[Bug] Zotero freezing upon notes sync

[macrospecter]

Is there an existing issue for this?

• I have searched the existing issues

Are you using the latest Zotero and the latest plugin?

• I have confirmed I'm using the latest Zotero and the latest plugin

Environment

• OS: Sequoia 15.3
• Zotero Version: 7.0.3
• Plugin Version: 2.2.5

Describe the bug

Almost every time I make a change to a note in Zotero, and it tries to sync, I get a popup showing a conflicted note issue and then the program freezes (I just get a beachball and can't click anything until I force quit); sometimes, I don't get the conflicted-note popup, but the program freezes anyway. It even sometimes happens when I am just inside a PDF in the PDF viewer in Zotero, but haven't yet changed a note. At this point Zotero is virtually unusable. I'm fairly certain the issue is Better Notes, because when I deactivate the plugin this doesn't happen.

I'm including the debugger info below, but I'm afraid that I can't capture it immediately after the error, because by then the program is frozen and I can't access the menu.

I have noticed that, in the conflicted-note errors, the conflict always seems to be in the links, e.g.: . I'm not sure if that's relevant.

Any idea what might be happening, and how I might fix it? Fwiw, this is only happening on my work computer, which is a Mac Studio running the above-mentioned OS.

Thanks!

Debug Output

1738777253718 addons.xpi-utils WARN disabling legacy extension zotserver@gazanchyan.com

1738777253719 addons.xpi-utils WARN disabling legacy extension zotfile@columbia.edu

1738777253719 addons.xpi-utils WARN disabling legacy extension zotero-authors-column@whacked.github.io

1738777253719 addons.xpi-utils WARN disabling legacy extension zutilo@www.wesailatdawn.com

1738777253725 addons.xpi-utils WARN disabling legacy extension night@tefkah.com

1738777253725 addons.xpi-utils WARN disabling legacy extension date-from-last-modified@iris-advies.com

1738777253725 addons.xpi-utils WARN disabling legacy extension ZoteroQuickLookNG@beaugunderson.com

1738777253726 addons.xpi-utils WARN disabling legacy extension ZoteroAbstractCleaner@carter-tod.com

1738777253726 addons.xpi-utils WARN disabling legacy extension daeda@mit.edu

[JavaScript Error: "TypeError: OS is undefined" {file: "jar:file:///Users/erinmiller/Library/Application%20Support/Zotero/Profiles/grye4vtm.default/extensions/zoteroreference@polygon.org.xpi!/chrome/content/scripts/index.js" line: 15953}]

[JavaScript Error: "TypeError: object[funcSign] is undefined" {file: "jar:file:///Users/erinmiller/Library/Application%20Support/Zotero/Profiles/grye4vtm.default/extensions/zoteroreference@polygon.org.xpi!/chrome/content/scripts/index.js" line: 696}]

[JavaScript Error: "uncaught exception: undefined" {file: "chrome://zotero/content/xpcom/file.js" line: 335}]

[JavaScript Error: "uncaught exception: undefined" {file: "chrome://zotero/content/xpcom/file.js" line: 335}]

[JavaScript Error: "uncaught exception: undefined"]

appName => Zotero, version => 7.0.3 (ARM64), os => macOS 15.3, locale => en-US, extensions => Obsidian Note for Zotero (1.0.1, extension), Zotero Reference (0.5.8, extension), Actions and Tags for Zotero (2.1.0, extension), Better BibTex for Zotero (7.0.5, extension), ZotMoov (1.2.11, extension), Better Notes for Zotero (2.2.5, extension), ZotServer (0.1.2, extension, disabled), ZotFile (5.1.2, extension, disabled), ZoteroAuthorColumn (1.0.1, extension, disabled), Zutilo Utility for Zotero (3.10.0, extension, disabled), Night for Zotero (0.4.23, extension, disabled), Zotero Date From Last Modified (0.1.0, extension, disabled), ZoteroQuickLookNG (2.0.0, extension, disabled), ZoteroAbstractCleaner (0.0.7, extension, disabled), MarkDBConnect (0.0.24, extension, disabled)

(4)(+0000374): SELECT COUNT(*) FROM settings WHERE setting='mImport' AND key='cleanup'

(3)(+0005180): Running /usr/bin/sw_vers '-productVersion'

Anything else?

No response

[windingwind]

Thanks for the report. Unfortunately, the debug output is not helpful.

I remember there was once a similar case, where the users has a super slow disk. Is this also your case?

Generally, for SSD disks, the sync-check should be insensible for at least thousands of notes. How many notes do you have in the plugin's sync manager?

Something that might be helpful with locating the bug:

I get a popup showing a conflicted note issue and then the program freezes (I just get a beachball and can't click anything until I force quit); sometimes, I don't get the conflicted-note popup, but the program freezes anyway.

1. Could you please describe or share a screenshot of the conflict window?
2. Could you please try to manually trigger a syncing in the sync manager and see what happens?
3. Could you please try to set the syncing period in settings to -1, then try to manually trigger a syncing again to see what happens?
4. If you can interact with the conflict resolve window, what happens if you choose to confirm the conflict-merge? Does it pop up again after manually trigger a syncing?

[windingwind]

Also seems like you have a lot of plugins. Is it possible to disable others plugins and try again? (you can call /path/to/zotero -p to create a new profile and only install this plugin there to see what happens)

[macrospecter]

Thanks for the reply. Pretty sure I don't have a slow disk. My Mac Studio is brand new, has an Apple M1 chip and lots of free space. I haven't experienced slowness anywhere—quite the opposite.

I actually only use BetterBibTex, your Tags plugin, and ZotMoov right now. The plugins that showed up in the bug report are just old, disabled plugins that don't work with Zotero 7 - for some reason Zotero registers them when I launch the program. Still, I've tried turning the other plugins off but still have the same issue.

I just tried what you suggested. At first, when I switched to -1 syncing, everything was better. In particular, when I manually synced a note, it worked fine. But when I went to sync all through the Sync Manager, the same thing happened—conflict window + freeze.

Usually I can interact with the popup before the freeze. I have tried all of the options: finish, skip, and unsync. All result in the freeze.

I'm attaching some captures of the conflict resolve window. I'm also attaching a weird distortion in the Tools menu, which seems to have popped up roughly when this started happening—not sure it's relevant.

[windingwind]

Thanks for the reply.

The menu issue is not related and is known for a long time; there will soon be an official API from Zotero to register menus, and that should hopefully fix this bug.

I just tried what you suggested. At first, when I switched to -1 syncing, everything was better. In particular, when I manually synced a note, it worked fine. But when I went to sync all through the Sync Manager, the same thing happened—conflict window + freeze.

How many notes (roughly estimate) you have in the sync manager? Specifically, if you only open the note that has the conflict and sync this note manually, does the program freeze?

[macrospecter]

Okay, great, thanks.

I have about 100 notes in the Sync Manager—maybe a bit more. With the syncing set to every -1 secs, I can sync one note at a time, including a conflict note; it's the syncing through the manager that is an issue. But when I turn the syncing back to my regular 30 or 60 secs, I cannot do any syncing whatsoever without the popup and freeze.

[windingwind]

Thanks, does it still freeze when you sync all notes again after all conflicts are resolved?

[macrospecter]

Yes, unfortunately so. I can unsync each note with conflicts, but still new notes get conflicts. Once I return to auto-sync every 30 seconds, my original setting, I now basically cannot do anything with any note (create new, export new) before the program freezes (without any popup). Also, in one of the screenshots you saw, there was actual no apparent conflict, but I was still getting the conflict resolution window.

…

On Feb 6, 2025 at 12:34 AM -0800, windingwind ***@***.***>, wrote: Thanks, does it still freeze when you sync all notes again after all conflicts are resolved? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[windingwind]

Thanks. Have you ever modified any of the builtin templates? Because this context in the conflict window seems to be part of an annotation/citation, while it's not in the format defined by the plugin.

[macrospecter]

I believe that at some point long ago I modified the File Name and File Header templates, according to templates that have been vetted on the Better Notes forum. I wouldn't have thought that was the problem, because in the past when that's been an issue the notes would fail to export. Below are my versions. I do have a custom template that inserts a hyperlink over the author/title/year and one that inserts a collection of annotations by color.  They don't include any annotations/citations in them, as far as I'm aware (though they do include the citation key). Export MD File Name: ${(noteItem.parentItem ? noteItem.parentItem.getField("citekey") : "")}.md Export MD File Header: ${await new Promise(async (r) => { let header = {}; header.author = noteItem.parentItem ? noteItem.parentItem.getCreators().map((au) => au.firstName + " " + au.lastName).join("; ") : "";header.title = noteItem.parentItem? noteItem.parentItem.getField("title"): "";header.date = noteItem.parentItem? noteItem.parentItem.getField("date"): "";header.tags = noteItem.parentItem.getTags().map((_t) => "#" + _t.tag);header.noteLink = Zotero.BetterNotes.api.convert.note2link(noteItem);r(JSON.stringify(header));})}

…

On Feb 6, 2025 at 2:49 PM -0800, windingwind ***@***.***>, wrote: Thanks. Have you ever modified any of the builtin templates? Because this context in the conflict window seems to be part of an annotation/citation, while it's not in the format defined by the plugin. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[windingwind]

Thanks, i see. these two templates does not affect though. The problem is I cannot reproduce...

If possible, could you please try to load the syncing settings in another device (if you have not tried this before):

Sync Manager -> Detect -> Choose the directory where the markdown files exists

Then the synced notes should be detected. Is it possible to reproduce this freezing bug in this device?

[macrospecter]

Thanks for the suggestion. I do have another computer. I hadn't realized that I could "detect" the notes on another device, but I will try it as soon as I have access to that computer again.

…

On Feb 7, 2025 at 1:01 PM -0800, windingwind ***@***.***>, wrote: Thanks, i see. these two templates does not affect though. The problem is I cannot reproduce... If possible, could you please try to load the syncing settings in another device (if you have not tried this before): Sync Manager -> Detect -> Choose the directory where the markdown files exists Then the synced notes should be detected. Is it possible to reproduce this freezing bug in this device? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[windingwind]

I investigated a bit and probably the freezing is from a large note, where the diff computation takes some time (arguably this computation should be moved to a separate thread, I may don't have much time for that, though)

But the empty diff window is quite weird. Thanks for the reply and please let me know if you have some findings.

[windingwind]

I will try to remake the diff window (the window itself is also too old and does not match the UI style) and hopefully this issue can be resolved. Keep tuned :)