Merge pull request #253632 from bzizou/irods-4.3.0

{ lib, stdenv, bzip2, zlib, autoconf, automake, cmake, help2man, texinfo, libtool, cppzmq, libarchive

, avro-cpp, boost, jansson, zeromq, openssl, pam, libiodbc, libkrb5, gcc, libcxx, which, catch2, nanodbc, fmt

, nlohmann_json, spdlog }:

, avro-cpp, boost, zeromq, openssl, pam, libiodbc, libkrb5, gcc, libcxx, which, catch2, nanodbc, fmt

, nlohmann_json, spdlog, curl }:

# Common attributes of irods packages

{

  nativeBuildInputs = [ autoconf automake cmake help2man texinfo which gcc ];

  buildInputs = [ bzip2 zlib libtool cppzmq libarchive avro-cpp jansson zeromq openssl pam libiodbc libkrb5 boost

                  libcxx catch2 nanodbc fmt nlohmann_json spdlog ];

  buildInputs = [ bzip2 zlib libtool cppzmq libarchive avro-cpp zeromq openssl pam libiodbc libkrb5 boost

                  libcxx catch2 nanodbc fmt nlohmann_json spdlog curl ];

  cmakeFlags = [

    "-DIRODS_EXTERNALS_FULLPATH_CLANG=${stdenv.cc}"

    "-DIRODS_EXTERNALS_FULLPATH_ARCHIVE=${libarchive.lib}"

    "-DIRODS_EXTERNALS_FULLPATH_AVRO=${avro-cpp}"

    "-DIRODS_EXTERNALS_FULLPATH_BOOST=${boost}"

    "-DIRODS_EXTERNALS_FULLPATH_JANSSON=${jansson}"

    "-DIRODS_EXTERNALS_FULLPATH_ZMQ=${zeromq}"

    "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ=${cppzmq}"

    "-DIRODS_EXTERNALS_FULLPATH_CATCH2=${catch2}"

  postPatch = ''

    patchShebangs ./packaging ./scripts

    substituteInPlace CMakeLists.txt \

      --replace "DESTINATION usr/bin" "DESTINATION bin" \

      --replace "INCLUDE_DIRS usr/include/" "INCLUDE_DIRS include/" \

      --replace "DESTINATION usr/lib/" "DESTINATION lib/" \

      --replace "{IRODS_EXTERNALS_FULLPATH_JSON}/include" "{IRODS_EXTERNALS_FULLPATH_JSON}/include/nlohmann"

    export cmakeFlags="$cmakeFlags

      -DCMAKE_INSTALL_PREFIX=$out

      -DIRODS_HOME_DIRECTORY=$out

      -DCMAKE_INSTALL_SBINDIR=$out/sbin

    "

  '';

{ lib, stdenv, fetchFromGitHub, bzip2, zlib, autoconf, automake, cmake, help2man, texinfo, libtool, cppzmq

, libarchive, avro-cpp_llvm, boost, jansson, zeromq, openssl, pam, libiodbc, libkrb5, gcc, libcxx, which, catch2

, nanodbc_llvm, fmt, nlohmann_json, spdlog }:

, libarchive, avro-cpp_llvm, boost, zeromq, openssl, pam, libiodbc, libkrb5, gcc, libcxx, which, catch2

, nanodbc_llvm, fmt, nlohmann_json, spdlog, curl }:

let

  avro-cpp = avro-cpp_llvm;

let

  common = import ./common.nix {

    inherit lib stdenv bzip2 zlib autoconf automake cmake

      help2man texinfo libtool cppzmq libarchive jansson

      help2man texinfo libtool cppzmq libarchive

      zeromq openssl pam libiodbc libkrb5 gcc libcxx

      boost avro-cpp which catch2 nanodbc fmt nlohmann_json

      spdlog;

      spdlog curl;

  };

in

rec {

  # irods: libs and server package

  irods = stdenv.mkDerivation (common // rec {

    version = "4.2.11";

  irods = stdenv.mkDerivation (finalAttrs: common // {

    version = "4.3.0";

    pname = "irods";

    src = fetchFromGitHub {

      owner = "irods";

      repo = "irods";

      rev = version;

      sha256 = "0prcsiddk8n3h515jjapgfz1d6hjqywhrkcf6giqd7xc7b0slz44";

      rev = finalAttrs.version;

      sha256 = "sha256-rceDGFpfoFIByzDOtgNIo9JRoVd0syM21MjEKoZUQaE=";

      fetchSubmodules = true;

    };

    # Patches:

    # irods_root_path.patch : the root path is obtained by stripping 3 items of the path,

    #                         but we don't use /usr with nix, so remove only 2 items.

    patches = [ ./irods_root_path.patch ];

    # fix build with recent llvm versions

    env.NIX_CFLAGS_COMPILE = "-Wno-deprecated-register -Wno-deprecated-declarations";

    postPatch = common.postPatch + ''

      patchShebangs ./test

      substituteInPlace plugins/database/CMakeLists.txt --replace "COMMAND cpp" "COMMAND ${gcc.cc}/bin/cpp"

      substituteInPlace cmake/server.cmake --replace "DESTINATION usr/sbin" "DESTINATION sbin"

      substituteInPlace cmake/server.cmake --replace "IRODS_DOC_DIR usr/share" "IRODS_DOC_DIR share"

      substituteInPlace cmake/runtime_library.cmake --replace "DESTINATION usr/lib" "DESTINATION lib"

      substituteInPlace cmake/development_library.cmake --replace "DESTINATION usr/lib" "DESTINATION lib"

      substituteInPlace cmake/development_library.cmake --replace "DESTINATION usr/include" "DESTINATION include"

      for file in unit_tests/cmake/test_config/*.cmake

      do

        substituteInPlace $file --replace "CATCH2}/include" "CATCH2}/include/catch2"

        -DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath,$out/lib

        "

      substituteInPlace cmake/server.cmake --replace SETUID ""

      substituteInPlace server/auth/CMakeLists.txt --replace SETUID ""

    '';

    meta = common.meta // {

  # icommands (CLI) package, depends on the irods package

  irods-icommands = stdenv.mkDerivation (common // rec {

    version = "4.2.11";

  irods-icommands = stdenv.mkDerivation (finalAttrs: common // {

    version = "4.3.0";

    pname = "irods-icommands";

    src = fetchFromGitHub {

      owner = "irods";

      repo = "irods_client_icommands";

      rev = version;

      sha256 = "0wgs585j2lp820py2pbizsk54xgz5id96fhxwwk9lqhbzxhfjhcg";

      rev = finalAttrs.version;

      sha256 = "sha256-90q1GPkoEUoiQXM6cA+DWwth7g8v93V471r9jm+l9aw=";

    };

    patches = [ ./zmqcpp-deprecated-send_recv.patch ];

    buildInputs = common.buildInputs ++ [ irods ];

    postPatch = common.postPatch + ''

diff -r -u irods-4.2.0.orig/scripts/irods/paths.py irods-4.2.0/scripts/irods/paths.py

--- irods-4.2.0.orig/scripts/irods/paths.py	2016-11-15 06:23:55.000000000 +0000

+++ irods-4.2.0/scripts/irods/paths.py	2016-12-21 15:17:07.437864606 +0000

@@ -10,7 +10,7 @@

     return os.path.join(root_directory(), 'var', 'lib', 'irods')

 def config_directory():

-    return os.path.join(root_directory(), 'etc', 'irods')

+    return os.path.join(os.path.abspath('/'), 'etc', 'irods')

 def plugins_directory():

     return os.path.join(root_directory(), 'usr', 'lib', 'irods', 'plugins')

@@ -37,7 +37,7 @@

 def version_path():

     return os.path.join(

-        irods_directory(),

+        home_directory(),

         'VERSION.json')

 def hosts_config_path():

@@ -64,7 +64,7 @@

 def log_directory():

     return os.path.join(

-        irods_directory(),

+        home_directory(),

         'log')

 def control_log_path():

@@ -110,8 +110,7 @@

 def server_bin_directory():

     return os.path.join(

         root_directory(),

-        'usr',

-        'sbin')

+        'bin')

 def server_executable():

     return os.path.join(

@@ -132,7 +131,7 @@

     return os.path.join(config_directory(), 'service_account.config')

 def genosauth_path():

-    return os.path.join(irods_directory(), 'clients', 'bin', 'genOSAuth')

+    return os.path.join(home_directory(), 'clients', 'bin', 'genOSAuth')

 def irods_user_and_group_entries():

     try:

diff -r -u source/src/irods-grid.cpp source.new/src/irods-grid.cpp

--- source/src/irods-grid.cpp	1970-01-01 01:00:01.000000000 +0100

+++ source.new/src/irods-grid.cpp	2020-05-05 16:34:35.566464346 +0200

@@ -412,7 +412,7 @@

             data_to_send.data(),

             data_to_send.size() );

         try {

-            if (!zmq_skt.send(req)) {

+            if (!zmq_skt.send( req, zmq::send_flags::dontwait )) {

                 std::cerr << "ZeroMQ encountered an error sending a message.\n";

                 return errno;

             }

@@ -426,7 +426,7 @@

         zmq::message_t rep;

         // wait for the server reponse

         try {

-            if (!zmq_skt.recv( &rep )) {

+            if (!zmq_skt.recv( rep, zmq::recv_flags::dontwait )) {

                 std::cerr << "ZeroMQ encountered an error receiving a message.\n";

                 return errno;

             }

  idevicerestore = callPackage ../tools/misc/idevicerestore { };

  inherit (callPackages ../tools/filesystems/irods rec {

    stdenv = llvmPackages.libcxxStdenv;

    libcxx = llvmPackages.libcxx;

    boost = boost179.override { inherit stdenv; };

    stdenv = llvmPackages_13.libcxxStdenv;

    libcxx = llvmPackages_13.libcxx;

    boost = boost178.override { inherit stdenv; };

    fmt = fmt_8.override { inherit stdenv; };

    nanodbc_llvm = nanodbc.override { inherit stdenv; };

    avro-cpp_llvm = avro-cpp.override { inherit stdenv boost; };