Zotero window never opens

SignalWalker
The application runs seemingly without issue (and I can even use the Firefox extension just fine), but no graphical window ever opens, and no icon appears in the system tray.

OS: NixOS 25.11 (Xantusia) x86_64
Compositor: Hyprland (Wayland)
Zotero version: 7.0.27 (installed with flatpak from Flathub)

Steps to reproduce:
1. `flatpak run org.zotero.Zotero`

I also tried running it after deleting `~/Zotero`, `~/.cache/zotero`, and `~/.zotero`, and got the same result.

The windows that should be opened by `-jsconsole` and `-ZoteroDebug` also don't appear.

`-ZoteroDebugText` output: https://gist.github.com/SignalWalker/5394a35f28be1c2ee686fdd90c389bae
  • poettli
    Please report the issue with this Flatpak in the issue tracker. Meanwhile, you should try with the official tarball (How do I install Zotero?).
  • SignalWalker
    This was also occurring in the Nixpkgs version of Zotero, so I assume it wasn't unique to the Flatpak version -- I just used the Flatpak version for this post because I assumed it was more officially supported, and I forgot to mention that I also tried the regular package manager version.

    ...and I'm using past tense here because, for some reason, when I went to try to get a debug text log for the Nixpkgs version, the GUI appeared perfectly fine. Which is really strange, because I don't think I changed anything between yesterday and today that could have affected it. This problem first appeared a couple months ago, so it doesn't seem like it could have been caused by some ephemeral bug, unless that bug coincidentally happened every time I tried to open Zotero since July.

    Both the Flatpak and Nixpkgs versions work fine today, and they're both still version 7.0.27, and I don't remember updating or changing any major system components between the first post and now.

    I messed with my Qt & GTK themes yesterday after posting this, so maybe that has something to do with it...? That's the only relevant thing I can think of.
  • dstillman
    edited 3 days ago
    I just used the Flatpak version for this post because I assumed it was more officially supported
    To be clear, we have nothing to do with the Flatpak and can only help with the official tarball available from this site (but you're still probably on your own with an esoteric distro like NixOS).
  • SignalWalker
    Oh, it happened again and I figured out the problem:

    1. My wayland compositor is Hyprland, which normally places windows into workspaces, and which has the concept of "special" workspaces, the visibility of which can be toggled with hotkeys.

    2. I'm using a utility called Pyprland to let me define special workspaces for specific applications such that I can toggle their visibility with various hotkeys (ex. Win+Shift+Z for Zotero)

    3. If you try to toggle an application that hasn't been started yet, Pyprland will execute it and then show any windows opened by the executed process.

    4. It seems like Zotero's GUI is managed by a child process, which breaks Pyprland's default process/window tracking and causes it to fail to display the window, leaving it trapped in the special workspace.

    5. I try to diagnose Pyprland's issue by killing Zotero and reopening it from the command line.

    6. Part of how Pyprland works is by applying a configuration at runtime to Hyprland, which is still applied, so the new Zotero window still gets sent to the special workspace and I never see it.

    It worked this morning because I ran it through a terminal (for the debug output) before I tried to use the hotkey I'd set up, so Pyprland never had a chance to tell Hyprland to apply special rules to Zotero windows.

    So this whole time I was just getting tricked by a weird edge case caused by my own hubris.
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