ZoteroDoctor is a Linux utility designed to fix integration issues between the Zotero Flatpak and LibreOffice. It addresses the common problem where the Zotero Flatpak cannot automatically install the required .oxt extension into the host system's LibreOffice installation.

Additionally, it provides fixes for common Zotero Flatpak stability issues, specifically Wayland crashes and interface scaling problems on high-DPI displays.

• LibreOffice Integration: Locates the Zotero_LibreOffice_Integration.oxt file hidden inside the Flatpak container (handling version-specific hash paths) and installs it into the host LibreOffice instance.
• Dependency Management: Automatically checks for and installs required Java dependencies (libreoffice-java-common, default-jre) necessary for the plugin to function.
• Crash Prevention: Applies Flatpak overrides to bypass Wayland socket issues that cause Zotero to crash when opening the citation picker. [Solved in flathub/org.zotero.Zotero#165]
• UI Scaling Fix: Forces the interface scaling factor to 1.0 to prevent the application from appearing too large on GNOME/Wayland setups.

• Python 3.6+
• Root privileges (required to install system dependencies and modify Flatpak overrides).
• Zotero (installed via Flatpak).
• LibreOffice.

Clone this repository or download the script directly.

git clone https://github.com/zoroaster1x/ZoteroDoctor.git
cd ZoteroDoctor
chmod +x zotero_doctor.py

You can run the script interactively or via command-line arguments for automated setups.

Running the script without arguments launches the interactive menu.

sudo ./zotero_doctor.py

The script supports flags for automated deployment or specific repairs.

Install the LibreOffice Plugin only:

sudo ./zotero_doctor.py --action plugin

Apply all fixes (Plugin, Wayland crash fix, UI scaling):

sudo ./zotero_doctor.py --action all

Specify a custom Flatpak ID (if using a fork or beta):

sudo ./zotero_doctor.py --action plugin --flatpak-id org.zotero.ZoteroBeta

Manually specify the location of the .oxt file: If the script cannot locate the extension automatically, you can provide the path explicitly.

sudo ./zotero_doctor.py --action plugin --oxt-path /path/to/Zotero_Integration.oxt

"javaloader error" in LibreOffice: If you see a Java error after installation, ensure you have a Java Runtime Environment (JRE) installed and selected in LibreOffice:

1. Open LibreOffice Writer.
2. Go to Tools > Options > LibreOffice > Advanced.
3. Ensure "Use a Java runtime environment" is checked and a vendor (e.g., Oracle, OpenJDK) is selected in the list.

Script cannot find the user: This script relies on SUDO_USER to identify the non-root account. If you are running this in a chroot or a clean environment where SUDO_USER is not set, specify the target user manually:

sudo ./zotero_doctor.py --action all --target-user myusername

MIT License