Merge pull request #165477 from rbreslow/dcm2niix-optional-modules

2 files changed, 78 insertions, 7 deletions

diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix
index 36dddad5db5ac..90eef027a8425 100644
--- a/pkgs/applications/science/biology/dcm2niix/default.nix
+++ b/pkgs/applications/science/biology/dcm2niix/default.nix
@@ -1,10 +1,26 @@
-{ lib, stdenv
+{ lib
+, stdenv
 , fetchFromGitHub
+, substituteAll
 , cmake
+, openjpeg
 , libyamlcpp
-, git
+, batchVersion ? false
+, withJpegLs ? true
+, withOpenJpeg ? true
+, withCloudflareZlib ? true
 }:
 
+let
+  cloudflareZlib = fetchFromGitHub {
+    owner = "ningfei";
+    repo = "zlib";
+    # HEAD revision of the gcc.amd64 branch on 2022-04-14. Reminder to update
+    # whenever bumping package version.
+    rev = "fda61188d1d4dcd21545c34c2a2f5cc9b0f5db4b";
+    sha256 = "sha256-qySFwY0VI2BQLO2XoCZeYshXEDnHh6SmJ3MvcBUROWU=";
+  };
+in
 stdenv.mkDerivation rec {
   version = "1.0.20211006";
   pname = "dcm2niix";
@@ -16,18 +32,37 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-fQAVOzynMdSLDfhcYWcaXkFW/mnv4zySGLVJNE7ql/c=";
   };
 
-  nativeBuildInputs = [ cmake git ];
-  buildInputs = [ libyamlcpp ];
+  patches = lib.optionals withCloudflareZlib [
+    (substituteAll {
+      src = ./dont-fetch-external-libs.patch;
+      inherit cloudflareZlib;
+    })
+  ];
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = lib.optionals batchVersion [ libyamlcpp ]
+    ++ lib.optionals withOpenJpeg [ openjpeg openjpeg.dev ];
+
+  cmakeFlags = lib.optionals batchVersion [
+    "-DBATCH_VERSION=ON"
+    "-DYAML-CPP_DIR=${libyamlcpp}/lib/cmake/yaml-cpp"
+  ] ++ lib.optionals withJpegLs [
+    "-DUSE_JPEGLS=ON"
+  ] ++ lib.optionals withOpenJpeg [
+    "-DUSE_OPENJPEG=ON"
+    "-DOpenJPEG_DIR=${openjpeg}/lib/${openjpeg.pname}-${lib.versions.majorMinor openjpeg.version}"
+  ] ++ lib.optionals withCloudflareZlib [
+    "-DZLIB_IMPLEMENTATION=Cloudflare"
+  ];
 
   meta = with lib; {
     description = "DICOM to NIfTI converter";
     longDescription = ''
-      dcm2niix is a designed to convert neuroimaging data from the
-      DICOM format to the NIfTI format.
+      dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.
     '';
     homepage = "https://www.nitrc.org/projects/dcm2nii";
     license = licenses.bsd3;
-    maintainers = [ maintainers.ashgillman ];
+    maintainers = with maintainers; [ ashgillman rbreslow ];
     platforms = platforms.all;
   };
 }
diff --git a/pkgs/applications/science/biology/dcm2niix/dont-fetch-external-libs.patch b/pkgs/applications/science/biology/dcm2niix/dont-fetch-external-libs.patch
new file mode 100644
index 0000000000000..493f0fb11f461
--- /dev/null
+++ b/pkgs/applications/science/biology/dcm2niix/dont-fetch-external-libs.patch
@@ -0,0 +1,36 @@
+diff --git a/SuperBuild/External-CLOUDFLARE-ZLIB.cmake b/SuperBuild/External-CLOUDFLARE-ZLIB.cmake
+index 9f064eb..fe74df5 100644
+--- a/SuperBuild/External-CLOUDFLARE-ZLIB.cmake
++++ b/SuperBuild/External-CLOUDFLARE-ZLIB.cmake
+@@ -1,8 +1,5 @@
+-set(CLOUDFLARE_BRANCH gcc.amd64) # Cloudflare zlib branch
+-
+ ExternalProject_Add(zlib
+-    GIT_REPOSITORY "${git_protocol}://github.com/ningfei/zlib.git"
+-    GIT_TAG "${CLOUDFLARE_BRANCH}"
++    URL file://@cloudflareZlib@
+     SOURCE_DIR cloudflare-zlib
+     BINARY_DIR cloudflare-zlib-build
+     CMAKE_ARGS
+diff --git a/SuperBuild/SuperBuild.cmake b/SuperBuild/SuperBuild.cmake
+index 2a0a956..81354a7 100644
+--- a/SuperBuild/SuperBuild.cmake
++++ b/SuperBuild/SuperBuild.cmake
+@@ -1,17 +1,3 @@
+-# Check if git exists
+-find_package(Git)
+-if(NOT GIT_FOUND)
+-    message(FATAL_ERROR "Cannot find Git. Git is required for Superbuild")
+-endif()
+-
+-# Use git protocol or not
+-option(USE_GIT_PROTOCOL "If behind a firewall turn this off to use http instead." ON)
+-if(USE_GIT_PROTOCOL)
+-    set(git_protocol "git")
+-else()
+-    set(git_protocol "https")
+-endif()
+-
+ # Basic CMake build settings
+ if(NOT CMAKE_BUILD_TYPE)
+     set(CMAKE_BUILD_TYPE "Release" CACHE STRING