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Merge pull request #253632 from bzizou/irods-4.3.0

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irods: 4.2.11 -> 4.3.0
This commit is contained in:
Weijia Wang 2023-09-06 18:10:10 +02:00 committed by GitHub
commit 4c6e02a683
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GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 22 additions and 108 deletions
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16
pkgs/tools/filesystems/irods/common.nix
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@ -1,13 +1,13 @@
{ 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=${stdenv.cc}"
@ -15,7 +15,6 @@
"-DIRODS_EXTERNALS_FULLPATH_ARCHIVE=${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}"
@ -31,13 +30,10 @@
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
"
'';

38
pkgs/tools/filesystems/irods/default.nix
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@ -1,6 +1,6 @@
{ 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;
@ -9,43 +9,33 @@ in
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 $file --replace "CATCH2}/include" "CATCH2}/include/catch2"
@ -56,7 +46,7 @@ rec {
-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath,$out/lib
"
substituteInPlace cmake/server.cmake --replace SETUID ""
substituteInPlace server/auth/CMakeLists.txt --replace SETUID ""
'';
meta = common.meta // {
@ -66,19 +56,17 @@ rec {
# 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 + ''

49
pkgs/tools/filesystems/irods/irods_root_path.patch
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@ -1,49 +0,0 @@
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:

21
pkgs/tools/filesystems/irods/zmqcpp-deprecated-send_recv.patch
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@ -1,21 +0,0 @@
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;
}

6
pkgs/top-level/all-packages.nix
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@ -9310,9 +9310,9 @@ with pkgs;
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; };