References in Document Z DB disappears after quiting Word, reopening

cforden
Error Report # 1147395323

I have an MS Word document that takes 650KB with the references embedded inside it. I had accepted the default choice of "Store references in document." It has 48 references. I have unfortunately reached a point where if I make a few simple edits to the document, all the Zotero citations break when I reopen the doc; the citation numbers embedded in my text remain, but they no longer refer to any references in the bibliography or anything else.

Everything seemed to be going OK, I edited text and added citations OK, then I quit Word, then re-opened the document. When I then click Zotero Refresh, I get a dialog box stating "You must insert a citation before performing this operation."

When this happened the size of the document shrunk from 650K to 140K. Selecting any citation and clicking Edit Citation brings up a dialog box stating "You must insert a citation before performing this operation."

If I add a new citation after this happens, it works OK, but I prefer not to re-enter all the citations I already did.

I am using Microsoft Office Home and Student 2010 v 14.0.6123.5001 (32-bit) on Win 7 Ultimate 64-bit with Zotero Standalone 3.0.11.1.

I have tried working with a version of my paper which has Track Changes off and all previously tracked changes previously accepted; it is still vulnerable to losing the internal Zotero Reference database. Your "Debugging broken documents" suggestions, although commendable, seem to not be relevant to docs that have lost their internal reference DB. I have uninstalled and reinstalled Zotero Standalone, to no avail.

The Word document in question is not private, and I could send it to you if it helps.

Would my citations have been safer if I had used Groups or some other online database for them instead of embedding them inside the doc itself?

Thanks,
--Chris
  • adamsmith
    In what format are you saving the document? What do you have selected under "Set Document Preferences"? (just tell us everything that's checked/selected in that window)
    It seems like for some reason the way you save the document strips out all links to Zotero - that's not actually related to storing the references in the document, you'd have the same problem with groups and w/o storing things in the document.
  • cforden
    I have always been saving my document in "Word 97-2003 Document (*.doc)" format.

    I always save and edit in Outline view. Sometimes I have been tracking changes inside the doc (as well as via Subversion), and sometimes there are no tracked changes in the doc, and that feature is turned off inside Word.

    I have been storing my revisions in a Subversion repository. This is convenient because it allows easy and arbitrary diff creation and viewing as well as labelling the different revisions. There is no compatibility problem inherent in storing the Word docs in Subversion, is there?

    This morning, I saved some previous revisions to the file system on my hard drive, from the repository, using TortoiseSVN to retrieve them from the repository. There is one revision, r614, that loses its reference info as soon as it is modified in any way, including renaming it, including saving it to .docx format. I could send it to you. It starts off (as it comes out of Subversion) being 695KB, then shrinks to 165KB when any modification is made and the revised doc is saved. In contrast, r612, coming out of the repo, never has any problem; I can revise it a little bit in any way I have been able to think of, then save it, and all the links that were live seem to still be connected, clicking Zotero Refresh doesn't seem to cause any problems, and the size doesn't shrink as reported by Windows (file) Explorer.

    The trouble is that after several times reverting back to that apparently uncorrupted version, then manually editing it to reinstate the changes I had made from r612 to r625, the resulting document always seems to develop the same loss-of-links-or-data problem. I have looked at various diffs to see which edits might be responsible, but I don't see any places where I edited part of a citation instead of correctly adding, removing, or replacing whole citations. So eventually I gave up and decided to seek professional help.

    Looking back at older revisions (before r612) in my Subversion repo, I notice that the Zotero-generated bibliography has changed its font from Calibri 11 to Times New Roman 12. I believe I did not manually change it. I don't know if that is related.

    I was worried about corrupted data in the doc going unnoticed for awhile, and then causing massive data loss later. It feels like that is what is going on. I have never been able to copy and paste a paragraph containing a citation, and have its citation survive as a link to reference-data. Sometimes I have been able to drag-and-drop paragraphs and the citation survives as a living link to a reference. Dragging-and-dropping in the Navigator Pane has never allowed citations to survive as other than dead characters that look correct but don't really link to any real reference in the bibliography or elsewhere. Is this the correct behavior?

    I also just noticed that in r612 and earlier, the citations were stored in Bookmark format, and in the problematic, later versions they somehow changed to Fields. I did not change that in Zotero Set Doc Prefs|Format Using: , although I can see the change revealed there in that dialog box, when brought up from inside the later document versions. What does "Microsoft Word Fields are less likely to be accidentally modified" mean, BTW?

    When I took one of the problematic revs (r614) of my doc, opened the Zotero Set Doc Prefs dialog and tried to change Format Using from Fields back to Bookmarks, I got the error message "[Exception... "Component returned failure code 0x80004005 (NS_ERROR_FAILURE) [zoteroIngerationField.getCode]" nsresult: "0x80004005 (NS_ERROR_FAILURE)" location: "JS frame :: chrome://zotero/content/xpcom/integration.js :: <TOP_LEVEL> :: LINE 1118" data: no]

    I have just sent Report ID 1950596957 to Zotero with this message.

    The other setting in (Zotero) Document Preferences is that I have been using my own Citation Style which should be almost identical to that I uploaded to the public .csl repo as Hypotheses in the Life Sciences (HyLS).

    Thanks,
    --Chris
  • adamsmith
    My suspicion would be that this is related to the diff feature that Tortoise uses for .doc files - maybe Simon knows more about that.
  • cforden
    I had suspected SVN/Tortoise myself, but tried and could not reproduce any problems by messing around with them. I was able to reproduce this problem by starting with r612 of my doc (from SVN's repo), then editing it without SVN/Tortoise for an hour or two.

    Doing a diff on Word revisions with TortoiseSVN, opens the same kind of window with the same info, that is opened from within Word by clicking the Review tab in the ribbon, then clicking Compare and selecting "Compare...", then comparing two files. So I suspect any problem diff'ing, resides in Word.

    So I don't know where the bug lies. Thanks for helping.
  • cforden
    I changed my Z plugin Settings in Word to Format Using: Fields (from bookmarks) on the last working revision of my paper. I was then able to make all the edits and then some, that caused problems when it had been set to Bookmarks. We shall see how long it keeps working, but no problems so far.
  • vinci8622
    I have a question about Zotero Standalone. I have not been using ZOtero for a month or two now and when I reopened it today, many of my references seem to be gone. The motherboard on my other computer crashed in November and I may have saved many of the references when working on that computer. However, I thought that ZOtero automatically syncs. Does this have anything to do with two computers or is it due to something else?
  • adamsmith
    Zotero _can_ automatically sync, but it doesn't necessarily (i.e. you need to input your username and password [correctly], you need to not disable auto-sync etc.).
    Check if your resources are available online (click on "My Library" at the top left of this page). If they are, you'll just need to sync your version of Standalone and they'll appear there.
  • vinci8622
    Thank you for the answer. No the references aren't online either. I saved the data from my old computer though, is there a way to get the references from Zotero from that data? Is it saved somewhere? Thank you.
  • adamsmith
    absolutely:
    this should help:
    www.zotero.org/support/zotero_data
    any further problems let us know.
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