I COMPLETELY LOST MY LIBRARY!!!!!

Hi everybody,
I really desperately need your help. This morning I have opened Zotero 5.0.94-beta.6+aeceb67a0 and I couldn't find any of my data inside!! Why is this happening? Funny is that in my storage folder there are still all my documents but the library on my Zotero app is completely empty.
Could you please help in setting back my library coz I really need it to finish writing my PhD? Thank you
  • Let us know the answers to the questions at the bottom of Locating Missing Zotero Data.
  • Thanks a lot for your quick reply.
    I have already gone through all the discussions here and did most of the steps you were suggesting on other posts but it does not work.
    What happened: Yesterday morning, I opened up my computer and Zotero and all my files inside are gone. Nothing happened before as far as I know (I didn't do anything intentionally)
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    What I did:
    1) Checked the directory ---> it is fine ( data directory is on my /Users//Zotero)

    2) Uninstalled Zotero and Re-installed Zotero (nothing changed) --> nothing changed

    3) Created an account (which I didn't have before) and launch sync --> nothing changed

    4) Updated my Apple system (so now I have the latest version) --> nothing changed

    5) Copied the folder "Zotero" from the data directory to the desktop, renamed the old folder "Zotero-Old" and put the (desktop) older in the data directory again --> nothing changed
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    Now my "Zotero" folder in the data directory /Users//Zotero, the file
    zotero.sqlite is 1MB

    The version of Zotero I am using now is 5.0.94-beta.6+aeceb67a0

    Never used Firefox ( I use Safari and Chrome) and I have a Zotero Standalone version.
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    Last point: Funny is that I still have the storage file in the Zotero fold with all the pdf files I had in my Library!

    I am a bit getting crazy with this problem and I would be very grateful if you could help me! Thanks
  • edited December 21, 2020
    You didn't provide this:
    The names, sizes, and dates of the zotero.sqlite* files in your current data directory
    The * means all the files that start with that name, if that's not clear.
  • But assuming all the zotero.sqlite files are 1 MB, you or something on your system (e.g., some sort of system-cleaning software) deleted your Zotero database, leaving behind just the 'storage' folder containing your attachment files. This isn't something Zotero would've done.

    You've never synced your data, so your only option would be to restore from a backup of your data directory.
  • Copied the folder "Zotero" from the data directory to the desktop, renamed the old folder "Zotero-Old" and put the (desktop) older in the data directory again --> nothing changed
    I'm also not sure what you mean by this. This is specifically about trying a different Zotero data directory that you find on your system. If you only have one, there's nothing to do. Can you explain what you thought this meant and what exactly you did?
  • zotero.sqlite (size 4.9 MB) created yesterday (last modified today)

    zotero.sqlite.bak (size 971KB) created yesterday
  • I have two Zotero folders: one folder stored in /Users/Zotero which was basically empty (I am giving you the info from this folder) and another one stored in /Users/Zotero/Library/Application Support which contains more information and more files including one zotero.sqlite (size 512 byte) created in May 2018.

    What I did:
    I renamed the Zotero folder located in /Users/Zotero "Zotero-Old" and I copied the Zotero folder from /Users/Zotero/Library/Application Support to the /Users/Zotero with the name "Zotero". So my data directory is not linked to the new folder I have exported from /Users/Zotero/Library/Application Support.
  • Anyway, I simply opened my Zotero one morning and the library was gone! So I did all this stuff just to try to solve a problem I didn't cause. Besides, I didn't even know about all these folders and all these files before I had this problem so I seriously doubt I deleted something.
  • edited December 21, 2020
    As the linked page notes, 1 MB (971 KB) and 5 MB (4.9 MB) databases are both empty, so those are just the empty database and backup file that Zotero creates when a database doesn't exist.

    And since you have no other .bak files in that folder, it's further evidence that something on your system deleted all the database files.

    Did you run any utility software on this computer in the last few days? I can't tell you what happened, but it wasn't Zotero that did this — there's simply no way for Zotero to delete your database files like this. If something deletes the Zotero database, your library will disappear.

    In any case, as I say above, your only option here would be to restore your zotero.sqlite database from a backup you made previously.
  • Thank you for your support.
    Basically I lost the work of 3 years... for something I still don't know. Well, it is very much frustrating and definitely shows that I cannot rely on Zotero for my work! I decided to use Zotero to make my life easier not more complicated.

    Anyway, thanks a lot for your support.
  • Again, Zotero absolutely did not do this. There's literally no code in Zotero that could delete your database files and leave 'storage' behind. You didn't answer my question as to whether you ran some utility/system-cleaning software in the last few days, but that's the most likely culprit.

    Regardless of the cause, note too that if you had been using Zotero syncing, you would have been able to restore your library simply by syncing.

    If you're doing any important work on your computer, you want to be making regular, automated backups of your entire computer. Time Machine, built in to macOS, makes this very easy.

    But once more, this isn't something that Zotero did. If Zotero's databases are deleted on disk and you didn't sync and don't have backups, you're going to lose your data, and there's absolutely nothing we can do about that.
  • I do backups every week and I use Time Machine for this. This morning I also reinstalled the old backup on my computer with the hope of having my library back. Nothing changed.

    What really drives me crazy is that I literally didn't do anything before I had this problem: one day I opened Zotero to regularly work and the library is completely gone. Now, as it has happened one time and I lost all (despite I follow all the instructions on this forum and I lost three days trying to solve the problem), I am definitely not sure that something similar could not happen again. So the question of Zotero affidability remains. And as I said, I use Zotero to make my life easier not more complicated as evidently this discussion shows.

    Thank you for your time again and support and please, consider that it is not my fault if I lost my library in which I put three years of work!
  • I do backups every week and I use Time Machine for this. This morning I also reinstalled the old backup on my computer with the hope of having my library back. Nothing changed.
    Wait, you have Time Machine backups? Then you can almost certainly restore your data. You need to go into the Zotero data directory in Time Machine and go back in the history until you see a zotero.sqlite file that's not 1 MB or 5 MB, and restore that.
    I lost three days trying to solve the problem
    If you're having trouble with Zotero, just post here. There's no reason to spend days struggling with something on your own. That's the point of these forums.
    So the question of Zotero affidability remains.
    No, it does not. Please stop suggesting this. Again, this is not something Zotero did, and this has absolutely no bearing on Zotero's reliability. Zotero will show you the data in your database. If the database file is deleted outside of Zotero, you'll see an empty library.

    We wrote the Zotero code. You're going to have to believe us when we tell you that there's no code in Zotero that can delete your database and all automatic backup files and leave the 'storage' folder behind. We can't fix something in code that doesn't exist.
    consider that it is not my fault
    I didn't say it's your fault. I said 1) Zotero couldn't have done this itself and 2) the most likely cause is some sort of software that tries to clean up your system, for example by deleting large files.

    In any case, if you have Time Machine backups, you almost certainly didn't lose your data.
  • Thanks for your reply and support.
    For the record: I have take all my stuff from the PC and put into an external hard-disk and when empty, I have used Time Machine to restore the last backup I did last week. I lost some papers, books and other small items that I have saved in the last week but I am finally happy to say that my Zotero library is back!!! So, for whoever has the same problem, I suggest to use Time-Machine and just upload your last backup and it should work.
  • edited December 21, 2020
    Just to be clear, all you had to do was go into Time Machine and restore the zotero.sqlite file in the Zotero data directory from before this happened. You certainly didn't have to restore an entire backup of your computer, if that's what you're saying you did. It's a 1-minute recovery.
  • edited December 21, 2020
    Again, though, I really wish you would comment clearly on whether you use any sort of utility or system-cleaning software. If there's some popular software that does this, we'd want to know so that we could report it to them.
  • I restored the entire "Zotero" folder from the backup in Time Machine which I believe it is safer and more lucky it works than just the zotero.sqlite file (as I did many things in my "Zotero" folder which was on my PC - as many others have also certainly done trying to fix the problem).
    However, I didn't use any system-cleaning software and I still do not know what happened and why it didn't work one day. (I had some space problems on my hardisk and I couldn't use Safari properly but I didn't touch Zotero or any other programs).
    Anyway, hope this discussion here helps somebody with the same problem.
  • edited December 21, 2020
    I had some space problems on my hardisk and I couldn't use Safari properly but I didn't touch Zotero or any other programs
    Did you do anything to try to clear up disk space? E.g., use the built-in tools macOS provides to clear out large files?

    How large is your zotero.sqlite file?
  • zotero.sqlite file is 140MB
    Yes, I use the built-in tools that MacOs provides you to clear large files
  • OK, so then when you ran low on disk space, you most likely deleted zotero.sqlite and the zotero.sqlite.bak files by accident using that tool. It lists large files out of context, and if you're not careful it's easy to delete an important file by mistake.
  • Yeah, that sounds like a reasonable explanation coz I allowed MacOs to delete large files to free some space and it could be that I accidentally deleted both zotero.sqlite files.

    By the way, I have created an account and I have sync my Library with zotero.org, does it allow me to store the Library online? How can I see which files are stored and which one are not - coz I don't have enough space to save all the library?
  • edited December 21, 2020
    You can see what's synced to your online library by clicking Web Library at the top of this page.

    Data syncing is free and unlimited, so all your library data will be available online if you've synced.

    File syncing is free up to 300 MB, and above that you'd need a storage subscription. You can tell what files are synced by which files you're able to view online. But it doesn't really make sense to think of that in terms of which files are synced — you either have enough space to upload all your files without getting a quota error or you'd want to just turn off file syncing and rely on other backups for the attachment files.
  • So if my data syncing if free and unlimited, why is file syncing up to a certain level -depending on your subscription. So what do I have in my "Web Library" and what does file syncing include more than the it is not already included in the "Web Library"?


  • Data syncing is the item title, authors, journal, etc., along with information about collections, tags, notes. That’s always unlimited.

    File syncing is attachment files like PDFs, images, or Word documents that you’ve attached to the items. That’s limited by your quota. If you don’t want to sync PDFs or other files, you can disable file syncing in the Preferences of the Zotero desktop app.
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