Missing items/pdfs, etc

delenca
Hi,

For reasons that I don't understand I've noticed that I've "lost" items from my Zotero library. This happened using the previous zotero 1.5 beta. I don't know when items + associated pdf were lost from the Zotero database. I can still find them if I search the Zotero storage folder directly but the zotero library itself has no record of them.

What is the recommended procedure to troubleshoot these kinds of problems? It scares me to think that articles I've painstakingly added to Zotero randomly and without warning disappear from my library.

Thanks,
-Alex
  • dstillman
    We've never seen any such problems, but if you don't mind uploading your database to the DB Repair Tool and sending the Upload ID to support@zot....org along with the folder names (e.g., "AH5E2NV9") of items you can't find in your library, we can take a look. If you have backup files with numbers above 1 (e.g., zotero.sqlite.36.bak), upload and include Upload IDs for those as well. You can ignore the download links the tool provides.

    Also, are you using syncing, or are you just working locally?
  • delenca
    Ah, this is a great idea. Will do. I'll send 2 examples.

    Syncing... I have turned off Zotero syncing. Instead, I am doing syncing via "Windows Live Sync".

    Question: is there a way to automatically determine what items in storage have become orphaned? (i.e. no longer anywhere in the library).

    Thanks,
    -Alex
  • dstillman
    So I don't see any references in your database to the two item keys you listed in your e-mail. This includes the log that Zotero 1.5/2.0 keeps of deleted items, which in your case shows eight deleted items between December and February. (I don't know what the date is on those two folders.) While I couldn't say for sure that Zotero didn't somehow wipe out those two items, it's pretty unlikely that it would have and that there'd be no record of them, particularly since you weren't even using syncing in the 1.5 previews/betas.

    I'd actually be much more wary of Windows Live Sync. I'm not familiar with how it works, but you would likely need to be extremely careful if you were keeping zotero.sqlite under its control—as far as I know, most people here who use third-party sync tools use them only for the 'storage' directory. When Firefox is open, Zotero can update its database even when you're not editing Zotero items, so, for example, if you left Firefox running on your other computer, Live Sync, depending on how it handles conflicts, might offer to overwrite your local database with the remote one simply because the remote one had been updated more recently than the changes you made locally—leaving you with a local database that was missing references to the 'storage' items you had created. It's hard to know for sure, but, if that all sounds plausible, that's my best guess as to what happened.

    (As a side note, I'm also a bit curious as to why there are no numbered backups above 1 in your data directory. Any time you upgrade Zotero to a new version that requires an update to user database tables, it should save a new copy...)
  • delenca
    Hi Dan,

    Ok, thanks for looking into it.

    Motivated by your comments, I learned how to look directly in the zotero.sqlite database myself and did some detective work using my daily backups of Zotero.

    Result:
    I think you're right. Although I've been diligent about never running Firefox/Zotero on 2 computers simultaneously something happened on 4/8/09. On that date 10-20 items got dropped from the db. Example:
    Item: 3FMGKDTG
    Created on 3/31/09 (with pdf) exists on zotero.sqlite on 040809 but is gone from the next backup 040909. Also dated 040809 is an extra zotero.sqlite file (let's call it zotero.sqlite-localcomputer) that indicates that Windows Live Sync saw a filename conflict. This extra file still had the item in question. Meaning that the zotero.sqlite 040909 lost quite a number of files.
    I still don't know why the files got lost. I really don't think it was as trivial a reason as what you mention (the remote computer didn't have the references/files, etc and that db got copied over to the local computer when a conflict occurred) - b/c the item that was lost -3FMGKDTG- existed on both local and remote computers. But I can't quite prove that the remote db on 4/8/09 had the reference (my backups on the remote computer don't go back so far), so I can't prove that's not what happened.
    Anyway, I'll have to change my synchronization strategy to ensure file conflicts never, ever occur - of course, this might be a good time to try the built-in zotero syncing again... :-)
    Thanks for your help,
    -Alex
  • mnilson
    Hi there,

    I'm facing a similar issue, but not sure of the cause-- or, more importantly-- the remedy. I'm missing huge chunks of my references and my five folders are completely empty. I'm not a techie, so I'm a lost babe in the woods here- Help! Please! I didn't notice until I was merrily saving new refs and went to see where they were going...ugh, I have this sinking feeling all is lost after four years of compiling.

    Thanks for any and all help.

    Michelle
  • adamsmith
    unlikely that you'd have lost much - if anything.
    First thing I'd do is to back up the current Zotero folder
    http://www.zotero.org/support/zotero_data
    and then restart. You might just have a search term or a tag or so selected...

    Second step would then be to tell us what - if any - syncing you have used: Zotero sync, dropbox, etc.

    The third step would then be to try to recover from an automatic back-up, but I'd hold off on that until we know what's actually going on.

    Finally, and only tangentially related to Zotero I'd encourage you to take the occasion of this (probably unwarranted) scare to think about a back-up solution for all your important files. External harddisks are cheap and easy to set up for automatic syncing. Anyone with important data should make sure to have frequent - at least weekly, preferably daily, back-ups.
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