"Zotero experienced an error updating your document. A bibliography in this document is corrupted"

stehle
Hi everybody,

I encountered a problem trying to refresh the references in my word doc: I cannot refresh, there pops up the error message "Zotero experienced an error updating your document. A bibliography in this document is corrupted".
After following instructions from the forum, the style refreshes, but in some cases (the doc is massive) not the references itself refresh. For example, insertions that have already been deleted and/ or transformed in the library keep showing up in the ref list.


Thanks for your help!
  • adamsmith
    Deleting references from Zotero won't delete them from your document.
    If changes in Zotero aren't reflected in references, the most like cause is that the citation is no longer connected to your database, but instead relies on citation data embedded in the document. That could have happened, e.g., when deleting a citation or even a duplicate of an item in Zotero (or, on a larger scale, when using import/export to transfer items)
  • nedasalahshour
    Hi
    I am having the same problem. I want to enter a citation but I get the following error. (please note I may have deleted references from my standalone zotero). What can and should I do now?
  • adamsmith
    sorry, "the following error"? Which error are you referring to?
  • nedasalahshour
    Hi again

    Sorry about that. There error is " Zotero experienced an error updating your document. A bibliography in this document is corrupted". I have a very long (77 000) words thesis and I want to add/edit citations and this is the error which pops up everytime and prevents me from doing so
  • adamsmith
    Have you tried just deleting the bibliography and reinserting it?
  • nedasalahshour
    Well i dont know which one bibliography it is? How can I know which bibliography /citation is corruputed?
  • nedasalahshour
    I have hundreds of citations and bibliographies in my thesis.
  • adamsmith
    I think you misunderstand what a bibliography is. That'd be the full list of references at the end, not an individual one.
  • nedasalahshour
    basically where ever on the document I click insert citation I get this error
  • nedasalahshour
    ok. so I meant hundreds of in-text citations and 1 bibliography list. The point is where ever on the document i click in order to insert or edit a citation I get this error.
  • adamsmith
    I understand that, but you haven't answered my question. Have you tried deleting the bibliography? (to later reinsert it).
  • nedasalahshour
    Ok now this makes sense. Let me try this and let you know.
  • nedasalahshour
    Ok. Thanks heaps for this. I was really getting worried. So now I am not getting that error. I deleted the bibliography and then re-inserted it. And now I tried to put in a citation and it states: "You have modified this citation since Zotero generated it. Do you want to keep your modifications and prevent future updates?

    I am not quite sure whether I should click yes or no? This has come up many times before and I have (ignorantly) just clicked yes, but could you please tell me what this means exactly?
  • DWL-SDCA
    edited May 18, 2016
    It probably means that you edited one or more of the citations after you inserted it. The edit was done not by using the Zotero edit citation command but using the word processor. It is best to edit citations via Zotero.

    Be sure to continue to save each iteration of your document so that you can go back to an earlier one if things go haywire.

    If the absolute worst case happens and you must reinsert all of your references, it won't be as bad as you think. When writing my doctoral thesis MS Word and EndNote melted down. I was about to complete my final draft. Then my Windows computer was stolen. Someone loaned me their Mac. It had OpenOffice instead of Word. Folks at the university computer center took my EndNote database and converted it into a format that worked with Zotero. (I had never heard of Zotero;this was back in the early days Zotero 1.) Within a day I was up and running. Replacing all citations in my 400 page document required only a few hours. I was using Vancouver style. An author date style might take a bit more time. There was actually a benefit to this exercise. I found a few typos and fixed couple of places where my prose was muddy. I, because of the detailed line-by-line reading found a place where (although what I wrote made sense) I had omitted a key tie-in and through a cut and paste error suggested a conclusion that I knew to be wrong. While I certainly can't recommend that to anyone who didn't need it; the result was a much better thesis.
  • nedasalahshour
    Thanks for sharing your story. It is good to know that is not a total disaster. I am in my final month of PhD so want everything to go as smoothly as possible. Back to the question. So shall I press yes or no? The reason why I change things in Word and not through Zotereo sometimes is because Zotereo doesnt make the changes I require. Just one example is that for some of the citations, it keeps on inserting the First name as well as the last name. It does it for only some of the citations strangely enough. and so I have to go and delete the first names through word.
    So when I click yes, what does Zotereo do? Does it transfer the changes I have made through Word (e.g. deleting the first name of the author) to Zotereo itself and save it like that in the future?

    The instructions are really confusing. It says clicking yes will prevent Zotero from updating this citation [i dont want that do I? I want the first names gone ], Clicking no will erase your cahnge [again I dont want it to erase changes]. See, I am left confused again.
  • nedasalahshour
    Or another time I make changes on Word is when I need just to insert a page number after a quote. Zotereo allows one to supress the author, but not to supress the date as well. In APA style, after a direct quote, you can use just the page number as in
    According to Smith (1998) " Zotero saves a lot of time" (p.20). I can't do this in zotereo so what I do is suppress the author and delete the date.

    No I ideally want to keep this changes [provided that there are not future drawbacks to me doing so]. What should I be pressing? YES or NO?
  • adamsmith
    When you click yes, Zotero stops updating that citation in the document -- regardless of whether you change citation style or if you update the data in Zotero. It doesn't change the item in Zotero itself, no.

    For initials, see https://www.zotero.org/support/kb/given_name_disambiguation
    if you're using APA, that might be a feature, not a bug. I'd avoid "fixing" that in the document.

    Since for page numbers after quotes the alternative would be to just type them in regularly -- which also doesn't update, of course-- clicking yes makes sense for those.
  • nedasalahshour
    Hi

    First of all thanks for the tip about putting in the page numbers. that does make sense.

    Secondly, I still have some problems with the given names which pop up in my document. For example, I have one author called Allan Bell and he has three publication all with different names and different years. I have made sure that the names is spelled consistently in all enteries. For some strange reason it keep adding his first name. There are not other Bell authors. They are all Allan Bell and all the entries belong to different years! I do not see why it would want to disambiguate in such instances. Could you advise me please?

    Thirdly, I still don't understand whether I should be clicking yes or no. Please note that I have a huge document, in some cases i have made changes in Word, in some cases I have made changes in Zotero. This has been done over a 4 year period. I dont remember which citations I have changed now.

    This is all so confusing ....
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