no field codes in any of my documents anymore. Libreoffice/Linux Mint LMDE

Hi,

Running Zotero all up to date on plugin and wp plugin. Linux Mint Debian edition, everything up to date including Libreoffice.

When I went of work in LibreOffice today, none of my documents as far as I can tell (I have hundreds dating back over years) is connected any more. All the gray is gone, all notes in every doc appear as straight unconnected text. I can add in new cites with no problem and they are gray but everything code, including all the cites in my current book manuscript, are gone. The notes and bibliographies are there as text, but not the codes.

I am set up to use all the defaults...store references in documents, use reference marks.

the last article I finished was formatted differently than usual, using parenthetical rather than footnotes, but I had no problems. I stripped the codes when it was done and saved it as a word docx file, so that one of course is just straight text, but all my other odf documents have lost all field codes too. Again, I can enter new cites and the field codes are there, but all the old ones are disconnected on everything.

Let me know if you need more details.
  • If I open up the odf files in an archive viewer and look in content.xml, there are still references to zotero in the xml
  • edited October 13, 2012
    I don't have an idea about the cause, but one thing you might try is to copy-paste the content of one of the files into a fresh document, to see if that wakes up the content.
  • Thanks, I just tried it. The code makes it over to the new doc, unpacking content.xml shows all the zotero codes, but it is not seeing anything. New cites go in fine. It is just missing all my previous cites for everything I have written with Zotero previously.
  • It has been a week with no response since the initial suggestion.

    I tried uninstalling and reinstalling zotero and the plugin, uninstalling the plugin from libreoffice and deleting the config files and then reinstalling the plugin.

    This is a real serious issue for me. I have a ton of documents I work on and I depend on the references to be there . Going through and reinserting the cites is hundreds of hours of pointless work. Hours I don't have. Dan? Adam? Simon? anyone have any ideas as to what may be wrong and what I can do to restore the citations? Is there more info needed? As noted above, the codes are still present in the OO document when I unzip them and look at the xml (copies only of course), but none of the codes show in the documents. everything acts like plain text, no gray fields. New citations, even of the same material go in fine.

    Please help or tell me what further info you need.
    Libreoffice from debian testing, latest zotero and plugins, up to date firefox, linux mint lmde.
  • Sent error report and followed other debugging procedures on troubleshooting page. error report is 893855195
  • I don't have any advice for you on this, but if the codes are all there this sounds like a LibreOffice problem, not a Zotero one. Zotero just inserts the fields into the document. It's not responsible for displaying them.

    Unrelated, but taking a look at your error report, it does look like you have your Zotero data directory stored in Dropbox, with a number of conflicted translator files. The Zotero data directory should absolutely not be stored in Dropbox—doing so will cause all sorts of problems, including potentially corrupting your database. Delete your 'translators' and 'styles' directories and let them be recreated, check your database integrity in the Advanced pane of the Zotero preferences, and move your Zotero data directory outside of Dropbox. (You should temporarily disable auto-sync and close Firefox before you move it, and then reopen Firefox and choose the new location from the Advanced pane of the Zotero prefs.)
  • Hi Dan, could you please check the libreoffice doc at http://way.net/tmp/02-%20ancient.zip ? It is just a renamed odt file and the content with the zotero field codes is in content.xml.

    I will also take the problem over to libreoffice and report back if I am able to find a solution.

    I will move zotero out of dropbox before doing that and check to see if that has fixed anything. I've run zotero out of that directory for several years now and never had a database problem, and one time it saved me when the sync server took my instructions to mean "delete everything". Because I had backups on dropboxI was able to restore a working version from the versions feature. (I know I also had the sqlite bak file too, but I think that might have been overwritten too before I figured out what was going on from me stopping and restarting things a couple of times). I'll move zotero outside of dropbox but I need some backup system that will keep an up to date copy made from whichever computer I am working from (mostly linux) that has a better versioning system than zotero's. I know versioning has been discussed elsewhere and you guys said it would be too expensive to implement server side, which is why I have kept the dropbox folder for zotero. Any ideas for a way to replace what dropbox is doing for me know on the backup front? Even a preference to set how many backups of the sqlite databse to keep locally, with perhaps some sort of thinning algorithm (e.g. 10 for the past week, 4 for the past month, and 1 for the past year), would be useful in this regard.

    I know this last part is a tangent from the original thread, so if you don't have anything, feel free to ignore, but please look at the zip file at http://way.net/tmp/02-%20ancient.zip and let me know if everything looks ok there while I take up the issue with the Libreoffice support community. I do hope I can get this resolved as it is a major problem for me.
  • edited October 23, 2012
    as for back-up: One obvious solution is to use a non-cloud back-up based on rsync to an external harddisk. Everyone should do that anyway.

    Otherwise - I don't know if you can set Dropbox (or any of the other sync services) to sync one-way only, but that's really what you'd want as a back-up system. The problem with Dropbox is the two way sync that can corrupt the database.
    That also means that if you're using Dropbox&Zotero _exclusively_ on one computer, there is not much of a risk keeping the Zotero folder in Dropbox, but the translator conflicts that Dan points to suggests that you're playing with fire.
  • Hi Dan, could you please check the libreoffice doc
    The plugins aren't my department—Simon would have to look—but, just logically, if all your old documents are suddenly displaying differently when you open them, it's by definition a LibreOffice issue. As far as I know the Zotero plugin doesn't do anything until you trigger an action.
  • edited October 23, 2012
    And all the references in that document display fine for me—in grey and with Zotero field codes intact—in LibreOffice 3.4.5.
  • edited November 11, 2012
    Regarding your LibreOffice bug report, the people testing it don't actually need to have Zotero or the plugin installed, since, again, how the fields show up in LibreOffice is completely unrelated to the Zotero plugin if the fields are already in the document.
  • edited November 11, 2012
    Also, FWIW, the Zotero fields in your document look OK to me in LibreOffice 3.6.3. Since you say this was affected by a LibreOffice version change, you should really test with the latest version of LibreOffice before reporting this to them. LibreOffice 3.5.4 came out in May, and 3.6.3 came out November 1.
  • update to 3.6x. One of the computers was running openjdk instead of Oracle java, so tried with java 7, no luck, but then upgraded libreoffice to 3.6 and downgraded JRE to 6 (latest version) and some docs have their zotero fields back, but some don't. still have the bug report open with libreoffice.
  • going back to modify bug report in light of Dan's correction about needing zotero installed.
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