Library gone, totally deleted – what happened?
Hello,
Emergency has brought me here. My whole library is completely gone, and it seems Zotero has deleted it by itself. Here is what happened:
After not having used Zotero during Christmas and New Year, I saw an article on Google Scholar that I wanted to save, so I opened up the Zotero application without looking at it and then hit the save button in the Zotero Firefox add-on, as usual. Action failed for some reason, but when I followed the article to its ScienceDirect page, it worked. I went back to the Zotero application and found that this article was the only article in my whole library.
All the bells and whistles went off in my head, but my last hope slowly drained as I followed this guide through: https://www.zotero.org/support/zotero_data#locating_missing_zotero_data and realised that none of the suggested actions would work, because none of the files associated with my library seems to exist anymore. In my Zotero folder at /home/username/Zotero all the files and folders were created only a few minutes ago, in the same instance that I fired up the application or saved the article (except for most of the translators, which were created a few months back). It seems all my old library files just got overwritten. Or somehow completely wiped out on an earlier occasion. Question is, how is this even theoretically possible? Is there some severe bug?
My Zotero is version 6.0.15 and I use Linux Mint 20.2 (Ubuntu 20.04) and I have not performed any disk cleanups or similar, and definitely not fiddled with the Zotero files myself. A couple of weeks ago everything was there, and now it isn't. What could possibly have happened? For various reasons (that mostly have to do with a shortage of storage space) my last backup is over a year old. I never thought the library files could just get deleted by themselves.
Any help much appreciated.
Emergency has brought me here. My whole library is completely gone, and it seems Zotero has deleted it by itself. Here is what happened:
After not having used Zotero during Christmas and New Year, I saw an article on Google Scholar that I wanted to save, so I opened up the Zotero application without looking at it and then hit the save button in the Zotero Firefox add-on, as usual. Action failed for some reason, but when I followed the article to its ScienceDirect page, it worked. I went back to the Zotero application and found that this article was the only article in my whole library.
All the bells and whistles went off in my head, but my last hope slowly drained as I followed this guide through: https://www.zotero.org/support/zotero_data#locating_missing_zotero_data and realised that none of the suggested actions would work, because none of the files associated with my library seems to exist anymore. In my Zotero folder at /home/username/Zotero all the files and folders were created only a few minutes ago, in the same instance that I fired up the application or saved the article (except for most of the translators, which were created a few months back). It seems all my old library files just got overwritten. Or somehow completely wiped out on an earlier occasion. Question is, how is this even theoretically possible? Is there some severe bug?
My Zotero is version 6.0.15 and I use Linux Mint 20.2 (Ubuntu 20.04) and I have not performed any disk cleanups or similar, and definitely not fiddled with the Zotero files myself. A couple of weeks ago everything was there, and now it isn't. What could possibly have happened? For various reasons (that mostly have to do with a shortage of storage space) my last backup is over a year old. I never thought the library files could just get deleted by themselves.
Any help much appreciated.
There's no code in Zotero to delete the database and 'storage' folder other than by unlinking or switching accounts from the Sync pane of the preferences.
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If you've gone through these steps and aren't sure what to do, post to the Zotero Forums with the following info:
• The names, sizes, and dates of all files beginning with “zotero.sqlite” in your current data directory
"zotero.sqlite", 1.4 MB, metadata says it was created in the same moment I launched the Zotero app yesterday night.
"zotero.sqlite-journal", 156 kB, created in the same moment.
"zotero.sqlite.bak" 1.4 MB, created half an hour after the first two files.
• Whether there's a 'storage' folder containing subfolders with dates corresponding to your previous usage of Zotero
There are three subfolders under 'storage', containing the files associated with the one article I saved yesterday. No other subfolders or files.
• Whether your current data directory is in the default location (“Zotero” in your home folder)
Yes, it's the default, /home/username/Zotero. I have also performed an extended file search on my computer, but the old library files are nowhere else to be found either.
• When you last used Zotero on this computer, and what happened on your computer since then
I can't remember exactly when I used it the last time, but it was some time before Christmas. Although it was probably even longer since I last saved an article into the library. Not much has happened on the computer since then. No new apps installed, no old apps uninstalled. A few regular system updates have been applied. If you'd like to look into the details, here's a part of the dpkg log with all the upgrades made on my computer since the beginning of December: https://pastebin.com/ywk72TYm
I would also like to add that I haven't had a Zotero account until today, so all of my usage has been offline and I have never configured any account or sync in the app. And I most definitely haven't touched the files myself. I haven't performed any type of file operations these last weeks, other than moving a few stuff around on my desktop and Downloads folder.
• What you've tried so far
I've confirmed the above. What now?
Whether it existed previously would determine whether to look for a way it has gotten deleted or whether it exists elsewhere.
Also, how did you install Zotero? I believe there are unofficial Flatpack and Snap packages out there, and it'd be good to know if you used either of those.
The details:
I installed Zotero on this computer when I got it about one and a half year ago, using the standard suggested way for Ubuntu Linux distros described here: https://www.zotero.org/support/installation, adding the https://github.com/retorquere/zotero-deb repository in my PPA. I then copied my Zotero folder from my old Windows machine (which should have been the default C:\Users\username\Zotero) to my new Linux Mint machine, pasted it in my home directory replacing the autogenerated Zotero folder there, and also kept a backup copy of it on my desktop. Not sure if I also had to do something else to make it work, but it has worked flawlessly since then anyway. Until what I described happened yesterday night. And now that I check the backup folder that has been lying on my desktop for almost a year and a half, the 'storage' folder in it is gone?!
It's as if some kind of file operation has deleted everything named */Zotero/storage on my computer, plus the corresponding sqlite files. How on earth could this be even theoretically possible? The Zotero app never knew about my backup folder on the desktop, and it all worked a couple of weeks ago. Since then I've had Christmas and New Year, and now suddenly my entire library has ceased to exist, including from the detached backup. Is there some kind of log to find out what has happened?
I really didn't think this was possible. I will have to start over from scratch. Are you sure there isn't some kind of log? Somewhere to see deleted files history? Or even better, somewhere where Zotero or the Firefox add-on logs what gets added to the library (URLs, DOIs, something)?
Zotero create a log during some version upgrades (e.g., Zotero 5 to 6), but it's stored in a 'logs' folder in the data directory. It doesn't sound like you have that either.
When people report this, it's almost invariably due to their running disk-cleaning software to free up disk space and accidentally deleting a large Zotero SQLite database file and the database backups in the same folder. Usually the 'storage' folder is left behind. But if a tool just identified large folders directly within the home directory and/or desktop, you might have accidentally deleted the entire Zotero folder.
If you had previously used Zotero syncing and tried to set up syncing with a different account, Zotero would warn you — quite clearly — that it was going to delete your existing local data and make you confirm before doing so. But that wouldn't be the case if you hadn't previously set up syncing with a different account, and it obviously wouldn't affect some other folder on your computer.
Other than that, the most likely explanation is that you're just misremembering where you had your Zotero data directory and the preference somehow got reset, though in that case you should of course be able to find your data directory somewhere else. If you actually had a full-disk backup, you could check the prefs.js file within the backup of the Zotero profile directory folder and look for a
dataDir
line to see if Zotero was perhaps pointed at another directory, but if you don't have a full-disk backup that wouldn't be possible.Anyway, this clearly isn't something that Zotero did, so I'm afraid we're not going to be able to help further. We always recommend regular, automated backups to an external device (i.e., not stored on your desktop) as well as using Zotero syncing, in case something happens to your local Zotero data.
The only other place that has *some* metadata would be documents in which you cited with the LibreOffice add-on