Corrupted database / Trouble with the DB Repair Tool

maeveish
Beginning this afternoon, I received the following error message: "The Zotero database 'zotero.sqlite' appears to have become corrupted. Your data was restored from the last automatic backup made on 12/12/2013 at 12:03:54. The damaged file was saved in your Zotero directory."

The "Check Database Integrity" tool shows errors in the database, and directs me to the Database Repair Tool. However, my troubleshooting attempts stall here, as I am unable to upload the 'zotero.sqlite' file. I have tried uploading the original file and a zipped file, and for each I get an error saying that the file "does not appear to be an SQLite database." Neither of the files exceed the 100 MB upload limit.

I get the errors in Zotero Standalone and in Firefox alike. I use a Mac with OS X 10.7.5.

Thanks in advance for your help!
  • dstillman
    Sorry, looks like this was broken in some server maintenance the other day. Try again now.
  • maeveish
    Thanks! It worked, and I was able to resolve my database problem.
  • reinhorn
    Server maintenance again today? I'm having the same problem today(also Mac and Firefox) and an endless loop trying to fix with restarts. Thanks for any help.

    BTW: I've also had trouble for the past few days with citations going to the version that sits in Firefox instead of the Standalone that has all my stuff in it. Is there any way to get rid of the one in the browser?

    Thanks again.
  • aurimas
    Idk about the DB repair tool, but...
    BTW: I've also had trouble for the past few days with citations going to the version that sits in Firefox instead of the Standalone that has all my stuff in it. Is there any way to get rid of the one in the browser?
    Start a new thread for further help on this issue, but it looks like you don't have your Zotero for Firefox and Zotero Standalone configured properly. Open Zotero Stadalone Preferences -> Advanced -> Files and Folders, then select Show Data Directory. Now open Zotero in Firefox, go to Preferences -> Advanced -> Files and Folders, click Custom (under Data Directory) and point it to the location that was shown for Zotero Standalone.
  • dstillman
    Server maintenance again today?
    No. What's the problem, exactly? The repair tool works for me.
  • dstillman
    Ah, maybe ZIP uploads aren't working. I'll look into that, but if your database isn't too big you can skip the compressing part and upload it directly.
  • dstillman
    ZIP upload should now be fixed. Thanks for letting us know.
  • reinhorn
    Sorry, I don't understand what the ZIP upload is. My problem is that I can't open my zotero database.

    I get an alert that zotero.squlite appears to have been corrupted and that my data was restored from the last automatic backup.

    I click okay to that but then get an error, that the database is corrupted and that I should attempt an automatic restore from the last backup.

    I click "restart now" and get the alert about zotero.squlite again, at which point I also get the spinning ball and have to "force quit" the program.

    Thanks for anything you can offer on this!
  • dstillman
    This thread is about the DB Repair Tool — that was what the server maintenance was affecting. If your database is corrupted, you need to upload the database to the repair tool.
  • pott
    My zotero file seems to be damaged and I tried to upload my file (first as .zip then as zotero.sqlite) on the DB repair tool site. But both weren't working. Answer of the site is "The file you uploaded is too big to process. The maximum upload size is 100MB." but my files have smaller sizes: 10 MB as .zip and 22 MB as not compressed.

    I can't start Zotero standalone at all. The Firefox plugin opens and I could save a resource but then again the plugin crashed. So I need to repair the sqlite file.
    I have troubles since a long time - Zotero crashed regularly as plugin, but then was working properly with the standalone version - until I've updated to Firefox 25.0.1.

    Thanks for hints and help.
  • dstillman
    pott: Try uploading again now.
  • hannah1987
    Have the same problem, tried with both zip and without and it is not working just get the "The file you uploaded is too big to process. The maximum upload size is 100MB." But my file is only 36 MB.
  • pott
    Tried again and it worked.
    Zotero standalone starts with the repaired file. I hope everything will work now properly again.

    Many thanks

    Petra
  • dstillman
    edited December 19, 2013
    hannah1987: I think your network connection may just be timing out. The error you're getting behind the scenes indicates a partial upload, and we're not seeing that from anyone else. I also can't reproduce any problem with large files, testing files up to 80MB unzipped.

    If this is a laptop, can you try from a different network? Alternatively, if you're able to upload the file to something like Dropbox, you could ask a friend to try the upload from another computer.

    How big is the file zipped? Is that 36MB, or is it smaller?
  • hannah1987
    It's 36MB, i tries the advanced option and fixed it. But when i opened my zotero standalone it broke again. What can i do next?
  • dstillman
    If there's a zotero.sqlite.is.corrupt file in the Zotero data directory, delete it. Otherwise, assuming you have Zotero 4.0.17, it's likely that you didn't replace the existing file correctly if you're still having trouble. Unless you have your data directory on a damaged disk or in Dropbox, etc., there's not really any way for a newly repaired file to be corrupt — it should start up properly and pass the DB integrity check in the Advanced -> Files and Folders pane of the Zotero preferences.
  • RebeccaAdami
    Hi, I am having the exact problem with Zotero as Pott and Maeveish. Zotero standalone does not open. Firefox does not open. tried to download both Firefox and Zotero again, but the same message keeps popping up every time I try to open them. "zotero is corrupted" and I tried like maeveish to exchange the damaged file, but it did not work.
    Please can you help me?
    Thank you so much in advance!
  • adamsmith
    You have tried to exchange the damaged file with what exactly?
  • RebeccaAdami
    With the file I received when sending the damaged file to zotero repair. I can now open Zotero, but the whole reference system I have build up during the past years is gone.
    How can I get it back?
    I am in desperate need of help for my PhD thesis.
    Thank you!
  • adamsmith
    Find and open your Zotero data directory: http://www.zotero.org/support/zotero_data
    In it you will see several files that contain zotero.sqlite in their filename (one should just be called that, others will be something like zotero.sqlite.bak1 etc.)
    Which files do you have and what are their respective sizes?
  • RebeccaAdami
    Hi Adam,
    I really hope you can help me on this, two years of references is not something I like to loose over a day...
    I have these files: profiles.ini
    zotero.sqlite 1MB
    zotero.sqlite kopia 3,4 MB
    zotero.sqlite kopia 2 3,9MB
    zotero.sqlite.bak 1MB
  • adamsmith
    ok, that's really odd, those copies make no sense there - do you have your data directory in a custom location? Dropbox or so?

    First, make a back-up of your Zotero folder:
    http://www.zotero.org/support/zotero_data#backing_up_your_zotero_library

    Then, follow the instructions on restoring from an automated back-up using the zotero.sqlite kopia 2 file (i.e. rename it to zotero.sqlite and replace the existing zotero.sqlite file with it). See if that helps.
    http://www.zotero.org/support/zotero_data#restoring_from_the_last_automatic_backup
  • Paul Simonin
    Greetings!
    Would anyone have any advice regarding how to use the database repair tool for databases larger than 100MB? I have started getting "database corrupted" messages every time I use Zotero. However, my database is currently 238MB with about 5300 entries and so is too large for the repair tool. I have also been unable to compress it a file less than 100MB (the file size limit).

    Any thoughts or tips? I am running Zotero on OSX 10.10.5, and just started to have this problem several months ago.

    (Rather than start a new discussion, I thought it best to post here, but let me know if this should be directed elsewhere)

    Thanks!
  • adamsmith
    @Paul -- try https://www.zotero.org/utils/dbfix/manual -- on Mac that's pretty easy to follow.
  • Paul Simonin
    Adam, thanks for this. I ran these commands yesterday, and so far I have not had any more database crashes, so am hoping the issue is resolved.
    Thanks again!
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