irods: 4.2.2 -> 4.2.7 + fixed + use fetchFromGitHub

pkgs/tools/filesystems/irods/common.nix

···
-{ stdenv, bzip2, zlib, autoconf, automake, cmake, gnumake, help2man , texinfo, libtool , cppzmq , libarchive, avro-cpp, boost, jansson, zeromq, openssl, pam, libiodbc, kerberos, gcc, libcxx, which }:
+{ stdenv, bzip2, zlib, autoconf, automake, cmake, gnumake, help2man , texinfo, libtool , cppzmq , libarchive, avro-cpp, boost, jansson, zeromq, openssl, pam, libiodbc, kerberos, gcc, libcxx, which, catch2 }:
 
 # Common attributes of irods packages
 
···
 {
   enableParallelBuilding = true;
 
-  buildInputs = [ bzip2 zlib autoconf automake cmake gnumake help2man texinfo libtool cppzmq libarchive avro-cpp jansson zeromq openssl pam libiodbc kerberos gcc boost libcxx which ];
+  buildInputs = [ bzip2 zlib autoconf automake cmake gnumake help2man texinfo libtool cppzmq libarchive avro-cpp jansson zeromq openssl pam libiodbc kerberos gcc boost libcxx which catch2 ];
 
   cmakeFlags = [
     "-DIRODS_EXTERNALS_FULLPATH_CLANG=${stdenv.cc}"
···
     "-DIRODS_EXTERNALS_FULLPATH_JANSSON=${jansson}"
     "-DIRODS_EXTERNALS_FULLPATH_ZMQ=${zeromq}"
     "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ=${cppzmq}"
+    "-DIRODS_EXTERNALS_FULLPATH_CATCH2=${catch2}"
     "-DIRODS_LINUX_DISTRIBUTION_NAME=nix"
     "-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=${builtins.nixVersion}"
     "-DCPACK_GENERATOR=TGZ"

pkgs/tools/filesystems/irods/default.nix

···
-{ stdenv, fetchurl, bzip2, zlib, autoconf, automake, cmake, gnumake, help2man , texinfo, libtool , cppzmq , libarchive, avro-cpp_llvm, boost, jansson, zeromq, openssl , pam, libiodbc, kerberos, gcc, libcxx, which }:
+{ stdenv, fetchFromGitHub, bzip2, zlib, autoconf, automake, cmake, gnumake, help2man , texinfo, libtool , cppzmq , libarchive, avro-cpp_llvm, boost, jansson, zeromq, openssl , pam, libiodbc, kerberos, gcc, libcxx, which, catch2 }:
 
 with stdenv;
 
···
     inherit stdenv bzip2 zlib autoconf automake cmake gnumake
             help2man texinfo libtool cppzmq libarchive jansson
             zeromq openssl pam libiodbc kerberos gcc libcxx
-            boost avro-cpp which;
+            boost avro-cpp which catch2;
   };
 in rec {
 
   # irods: libs and server package
   irods = stdenv.mkDerivation (common // rec {
-    version = "4.2.2";
-    prefix = "irods";
-    name = "${prefix}-${version}";
+    version = "4.2.7";
+    pname = "irods";
 
-    src = fetchurl {
-      url = "https://github.com/irods/irods/releases/download/${version}/irods-${version}.tar.gz";
-      sha256 = "0b89hs7sizwrs2ja7jl521byiwb58g297p0p7zg5frxmv4ig8dw7";
+    src = fetchFromGitHub {
+      owner = "irods";
+      repo = "irods";
+      rev = version;
+      sha256 = "1pd4l42z4igzf0l8xbp7yz0nhzsv47ziv5qj8q1hh6pfhmwlzp9s";
+      fetchSubmodules = true;
     };
 
     # Patches:
···
       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 $file --replace "CATCH2}/include" "CATCH2}/include/catch2"
+      done
       export cmakeFlags="$cmakeFlags
         -DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath,$out/lib
         -DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath,$out/lib
···
 
   # icommands (CLI) package, depends on the irods package
   irods-icommands = stdenv.mkDerivation (common // rec {
-     version = "4.2.2";
-     name = "irods-icommands-${version}";
-     src = fetchurl {
-       url = "https://github.com/irods/irods_client_icommands/archive/${version}.tar.gz";
-       sha256 = "15zcxrx0q5c3rli3snd0b2q4i0hs3zzcrbpnibbhsip855qvs77h";
+     version = "4.2.7";
+     pname = "irods-icommands";
+
+     src = fetchFromGitHub {
+       owner = "irods";
+       repo = "irods_client_icommands";
+       rev = version;
+       sha256 = "08hqrc9iaw0y9rrrcknnl5mzbcrsvqc39pwvm62fipl3vnfqryli";
      };
+
+     patches = [ ./zmqcpp-deprecated-send_recv.patch ];
 
      buildInputs = common.buildInputs ++ [ irods ];
 
···
        description = common.meta.description + " CLI clients";
        longDescription = common.meta.longDescription + ''
          This package provides the CLI clients, called 'icommands'.'';
-       broken = true;
      };
   });
 }

pkgs/tools/filesystems/irods/zmqcpp-deprecated-send_recv.patch

···
+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;
+             }