unclear. I'll edit to make it clearer.
hmmm so you were using grobid. I think this could be a separate issue. Maybe related to
- a3a886e04fac61733b73ae500dea9af00396a162? @calixtus
- 16de272317ee0f50b4abd5efcd84c56e9621bb76