From 77a7609eb727c53028846d0bf54204cdf9f58f9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= <tclaesson@gmail.com>
Date: Sat, 14 Jan 2023 23:56:43 +0200
Subject: [PATCH] gnu: gdcm: Use system packages where possible.

---
 gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++--
 1 file changed, 45 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e45d33ec2b..41709fd9ed 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17853,7 +17853,29 @@ (define-public gdcm
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))))
+                "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))
+              (modules '((guix build utils)
+                         (ice-9 ftw)))
+              (snippet
+               '(begin
+                  (define (unbundle? file)
+                    (member file '("dicom3tools"
+                                   "gdcmexpat"
+                                   "gdcmutfcpp"
+                                   "gdcmuuid"
+                                   "gdcmzlib"
+                                   "getopt"
+                                   "KWStyle"
+                                   "pvrg"
+                                   "Release"
+                                   "Release"
+                                   "VTK")))
+                  (with-directory-excursion "Utilities"
+                    (for-each (lambda (utility)
+                                (delete-file-recursively utility)
+                                (substitute* "CMakeLists.txt"
+                                  (((string-append ".*/" utility "/.*")) "")))
+                              (scandir "." unbundle?)))))))
     (build-system cmake-build-system)
     (outputs '("out" "bin" "doc"))
     (arguments
@@ -17882,6 +17904,20 @@ (define-public gdcm
                              "|gdcmscu-find-dicomserver"
                              "|TestEcho"
                              "|TestFind'")
+              ;; Libraries
+              "-DGDCM_USE_SYSTEM_EXPAT:BOOL=ON"
+              "-DGDCM_USE_SYSTEM_JSON:BOOL=ON"
+              "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=ON"
+              "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=ON"
+              "-DGDCM_USE_SYSTEM_POPPLER:BOOL=ON"
+              "-DGDCM_USE_SYSTEM_UUID:BOOL=ON"
+              "-DGDCM_USE_SYSTEM_ZLIB:BOOL=ON"
+              ;; TODO: Unbundle these if possible.
+              "-DGDCM_USE_SYSTEM_CHARLS:BOOL=OFF"
+              "-DGDCM_USE_SYSTEM_LJPEG:BOOL=OFF"
+              "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=OFF"
+              "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=OFF"
+              "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=OFF"
               ;; Documentation
               "-DGDCM_DOCUMENTATION:BOOL=ON"
               "-DGDCM_PDF_DOCUMENTATION:BOOL=ON"
@@ -17890,7 +17926,14 @@ (define-public gdcm
               "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF" ;; TODO: need ‘xsl-ns’
               ;; Utilities
               "-DGDCM_BUILD_APPLICATIONS:BOOL=ON")))
-    (native-inputs (list doxygen ghostscript graphviz texlive))
+    (inputs (list expat
+                  json-c
+                  libxml2
+                  openssl
+                  poppler
+                  `(,util-linux "lib")
+                  zlib))
+    (native-inputs (list doxygen ghostscript graphviz pkg-config texlive))
     (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page")
     (synopsis "Grassroots DICOM library")
     (description
-- 
2.38.1