Citation problems with updated document

I wrote my doctoral thesis in OpenOffice using Zotero 1. Since then I've written another book using Zotero 2 and have the most up-to-date OOo plug-in. I'm now editing my thesis as a book. Trying to insert a new citation I was told I had to specify my document preferences, and was offered the choice of two formats: stable-but-can't-be-saved-as-Word and savable-as-Word-but-less-stable. My publishers will need it in Word so I chose that -- even though that will mess up the citations I already have in a few footnotes.

It's letting me insert new citations, but a. they're not shown highlighted, as the old ones are, and b. the paragraph the new citation is in becomes single-spaced rather than the 1-1/2 spaced it was before.

This all seems a bit flakey, and I'm concerned for the integrity of my work. Any advice?
  • What I would recommend you do is to use Reference Marks and only convert the document at the end of the process. That said, the issues you note are no reason for concern.
    Bookmarks are nor highlighted (that's one of the reasons they're easier to corrupt) and the formatting issue has always been the case, here for a solution/workaround.
    http://www.zotero.org/support/kb/word_default_font
  • The "highlighting" is because of the way that OpenOffice shows what's in a field (the "stable" kind of citation); OpenOffice doesn't show you the contents of a bookmark (the "unstable" kind of citation) in the same way. So the lack of highlighting shouldn't be cause for concern. And the Zotero team is dedicated to making both kinds of citations work correctly-- there shouldn't be problems with fields or bookmarks on the Zotero end-- it's just that, I think, bookmarks more easily broken while editing, rearranging, etc. the document.

    Since your publisher probably does not need to edit your citations using Zotero, you can actually continue to compose in ODT format and use fields, as you prefer doing. Just remove field codes and save to DOC or DOCX when you're done whenever you submit the manuscript to the publisher. The citations will still display correctly; your editor just won't be able to interact with them using the Zotero integration plugin.

    I'm not sure what's causing the spacing issue-- hopefully someone else can chip in on that one. Is that only when you use bookmarks (Word-compatible citations)?

    Finally, the word processor integration has improved and become more stable since Zotero 1.0 and 2.0, so your work is at least as safe as it was before. And, as always, you have the complete support of the forums and developers for troubleshooting if problems do arise. You may actually want to explore moving to Zotero 2.1, which is about to come out of its long beta, and which has somewhat improved word processor integration (and is more likely to receive developer attention and fixes if you run into any actual defects).
  • Thanks to both of you; as always the responses on this forum are expert and helpful.

    I changed to bookmarks because I (mis?)understood the document preferences choice to say that if I used reference marks I wouldn't be able to save it in Word when I was ready to send it to my publishers, but you're saying I can do so, Adam -- so would it make sense to switch back to reference marks, or might that cause further trouble? (Was the actual meaning that with bookmarks the citations themselves can be edited in both OOo and Word? If so, that wasn't clear.)

    Odd that I've never met the formatting problem before. The problem with changing the default is that (I think) this would be for all my documents, not just for this one, and most of what I write is single-spaced. I think I'll stick with the problem and just reformat any para that gets changed.

    ajlyon: I'm always loath to use beta s/w, in case I trip over an unfixed or even unreported glitch (back in my programming days 20+ years ago we called them "undocumented features"!). I'm currently using 2.0.9; do you think the advantages of moving to 2.1 would outweigh the possible risks? (I'm not asking for guarantees, just an opinion.) Oh, and I don't understand "Just remove field codes"; is that something I'd need to do myself, or would saving as .doc do it?

    Thanks again for your help.

    David
  • edited February 26, 2011
    (Was the actual meaning that with bookmarks the citations themselves can be edited in both OOo and Word? If so, that wasn't clear.)
    Yes, that's precisely what the intended meaning is.
    I'm currently using 2.0.9; do you think the advantages of moving to 2.1 would outweigh the possible risks?
    Zotero 2.1 is on the verge of being released (it will be required for Firefox 4), and I am fairly confident that it is less prone to cause problems than 2.0.9. But, of course, there's no harm in waiting a little.

    See http://forums.zotero.org/discussion/3704/ for information on removing field codes. If you continue to write in ODT, saving the document as DOC should be sufficient to make sure the citations aren't mangled by your publisher.
  • Thanks.

    On removing field codes: the reason I hadn't met this issue before is that my thesis went to the examiners in printed form (though I sent it to OUP as a Word file) -- and with the other book I just used Zotero to create the bibliography, not for in-text citations.

    Whichever format I use I'll output it in Word, and any copy-editing by the publisher will be in Word. I'll then turn it back to OOo for any final editing -- and at that stage I may need to edit or add citations, so will need them still to exist -- so that may be the factor that determines whether I should use bookmarks or reference marks. But whichever I use, do I lose anything when I switch from one to the other?

    I don't know when FF4 will arrive, but I'll take a leap of faith and move to Zotero 2.1 now.

    Incidentally, I don't know if you two are Zotero developers or expert users -- but it's so vastly preferable to the clunky EndNote I used when I first started working on my thesis that I've been recommending it to every academic and non-fiction author I know since I first came across it. Thank you Zotero!
  • Looks like I'm stuck with bookmarks; I tried changing back to reference marks, and then I tried starting afresh with reference marks on a backup document that hadn't been changed either way, and in each case I got a screen full of error messages that wouldn't go away; I had to use Ctr-Alt-Del to kill OOo each time I tried it.

    I haven't risked changing to Zotero 2.1 in case that makes things worse -- unless the screen full of errors is one of the things it fixes...
  • I am having a possibly related problem. I have a document with references in referencemark format, but my colleagues all work in word and it's time for some editing etc. I have both LibreOffice & Word on my machine, so I figured I would just convert to bookmarks, save as word, and proceed from there. The trouble is, when I try to convert, it eats my work - for example, reference 1 should show a little "1" - it does, but then it shows another one, and another, and another, with each one on a new line, and each one replacing a successive character of my manuscript. Eventually it stops doing that, and starts on the "2"s. Has anyone seen this before?

    Windows 7, 64-bit, LibreOffice 3.3.0, Firefox 3.6.13

    thanks!
  • what style is this?
    Can you replicate this with an empty document? I.e. star an empty document in LO/RefMarks insert two citations, then "convert" to bookmarks.

    And no, I've never seen this before.
  • adamsmith: yes, it's replicable that way - I have saved the doc pre & post & can email it to you if you want. To give a quick idea I will ctrl-A / ctrl-C / ctrl-V here

    As made with Refmarks:
    ==============================================
    Here is a document with a reference1 to something.

    1. Anderson, J.R. et al. A Computational Framework for Ultrastructural Mapping of Neural Circuitry. PLoS Biology 7, e74 EP - (2009).
    ==============================================


    After converting to Bookmarks (gear icon / bookmarks radio button / OK button):
    ==============================================
    Here is a document with a reference1
    1
    1
    1
    1something.

    {Citation}
    ==============================================

    PS the "1"s are all superscript after conversion, the first one can be edited as normal for a citation, if I try to edit the others another "1" appears and then blinks out & that's it, except for the third "1", if I try to edit that it starts spewing out more "1"s (some superscript some not) and eating more text.
  • PS style is "Nature Journal"
  • I can confirm that on Ooo 3.2 and Ubuntu and not just for Nature style.
    Here's a screenshot of the error message I get repeatedly
    http://img193.imageshack.us/i/screenshotggx.png/
    no error is triggered in Zotero itself.

    Simon is currently revamping the Ooo/Lo integration - it would be nice if the new version didn't have this problem, which make co-authoring with word users even harder.
  • any thoughts on a workaround?
  • can't think of anything at the moment, no.
  • how is the reference stored? maybe I can kludge up a script or something to get my paper out without having to re-enter everything...
  • edited March 1, 2011
    I can reproduce this on my Mac with LibreOffice 3.3.1, but OpenOffice.org 3.3 seems to work fine. The version of OpenOffice.org that ships with Ubuntu is based on go-oo, which contains many of the same patches as LibreOffice. It looks like one of these patches has broken functionality that we've been relying on. (Ugh.) I'll see if I can fix this, but for now, using OpenOffice.org may be a workaround.
  • Back to my problems with reference marks and bookmarks, I'm afraid. As I said, I seem to be stuck with bookmarks, because any attempt to set up the document with reference marks (which I would far prefer, if only because I can see them!) causes repeated pages of error messages and a forced exit from OOo.

    So I have a 100,000-word document with hundreds of old reference mark citations and a few new bookmark citations. But if I try to edit a reference mark, to change the cited pages for example, I get a horrible metallic thud sound and the message "You must place the cursor in a Zotero citation to edit it." Of course it is -- but Zotero/OOo doesn't seem to recognise it. Does this mean that I shall have to reinsert any old citation I need to edit as a bookmark? And a far more serious consequence: when I come to generate a new bibliography will Zotero recognise both reference marks and bookmarks? Or will it generate a bibliography of just half a dozen items?

    As I've also said, I haven't risked changing to Zotero 2.1 in case that makes things worse. But would it be more likely to make things better?
  • edited March 2, 2011
    you don't have both bookmarks and reference marks in a document.
    I'm not quite sure how you got where you are, but a document is either/or.

    just to clarify, if you, at any point in time, saved a document with reference marks as .doc, those no longer exist as Zotero citations and there is no way to bring them back (except a back-up of the document prior to saving it as .doc)

    edit: And in case of that latter scenario (and this is what this sound like) the bibliography will consist only of the newly added items. Zotero doesn't know that there are any others.
  • What version of OpenOffice.org are you using? As I noted above, the official version (i.e., the one from OpenOffice.org, not the version distributed with Ubuntu and several other Linux distributions) should work. If you're still having issues, if you could take a screenshot of the error and send it along with the document to support@zot...org, I can take a look.
  • to avoid confusion: while Simon knows much (much!) more about the plugins, I believe my understanding of what's going on in your case is actually correct. Using the official Ooo version would likely help with the issue you described above (in the "looks like I'm stuck with Bookmarks" post), but not with this one.
  • edited March 2, 2011
    If conversion fails with an error, it's possible for the document to contain both Bookmarks and ReferenceMarks. If this is the case, new citations will be added according to the setting in Document Preferences, and Zotero will only recognize the type of references set in Document Preferences when editing citations or creating a bibliography. I'm not sure if this is the case here, or if the ReferenceMarks are simply gone, but it's a possibility.
  • edited March 2, 2011
    Adam: I finished the thesis over a year ago, using Zotero 1. I then wrote another book, and went up to Zotero 2 (currently 2.0.9). When I returned to edit the thesis as a book and tried to add a new citation I was told I had to specify my document preferences, with the choice of reference marks or bookmarks. I went for the latter, for the reasons mentioned above.

    The old citations are nicely highlighted, and when I hover the cursor over them they tell me that they're reference citation items, but I can't edit them; the new citations aren't highlighted, don't say anything when I hover the cursor, but I can edit them. So I do have both types in the document.

    Yes, I saved the document as a .doc file to send to OUP -- but I'm editing the OOo file, not the .doc file.

    Fortunately I generated a bibliography when I completed my thesis, and this is now at the end of the document, so that situation isn't as dire as it might have been; I'll just have to remember which new titles I've added to the database and manually type them into the bibliography -- a pain, but not a major one.

    Simon: I'm using OOo 3.30, downloaded direct from OOo, with the add-on Zotero OpenOffice Integration 3.0. Someone (Adam?) told me a while ago that I might be experiencing problems because between originally writing the thesis and now editing it I went from the Zotero-1.oxt add-on to 3.0 (via version 2, but my thesis doesn't know that).

    I think I'm just going to have to muddle through with this book -- If I need to edit an old (reference) citation I'll just create a new (bookmark) one instead -- and hope that when I eventually save it as .doc to send to my publishers, all the citations, of both types, will remain in the text. (Do I need to Remove Field Codes first, or does saving as .doc do that anyway?)

    And the next book I'll start from scratch with reference marks -- and with Zotero 2.1.

    **Edit: You both responded again while I was writing this -- but I think it still stands.
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