Automatically updating bibliography after citation changes

jphekman
I'm in the process of manually filling out the "journal abbrev" field for a bunch of citations. My citation style (AMA) will automatically use those abbreviations once they're added (good!). However, I have a document which already has a lot of references in it. I see that when I modify a citation (to add the "journal abbrev" field), the actual reference in the document's bibliography doesn't update, even when I delete and re-add the bibliography. I have to delete and re-add the individual reference in order to get it to update.

I really don't want to have to delete and re-add all 76 references -- it would be nice to get the bibliography to just update once I have added all those "journal abbrev" fields.

To be clear, I am not complaining about having to add the "journal abbrev" fields by hand; I see that that is still necessary, but that work is being done to fix the problem. I was just hoping that my references would update in my document once they had been modified. Is there any way to make that part of the process easier?

Thanks!

Jessica
  • adamsmith
    Let me make sure I understand correctly what you're doing:
    You have a reference (1)
    and in the bibliography
    (1) Smith et al 2010, The Cure for Everything, New England Journal of Medicine

    Now, in Zotero - you put in NEJM into the Journal Abbr. field.

    You go back to the document, you click the "Refresh" button - nothing.
    You delete and re-insert the bibliography - still the full New England Journal of Medicine.

    That's neither expected nor normal behavior. Indeed, the citation(s) should update to any changes in the database once you click Refresh - and that's what Zotero normally does, too.

    There is only one way I can replicate what you see: If you, at some point before, used "Edit Bibliography" and manually edited the entries using the "Show Editor" function (e.g. to put in the abbreviations manually) this would lead to the problems you're experiencing - that's why a warning is displayed when you use the editor. This seems to be the most likely scenario.
  • jphekman
    Your summary is correct. However, when I first posted my question, I had only tested after changing one or two references. After posting, I added journal abbrevs for all the references, and refreshed again. I now see that some number of them did update, and some number did not. I can't see a pattern for which ones updated, at this point, though it's possible a pattern exists. I double-checked in my Zotero db, and the abbreviations do exist for the ones that didn't update.

    I probably did "Edit Bibliography" at some point as I was figuring out how to make the short form of the journal title appear. I don't remember for sure, but I am positive that I wouldn't have edited more than one or two entries, so I don't think that would explain why there are non-updating references scattered throughout the bibliography. Just to be sure, I found a saved version of the document, from before I started messing with the bibliography (so definitely I had not edited any entries in that). I refreshed the bibliography in that document. Same problem (some entries update, some do not).

    Sorry to present you with a confusing problem. Computers suck :)
  • adamsmith
    Try toggling field codes (for the citation in the text) using alt+F9 - copy some of the offending ones here. If they say "custom" somewhere they have been modified and will not update anymore.
  • jphekman
    I'm not sure what you mean by toggling the field codes. I tried alt+F9 in the main document (with the cursor in a reference number, and in the actual reference in the bibliography) to no effect. I also brought up the edit window for an individual citation and tried alt+F9 there, again, no effect. What's supposed to happen?
  • adamsmith
    might not work with your Office version -
    this would show you the entire code that Zotero inserts with a citation.
    can you hover over the citation with your mouse and see what it says?

    Which word processor and OS are you using?
  • jphekman
    OpenOffice 3.2.1, Ubuntu Lucid. (Sorry. I should have said that at the start.) I am saving as ReferenceMarks. I don't mind using Bookmarks in the future -- whatever is more reliable would be what I'd prefer.

    Hovering over a citation with the mouse does nothing.

    Thanks!
  • adamsmith
    ah yes, alt+F9 is for MS Word.
    don't use Bookmarks, no - Reference Marks are better and more reliable.
    Your references are highligted in gray, right? You should really be able to see a long string (I think in black or so) when you move your cursor over them - I just tried that on the same set-up and it works. Could you try again?
  • jphekman
    They are indeed highlighted in grey, but honestly I get nothing when I hover. (I did try again.) I can send you a screenshot if you want. I have never seen any text when I hover over them, actually, although I've been using the Zotero plugin to generate them for six months or so now... Why could that be?

    This is a side question, but I wonder if it is relevant. It has always been true that some of my citation numbers will become too small to read after I add a new citation (when the system goes through and regenerates all of them, I am guessing). Restarting OpenOffice fixes the problem, until the next time that I add a new reference to the document, when it will shrink a bunch of them again. Not related? Or possibly symptomatic of a larger problem?
  • adamsmith
    I'm not super concerned by the change in font - that sometimes happens - but I don't understand why you don't see the field codes. I can't manage to turn that off in my Ooo even if I try.
    Anyone else has an idea?

    In your place I think for the one article I'd suck it up and replace the citations - seems unlikely that can be fixed now.
  • jphekman
    OK, it's not the end of the world as workarounds go! If anyone else does have insights I would love to know why I'm not getting the mouseover text, though. Maybe a problem with the version of Ooo or something.
  • adamsmith
    if you're using the Ooo version shipped with Ubuntu Lucid - no - that's the one I'm looking at.
  • jphekman
    No, I updated to Ooo 3.2.1 (actually in order to try to overcome problems with Bookmarks I was having -- failed to fix those problems but figured I may as well stay with the newer version).
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