Ubuntu LibreOffice bookmark issues: new lines, junk bookmarks, etc

yigit

Hello,

Thanks for developing Zotero. I have Linux (Ubuntu), and I don't want to boot windows just to type. Collaborators have windows/mac and use word, but don't use citation managers. I figure LibreOfficde bookmarks are the best way to go for Zotero.

I'm just starting the paper and noticing some odd behaviours; apologies if these are LibreOffice issues not Zotero.

1. Every time I insert a citation with zotero, I want it to be like this
''Some text (Author, 2011). The text continues''

But sometimes, I get this:
Some text(Author, 2011)
. The text continues

So it's deleting any spaces I had before the "(" and adding a paragraph mark after the ")" Occasionally.

2. The bookmarks (when I view them in libreoffice menu > insert > bookmarks...) start out normal, ie a bookmark for each citation and the bibliography. Then as I open and close the document (saving in docx format, alas) each time, random additional bookmarks start to multiply with names like this "__UnoMark__2165_1855068224". Everytime I save and reopen the docx, there are more of these.

3. I start getting some duplicate in text citations as well, sometimes nested in each other, and when I open the document and sometimes when I hit the refresh button it starts telling me, for every citation in the doc, "you've modified this citation since zotero generated it. etc etc" and I click "no, just keep updating it" and then I have these duplicating in-text citations.

So basically, I am not able to use Zotero this way. Can anyone suggest what I'm doing wrong? Or an alternative workaround if necessary?

This occurs even with a brand new lorem ipsum docx I create and use only on ubuntu with zotero bookmarks.


ubuntu version: 17.10 with Gnome 3.26.2
Libreoffice version: 5.4.6.2
Zotero version: 5.0.45
Libreoffice plugin for zotero: Reinstalled as of 27.4.2018
Citation style: Geoarchaeology

adomasven

But sometimes, I get this:
Some text(Author, 2011)
. The text continues

Are there steps to reproduce this consistently? Perhaps citing a particular item does?

2. The bookmarks (when I view them in libreoffice menu > insert > bookmarks...) start out normal, ie a bookmark for each citation and the bibliography. Then as I open and close the document (saving in docx format, alas) each time, random additional bookmarks start to multiply with names like this "__UnoMark__2165_1855068224". Everytime I save and reopen the docx, there are more of these.

I see this too, but the bookmarks are inserted by LibreOffice, so you will have to ask them about it.

3. I start getting some duplicate in text citations as well, sometimes nested in each other, and when I open the document and sometimes when I hit the refresh button it starts telling me, for every citation in the doc, "you've modified this citation since zotero generated it. etc etc" and I click "no, just keep updating it" and then I have these duplicating in-text citations.

This is indicative of broken bookmark markers. Unfortunately, weird editing, cutting and pasting, etc can lead to overlapping bookmark markers. There is usually no easy resolution for it, aside from going over the debugging broken documents steps.

yigit

Hi adomasven. #1 ... yes ok it may be related to particular funky handmade citations.

#2 ok... I don't use the bookmarks for anything else, but this is basically breaking bookmarks if people use them for any other purpose since the list is going to be full of thousands of junk bookmarks in a fulllength research paper with maybe hundreds of zotero citations. + thousands of junk UnoMark citations.

#3. I am not doing anything but citing things into a lorem ipsum doc I just made; nothing fancy like track changes or copy pasting. Add a new citation. Close document. Change date or something else about citation in zotero. Reopen doc, refresh-- these double citations get generated.

adomasven

(2) I am not seeing the UnoMarks replicating infinitely, but they do indeed not get cleaned up properly, if you remove the Zotero-citation related bookmarks. Either way, this is a LibreOffice bug, so that's still who you have to talk about this. Although I don't think there is any harm in removing those manually when they accumulate.

(3) I cannot reproduce this with the Geoarchaeology style on Ubuntu 16.04, LO: 6.0.2.1

yigit

Focusing on number 3 then, which is now the only part that makes the setup unusuable (as the junk bookmarks can be ignored for most people). Here's what happened to me more exactly.

1. Start a new blank document in LO.

2. hit new citation button.

3. Prefs dialogue pops up.
-Choose style Geoarchaeology (or Quaternary Science Reviews, happens with that too; haven't tried others so far)
-Choose bookmarks
-Auto update is on

4. Add the citation.

5. Save document as docx, then close

6. Reopen document.

7. Hit refresh. It tells me the citation has been modified. Regardless if I click yes (stop updating it) or no (keep updating it normally), a duplicate in text citation will be created next to the first one.

If this doesn't happen on your setup it means... something? I haven't tried LO 6 yet, and I haven't tried it with LO on my mac laptop yet either. That will be next step.

(I note that even though auto-update is on in the prefs, with bookmarks it doesn't automatically refresh when you open the document, ie if you've changed the entries in zotero, changes won't be reflected in document until you hit refresh. I guess this is an inherent limitation of bookmarks, correct?)

adomasven

Could you email this broken document to support@zotero.org with a link to this thread? We haven't had any other reports about something like this.

I note that even though auto-update is on in the prefs, with bookmarks it doesn't automatically refresh when you open the document, ie if you've changed the entries in zotero, changes won't be reflected in document until you hit refresh. I guess this is an inherent limitation of bookmarks, correct?

The auto-update preference only deals with citation updates caused by disambiguation or renumbering. If you change the metadata of your citations, you need to click refresh for Zotero to check over every citation in the doc.

yigit

Ok, thanks for the info. I will send a long the test document; with nothing but a citation. If you open it (and you were me) and hit refresh, you would see the prompt for "You have modified this citation," to which answering either yes or no creates a duplicate in text citation.

EDIT: ok, now it seems that clicking YES doesn't create the duplicate. I really thought that wasn't the case a few minutes ago. But anyway, I need to click NO, because I don't want to prevent future updates of the citation in case I change styles, edit the object it refers to, etc.
EDIT2: Also, I never did modify the citation


Longtime zotero user with Mac/Office, but I'm not so experienced LO or Ubuntu, it's possible there's some stock setting that needs to be changed before this works as it should. Thanks for your help.

adomasven

I have not seen this bug before, but the document you sent indeed is corrupt. I'd advise updating LibreOffice as a first step and seeing whether that has any effect.

yigit

Just for future reference in case this is ever useful to anyone else, I purged libreoffice, and reinstalled it (stable) from the ubuntu repository (as recommended on the libreoffice website)

Still having the same problem. Create a new document, add citation, save document as docx. reopen document, refresh document -- it claims the citation has been modified even though I didn't touch it, and then it inserts a duplicate.

Doesn't occur with odt document using bookmarks, only docx using bookmarks.

If I ever have time to post and get an answer from the libreoffice people I'll probably add it to this thread

adamsmith

Try .doc instead of .docx in a pinch? It's been a while since I looked at this, but last time I tried, LO's docx implementation wasn't terribly good (issues unrelated to Zotero).

yigit

Using .doc seems to work so far... the issue does not appear using the steps I listed above to recreate it. thank you. Recommend this as the workaround for anyone else experiencing this issue.