From cfeca3278464cf6eff7d3620c921a8d238b44404 Mon Sep 17 00:00:00 2001
From: "Markus S. Wamser" <github-dev@mail2013.wamser.eu>
Date: Wed, 21 Oct 2020 23:03:48 +0200
Subject: jabref: 3.8.1 -> 5.1

---
 pkgs/applications/office/jabref/default.nix | 52 +++++++++++++++++++++--------
 1 file changed, 39 insertions(+), 13 deletions(-)

(limited to 'pkgs/applications/office')

diff --git a/pkgs/applications/office/jabref/default.nix b/pkgs/applications/office/jabref/default.nix
index 7ab53b19ce04..03da2170b3d3 100644
--- a/pkgs/applications/office/jabref/default.nix
+++ b/pkgs/applications/office/jabref/default.nix
@@ -1,14 +1,17 @@
-{ stdenv, fetchurl, makeWrapper, makeDesktopItem, jdk, jre, wrapGAppsHook, gtk3, gsettings-desktop-schemas }:
+{ stdenv, fetchurl, makeWrapper, makeDesktopItem, wrapGAppsHook, gtk3, gsettings-desktop-schemas
+, zlib , libX11, libXext, libXi, libXrender, libXtst, libGL, alsaLib, libav, cairo, freetype, pango, gdk-pixbuf, glib }:
 
 stdenv.mkDerivation rec {
-  version = "3.8.1";
+  version = "5.1";
   pname = "jabref";
 
   src = fetchurl {
-    url = "https://github.com/JabRef/jabref/releases/download/v${version}/JabRef-${version}.jar";
-    sha256 = "11asfym74zdq46i217z5n6vc79gylcx8xn7nvwacfqmym0bz79cg";
+    url = "https://github.com/JabRef/jabref/releases/download/v${version}/JabRef-${version}-portable_linux.tar.gz";
+    sha256 = "04f612byrq3agzy26byg1sgrjyhcpa8xfj0ssh8dl8d8vnhx9742";
   };
 
+  preferLocalBuild = true;
+
   desktopItem = makeDesktopItem {
     comment =  meta.description;
     name = "jabref";
@@ -19,21 +22,44 @@ stdenv.mkDerivation rec {
     exec = "jabref";
   };
 
-  buildInputs = [ makeWrapper jdk wrapGAppsHook gtk3 gsettings-desktop-schemas ];
+  nativeBuildInputs = [ makeWrapper wrapGAppsHook ];
+  buildInputs = [ gsettings-desktop-schemas ] ++ systemLibs;
 
-  dontUnpack = true;
+  systemLibs = [ gtk3 zlib libX11 libXext libXi libXrender libXtst libGL alsaLib libav cairo freetype pango gdk-pixbuf glib ];
+  systemLibPaths = stdenv.lib.makeLibraryPath systemLibs;
 
   installPhase = ''
-    mkdir -p $out/bin $out/share/java $out/share/icons
+    mkdir -p $out/share/java $out/share/icons
 
-    cp -r ${desktopItem}/share/applications $out/share/
+    cp -r lib $out/lib
+
+    for f in $out/lib/runtime/bin/j*; do
+      patchelf \
+        --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
+        --set-rpath "${ stdenv.lib.makeLibraryPath [ zlib ]}:$out/lib/runtime/lib:$out/lib/runtime/lib/server" $f
+    done
+
+    for f in $out/lib/runtime/lib/*.so; do
+      patchelf \
+        --set-rpath "${systemLibPaths}:$out/lib/runtime/lib:$out/lib/runtime/lib/server" $f
+    done
 
-    jar xf $src images/icons/JabRef-icon-mac.svg
-    cp images/icons/JabRef-icon-mac.svg $out/share/icons/jabref.svg
+    # patching the libs in the JImage runtime image is quite impossible as there is no documented way
+    # of rebuilding the image after it has been extracted
+    # the image format itself is "intendedly not documented" - maybe one of the reasons the
+    # devolpers constantly broke "jimage recreate" and dropped it in OpenJDK 9 Build 116 Early Access
+    # so, for now just copy the image and provide our lib paths through the wrapper
+
+    makeWrapper $out/lib/runtime/bin/java $out/bin/jabref \
+      --add-flags '-Djava.library.path=${systemLibPaths}' --add-flags "-p $out/lib/app -m org.jabref/org.jabref.JabRefLauncher" \
+      --run 'export LD_LIBRARY_PATH=${systemLibPaths}:$LD_LIBRARY_PATH'
+
+    cp -r ${desktopItem}/share/applications $out/share/
 
-    ln -s $src $out/share/java/jabref-${version}.jar
-    makeWrapper ${jre}/bin/java $out/bin/jabref \
-      --add-flags "-jar $out/share/java/jabref-${version}.jar"
+    # we still need to unpack the runtime image to get the icon
+    mkdir unpacked
+    $out/lib/runtime/bin/jimage extract --dir=./unpacked lib/runtime/lib/modules
+    cp unpacked/org.jabref/icons/jabref.svg $out/share/icons/jabref.svg
   '';
 
   meta = with stdenv.lib; {
-- 
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