D1512259298 Citations not being added Feb 2, 2020 - sudden problem among others

Greetings,
I have a due date to deliver the revised manuscript to the peer review journal and I need to resolve this issue urgently. My due date is in 1 week.
When I try to add a citation to the list of bibliography, the pop-up red tab appears, I am able to see the list of all citations available, I click on the one I want, and the number is added in the manuscript where the citation is supposed to be referred to. However, the citation is not added to the list of bibliographical references located below the article text. I reinstalled the app version 5.0.82, and also re-installed the word add-in several times (around 3 times). Each time I turned off my Mac and restarted it. It didn't not work. I also tried to install a earlier version as some threads talk about it, and it didn't work either. Everything was working fine until this morning, and then all of a sudden it wasn't. I also opened a new word doc and verified that Zotero is not working even with a new doc. Same thing... I try to add citation, the number comes up on the text, but the reference is not added to the list of bibliography. After I discover this problem today, something else happened too when I was trying to make sure I was using the style required: American Medical Association. I went to the app and changed the default style to AMA. All of a sudden my paper had two lists of references one on top before the text which looked the correct AMA style, and the second one below the text which looked wrong. So, I am not even sure if the style I have on my paper now is from the AMA because it looks very different from when I first wrote the article and sent to the journal. The editor did not complain about the style. So, I am assuming the first one was right which is different from the one on paper now. Last week I also had another similar problem. Citations could not be added. I had to get a previous early version of my article and start adding the citations again from there which worked. So I went around the problem, but this feel like a bug... Lucky I made several copies in different stages of my research article anticipating problems like this., now nothing works. Can you guys please help me out here? Getting concerned with the due date. Thank you. Andréa.
  • In general, see Debugging Broken Documents.

    The first thing you should do is delete any existing bibliographies from the document and reinsert a bibliography.
    I also opened a new word doc and verified that Zotero is not working even with a new doc. Same thing... I try to add citation, the number comes up on the text, but the reference is not added to the list of bibliography.
    If you start a completely new document, click Add/Edit Citation and insert a citation, and then click Add/Edit Bibliography, what exactly happens? It's extremely unlikely that that wouldn't insert a bibliography with the citation you just inserted.
  • 1. So, this is about 100 bibliographical references... not really easy to do because I it's difficult to keep track of where each one goes. With 100 references, I probably have 3 x times more places in the text to insert them. One reference does not imply in one insertion only in the text. This would take me many days to do, with no guarantees that this is going to work. This does not fix the problem that Zotero is having. It's the second time it happens. The first time I went back to an early version of the article and somehow was able to start inserting citations again.
    2. "If you start a completely new document, click Add/Edit Citation and insert a citation, and then click Add/Edit Bibliography, what exactly happens? It's extremely unlikely that that wouldn't insert a bibliography with the citation you just inserted" - it happens exactly how I said. In a new word doc, the number comes up like 1, 2, etc... but the list of references does not form down below. That's exactly my point - Zotero is having some problem, a bug or similar... this should be working but it's not.
    So, are you from Zotero administration, or a user from the Zotero community? I would love to have someone from Zotero admin answering. I enabled the debug output and got the number. Does it mean that Zotero admin will look into it for bugs? Txs!
  • edited February 2, 2020
    So, this is about 100 bibliographical references... not really easy to do because I it's difficult to keep track of where each one goes.
    I'm not sure what you're responding to here in my comment. I said to 1) try the debugging steps, which can be done quickly regardless of how many citations you have and 2) try deleting any existing bibliographies (not citations) and inserting a new bibliography, since you seemed to suggest you had multiple bibliographies in the document.
    it happens exactly how I said. In a new word doc, the number comes up like 1, 2, etc... but the list of references does not form down below.
    It's still not clear to me that you tried exactly what I asked — I didn't say anything about inserting multiple citations, and you don't say that you actually inserted a bibliography or explain what happened after you did. Again, if the steps I describe didn't work, that would be extremely unusual and not something anyone else has reported in recent memory.

    See Steps to Reproduce. That's what we need from you — the precise steps, starting with a completely new document, to reproduce the problem, and a complete explanation of exactly what you expect to happen and exactly what's actually happening, with every single thing you're clicking on or looking at on screen.
  • And your Debug ID doesn't show anything related to word processor integration at all — it just shows a lot of unrelated syncing activity.
  • So, I followed the link and tried those steps: https://www.zotero.org/support/kb/debugging_broken_documents

    Still, the problem persists.

    So, I am going to try to explain better. See the steps below:

    A. WITH THE ARTICLE I WAS ALREADY WORKING ON:
    1. Everything was working fine, until today afternoon. I wrote a sentence. Put the cursor at the end of the prhase and clicked to determine where the number would be.
    2. Then I opened the Zotero app, and I listed the article name, authors, publication, date, etc..
    3. On word doc, I clicked on the upper tab where it's written Zotero. Then I clicked on Add/Edit citation, then wrote the name of the article (e.g. Zhang 2017); A list of possible articles by Zhang shows and I clicked on the correct one. Then I clicked on the "return" on keyboard. (I have a Mac)
    3. Immediately, a number showed at the end of the phrase in the manuscript where the cursor was (e.g. 70).
    4. To check if the article was listed in the reference list at the end of the article, I scrolled down. The new article was not there. I repeated this process several times and in other places of the article, and it didn't work anymore.
    So, this is the main problem. I have been working for days with the same MO and had no problem. This problem appeared suddenly. The only thing different that I did was transferring the file that contained the word doc to iCloud for security reasons. However, I don't remember if the problem started after I did this, or before. Anyway. I moved the file back to my Mac, and re-started it just in case. It still does not work.

    B. WITH A NEW WORD DOC - I just tried again with a new blank doc:
    1. I did everything the same as described above; opened the new doc, opened Zotero app; click on Zotero upper tab on word; clicked on "Add/Edit citation".
    2. The app with the list of bibliography opened with no problem
    3. However, this time when clicked on "Add/Edit Citation" button, the red tab to type in the name of the article did not pop up.
    4. I tried this several times and it does not work.

    I did not receive any error message in any moment today when trying to fix this.

    C. DOUBLE BIBLIOGRAPHY THAT APPEARED AFTER I CHANGED THE DEFAULT STYLE TO THE AMERICAN MEDICAL ASSOCIATION:
    I decided to mention this problem because it happened at a certain point today when I was trying to fix the problem described in item A. I thought that problem A could be a problem with the style since it does not look like the style I had before when I sent the article to the editor. So, a changed the default style, but problem A did not go away. I resolved the problem with double bibliography list by discarding the copy of the doc (I delete it) and used a copy of the article before the error happened. So, I didn't really fix the problem. But, I thought of mentioning this so you can evaluate if this is related with the problem A. They may be disconnected problems. I don't know.

    So, I hope that it is better explained now. Thank you for helping. A.


  • B. WITH A NEW WORD DOC - I just tried again with a new blank doc:

    […]

    B. 2. The app with the list of bibliography opened with no problem
    3. However, this time when clicked on "Add/Edit Citation" button, the red tab to type in the name of the article did not pop up.
    Let's focus on this for the moment, since this is the baseline process that we need to make sure is working.

    When you say "The app with the list of bibliography opened with no problem", you're referring to the main Zotero window? That's not supposed to appear when you click Add/Edit Citation. Check to see if the red bar is behind the Zotero window. That's the most likely scenario, so you should cycle through Zotero's windows to see if you can find it. If you can't, restart Zotero and Word and try again, or restart your computer. If you still can't find it, provide a Debug ID for clicking on Add/Edit Citation and having the red bar not appear.

    For A and C, as I say, you should delete all bibliographies in the document and just try re-inserting one. Unless you make manual changes to the bibliography separate from your in-text citations, a Zotero-inserted bibliography is just a tiny field in the document that tells Zotero to generate a bibliography from the list of citations in the document, so you can delete it at any time and just reinsert it. That's what the debugging steps say to do, and it's what you should try. You can toggle field codes in the document to more easily see the citations and bibliography. With field codes displayed, a bibliography will say "ZOTERO_BIBL", so you can search for that to make sure you've fully deleted any bibliographies before you reinsert a new one at the end of the document.
  • edited February 3, 2020
    Thank you. Let's go over what you told me to do:

    1." When you say "The app with the list of bibliography opened with no problem", you're referring to the main Zotero window?" - yes, exactly.
    2. "Check to see if the red bar is behind the Zotero window" - yes, I did this. I tried several times and the red pop-up bar is not anywhere. When I first posted on this forum today, the red bar was showing. Then, when I wrote the last message to you, the red bar starting not showing.
    3. "If you can't, restart Zotero and Word and try again, or restart your computer".- So, I restarted the computer and this is what happened:
    I opened a new doc on word > clicked on Zotero > clicked on "Add/Edit citation" button > the window "Zotero - Document preferences" opened > I clicked on Ok > THE RED POP-UP BAR APPEARED THIS TIME. I typed the name of the article > number 1 appeared where I left the cursor > the reference did not show below.
    I tried several times and still the same.

    So, the red pop-up bar showed, the number appeared where the cursor was, but still no article reference was added on the bibliography list at the end of article.

    YOU SAID: "For A and C, as I say, you should delete all bibliographies in the document and just try re-inserting one" > so this is not clear to me. Are you saying that I should try deleting the bibliography in Zotero app or the bibliography at the end of the word document?

    I deleted the list of references at the end of the article. Then I tried to do what I described in A, to reinsert one article. It did not work. The software did not respond. For example, I deleted the bibliography list at the end of the article, went back to the text and where the number 1 was, I deleted it and tried to insert it again. The number 1 appear again, but the article reference was not added the end of the article... unfortunately.

    The problem seems to be consistently the same... the number shows but the article is not added to the bibliography list at the end of the article.

    YOU SAID: "You can toggle field codes in the document to more easily see the citations and bibliography. With field codes displayed, a bibliography will say "ZOTERO_BIBL", so you can search for that to make sure you've fully deleted any bibliographies before you reinsert a new one at the end of the document".

    So about the filed codes, I went to word preferences > view > field shading > always (I am assuming I should opt for "always" so I can see where the codes are changed, correct?). Going back to the word document, whenever the "unknown filed code changed" appeared, I "accepted the change". So, I accepted all changed of field codes and then I tried to insert the an article. Still didn't work. When I click on "Add/Edit citations", the number shows, but the article is not added at the list of bibliography references at the end of the article.

    Am I doing something wrong???!!!
  • edited February 3, 2020
    I typed the name of the article > number 1 appeared where I left the cursor > the reference did not show below.
    OK, this sounds like it might just be a basic misunderstanding. If you're following what I asked you to do, that would be entirely normal and expected, as you wouldn't have yet inserted a bibliography, as I said to do in a later step. AMA is a numeric style, so all it shows you is a superscripted number in the text until you actually insert a bibliography.

    Let's make sure we're on the same page here before we worry about your existing document.

    But:
    So about the filed codes, I went to word preferences > view > field shading > always (I am assuming I should opt for "always" so I can see where the codes are changed, correct?).
    Leaving that on Always is good, yes, but that's not what I said to do for this — I said to toggle field codes, as explained on the linked page, so you can search for bibliographies in your document by searching for "ZOTERO_BIBL", delete those completely and then insert a new bibliography.
    Going back to the word document, whenever the "unknown filed code changed" appeared, I "accepted the change".
    This is the first you've mentioned that you're using Track Changes, but as the debugging page says, you should accept all changes and then disable Track Changes before proceeding.
  • Good morning,
    So, let's go one-by-one:

    1. YOU SAID: "OK, this sounds like it might just be a basic misunderstanding. If you're following what I asked you to do, that would be entirely normal and expected, as you wouldn't have yet inserted a bibliography, as I said to do in a later step. AMA is a numeric style, so all it shows you is a superscripted number in the text until you actually insert a bibliography" >

    Correct, this is what is expected. However, still the list of bibliography does not form at end of the doc after the article.

    2. YOU SAID: "Leaving that on Always is good, yes, but that's not what I said to do for this — I said to toggle field codes, as explained on the linked page, so you can search for bibliographies in your document by searching for "ZOTERO_BIBL", delete those completely and then insert a new bibliography" >

    I don't understand this. The title of the page says: "Why do I see code beginning with ADDIN ZOTERO_ITEM CSL_CITATION in my document instead of formatted citations?". This page explains why one sees the track codes, how to hide it or turn it off and on on word setting, and how to accept changes. I CANT FIND ANYTHING THAT EXPLAINS HOW TO TOGGLE FIELD CODES TO SHOW ZOTERO_BIBL. Can you please explain this better?

    3.YOU SAID: "This is the first you've mentioned that you're using Track Changes, but as the debugging page says, you should accept all changes and then disable Track Changes before proceeding" >

    I did all the debugging. I just repeated it now. I duplicated my article > accepted all changes > turned off the track changes > tried to insert the article and it did not work. Still same problem. The exact number in the order (e.g. 70) shows but the article is not added to the list after article. Using the same document, I changed the style from AMA to Nature. Still, same problem. Then I deleted the whole list of bibliography at the end of the article, and tried to insert some article, and still the same problem. The problem is very consistent - when I try to insert an article, the exact number (the number which is next in line) shows but teh article is not added to the list of references at the end of the page.

    The editor of the journal requires the revised manuscript to be sent with track changes and in red. However, It seems that the tracking changes being on is not the cause of the problem.

    Thank you for helping. Please let me know how to locate the ZOTERO_BIBL.
    Andréa.
  • edited February 3, 2020
    (Please avoid all-caps. It's seen as shouting in internet forums.)
    Correct, this is what is expected. However, still the list of bibliography does not form at end of the doc after the article.
    I still don't know what you mean here. Again, there won't be a bibliography until you insert a bibliography. So far you still haven't said a single time that you're actually inserting a bibliography into this document or said exactly what's happening when you do.

    Can you save this test document that you believe shows a problem and email it to support@zotero.org with a link to this thread?
    This page explains why one sees the track codes, how to hide it or turn it off and on on word setting, and how to accept changes. I CANT FIND ANYTHING THAT EXPLAINS HOW TO TOGGLE FIELD CODES TO SHOW ZOTERO_BIBL.
    The page is about Word fields, not Track Changes — it only mentions Track Changes in passing. The page explains how to toggle field codes:
    If Word or LibreOffice is showing the field codes, rather than the formatted text, you can hide the field codes by pressing Alt/Option-F9 (or Option-Fn-F9) in Word or Ctrl-F9 in LibreOffice.
    It's the same to go the other direction.
  • @PandoraBox: I asked you to send the new, empty test document, in which you say the bibliography isn't appearing, not the document you've been working on.

    But in the document you sent, you haven't accepted all changes or turned off tracking. You need to do that, and then just delete the existing bibliography — which has become plain text somehow — and reinsert a bibliography using the Add/Edit Bibliography button. Then wait — potentially 5–10 minutes — for the new bibliography to appear, and you'll have a new bibliography based on the citations in the document.
  • One-by-one below:

    1. "Please avoid all-caps. It's seen as shouting in internet forums" > Sorry, I just wanted to highlight some things. There is no bold option here. This is my first time in a public forum.

    2. You wrote: "I still don't know what you mean here. Again, there won't be a bibliography until you insert a bibliography. So far you still haven't said a single time that you're actually inserting a bibliography into this document or said exactly what's happening when you do" >

    Yes, i did explain in a detailed message before. I am transcribing again what I wrote below. I did insert the bibliography and did everything as it is supposed to be done. I have been using Zotero for quite some time. Past articles that I wrote using it were fine. See again what I wrote before. Number 3 says I "entered the name of article, author, date, publication etc... So, no problem here:

    "A. WITH THE ARTICLE I WAS ALREADY WORKING ON:
    1. Everything was working fine, until today afternoon. I wrote a sentence. Put the cursor at the end of the prhase and clicked to determine where the number would be.
    2. Then I opened the Zotero app, and I listed the article name, authors, publication, date, etc..
    3. On word doc, I clicked on the upper tab where it's written Zotero. Then I clicked on Add/Edit citation, then wrote the name of the article (e.g. Zhang 2017); A list of possible articles by Zhang shows and I clicked on the correct one. Then I clicked on the "return" on keyboard. (I have a Mac)
    3. Immediately, a number showed at the end of the phrase in the manuscript where the cursor was (e.g. 70).
    4. To check if the article was listed in the reference list at the end of the article, I scrolled down. The new article was not there. I repeated this process several times and in other places of the article, and it didn't work anymore.
    So, this is the main problem. I have been working for days with the same MO and had no problem. This problem appeared suddenly. The only thing different that I did was transferring the file that contained the word doc to iCloud for security reasons. However, I don't remember if the problem started after I did this, or before. Anyway. I moved the file back to my Mac, and re-started it just in case. It still does not work.

    3. You said: "Can you save this test document that you believe shows a problem and email it to support@zotero.org with a link to this thread?" >
    Yes, I just sent you an email with a test doc. However, I sent you the article by mistake. Please, do not disseminate it as it is copyright protected and the journal owns it. I sent you the correct test doc right after. Thank you.

    I tried to send the link but it did not work.... not sure how to post the link here... sorry.. My email is pretty easy... it's starts with pandora box. I just sent it.

    4. You said: "If Word or LibreOffice is showing the field codes, rather than the formatted text, you can hide the field codes by pressing Alt/Option-F9 (or Option-Fn-F9) in Word or Ctrl-F9 in LibreOffice". >

    Sorry I was very exhausted yesterday. I went online and watched a video about this (see link below). I opened the word doc, and clicked on Control/F9. The filed code did not show. I opened a blank doc as shown in the video, and the field code did not appear.
    Video I watched: https://www.youtube.com/watch?v=hEMgyMaenuQ

  • Yes, I got your last message. I explain above that I sent the wrong doc by mistake. I just sent you the test doc. Sorry about that. As explained, I did replicate the article, accepted all changes, turned off the tracking, deleted the bibliography and tried to reinsert. I did all that several times, but it did not resolve the issue. Hopefully you will be able to figure out the issue with the test doc that I just sent. Thank you!
  • This is simply a misunderstanding of how to use Zotero, or you're not waiting long enough for a bibliography to appear.

    In the test document you sent, you just haven't inserted a bibliography — that's all there is to it. You inserted two citations, but no bibliography. With AMA style, you won't see references until you insert a bibliography.

    In the real document you sent, there was a plain-text bibliography that would never update on its own. You either inserted that the wrong way (e.g., by generating it in Zotero and pasting it in) or it was somehow flattened through the use of Track Changes. Regardless, you need to accept all changes, delete the plain-text bibliography, reinsert a proper bibliography via the plugin's Add/Edit Bibliography button, and wait a number of minutes for the bibliography to appear.
  • So, when you say "You inserted two citations, but no bibliography", what do you mean exactly? By inserting the bibliography do you mean I need to input the article info (name of author, title of article, date, publication, etc) into Zotero? Because I did that... I wrote other articles with Zotero and never had this problem before. Can you please explain what do you mean by inserting the bibliography?

    You said: "Regardless, you need to accept all changes, delete the plain-text bibliography, reinsert a proper bibliography via the plugin's Add/Edit Bibliography button, and wait a number of minutes for the bibliography to appear" >

    yes, I explained it. Because I can't risk messing up with this article, I replicated it and did all that. I sent the article to you by mistake. The one I sent you is not the article I did the debugging. Just so you understand that I understand what you have been saying and I am following your instructions. I tried all that. I accepted all changes, turned off the track changes, delete all bibliography at the end of article, and tried to insert the article again.



  • By inserting the bibliography do you mean I need to input the article info (name of author, title of article, date, publication, etc) into Zotero?
    No. Absolutely nothing to do with that. "Inserting a bibliography" means clicking the Add/Edit Bibliography button in the Zotero toolbar in Word, the exact same way that you click Add/Edit Citation to insert a citation.
  • Ok I get it now...

    1. Yes, I forgot that to start the list of references one needs to click on the "Add/Edit bibliography". So, yes... you are correct. I have been working on the same article for months, so I forgot about this detail. However, having said that, in all the papers that I used Zotero with, I only clicked on the "Add/Edit bibliography" button to start the list of references. Once the list started, I clicked the button "Add/Edit citation", and every time the system would do everything by itself adding each reference on the list. Also, when I added a citation in the middle of the article, It updated the order by itself automatically. So, for me it is really the first time that I need to click on the "Add/Edit Bibliography" button in the middle of an article. It seems straightforward to you, but I never needed to click on it after the reference list had started. The way I was doing worked for me for many articles. I am not sure why now it's not working. So, simple issue but it took us many 1 1/2 day.

    2. I appreciate your help. I would like to suggest that the terms "add/edit citation" button and "add/edit bibliography" buttons are used. I got really confused when you said that I did not add the bibliography. I was understanding the whole time that "add bibliography" meant inserting name, author, date, etc. of the article. So, using the word "button" may facilitate the understanding in future explanations.

    3. So, I would also like to suggest a system that many companies use to troubleshoot issues. Companies are using "screen sharing" which I think is fast and practical. If we had done that, we could have clarified my problem in a few minutes. No need to exchange so many messages, emails. Some people may not like it, but I had IT troubles with apple and another company that sells external hard drives before... one screen sharing with a tech person and things were resolved in just a few minutes. Having to level the vocabulary, clarify misunderstandings and interpretations, and understand how thing are supposed to work takes a long time. Some of us are pressed by time and stressed with due dates. Some of us are not IT people. So, just a constructive suggestion here. Also, sending video links on the step-by-step troubleshooting and how to work with Zotero would be great. Not sure if Zotero has its own videos.

    Anyway, Thank you for the help. I appreciate it!
  • edited February 3, 2020
    Once the list started, I clicked the button "Add/Edit citation", and every time the system would do everything by itself adding each reference on the list.
    Yes, that's how it normally works. But somehow — possibly because of Track Changes — the existing bibliography in your document had become a flattened version, which is why I said to delete it and reinsert it.
    I would like to suggest that the terms "add/edit citation" button and "add/edit bibliography" buttons are used.
    To be fair, I did say "Add/Edit Bibliography button" twice. And in my very first response to you, I said to "click Add/Edit Bibliography" after clicking "Add/Edit Citation". I understand that you're stressed, and not understanding something immediately is fine, but we do try to use very precise language here.
  • edited February 3, 2020
    Yep, you did. It's true. Not trying to blame anybody here. I didn't even remember there was the button "Add/Edit Bibliography". I never use it.. On your 1st response there was no "button" word; you said "click Add/Edit Citation and insert a citation, and then click Add/Edit Bibliography". Then my head went immediately to my MO which was to click on the "add/edit citation" button and then add the name of the article that shows in the pop-up red tab... That's what I understood then. So, now I get it. I am just trying to suggest things for other people that might have a similar problem. All resolved. Thank you so much!! I appreciate your efforts. I do!!! :-) Have a great day!
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