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Full home directory access was removed in #70 after the discussion in #65, which unfortunately has led to a spate of confused people in the Zotero Forums and on Twitter not understanding why they can't see all their folders. (Most recent is here.)

Many Zotero users on Linux are unfamiliar with sandboxes (and/or don't even realize they're using a third-party package) and are confused by this behavior, which just seems like a bug in Zotero to them. As suggested by @danielwe in #65 (comment), it's common for people to want to interact with other parts of the home directory, both when using native Zotero functions and particularly when using plugins.

We (the Zotero team) would like to ask that full home directory access be restored, which brings this package more in line with Zotero's intended behavior. People who want more restrictive access can manually disallow access.

Known issue for some flatpak apps (e.g. GIMP). When running Zoetro, a second icon is shown in the Dock (plank). Here's a workaround, but not sure how to implement it for Zotero:

https://elementaryos.stackexchange.com/questions/18/one-of-my-apps-has-a-second-fuzzy-icon-in-plank-how-can-i-workaround-this

OS: elementaryOS 5.1.7 Hera

The Ztero 7 Beta FLATPAK closes whenever I insert a citation into a document (GDocs or Libre Writer on Linux). The problem is unique to the Flatpak install (the tarball version works fine). Saving documents via the Firefox connector works fine.

Anybody got a clue why or how we can fix it?
Thanks

Thanks for maintaining this package.

It's not clear from the Flatpak description that this is a third-party package that's not produced by the Zotero team, and when people encounter confusing issues with the package they believe they're experiencing a Zotero bug.

We'd like to ask that a message similar to the one on various other packages be added:

NOTE: This wrapper is not verified by, affiliated with, or supported by the Zotero project.

If people come to the Zotero Forums with issues unrelated to the packaging, we'll do our best to help them, but they should know that they're using an unofficial version.

The "Developer" field should also be changed to "Corporation for Digital Scholarship", not "The Corporation for Digital Scholarship".

There will be updates for this flatpak?
The actual version is 5.0.56 (October 9, 2018) and there was 2 versions after that.
Maybe be a option try contact the developers of Zotero to mantain the flatpak version?

The zotero addon for libreoffice can't insert items from zotero, and the webpage can't be saved to zotero using zotero addon for chrome.

Zotero 6 has just been released and I'd be happy to use the updated version :)

I've never contributed here but if you point me in the right direction I may be able to make a PR.

Thanks for your work!

I have my zotero folder installed on a separate NTFS partition, so that I can share it between windows and linux (I really need to work in Windows sometimes). However using this flathub package I can not acces the external disk. I found also this on stackexchange. What do you think about changing the filesystem permissions (possibly in an alternative flathub package)?
It was an annoying surprise to see that the package did not work and it took precious time to find out why it did not work? Otherwise shouldn't this issue be mentioned in the package description?

It's possible this is a result of me not having configured the sandbox permissions properly, but merging duplicates in this release does not result in the duplicate entries disappearing. You select the one whose metadata you want to keep, then press merge. The metadata is shared between both items, but the duplicate item has to be deleted manually.

Am I missing something here?

Hello,

Since the last Zotero flatpak update, I'm having issues with extracting annotations from pdfs with the Zotfile plugin (http://zotfile.com/) whereas it was working perfectly before. The option simply disappeared from the "attached files" contextual menu.

Since the behaviour only appeared after a Zotero update, could it be related to the update? Could for instance a dependency not been met (zotfile uses pdf.js to extract annotations)?

I have configured the Zotero data dir to a custom location ~/.zotero_data, and I allowed it access to it via flatpak override. This works all fine, however, on every launch, the folder ~/Zotero gets created (empty) nonetheless... This is really annoying.

I don't know whether this is an issue of Zotero or the flatpak, but it is new. Didn't had an issue like that before upgrading today.

It would be helpful to have a flathub ARM build (e.g. Chromebooks, Raspberry Pi, Pinebook Pro). The latest version has been packaged on Arch (https://aur.archlinux.org/packages/zotero-arm-bin/), with the exception of PDF indexing.

In the preferences I set that Zotero should use the system's default PDF viewer to open PDFs. However, every time I open a PDF, Zotero asks which viewer to use.
Is there a way to fix this?

Zotero has a repo for beta build: https://www.zotero.org/support/beta_builds, and flathub supports beta channel: https://discourse.flathub.org/t/how-to-use-flathub-beta/2111

Is it possible to package beta build of Zotero on flathub?

The reason I want beta build is that Zotero 7 beta finally supports wayland windowing session. Thank you so much!

I am on Debian 9.6, and I am currently unable to open pdf files or nautilus through Zotero. It seems to be a problem with the connection with xdg-open.

When I try to open a pdf file I get the following:

Jan  9 10:35:39 baltra org.zotero.Zotero.desktop[5250]: Possibly unhandled rejec
tion:
Jan  9 10:35:39 baltra org.zotero.Zotero.desktop[5250]: /usr/bin/xdg-open returned exit status 4
Jan  9 10:35:39 baltra org.zotero.Zotero.desktop[5250]: Error: /usr/bin/xdg-open returned exit status 4
Jan  9 10:35:39 baltra org.zotero.Zotero.desktop[5250]:     Zotero.Utilities.Internal.exec</<.observe@chrome://zotero/content/xpcom/utilities_internal.js:516:22
Jan  9 10:40:46 baltra gnome-shell[1965]: Ignoring excess values in shadow definition
Jan  9 10:40:46 baltra gnome-shell[1965]: Ignoring excess values in shadow definition
Jan  9 10:40:46 baltra gnome-shell[1965]: Ignoring excess values in shadow definition
Jan  9 10:40:46 baltra gnome-shell[1965]: Ignoring excess values in shadow definition
Jan  9 10:40:46 baltra gnome-shell[1965]: cr_parser_new_from_buf: assertion 'a_buf && a_len' failed

When I try to open the folder:

Jan  9 10:41:48 baltra zotero-bin[5297]: Cannot launch default application: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such method 'OpenFile'
Jan  9 10:41:48 baltra zotero-bin[5297]: Cannot launch default application: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such method 'OpenFile'
Jan  9 10:41:48 baltra org.zotero.Zotero.desktop[5250]: Failed to call portal: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such method 'OpenFile'
Jan  9 10:41:48 baltra org.zotero.Zotero.desktop[5250]: Possibly unhandled rejection:
Jan  9 10:41:48 baltra org.zotero.Zotero.desktop[5250]: /usr/bin/xdg-open returned exit status 4
Jan  9 10:41:48 baltra org.zotero.Zotero.desktop[5250]: Error: /usr/bin/xdg-open returned exit status 4
Jan  9 10:41:48 baltra org.zotero.Zotero.desktop[5250]:     Zotero.Utilities.Internal.exec</<.observe@chrome://zotero/content/xpcom/utilities_internal.js:516:22

Is it a config problem perhaps?

How can i change which browser zotero uses to open a HTML file?
It's seems to be stuck with the default browser at the time of installation, which i've since changed.

The download URL of latest version can be read from

curl -I 'https://www.zotero.org/download/client/dl?channel=release&platform=linux-x86_64' | grep Location

Additionally do not forget https://www.zotero.org/download/client/dl?channel=release&platform=linux-i686

All the releases and their corresponding dates can be read from
https://api.github.com/repos/zotero/zotero/git/refs/tags

For app store visibility this needs a category. I've created a downstream issue and PR to track this: zotero/zotero-standalone-build#63 but it could also be patched here in the interim with desktop-file-edit

The current screenshot is from the macOS version :/

Attached, is the error I keep receiving. Which folder would I need to modify permissions so it updates?

This flatpak should do a better job at isolating the software from the rest of the system:

... the use of portals for documents, desktop and downloads is great, but why do we need access to the entire $HOME directory? (And arguably, do we really need access to the other directories as well?) I understand it might be necessary to access the zotero database (say in ~/Zotero?) but in that case, shouldn't we restrict to that directory only?

It would be great to have instructions on how to secure this a little further, in any ways...

An attempt to view a PDF file stored in the Zotero database (right click on entry, select "View PDF") on standard Fedora installation fails, with the error message below. Same for other means to access the stored PDF files (open folder etc.). Without this, the user must manually search for PDF files in the Zotero data directory, perhaps the required permissions to do xdg-open should be added to permit this ?

** (zotero:6): WARNING **: Cannot launch default application: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.portal.Desktop was not provided by any .service files
Failed to call portal: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.portal.Desktop was not provided by any .service files
Possibly unhandled rejection:

/usr/bin/xdg-open returned exit status 4

Error: /usr/bin/xdg-open returned exit status 4
Zotero.Utilities.Internal.exec</<.observe@chrome://zotero/content/xpcom/utilities_internal.js:516:22

In short: the better-biblatex plugin looks for git in PATH, and uses it to push auto-exported files to the default remote. (Feature documented here)

Problem: It doesn't work with Zotero from flathub, and my guess it that git most likely isn't available in the virtual environment.

Solutions would most likely be to either include a copy of git, or somehow let Zotero access the system-wide git.

https://www.zotero.org/support/dev/translators/scaffold which is probably related to sandboxing.

When trying to update to the latest version I'm getting the following error:
Error: While pulling app/org.zotero.Zotero/x86_64/stable from remote flathub: GPG signatures found, but none are in trusted keyring

Might be related to this? I'm only facing it with Zotero at the time being though.

When I run zotero-ocr plugin with tesseract installed in the system, I get

No tesseract executable found.

Is there a way to allow Zotero to execute a system executable? I read the docs on permissions, but could not get it right.

Linux distribution and version: Fedora 32
Flatpak version: 5.0.93

Description of the problem

After finishing installation, settings (like data sync info) and library won't be saved without further action.
I'm not sure if this is due to recent changes in flatpak permissions or what happened but Zotero needs these directories in order to store preferences/library:

• ~/Zotero
• ~/.zotero/zotero

Steps to reproduce

1. Install the flatpak and launch the application.
2. After syncing or doing any changes to setings/library, close it.
3. Next launch won't have any of the previous changes.

Workaround / Temporary Fix

1. Finish installation.
2. Manually create the necessary directories by running: mkdir -pv ~/Zotero ~/.zotero/zotero

Again, I'm not sure this is an issue with the flatpak (I hope the maintainers will confirm that) but I guess this is the best place to share this workaround/document the problem for future users.

cf. https://www.zotero.org/blog/zotero-5-0-36/

Zotero flatpak should never ask to self-update to avoid users gettting update warning (e.g. #6 ) when in fact the updates are through the flatpak system.

according to dan stillman this is as simple as setting app.update.enabled to false in the bundled prefs.js. I got that spurious update message again today so presumably this is still a problem.

I'm trying to install the Better BibTex extension but Zotero doesn't even show the .xpi file on the the addon manager. Trying to drag the addon inside the addon manager windows gives the following incompatible error message:

Since the Zotero flatpak version is the last one available and the plugin version is only 16 days old, I believe it's not likely to be a version compatibility problem.

Zotero: 5.0.80
Flatpak: latest version from flathub (December 3, 2019)

Recently I haven't been able to drag and drop files into my collection of papers. I am using wayland with fedora 31, however that hasn't been an issue before. The pdf's I am trying to add are in my home directory, so Zotero should have access to them.

This app needs one or more screenshots added to the appdata

I have the flatpak installed on an Arch box and Zotero closes on its own after a short time. None of the error console, debug logs, or the cli output show the same thing each time this happens, so I'm not sure how do even triage it.
Here's my flatpak info org.zotero.Zotero:

Zotero - Collect, organize, cite, and share research

          ID: org.zotero.Zotero
         Ref: app/org.zotero.Zotero/x86_64/stable
        Arch: x86_64
      Branch: stable
     Version: 6.0.13
     License: AGPL-3.0
      Origin: flathub
  Collection: org.flathub.Stable
Installation: system
   Installed: 139.0 MB
     Runtime: org.freedesktop.Platform/x86_64/21.08
         Sdk: org.freedesktop.Sdk/x86_64/21.08

      Commit: fafbc2d63f1b8f02b0f9d4bb3975ec949e03d2539eb9c8af3c02504e6e6f516f
      Parent: 7e2a7c3b2c24154b7b5f0fb6fcbcef496164c277fbff2d70ce7ce9fd912f22d7
     Subject: Update to Zotero 6.0.13 (25744627)
        Date: 2022-08-22 01:00:32 +0000

When running flatpak run org.zotero.Zotero, I get Error: no DISPLAY environment variable specified. I tried running DISPLAY=Wayland flatpak run org.zotero.Zotero, but I get the same error.

How could I debug this? Could you help me?

Thanks a lot!

This flatpak app seems to ignore my system wide proxy settings and can therefore not connect to the internet.
System: Ubuntu 22.04
DE: Gnome 42.9
Proxy set in Gnome settings / Network / Network Proxy

Since some webdav servers are not directly accessible in some regions (like mine, China), a proxy must be used to connect to them. Also, some zotero plugins that rely on google translate must use a proxy to work properly.

Also, proxy is needed if you need to access webdav servers through tor network.

Can I convince zotero somehow to use a specific proxy server or to obey the system proxy settings? Note that the chromium flatpak had the same issue before, but that was fixed. Maybe something similar needs to be done for zotero?

As Zotero Flatpak is now, it just can access files in home. If the user has his documents or database at another partition (a normal scenario), the user needs to override permissions via CLI to access his Zotero.

Because at this situation the Zotero description in Flathub has a "hint" to new users.

We could improve this, giving permission to xdg-desktop. xdg-documents and xdg-download. With this simple change, Zotero could access files at default dirs to Desktop, Downloads and Documents (without problems if these dirs are located at another disk).

This probably will cover the majority of use cases (e.g.: Zotero database at somewhere in xdg-documents, new PDF files to add located at xdg-download) ... bringing a better initial experience and we could remove the "frightening hint" of Flatpak CLI commands at Zotero Flatpak description.

Someone has any objections?

Is this an issue with the flatpak or a general issue with Zotero? Because on some places there is white text on white background in dark mode for example...

I think the desktop file should be patched with the MimeType=x-scheme-handler/zotero; directive to enable the zotero:// URL scheme.

More info: https://forums.zotero.org/discussion/78550/getting-zotero-to-work-under-ubuntu-linux-solved

The Better BibTex add-on has a feature to push citation keys to TeXstudio which does not work with this version of Zotero because it cannot find TeXstudio (I already mentioned that here). I'm no Flatpak expert. Can you tell me how I can allow Zotero to find TeXstudio (installed in the host system)?

Use the Persistent path permission for both Zotero and .zotero folder:

This change will enable

• better sandboxing: app with user home path permission will not be able to see zotero content
• Less pollution in the home folder

We might also need to remove home folder permission as well, for this change to work.

Similar to #6. It seems that I am not able to update Zotero since 6.0.0. Now the latest version is 6.0.3. Thank you!