The Zotero database 'zotero' appears to have become corrupted.

richfaun@gmail.com
The Zotero database 'zotero' appears to have become corrupted.

Please restart Firefox to attempt an automatic restore from the last backup.

The above message appeared when entering Zotero from the "Z" at the bottom bar of my screen. It keeps repeating itself with the only choices "restart now" or "restart later" - I have rebooted my iMAC twice and restarted Firefox twice. It says the corrupted file in is Zotero. Is there a way for me to identify the file and once I do (if I can) how do I dispose of it?

Thanks for you kind assist.

Richard
  • dstillman
    Use the DB Repair Tool.

    Also, database corruption should absolutely not happen, so there may be a problem with your disk (or you're using some external syncing tool such as Dropbox incorrectly).
  • richfaun@gmail.com
    Is "dropbox" a part of Zotero? When I saw the word - it seemed familiar, but I can't recall in what context.. a hint would be helpful... I think
  • dstillman
    edited July 26, 2010
    (Google?)

    Dropbox is a third-party syncing tool. You're probably not using it unless you know that you are (and you would have had to move your Zotero directory into it).

    Try the DB Repair Tool.
  • richfaun@gmail.com
    I believe I read about it - Once I go into it - is it correct to assume that if it doesn't work, ALL that I have created (which is six month of research) will be gone forever?

    I do very much appreciate your kind assist.
  • adamsmith
    edited July 26, 2010
    I believe I read about it - Once I go into it - is it correct to assume that if it doesn't work, ALL that I have created (which is six month of research) will be gone forever?
    short answer is no - if the db repair tool doesn't work there might be a couple of other things you can do. But in many cases it does, so why don't you try it?
    When you say "Once I go into it" - do you think that the db repair tool is doing something irreversible? Because, of course, it doesn't - you should make a backup copy of your Zotero folder
    (and you should take this occasion to start backing up your work at least weekly, preferably daily. Working on a research project for several months without frequent back-ups is - to be blunt - incredibly stupid. Several hundred GBs of Flash cost 50$ or less and automatic backup software makes this no hassle).
  • richfaun@gmail.com
    I'll accept the crown of stupidity on this one.. and I will also accept your good advice. I have yet to to to www.zotero.com and see what is there.. as I have purchased space and see if there is something there.. that I may use for backup??

    Again, I thank you and those others who have responded to my call for assistance. I am most appreciative.

    BTW - I was unaware that Zotero could be backed up on a flash drive...
  • richfaun@gmail.com
    Hoping not to be a "bore." I just checked via Zotero.com and found ALL my library there, and that's a good thing.

    When I enter Z from my browser window (Z on the bottom right side) it tells me to restart Firefox (now or later) and when I select "later" it repeatedly asks me the same questions. and after selecting "later" three or four times, it ceases to ask the question again.

    It's then that I notice it is "syncing" and the green arrow is rotating - - -

    My questions is, if I wait until it is through "syncing" will my Library eventually sync and rid my computer of the "error of corrupt database" resolve itself?

    More thank for your golden advice
  • dstillman
    We've recommended three times already to use the DB Repair Tool.
  • richfaun@gmail.com
    Dan, thanks again. I am having problems "finding" the DB Repair Tool. I have looked for it by going to www.zotero.com and ran I search - but don't find it.

    Once again, I can reach My Library and all it's contents by signing in and pulling it up. I have tested retrieving different items and am satisfied that it is intact. However, in that mode, it's extremely slow and obviously not operating at it's optimum. If you or anyone might help me locate the DB Repair Tool, I'll work through it. In the meantime, I'm going to try and find the necessary method of "backing up" my library onto a flash or hard drive, your assist is so very appreciated.
  • dstillman
    edited July 27, 2010
    I linked to it in my first response to you (though, for what it's worth, typing "Zotero DB Repair Tool" into Google would also do the trick).

    https://www.zotero.org/utils/dbfix/
  • richfaun@gmail.com
    Thanks Dan - BTW the reason for my problem, which I didn't think of until this morning.. on Sunday here in Maryland, we had a power outage that lasted for over 20 hours and in which my mac was shut down, needless to say abruptly.

    I'm backtracking to your original assist and will post my (hopefully) good results in a bit.

    With appreciation
  • richfaun@gmail.com
    I have gotten to the point where using the tool in Zotero (gear box) and found the zotero.sqlite file - however in the instructions, I am supposed to:

    A) shut down firefox
    B) Find and copy zotero.sqlite
    C) Control-click zotero.sqlite (to create zip file)
    D) Upload Zotero Database

    In this scenario I cannot find zotero.sqlite once I have closed Firefox, nor can I find the "Create Archive of zotero.sqlite from the drop down menu... while I am in the Advanced Tab of the tool box and lastly I cannot find a means of "uploading" the zotero.sqlite file to... where??

    I pledge if I am ever able to execute the DB Repair process, I will keep the forum open to help anyone as lame as I am... to perform the task, as I am hoping will the be the outcome for me today.

    Here is a screen shot of more "hidden" zotero file on my OS 10.5.8 iMac
  • richfaun@gmail.com
    With regrets, my attempt to include the screen shot was unsuccessful - perhaps it's not allowed in the forum..
  • adamsmith
    how to find zotero.sqlite with Firefox closed:
    Follow 1-7 here:
    http://libguides.northwestern.edu/content.php?pid=68444&sid=676064
    after that, just worry about zotero.sqlite, not the rest of the folder.

    I can't tell you how to compress a file on your Mac - but surely you must be able to create a .zip file? If not, it's not strictly necessary, just a lot faster.

    upload here: https://api.zotero.org/utils/dbfix/
    click the browse button, go to your zotero.sqlite.zip and click OK, then click upload and wait.

    Screenshots: upload screenshots to a free image hosting site (imageshack or whatever) and post a link here
  • richfaun@gmail.com
    Screen Shots unintentionally left out.

    http://www5.snapfish.com/snapfish/thumbnailshare/AlbumID=4984625014/from_loggedout=share_main/

    Thanks to you Adam
  • richfaun@gmail.com
    Thanks Adam - but I have an iMac OS 10.5.8

    I have found the zotero.sqlite file - just can't find it in the hidden files of the iMac.

    Regards and Thanks, I'm still in a quandry on the subject.
  • adamsmith
    copy it somewhere you can find it
  • richfaun@gmail.com
    I trust the following describes where I am at in attempting to repair my "corrupted" zotero library.

    In response to the following instruction:

    To use this tool, first locate the zotero.sqlite file in your Zotero data directory, close Firefox, and make a copy of the file. Then upload the copy using the form below.

    While I was able to locate the zotero.sqlite file via the gear box, I closed Firefox as instructed, but could not locate the file in my "MAC 10.5.8) hard drive. I was able to "copy" the zotero.sqlite while "in FIrefox" and also create a zip file.

    I am trying to understand, "if I have copied it from within firefox" will the process still work, as the instructions state "close Firefox and then make the copy/zip file."

    I trust someone will kindly give me an assist. I don't mean to take up people's time - but I have searched for a solution, but to no avail - I believe this is the best place to find a solution.

    Thanks for everyone's patience, it's most appreciated.
  • adamsmith
    edited July 28, 2010
    if you open the Zotero folder from within Firefox and then close Firefox, while keeping the folder open, you're not "within Firefox" anymore. If you use the "Show data directory" button, the directory opens in your OS not in Firefox.

    What you should not do is to try to repair a copy of zotero.sqlite that you made while Firefox is running.

    For a moment, don't try to understand, just follow the instructions for steps 1-6 here:
    http://libguides.northwestern.edu/content.php?pid=68444&sid=676064
    You will now have a) the Zotero folder (with zotero.sqlite) open and b) Firefox closed (step 6).
    You can then copy sqlite, if possible convert it to a .zip file and upload it to the database.

    This is really as good as I am able to explain things. Is there really no way you can have someone a little computer savvy look over your shoulder? The person wouldn't need to know anything about Zotero.
  • richfaun@gmail.com
    Adam, thanks for your good assist.

    I have executed the zip file issue for zotero.sqlite and now have the "new" zotero.sqlite file ready to replace the old one.

    Before doing so, I know I must dump the old file, and also the zotero.sqlite.is.corrupt file and replace it with the new... what about all the other files (damaged 1-11, zotero.sqlite.damaged and all the others?) I'd appreciate your thoughts, or anyone else that may be viewing this.

    Thanks again in advance.
  • richfaun@gmail.com
    Sorry I forgot to send a screen shot of my zotero folder

    http://www5.snapfish.com/snapfish/thumbnailshare/AlbumID=4984625014/a=122875315_122875315/otsc=SHR/otsi=SALBlink/COBRAND_NAME=snapfish/
  • richfaun@gmail.com
    To: Adam and Dan

    Thanks for your help. Everything is running smoothly once more.. your assistance is appreciated and my apology for being so dim on picking up the issues you were helping me with.

    Enjoy your day..
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