jabref: 5.13 -> 6.0-alpha.3 (#370839)

{

  lib,

  stdenv,

  fetchurl,

  fetchFromGitHub,

  wrapGAppsHook3,

  makeDesktopItem,

  copyDesktopItems,

  makeShellWrapper,

  unzip,

  zip,

  xdg-utils,

  gtk3,

  jdk21,

  jdk25,

  openjfx25,

  gradle_8,

  gradle_9,

  python3,

  postgresql,

  jbang,

}:

let

  jdk = jdk21.override {

    enableJavaFX = true;

    openjfx_jdk = openjfx25;

  jdk = jdk25;

  openjfx = openjfx25;

  gradle = gradle_9;

  ltwaUrl = "https://www.issn.org/wp-content/uploads/2021/07/ltwa_20210702.csv";

  ltwa = fetchurl {

    url = ltwaUrl;

    hash = "sha256-jnS8Y9x8eg2L3L3RPnS6INTs19mEtwzfNIjJUw6HtIY=";

  };

  # "Deprecated Gradle features were used in this build, making it incompatible with Gradle 9.0."

  gradle = gradle_8;

in

stdenv.mkDerivation rec {

  version = "5.13";

  version = "6.0-alpha.3";

  pname = "jabref";

  src = fetchFromGitHub {

    owner = "JabRef";

    repo = "jabref";

    rev = "v${version}";

    hash = "sha256-inE2FXAaEEiq7343KwtjEiTEHLtn01AzP0foTpsLoAw=";

    tag = "v${version}";

    hash = "sha256-ZX4LQe8xKZCDJqVh+L9BHkJK82Pz/qPhlaE8SrAin6o=";

    fetchSubmodules = true;

  };

      comment = meta.description;

      name = "JabRef";

      desktopName = "JabRef";

      genericName = "Bibliography manager";

      genericName = "BibTex Editor";

      categories = [ "Office" ];

      icon = "jabref";

      exec = "JabRef %U";

  };

  postPatch = ''

    sed -i -e '/vendor/d' -e '/JavaLanguageVersion/s/24/25/' build-logic/src/main/kotlin/org.jabref.gradle.feature.compile.gradle.kts

    sed -i -e '/javafx-base/s/24.0.1/25/' build-support/src/main/java/*.java

    substituteInPlace build-support/src/main/java/*.java \

      --replace-fail 'JAVA 24' 'JAVA 25'

    sed -i -e '1a //REPOS file://${mitmCache}/https/repo.maven.apache.org/maven2,file://${mitmCache}/https/plugins.gradle.org/m2' build-support/src/main/java/*.java

    pushd jablib

    # Disable update check

    substituteInPlace src/main/java/org/jabref/preferences/JabRefPreferences.java \

      --replace 'VERSION_CHECK_ENABLED, Boolean.TRUE' \

    substituteInPlace src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java \

      --replace-fail 'VERSION_CHECK_ENABLED, Boolean.TRUE' \

        'VERSION_CHECK_ENABLED, Boolean.FALSE'

    # Find OpenOffice/LibreOffice binary

    substituteInPlace src/main/java/org/jabref/logic/openoffice/OpenOfficePreferences.java \

      --replace '/usr' '/run/current-system/sw'

      --replace-fail '/usr' '/run/current-system/sw'

    sed -i -e '/setOutputRedirector/d' src/main/java/org/jabref/logic/search/PostgreServer.java

    substituteInPlace build.gradle.kts \

      --replace-fail '${ltwaUrl}' 'file://${ltwa}'

    popd

  '';

  nativeBuildInputs = [

    jdk

    gradle

    (jbang.override { inherit jdk; })

    wrapGAppsHook3

    copyDesktopItems

    unzip

    zip

    makeShellWrapper

  ];

  buildInputs = [

    install -dm755 $out/share/java/jabref

    install -Dm644 LICENSE $out/share/licenses/jabref/LICENSE

    install -Dm644 src/main/resources/icons/jabref.svg $out/share/pixmaps/jabref.svg

    install -Dm644 jabgui/src/main/resources/icons/jabref.svg $out/share/pixmaps/jabref.svg

    # script to support browser extensions

    install -Dm755 buildres/linux/jabrefHost.py $out/lib/jabrefHost.py

    install -Dm755 jabgui/buildres/linux/jabrefHost.py $out/lib/jabrefHost.py

    patchShebangs $out/lib/jabrefHost.py

    install -Dm644 buildres/linux/native-messaging-host/firefox/org.jabref.jabref.json $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json

    install -Dm644 jabgui/buildres/linux/native-messaging-host/firefox/org.jabref.jabref.json $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json

    sed -i -e "s|/opt/jabref|$out|" $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json

    # Resources in the jar can't be found, workaround copied from AUR

    cp -r build/resources $out/share/java/jabref

    cp -r */build/resources $out/share/java/jabref

    tar xf build/distributions/JabRef-${version}.tar -C $out --strip-components=1

    DEFAULT_JVM_OPTS=$(sed -n -E "s/^DEFAULT_JVM_OPTS='(.*)'$/\1/p" $out/bin/JabRef | sed -e "s|\$APP_HOME|$out|g" -e 's/"//g')

    for tarball in */build/distributions/*.tar; do

      tar xf $tarball -C $out --strip-components=1

    done

    # Temp fix: openjfx doesn't build with webkit

    unzip $out/lib/javafx-web-*-*.jar libjfxwebkit.so -d $out/lib/

    # Use postgresql from nixpkgs since the bundled binary doesn't work on NixOS

    ARCH1=${if stdenv.isAarch64 then "arm64v8" else "amd64"}

    ARCH2=${if stdenv.isAarch64 then "arm_64" else "x86_64"}

    mkdir postgresql

    cd postgresql

    ln -s ${postgresql}/{lib,share} ./

    mkdir -p bin

    ln -s ${postgresql}/bin/{postgres,initdb} ./bin

    # Wrap pg_ctl to workaround https://github.com/NixOS/nixpkgs/issues/83770

    # Use custom wrap to workaround https://github.com/NixOS/nixpkgs/issues/330471

    makeShellWrapper ${postgresql}/bin/pg_ctl ./bin/pg_ctl \

      --add-flags '-o "-k /tmp"'

    chmod +x ./bin/pg_ctl

    jar=$(ls $out/lib/embedded-postgres-binaries-linux-$ARCH1-*.jar)

    tar -cJf postgres-linux-$ARCH2.txz *

    zip $jar postgres-linux-$ARCH2.txz

    cd ..

    runHook postInstall

  '';

  postFixup = ''

    rm $out/bin/*

    for bin in jabgui jabkit jabsrv-cli; do

      DEFAULT_JVM_OPTS=$(sed -n -E "s/^DEFAULT_JVM_OPTS='(.*)'$/\1/p" $out/bin/$bin | sed -e 's/"//g')

      MODULE_PATH=$(sed -n -E 's/^MODULE_PATH=(.*)$/\1/p' $out/bin/$bin | sed -e "s|\$APP_HOME|$out|g")

      MODULE=$(sed -n -E 's/\s*--module (.*) \\/\1/p' $out/bin/$bin)

      rm $out/bin/$bin*

      # put this in postFixup because some gappsWrapperArgs are generated in gappsWrapperArgsHook in preFixup

    makeWrapper ${jdk}/bin/java $out/bin/JabRef \

      makeWrapper ${jdk}/bin/java $out/bin/$bin \

        "''${gappsWrapperArgs[@]}" \

      --suffix PATH : ${lib.makeBinPath [ xdg-utils ]} \

      --add-flags "-Djava.library.path=$out/lib/ --patch-module org.jabref=$out/share/java/jabref/resources/main" \

      --add-flags "$DEFAULT_JVM_OPTS"

        --suffix PATH : ${

          lib.makeBinPath [

            xdg-utils

            postgresql

          ]

        } \

        --add-flags "$DEFAULT_JVM_OPTS \

          -Djava.library.path=$out/lib/:${openjfx}/modules_libs/javafx.graphics:${openjfx}/modules_libs/javafx.media \

          --module-path $MODULE_PATH \

          --module $MODULE"

    done

    # lowercase alias (for convenience and required for browser extensions)

    ln -sf $out/bin/JabRef $out/bin/jabref

    ln -sf $out/bin/jabgui $out/bin/jabref

    ln -sf $out/bin/jabgui $out/bin/JabRef

  '';

  gradleUpdateScript = ''

    runHook preBuild

    # Add jbang deps to gradle

    sed -n 's|//DEPS \(.*\)|    implementation("\1")|p' build-support/src/main/java/*.java | sort -u | sed -i '/dependencies {/r /dev/stdin' build-logic/build.gradle.kts

    gradle nixDownloadDeps -Dos.arch=amd64

    gradle nixDownloadDeps -Dos.arch=aarch64

    gradle assemble -Dos.arch=amd64

    gradle assemble -Dos.arch=aarch64

  '';

  meta = with lib; {

  meta = {

    description = "Open source bibliography reference manager";

    homepage = "https://www.jabref.org";

    sourceProvenance = with sourceTypes; [

    sourceProvenance = with lib.sourceTypes; [

      fromSource

      binaryBytecode # source bundles dependencies as jars

      binaryNativeCode # source bundles dependencies as jars

    ];

    license = licenses.mit;

    license = lib.licenses.mit;

    platforms = [

      "x86_64-linux"

      "aarch64-linux"

    ];

    maintainers = with maintainers; [

    maintainers = with lib.maintainers; [

      linsui

    ];

  };