Needed to re-install Zotero but it won't re-import any PDFs or annotations

NicolaJohnson
Hi, I used Zotero for the last 18 months and backed up literally every day using Zotero>Export to 2 places....1) external hard drive 2) onedrive.

My last backup was last week just before I had to delete my Mac's hard drive because it had got corrupted. I had to reinstall the Mac's hard drive with Apple's help.

I have now reinstalled Zotero. I can import the 'My Library' files ok - but it re-imports them all as a list and has multiple issues:
1) it's lost all my folders
2) it's lost all the PDFs
3) it's lost all my annotated files.

The above 3 things represent weeks of work.

I have been trying for the past 3 hours to problem solve with AI and it keeps tellng me to locate the Zotero.sqlite file. I can see two of these: the first is on my Mac and it's from today. The second is on OneDrive and it's from April 2024 which is when I originally installed it. I can see nothing in between those dates.

Please can you help.
  • dstillman
    edited yesterday at 3:50pm
    An export isn't a backup, and what you'll get back depends on the format you used.

    Did you make a proper backup of your disk (e.g., with Time Machine) before wiping it? You should absolutely never wipe your disk without making a complete backup.
  • dstillman
    edited yesterday at 3:54pm
    You do appear to have been using Zotero syncing, though, so you can just sync from an empty library to pull down all your data. (You should first delete zotero.sqlite in the Zotero data directory and restart Zotero to remove the imported items.)

    But you were at your Zotero Storage quota, so some files won't be available. You'd have to manually redownload those PDFs from the publishers' sites and relocate them via the file-not-found dialog to add them back to your library.
  • NicolaJohnson
    Thanks for your support.

    I made a complete backup of all things using onedrive and my external disk with Apple's support. This included logging into Zotero and exporting one more time (although I also did this two weeks ago and in September).

    My head is about to burst and I do not understand how to "just sync from an empty library to pull down all your data. (You should first delete zotero.sqlite in the Zotero data directory and restart Zotero to remove the imported items.)" or how to " manually redownload those PDFs from the publishers' sites and relocate them via the file-not-found dialog to add them back to your library.". Is there anyone who can talk me through on the phone?
  • dstillman
    edited yesterday at 4:05pm
    This is where all support happens. If there's something you don't understand, you'll need to ask a more specific question.
    I made a complete backup of all things using onedrive and my external disk with Apple's support. This included logging into Zotero and exporting one more time (although I also did this two weeks ago and in September).
    Again, an export isn't a backup, so if that's all you did, you didn't make a backup. A backup would be making a backup of your Zotero data directory or, ideally, just using Time Machine, built into macOS, to back up your entire disk to an external drive. It would be malpractice for Apple not to have you do that before they had you wipe your disk.
    I do not understand how to "just sync from an empty library to pull down all your data. (You should first delete zotero.sqlite in the Zotero data directory and restart Zotero to remove the imported items.)"
    Close Zotero, go to your Zotero data directory, delete zotero.sqlite, restart Zotero, and click the Sync button. All the data you see in your web library on this site will reappear in the app. But some files will be missing, because you were at your storage quota, and they wouldn't have ever been uploaded to our servers.
    how to " manually redownload those PDFs from the publishers' sites and relocate them via the file-not-found dialog to add them back to your library."
    When you try to open a file that's not available (because you were at your storage quota and it wasn't uploaded), Zotero will tell you that the file can't be found. There's a Locate button in that dialog. You'd have to find the PDF online — by going to the publisher page linked from the item — and redownload the PDF manually, and then point Zotero to that file by pressing the Locate button. Zotero will then copy it back into your library files, and you can delete the file from your downloads folder. (Note that if the file isn't a precise match for the version you had earlier, some annotations could be misaligned.)
  • NicolaJohnson
    Thank you. You have already been of great help. AI apparently did not know what you know :)

    I can promise you that Apple did not get me to use Time Machine. That's another story.

    I have pressed sync and it is pulling in lots of my files including the annotations etc.

    Questions:
    1) can I tell which date it got to before my storage quota got 'full up'?

    2) what do I need to do right now to back up what it has synced just now so this does not happen again?

  • NicolaJohnson
    More questions:
    3) how can I tell how full up my storage quota is, eg if I delete some old stuff, can I see whether I am under the quota then?
  • dstillman
    1) It looks like you ran out of space last December, so only a small number of files have been uploaded since then (e.g., as you deleted others).

    2) See Backing Up Your Zotero Data. As it says there, you really just want to use Time Machine.

    3) See your storage settings page. Also see Storage Quota and Local Storage.
  • NicolaJohnson
    Thank you. I did not know any of this previously, I thought exporting was the same thing as back up :(

    Time Machine being installed as we speak.

    More questions please:

    4) Will the system have lost all my annotatations since Dec 2024? Is there no way of uploading them from the hundreds of 'export library' to one drive I did over that time?


    5) How can I tell what size my current library uses so I can select the correct upgrade plan?



  • dstillman
    (Time Machine isn't something you install — it's built into macOS — but you'd need to set it up to back up to an external disk.)

    4) If you made the annotations within Zotero, the annotations would still exist in your database, but you'd need the associated files to view them on the PDF. That's why I explain how to download and reassociate those files.

    5) You can get a rough estimate by checking the size of the 'storage' folder in your data directory. But if you get a plan that's too small, you can also change it to a larger one without paying again — it will just adjust your expiration date forward.
  • NicolaJohnson
    4) Thank you, I have done the first one (Gregson) now.

    I can see in the desktop app that it is in MyLibrary with the PDF now attached.

    However although I have synced the PDF is not on the online version. Is this because my storage is full?

    Also, a search cannot find anything. So eg the Gregson file is in My Library>AAA folder and then multiple groups under that AAA folder eg >3>3.2 But a search of the 'AAA' folder does not locate it. And a search of the '3' folder does not find it. It ONLY finds it if I have already navigated to 3.2, which defeats the purpose of search. Please help with this key issue.

  • dstillman
    Yes, no new files will be uploaded unless you increase your storage, and Zotero will be showing you a warning icon in the toolbar on every sync.

    For other questions (e.g., search), start a new thread and provide screenshots of what you're trying.
  • NicolaJohnson
    I have worked out my last question (needed to show all items).

    Sync has NEVER shown me any warning on the desktop app that my storage was full up (and still doesn't). That is a major cause of the situation I find myself in now. How can I force it to tell me in the future?
  • dstillman
    Click the sync button and provide a screenshot of your toolbar.
  • NicolaJohnson

    https://s3.amazonaws.com/zotero.org/images/forums/u13832981/kzz6syr0cli8n5ybdt6h.png
  • dstillman
    I don't see any file upload attempts from your recent syncs. Can you provide a Debug ID for adding a file and clicking the Sync button?
  • NicolaJohnson
    D1869087879
  • NicolaJohnson
    oh hang on i did it wrong, let me do it again
  • dstillman
    That doesn't show a file being added, and it shows a successful sync with no files to upload. Again, we'd need a Debug ID for 1) adding a file and 2) clicking the Sync button.
  • NicolaJohnson
    ok, I added a file and synced. this is the ID: D1256213130
  • dstillman
    Relocating a missing file currently might not always cause it to be reuploaded — this isn't a common situation, so this isn't something we've extensively tested. You can try going to the Sync → Reset section of the settings and running Reset File Sync History. (Don't use other reset options.)

    I suggested generating a Debug ID for adding a new file — not relocating an existing one — because that should certainly trigger a file upload and show you the icon, which, again, should've appeared on every sync on the computer where you were actually adding the files originally, unless you disabled file syncing.
  • NicolaJohnson
    Ok, have just done it and added a new file and it synced and now has an exclamation mark next to sync. Literally never seen that before. ID: D1252301153
  • dstillman
    Yes, that's what would've been appearing in the toolbar on the other computer (unless you disabled file syncing when you first hit your quota). People often don't notice it, and we're going to show a more prominent warning in a future update.
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