Bibliography not being generated

pmgoa

Hi,
I’m working on a word document in mac with almost 200 pages.
When I try to generate the bibliography nothing happens. I also experience a quite slow process to add any in-text citation. It can takes more than a couple of minutes to add one citation.
I’m also using the add-in Grammarly. I noticed that Grammarly slows down the performance of the computer, but do you think that there are any incompatibility between these softwares?
Thanks

dstillman

For the bibliography, you're almost certainly just not waiting long enough. A large document in Word for Mac can take a very long time. You can go to Help → Debug Output Logging → View Output to confirm that it's still processing. If you think it's stuck, restart Zotero and try again, and be prepared to wait a while — possibly hours.

For adding a citation, make sure you have "Automatically update citations" disabled in the plugin's Document Preferences window, which will greatly speed up inserting citations in large documents.

pmgoa

Thank you for your help.
I waited the whole night and nothing happened.
Where do I find the command Debug Output Logging? I cannot find it in the help menu.
I will restart everything because not even the document preferences command in the Zotero tab seems to be working.

dstillman

It's exactly what I say: Help → Debug Output Logging → View Output. If you're using a non-English locale, it could be called something else.

To be clear, this is in Zotero, not Word.

pmgoa

Sorry. I was looking for it in word.

pmgoa

I just restarted both apps and retried adding the bibliography.
In the debug output window I got:
"(3)(+0000009): Integration: Request already in progress; not executing MacWord16 addEditBibliography"
Does this mean that it is not running?

dstillman

No, that means you already started an operation and it hasn't finished, so that's not relevant. You need to restart and log from the beginning. And don't press a button more than once until something has happened.

pmgoa

I did and got the following:

(3)(+0046377): Integration: MacWord16-addEditBibliography:'/Applications/Microsoft Word.app/' invoked

(3)(+0000006): Integration: Instantiating @zotero.org/Zotero/integration/application?agent=MacWord16;1 for command addEditBibliography with doc /Applications/Microsoft Word.app/

(3)(+0000003): MacWord: M1 Mac detected. Checking macOS version.

(3)(+0000050): MacWord: macOS version: 13.4.1

(3)(+0000001): MacWord: parsed macOS version: 13,4,1

(4)(+0000140): ZoteroMacWordIntegration: getDocumentData

(4)(+0000347): ZoteroMacWordIntegration: getFieldsAsync

(3)(+0015879): Getting contents of /Users//Library/Application Support/Zotero/Profiles/0pc4zg8u.default/treePrefs.json

(3)(+0000003): Writing column prefs of length 4355 to file /Users//Library/Application Support/Zotero/Profiles/0pc4zg8u.default/treePrefs.json

(3)(+0018283): Checking for unprocessed full-text content

(4)(+0000002): SELECT itemID FROM fulltextItems WHERE synced=2

(3)(+0000002): No unprocessed full-text content found

(3)(+0000000): Unregistering full-text content processor idle observer

(3)(+0000000): Stopping full-text content processor

dstillman

There's nothing wrong there. It's just in the middle of processing.

pmgoa

Zotero just crashed...
I got the following prompt "Zotero fields cannot be inserted here."
I just minimized both windows to have it running in the background.
I'll restart it, but I'm starting to panic... This is my doctoral thesis...

dstillman

Don't minimize anything. That can dramatically slow down processing. Restart Word and Zotero and try again, and just leave it. It will very likely finish if you wait long enough.

dstillman

But also, for "Zotero fields cannot be inserted here.", make sure you're putting your cursor on a new line in the normal body text at the end of the document before clicking Add/Edit Bibliography. The bibliography will be inserted where your cursor is.

(This is assuming you haven't inserted a bibliography already and don't have the placeholder message that's shown for the bibliography when "Automatically update citations" is disabled. If you've already inserted the bibliography once before, you just need to use Refresh to update the bibliography, as the placeholder message will tell you.)

Beyond that, if you have access to a Windows computer, you can also do the final bibliography generation on that computer, even without access to your library. You just need Zotero and the document.

In any case, with "Automatically update citations" disabled, actually inserting citations should be fairly quick, so it's just the final bibliography generation that may take quite a while.

pmgoa

Thank you so much. I think it worked.
At least I have a bibliography. Not sure if it is complete as I got an error message when I got back to the computer. Something like "An error has occurred...".
I'm just going to create a new document version, and unlink citations in this one before it disappears.
But even the unlink citations process is taking a while, but I think it is normal as the document is too big.
I already disabled "Automatically update citations". Let's see how it goes.
Thank you so much for your help.

pmgoa

Just one more question.
Due to the dimension of the document and the number of references in use, when I try to add a new reference, Zotero doesn't show me those already cited, so the probability of duplicating some references is quite high.
There is a way to work around this issue or to check for duplicated references in Word automatically?

dstillman

It will show options under Cited if you wait long enough, but Zotero has to get the list of cited items from Word, and that's what's particularly slow with Word for Mac, so in a large document, it can take a while. There's no workaround here. We're hopefully that we'll be able to speed up performance with Word for Mac in a future version, but that's still a little ways off.

It's a bit odd to frame it as "duplicating" references, though. You cite what's relevant for what you're writing. The point of Cited is mainly to let you quickly add items you've already cited, not to avoid them.

If you really want to avoid cited items, you'd want to just add items you cite to a collection. You could then create a saved search for items not in that collection. You can use Reference Extractor to select the items in Zotero that you've already cited in the document and drag those to a collection to start.

pmgoa

The issue with duplicated references is my fault, due to the organization of the articles in Zotero. I have created several collections, each for a specific subject. But when I find an article to be relevant in different fields, I just drag it into other collections. At first I thought that it would just create an image of the article, but I happen to have duplicated a few.
So when I can’t see those already cited in a document, I may choose a different version of that same article.

dstillman

I'm not sure what you mean here. Dragging the same item to different collections doesn't duplicate anything — it just adds the item to the new collection as well. It's the same item.

pmgoa

I meant dragging from a mac’s folder to Zotero to different collections…
I have to reorganize it all, but now I can’t until I submit my thesis.

dstillman

Note that if you merge the items in Zotero (e.g., in the Duplicate Items view), they’ll be considered the same citations.

pmgoa

I’m trying to do that but it takes time. We can only do that one at a time to select which metadata to keep for the file, right?
I’m trying to reset the manual changes I did to a in-text citation. Is this possible? Or I have to delete and add it again?

dstillman

Duplicate merging is currently one by one, but batch merging will be possible soon.

If you click a modified citation and press Add/Edit Citation, it will prompt you to reset it.

pmgoa

It doesn't prompt me to reset it. Is it available in word for mac?
But I have disabled "Automatically update citations". Since then, every change to references (e.g., adding) will underline with a slashed line.
Is it because this option is disabled? When I try to enable it, both Zotero and word crash.

dstillman

https://www.zotero.org/support/kb/citations_underlined