Zotero Library Gone After Update But Files Still On Computer

I am using Zotero 5.0.81 for Mac. Just decided to open it after like 4 days ago when it was working fine, and my library is blank, as if I had just opened Zotero for the first time.

The data directory is normal (/Users/Name/Zotero), and there is the Zotero folder at the end, with what appears to be a normal Zotero folder that should have my library in it. I know my library is in it somewhere, because looking into the storage folder inside of the Zotero folder, I see a lot of randomly named folders that contain things that look like the papers that were in my library.

Why isn't this working?
  • What are the sizes and dates of the zotero.sqlite* files within /Users/Name/Zotero?
  • They are all created jan 7 2020 (I think this is when I opened it to find my library was gone) and less than 10MB so I assume I am screwed, I had a bibliography in an older word file and just used that to manually recreate the library folder for my current project, not the end of the world but definitely concerning.
  • edited January 16, 2020
    Is there a 'storage' subfolder, and if so do the modification times of its subfolders (with 8-character names) correspond to the dates of your previous usage of Zotero, or do they only correspond to your most recent usage?

    The goal here is to determine if this actually was the Zotero data directory you were using and something happened to your database or if you were previously using a different data directory that might still be elsewhere on your computer.

    Basically, though, see Locating Missing Zotero Data. If you've already rebuilt a library you'll want to be careful changing things around, but that explains the files you could at least look for elsewhere on your computer and places they might be.
  • edited January 16, 2020
    Oh, sorry, you answered the 'storage' question already in your previous message.

    The exact filenames and sizes of the zotero.sqlite* files would still be helpful. How long had you been using Zotero previously?
  • Yeah so in that storage folder there are plenty of weirdly named folders dated all over the place with larger sizes and contents that correspond to my previous work.

    As for the sqlite files, there is:

    zotero.sqlite (not a capital Z if that matters) - Jan 9 2020, 7.6MB

    zotero.sqlite.1.bak - Jan 11 2020, 7.6MB

    zotero.sqlite.bak - Jan 12 2020, 7.6MB

    zotero.sqlite.105.bak - Jan 9 2020, 5.1MB

    (Also, maybe Jan 9 is when I noticed my library was gone as that matches with my original post of 6 days ago, probably doesn't matter that much though)





  • Would you mind uploading the zotero.sqlite.105.bak file to the DB Repair Tool and posting the Upload ID here? That looks like an empty database, but we may be able to tell more by looking at its exact contents. You can ignore the download link the tool provides, which won't fix anything.
  • This is the Upload ID: 5e200e2faaca3
  • Oh and to answer your question, I have been using Zotero for a few years, I see folders in the storage folder dated all around 2019 and 2018
  • edited January 16, 2020
    And just to be sure, you haven't synced or backed up your computer (or the Zotero data directory specifically) during that time? Time Machine, etc.?
  • I have done one Time machine backup in November 2019, after my display failed. I got a new Macbook air as a loaner until I could fix it, but the display spontaneously recovered (I have diagnosed it as a sketchy display cable), so I returned that Macbook air, and since I needed my external SSD to be used with a Windows computer, I deleted my time machine backup and decided to copy the Users folder onto it instead. I figured copying the Users folder wouldn't cause this but maybe it did? Also, since I did the time machine backup in November I was not using this macbook so I couldn't tell you if this occurred after the time machine backup, or after the copying of my Users folder
  • Also, I have never used Zoteros online syncing thing until that night of Jan 9
  • edited January 16, 2020
    You're saying you copied the Users folder from the loaner MBA back to your main computer? Did you do that manually, rather than using Migration Assistant? (I would strongly recommend always using Migration Assistant, which is much safer, when migrating between Macs.)

    I'm a bit confused by the timeline here, since you say that you were using Zotero four days before this happened. But if it might have been earlier, or on a different computer, then yes, I would guess that when you copied the Users folder, the database for some reason wasn't copied, leaving you with a 'storage' directory and no database. That could certainly have happened if you had Zotero open on the source computer at the time of the copy.

    Your zotero.sqlite.105.bak is indeed empty. That file is a backup that Zotero would've made when you updated to Zotero 5.0.78 or later. But the file was created on January 9th with Zotero 5.0.76, which hasn't been the current version since Oct. 31, so it'd be a bit odd if you had actually been using Zotero during that time. I'm guessing that you lost the database in the computer swaps, started up an old version of Zotero (because you hadn't actually opened Zotero on this computer since the copying was done) that created a new database, and then it auto-updated to the current version, which renamed the empty zotero.sqlite to zotero.sqlite.105.bak file.
  • Sorry for being so confusing and thanks so much for helping me out here! The timeline is brutal even for me...

    I didn't copy the User folder from the loaner MBA to my main computer. Before returning the loaner MBA, all I did was save the User folder of that loaner MBA onto my external drive, so no loaner MBA data should be on my current computer. If I look at the loaner MBA User Folder through my external SSD, I can see that there is a Zotero folder containing the zotero sqlite files that I created Dec. 17 2019, as I installed Zotero on that computer and used it for a paper, my current computer's zotero library was never on the loaner MBA.

    Now that you mention it, I must have been using Zotero "just fine 4 days ago" on my loaner computer, but still I would have expected to return to my main computer with my original library intact, so I guess I was using it fine around a month before I noticed this. Now I think that copying the user folders had something to do with it, because I just realized that there is only one User folder on my external hard drive, and it is the one from the loaner MBA, which means I don't have a backup of this main computer when I thought I did... ugh

    By the way, I know time machine would be optimal, I did that, used migration assistant with my brand new loaner MBA, instantly bricked the computer same day I got it because the migration failed somehow, so I actually got a 2nd loaner.

    I think what I ended up doing was I copied my main computer User folder onto the SSD, so any important files I could grab and use on the loaner MBA. This is why I am confused when I don't see the main computer User folder on my external drive, so I most likely chose replace when copying my loaner User folder.

    Still, since my main computer should have been untouched and I see what looks like an intact storage subfolder, I was hoping there would be a way to make it work, but without intact sqlite files.. I don't know!!
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