sync corrupted my library and I lost more than half of my pdfs

ankushaggarwal
I had been using Zotero for more than a year. Finally I committed to it and bought 2 GB of online space so that I could sync my 350+ papers across devices. Then I spent 2 full days nicely organizing them into categories and tagging them.

Then I went ahead and synced the library to my laptop. There were some errors and I had to "reset" the sync. At the end I lost more than half of my papers as Zotero says pdf file not found. I did not backup my library before trying to sync it. And now I am reconsidering my decision of committing to Zotero. I don't know how to fix it, other than manually downloading each paper again.

Any ideas?
  • dstillman
    There were some errors and I had to "reset" the sync.
    What does that mean, exactly?

    For "missing" files (which it's fairly unlikely are actually missing, though it depends exactly what you did) start here: Files Not Syncing.
  • adamsmith
    Then I went ahead and synced the library to my laptop. There were some errors and I had to "reset" the sync.
    The Reset tab specifically warns that the reset options are for "specific, rare situations and should not be used for general troubleshooting". Let's maybe start there. What errors did you get and which reset options specifically did you use?

    As for back-ups -- Zotero would be backed-up by any full back-up of your harddisk. You don't have that, either?
  • ankushaggarwal
    It is a long store, but here it is: before I bought the zotero account space, I used to occasionally copy the library myself from desktop to laptop. So when I tried to sync with the online, it was asking me to merge the entries, which I first clicked through all of them. Then I found that there were some papers not correctly synced. So, I reset in the sync so that everything will be copied from the server.

    Now, on all of my Zotero library copies (desktop, laptop and online), the pdf files are missing. So I don't think the issue is about files not syncing, just that the sync introduced some problems into the library and it is all corrupted now.
  • ankushaggarwal
    I have back-up of Zotero before I spent 2 days of work on organizing my papers. But not after that.
  • dstillman
    The sync did exactly what it was supposed to do. The reset options, as it warns, are for specific, rare situations and not for troubleshooting, and if you don't understand exactly what they do they're dangerous to use.

    You have no synced files online at all under your current account. Doing a Restore to Zotero Server — which you appear to have done — does indeed wipe out all uploaded file connections, and you have to resync the files again afterward. If you don't have those locally, it'd be because you're using a different Zotero data directory than you were before or they weren't created on your current computer and never synced to it.
  • adamsmith
    yeah, so my guess would be that the files may not all have been online when you told Zotero to overwrite the local copy of your library with the copy from the server and thus deleted the PDFs.
    I'm sorry about this, but again, there is a very clear warning attached to the "Reset" options that you disregarded.

    As for restoring this -- do you have a harddisk backup from before that happened? That'd be your best hope. Otherwise I don't have a good idea on how to get them back.
  • adamsmith
    Yeah, sounds like you're probably still best of restoring from your most recent back-up:
    https://www.zotero.org/support/zotero_data#restoring_your_zotero_library_from_a_backup

    You should disable auto-sync while doing all of this.

    You could also experiment with combining restore from your harddisk backup with restoring from the last automated back-up. Moving around and tagging files in Zotero doesn't change their storage location, so you might be able to combine the two.
  • dstillman
    Before you overwrite anything, try these things:

    1) You can look in the 'storage' directory in your Zotero data directory and see what's there.

    2) If you view the debug output for trying to open a missing file, you can see the path where Zotero is look for the file, with a random eight-character directory name. Presumably you won't find that in your active Zotero data directory, but you can try to figure out where else those files are (on another computer, in a backup, etc.).

    Your database itself may not be the issue here — just the 'storage' directory. But it depends exactly what you did to end up in this situation.
  • ankushaggarwal
    No, actually all the files were online. I did sync them to Papership on my ipad and they were all loading very nicely. After that I tried to sync them to my laptop when all this happened.

    Also I did a "reset" only on my laptop, but the files disappeared on my desktop as well. May be I shouldn't have done that. But nevertheless, I think this does point out a weakness of Zotero. And there is no way of conveying this message to the developers. I just thought this discussion forum was to report some bugs in Zotero and finding some ways to fix them.
  • aurimas
    You're speaking with the developers right now (Dan is the lead developer of Zotero). See what Dan has posted above, but basically
    I have back-up of Zotero before I spent 2 days of work on organizing my papers. But not after that.
    If you did back up your "storage" directory, then you should be able to restore the PDFs you had by copying the contents of the old storage directory into the new storage directory. You won't get back any of the new PDFs you may have downloaded during your organizing, of course. Before you experiment with this, make new backups of your Zotero data directory.
  • ankushaggarwal
    So I fixed my library while the automatic syncing was switched off. My library has 306 papers with a storage of approximately 1.2 GB. I have synced multiple times, however still in Home > Settings > Storage it shows my current usage is 0 MB. Somehow my files are not uploading to the server?
  • aurimas
    Make sure your file syncing is enabled https://www.zotero.org/support/preferences/sync

    If it is, see #4 here https://www.zotero.org/support/kb/files_not_syncing

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