zotero can't open pdf/open links

[teto]

Issue description

I've installed zotero via nix-env and met 2 annoying problems:

• (zotero:2956): WARNING **: Could not launch default application for URI: Operation not supported => can't click on links
• and

qt.qpa.plugin: Could not find the Qt platform plugin "xcb" in ""
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

which prevents me from opening pdfs for some reason :/

Steps to reproduce

Install zotero and try to open pdf/click link.

Technical details

nixos-unstable/sandboxed mode.

[Ma27]

currently building this locally, I'll try to reproduce it :)

[Ma27]

regarding the URL opening issue, thebig problem with zotero is that it seems to love hardcoding things into /usr/bin, so the easiest workaround is to add all of the needed things into our artificial FHS environment:

diff --git a/pkgs/applications/office/zotero/default.nix b/pkgs/applications/office/zotero/default.nix
index b070958b756..29172bff28e 100644
--- a/pkgs/applications/office/zotero/default.nix
+++ b/pkgs/applications/office/zotero/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, buildFHSUserEnv, makeDesktopItem, runCommand, bash, wrapGAppsHook, gsettings-desktop-schemas, gtk3, gnome3 }:
 
 let
-version = "5.0.35.1";
+version = "5.0.57";
 meta = with stdenv.lib; {
   homepage = https://www.zotero.org;
   description = "Collect, organize, cite, and share your research sources";
@@ -15,7 +15,7 @@ zoteroSrc = stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://download.zotero.org/client/release/${version}/Zotero-${version}_linux-x86_64.tar.bz2";
-    sha256 = "0d2imvp84svllrnja1dl4nldp634z632g5xkm2q9v7j3dwbzw1hw";
+    sha256 = "030x780cz178wrd2q75yzibcz9wnxxyb12bblvcjpdsjrd09d5ij";
   };
 
   buildInputs= [ wrapGAppsHook gsettings-desktop-schemas gtk3 gnome3.adwaita-icon-theme gnome3.dconf ];
@@ -34,7 +34,7 @@ fhsEnv = buildFHSUserEnv {
   targetPkgs = pkgs: with pkgs; with xorg; [
     gtk3 dbus-glib
     libXt nss
-    libX11
+    libX11 xdg_utils coreutils firefox which
   ];
 };

But the question is if the can't provide a better solution, we shouldn't force folks to use firefox,but $BROWSER in general, however we can't add all browsers into the FHS closure and I'm currently not sure whatto do about this, but such a patch may solve at least your issues :)

[iimog]

@Ma27 thanks for looking into this. Had the same problem as @teto and can confirm that on my system your solution works. I also added evince to the list of targetPkgs to have pdfs opened there. I see that this is not the best generic solution. Might it be possible to add just the basics (xdg_utils, coreutils, which) by default and controll additional tools like browser or pdf viewer via overlays? This would probably need documentation... Or maybe provide a default browser/pdf viewer and have it adjustable via overlay?

[teto]

thanks for looking into it. Zotero is open source any reason we use a FHS ? I am not familiar with FSH much but it seems to be a pain/break normal expectations.
I guess it's because it relies on firefox one way or another and is not easy to build ?

[Ma27]

@iimog yeah, I thought which packages to add, but I'm not entirely sure how to proceed here.

@teto I had a look into the history of the derivation and it seems as this decision was taken intentionally to work around the excessive /usr/bin usage. There are several examples of package types (such as electron applications) that are fairly hard to build from source, maybe zotero is a similar case. In the long term I guess that this is the best solution (and also avoids FHS hackery), but I'm not sure when I have sufficient time to look into the source and package build (given that it seems to be quite an effort). If you want to do this, feel free, otherwise I'd try to reserve some time to give it a try :)

[teto]

My focus is now on trying to sync my zotero files via webfs otherwise I will fallback on mendeley (which doesn't fully work either and is closed source arg..). I have been trying to use nextcloud but while it works locally, I have some trouble installing it on my server.

Getting rid of the FHS would be better but yeah it's probably quite an effort as zotero is firefox-based (if i get it right). Until I can sync my zotero files via webfs, I can't really ask anything from you so no pressure :)

[Ma27]

whats the problem with the sync? A missing library as well or is there a reported upstream bug? I guess for now it's the best solution IMHO to override targetPkgs of the FHS expression until somebody (maybe me in the next weeks, hopefully) actually implements a source build for this package.

Regarding nextcloud: we can talk in the IRC if you're experiencing issues, I may help (running nextcloud for ~2 months successfully on one of my NixOS servers :))

[teto]

no problem, just you are limited to 300M in the freeplan and I needed more space but I don't want to pay for it. I managed to make nextcloud work, just need to try it with zotero now.

[teto]

zotero's webfs sync work perfectly with nextcloud so consider me interested in an improved zotero :)

[lambdafu]

I just encountered this bug, but I am pretty much a NixOS noob. Maybe it's possible to replace the firefox in the FHS with a script that calls xdg-open?

[Ma27]

Yeah that's an idea. I'm not sure anymore how exactly this worked (it's been a while since I debugged this), but IMHO this is something that could go upstream as well :)

[matthewbauer]

Discussion on this issue is in #42893.

[NickHu]

@matthewbauer The solution described in #42893 doesn't seem to work for me, I'm still unable to get zotero to launch okular

[NickHu]

I managed to get zotero to launch okular (both installed system-wide) without modifying either derivation and setting QT_QPA_PLATFORM_PLUGIN_PATH=/run/current-system/sw/lib/qt-5.12/plugins

[timor]

@NickHu

... and setting QT_QPA_PLATFORM_PLUGIN_PATH=/run/current-system/sw/lib/qt-5.12/plugins

Could you tell me where exactly you set that?

[knedlsepp]

Let's hope for #54525 to fix this

[NickHu]

@NickHu

... and setting QT_QPA_PLATFORM_PLUGIN_PATH=/run/current-system/sw/lib/qt-5.12/plugins

Could you tell me where exactly you set that?

In $HOME/.xprofile, add something like

export QT_QPA_PLATFORM_PLUGIN_PATH=/run/current-system/sw/lib/qt-5.12/plugins

[teto]

i don't use zotero anymore, I suppose this has been fixed.