Issues with Scrivener, LibreOffice, and Zotero citation plug-ins

After compiling a document in Scrivener, opening in LibreOffice, I am trying to select an idea citation style setting document preferences on the Zotero toolbar in LibreOffice, but I am facing serious issues.

1) I opened the .odt file with citations and noticed they are in a LASTNAME, YEAR format. They are also in different fonts.

2) Clicked on Set Doc Preferences and chose Bluebook Law Review, footnotes, ReferenceMarks, Use MEDLINE journal addr, and automatically update citations.

3) Get a warning box: The highlighted citation no longer exists in your Zotero database. Do you want to select a substitute item? When I click "no" LibreOffice begins to populate the citations, which appeared in i.e., 96. CITATION format

4) Get another warning box:
Updating citations in this document is taking a long time. Would you like to disable automatic citation updates?
You will need to click Refresh in the Zotero toolbar when you are done inserting citations.
You can change this setting later in the document preferences.

5) After clicking "yes" I have a citation number followed by a shaded number through half of a page, then a line followed by a full citation. When I erase the number above the line, the citations below the line are automatically deleted accordingly.

I updated LibreOffice (7.1.3.2), reinstalled the LibreOffice-Zotero plug-in successfully. I tried every which way to make this work to no avail. Would someone help me understand what I am doing wrong?
  • 3. Sounds like the item cited is no longer in your local Zotero library. Not much you can do about that other than re-insert
    4. Try clicking "no" and waiting. You want the citations to update initially, even if it takes some time.
  • That's the thing. This is not a message for one or two but for all. No items have been deleted or moved from the library.

    Here is what it looks like on two citations where everything after 35 and 36 is shaded and populated with the respective citation info:
    35 Rabuy, & Kopf, 2016; Quigley, 2016
    36 Wiesel, 1999

    When I click "no" LibreOffice begins to update. Then, the two citations above show:
    35 58 shaded; 59 shaded
    36 60 shaded
    -------------
    58 Bernadette Rabuy & Daniel Kopf, Detaining the Poor: How money bail perpetuates an endless cycle of poverty and jail time, Prison Policy Initiative, May 10, 2016, https://www.prisonpolicy.org/reports/incomejails.html (last visited Apr 25, 2021)
    59 Bill Quigley, 40 Reasons Why Our Jails Are Full of Black And Poor People, HuffPost, June 2, 2016, https://www.huffpost.com/entry/40-reasons-why-our-jails-are-full-of-black-and-poor-people_b_7492902 (last visited Apr 25, 2021).
    60 Wiesel, supra note 57.

    Then, three boxes appeared:
    1- Zotero Integration (as in 4) above)
    2- Zotero integration error - Zotero experienced an error updating your document. Would you like to troubleshoot?
    3- Zotero integration - Zotero experienced an error updating your document. Would you like to troubleshoot?
  • We'd want to see a Report ID to start. But generally if you're having problems in a specific document you'll want to follow the Troubleshooting Errors in Word Processor Documents steps linked from that dialog.
  • Report ID: 210542810

    I tried troubleshooting errors to no avail.
  • Just FYI, I am working on a mac. Thank you!
  • @adomasven can take a look at the error you're getting, but just to be clear, unless the problem still occurs after clearing the document completely, the troubleshooting steps — specifically the last step — will by definition fix or isolate the problem.
  • @santorio You'll have to follow step 10 of the debugging instructions. Your Report ID suggests that at least something is going wrong with Zotero trying to display an alert within LibreOffice, but it's hard to say why.
  • @dstillman @adomasven

    Ok, I redid the steps. Just in case I am doing something different. I am working on LibreOffice. Here are some questions on the steps:
    3 - image captions - I checked all citations, and they were all drag/dropped from Zotero into scrivener. I am unsure if this is what you mean.
    4 - Since your instructions are for Google Docs, I used "save a copy" in LibreOffice. Does this suffice? Working on the COPY document, I used the ODT scan and I clicked “Set Document Preferences” button. I received the warning: Zotero Integration
    Updating citations in this document is taking a long time. Would you like to disable automatic citation updates? I clicked yes.
    Scrolling down to the area of the citation, I see the same problem.
    5 - Made a copy
    6 - Not using OneDrive here
    7 - I opened the copy, switched the style, and the citations are still screwed up
    8 - No biography, just endnotes
    9 - I have a Mac, so when using Fn+Opt and then pressing F9 when it appears on the touch bar, the menu "tools" on LibreOffice appears as if I had the cursor hovering over it, but nothing else happens
    10 - Deleted portion of the document and the problem persists

    Just in case, here is a new Report ID: 783955876. I also emailed a screenshot of the problem so you can see what I see.
  • You should keep repeating step 10 and removing portions of the document until it starts working which helps you identify which part of the document is the culprit, then you restore other parts of the document and make sure it still works.
  • @adomasven

    Ok, I went through the document deleting parts and changing the style every time. The problem persisted. When I deleted the whole thing, I could still see all the citations despite no text corresponding to these citations.
  • Where do you see the citations? Did you do something first to see the citations?
  • They are at the bottom of the document. I kept deleting portions of the document, changing citation style, and waiting until changes were implements. Once I "set document preferences" on the (citations) version of the initial document, the problem appears.
  • I'm wondering if the problem is something about Scrivener and its ODT export?
    Could you try the same thing with a document compiled to RTF in Scrivener, then open that doc in LibreOffice, save as .odt, then run the scan? If you want to, you can do this with a small subsection of the document since this is just for testing.
  • Ok, I just tried that. Same problem. Report ID: 1482716146
  • UPDATE: I tried working on another document, and the problem does not occur.

    I tried opening a brand new Scrivener document and copy/paste from the problem document, but it also brought over the issue.
    I made a folder into the project where the issue if not happen and copy/paste a section from the problem document as plain text.
    I manually drag/dropped citations accordingly. I compiled and test and the issue is gone.

    Is there something you can suggest to avoid having to manually add every citation or find out what happens with that document?
  • It's hard to say, but it's not out of the question that what you're seeing is a Scrivener bug in saving your document as .odt/.rtf, although we'd need to see a broken excerpt ourselves to figure out what's wrong. If you can send support@zotero.org a 1 page snippet of a broken document we can take a look. Make sure to include a link to this thread in the email.
  • I just sent the email with the document. Please let me know if there is anything else you may need. Thank you for helping to find an answer to this puzzling issue.
  • edited May 21, 2021
    Could you send us the file after you run ODF (to citations) export on it?
  • Just sent. I assume you were referring to the rtf file since I sent the odt with citations already.
  • No, I meant the odt. You have attached a sample (citations).odt file in an earlier email, but it seems to be empty and/or corrupt. We need a document that has LibreOffice ReferenceMarks in it after running ODF (to citations) export with Zotero on a file saved from Scrivener.
  • Ok. I just sent it. Please let me know if that works. Thanks!
  • Ok, that's a whole lot of citations and unfortunately even after the export I don't have much to work with to identify the issue. You did say that manually copying citations from this problem document to a new working one worked. Doing that will be your best bet, but you can speed up the process of elimination significantly by copying citations in clusters - half of the citations at the time. Once you run into the error after such a copy, take a half of that half and see if it still breaks. Keep halving the number of citations you copy until it works, which will help you quickly narrow down the citation that is causing issues.
  • What would help you find the issue?

    I used an existing paper where the issue was not happening. I deleted everything on that document, then copy/paste the text unformatted, and finally went through the whole document manually, inserting each citation. I want to find out why it happened and hopefully spare anyone else the laborious ordeal.
  • It's hard to tell. We don't officially support Scrivener or RTF/ODF export (it's a community created plugin), but it seems to be a bug originating on Scrivener's end.

    You shouldn't need to manually redo every citation, you just need to keep copying them from the broken document to find the one causing problems and remove/reinsert that one from Scrivener.
  • I submitted a ticket to Scrivener.

    Is there anything we can do on this end?
  • I'm afraid not, but even for Scrivener you will have to narrow down to a specific short part of the document that is causing breakage. It's likely just one or two fields/lines in the document, so you'll have to do the manual debugging.
  • @sartorio We got your email (although you should generally post on the forums for support - email is only for private information), but that Scrivener message does not help to fix this. Ultimately unless you can narrow down the issue to a few lines that reproduce the error it's impossible to debug it for us.
  • I understand. Speaking with Scrivener support, they suggested compiling to RTF and opening in TextEdit to confirm that Scrivener handled the citations correctly and behaved as expected. Then ask Zotero support what to do next.

    I did just that, and indeed, the citations come through in the expected order.

    I went back and created a new doc on Scrivener, copied and pasted it from the problem document, and the issue did not appear. There must be something wrong with the specific document.
Sign In or Register to comment.