Subject: [bug#55538] [PATCH] gnu: virtuoso-ose: Update to 7.2.7.

From: Roel Janssen <[email-masked]>
Date: Fri, 27 May 2022 12:47:18 +0200

On Wed, 2022-05-25 at 17:51 +0200, Roel Janssen wrote:
> On Wed, 2022-05-25 at 10:29 -0400, Maxim Cournoyer wrote:
> > Hi Roel,
> > 
> > Roel Janssen <[email-masked]> writes:
> > 
> > > Dear Guix,
> > > 
> > > I'd like to update Virtuoso OSE to the latest release (see attached patch).
> > > 
> > > Other than the version number and checksum bump I noticed that some JAR files made it in the
> > > build
> > > output.  I tried removing them from the source tarball using a snippet, but then one needs to
> > > include a patch for various Makefile.am files and run the autogen.sh script.  I thought this
> > > was
> > > simpler and clearer on what's actually achieved.
> > 
> > I fear in the future it would be easy to overlook the introduction of
> > extra bundled jars in the source, that'd get installed.  I feel it'd be
> > preferable if we removed them all from a source snippet, at the cost of
> > having to patch the build system (the extra complications you
> > mentioned).
> > 
> > Could you try it and send a revised patch?
> > 
> 
> Thank you for taking a look at it! To be fair, what the patches would do, would be to avoid
> including the directories that I remove. So removing the current pre-built binaries in a snippet
> will be equally error-prone.
> 
> But I agree that you would preferably want to have a source tarball without pre-built binaries in
> it
> when running `guix build -S virtuoso-ose`.
> 
> A naive patch leads to the build getting stuck, so I need to investigate the impact further.
> I'll report back when I have adapted the patch.
> 
> THank you again for your time!

I attached an updated patch that removes the pre-built binaries in a snippet. It then removes these
directories from the build system which in turn requires one to re-run autogen.sh.

Kind regards,
Roel Janssen

From 1f3b9db55cac790711ece613f5ebeb51474764a7 Mon Sep 17 00:00:00 2001
From: Roel Janssen <[email-masked]>
Date: Fri, 27 May 2022 12:40:46 +0200
Subject: [PATCH] gnu: virtuoso-ose: Update to 7.2.7.

* gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen
  after applying the patch below.
* gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch:
  New file.
---
 gnu/packages/databases.scm                    |  26 +++-
 ...tuoso-ose-remove-pre-built-jar-files.patch | 117 ++++++++++++++++++
 2 files changed, 141 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 2161340ef9..58b6dd088c 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -100,6 +100,7 @@ (define-module (gnu packages databases)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages gperf)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages icu4c)
@@ -3229,14 +3230,30 @@ (define-public python-lmdb
 (define-public virtuoso-ose
   (package
     (name "virtuoso-ose")
-    (version "7.2.6")
+    (version "7.2.7")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/virtuoso/virtuoso/" version "/"
                            "virtuoso-opensource-" version ".tar.gz"))
        (sha256
-        (base32 "0ly7s7a3w2a2zhhi9rq9k2qlnzapqbbc1rcdqb3zqqpgg81krz9q"))))
+        (base32 "1853ln0smiilf3pni70gq6nmi9ps039cy44g6b5i9d2z1n9hnj02"))
+       (patches (search-patches "virtuoso-ose-remove-pre-built-jar-files.patch"))
+       (modules '((guix build utils)))
+       ;; This snippet removes pre-built Java archives.
+       (snippet
+        '(begin
+           (delete-file-recursively "libsrc/JDBCDriverType4")
+           (delete-file-recursively "binsrc/hibernate")
+           (delete-file-recursively "binsrc/jena")
+           (delete-file-recursively "binsrc/jena2")
+           (delete-file-recursively "binsrc/jena3")
+           (delete-file-recursively "binsrc/jena4")
+           (delete-file-recursively "binsrc/rdf4j")
+           (delete-file-recursively "binsrc/sesame")
+           (delete-file-recursively "binsrc/sesame2")
+           (delete-file-recursively "binsrc/sesame3")
+           (delete-file-recursively "binsrc/sesame4")))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; Tests require a network connection.
@@ -3247,6 +3264,9 @@ (define-public virtuoso-ose
                            "--enable-static=no")
        #:phases
        (modify-phases %standard-phases
+         (add-before 'configure 'autogen
+           (lambda _
+             (invoke "./autogen.sh")))
          ;; Even with "--enable-static=no", "libvirtuoso-t.a" is left in
          ;; the build output.  The following phase removes it.
          (add-after 'install 'remove-static-libs
@@ -3256,6 +3276,8 @@ (define-public virtuoso-ose
                            (delete-file (string-append lib "/" file)))
                          '("libvirtuoso-t.a"
                            "libvirtuoso-t.la"))))))))
+    (native-inputs
+     (list autoconf automake libtool bison flex gperf))
     (inputs
      (list openssl net-tools readline zlib))
     (home-page "http://vos.openlinksw.com/owiki/wiki/VOS/")
diff --git a/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch
new file mode 100644
index 0000000000..17413c71ae
--- /dev/null
+++ b/gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch
@@ -0,0 +1,117 @@
+This patch disables build targets that contain pre-built Java archives that
+would be copied to the build's output.
+
+Patch by Roel Janssen <[email-masked]>
+*** a-virtuoso-opensource-7.2.7/binsrc/Makefile.am	1970-01-01 01:00:01.000000000 +0100
+--- b-virtuoso-opensource-7.2.7/binsrc/Makefile.am	2022-05-27 12:20:52.909135774 +0200
+***************
+*** 19,25 ****
+  #  
+  #  
+  
+! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql jena jena2 jena3 jena4 sesame sesame2 sesame3 sesame4 redland hibernate dbpedia rdb2rdf rdf4j
+  
+  
+  # ----------------------------------------------------------------------
+--- 19,25 ----
+  #  
+  #  
+  
+! SUBDIRS = dav mono virtuoso tests rdf_mappers driver maildrop sqldoc hosting bpel fct tutorial conductor samples vsp ws sync vspx vad cached_resources virtodbc virtoledb virtuoso_sink xddl VirtuosoClient.Net oat isparql redland dbpedia rdb2rdf
+  
+  
+  # ----------------------------------------------------------------------
+*** a-virtuoso-opensource-7.2.7/configure.ac	1970-01-01 01:00:01.000000000 +0100
+--- b-virtuoso-opensource-7.2.7/configure.ac	2022-05-27 12:27:51.879208018 +0200
+***************
+*** 57,64 ****
+  dnl	AM_INIT_AUTOMAKE([1.8])
+  dnl	AM_INIT_AUTOMAKE([1.9 tar-ustar])
+  dnl
+! AM_INIT_AUTOMAKE([1.9 tar-ustar])
+! 
+  AM_MAINTAINER_MODE
+  
+  
+--- 57,63 ----
+  dnl	AM_INIT_AUTOMAKE([1.8])
+  dnl	AM_INIT_AUTOMAKE([1.9 tar-ustar])
+  dnl
+! AM_INIT_AUTOMAKE([1.9 tar-ustar subdir-objects])
+  AM_MAINTAINER_MODE
+  
+  
+***************
+*** 3157,3163 ****
+  	binsrc/dbpedia/Makefile
+  	binsrc/driver/Makefile
+  	binsrc/fct/Makefile
+- 	binsrc/hibernate/Makefile
+  	binsrc/hosting/Makefile
+  	binsrc/hosting/mono/Makefile
+  	binsrc/hosting/mono/tests/Makefile
+--- 3156,3161 ----
+***************
+*** 3169,3184 ****
+  	binsrc/hosting/ruby/Makefile
+  	binsrc/hosting/shapefileio/Makefile
+  	binsrc/isparql/Makefile
+- 	binsrc/jena/Makefile
+- 	binsrc/jena2/Makefile
+- 	binsrc/jena3/Makefile
+- 	binsrc/jena4/Makefile
+  	binsrc/maildrop/Makefile
+  	binsrc/mono/Makefile
+  	binsrc/oat/Makefile
+  	binsrc/rdf_mappers/Makefile
+  	binsrc/rdb2rdf/Makefile
+- 	binsrc/rdf4j/Makefile
+  	binsrc/redland/Makefile
+  	binsrc/samples/demo/Makefile
+  	binsrc/samples/hslookup/Makefile
+--- 3167,3177 ----
+***************
+*** 3191,3200 ****
+  	binsrc/samples/webapp/Makefile
+  	binsrc/samples/xpath/Makefile
+  	binsrc/samples/xquery/Makefile
+- 	binsrc/sesame/Makefile
+- 	binsrc/sesame2/Makefile
+- 	binsrc/sesame3/Makefile
+- 	binsrc/sesame4/Makefile
+  	binsrc/sqldoc/Makefile
+  	binsrc/sync/Makefile
+  	binsrc/tests/biftest/Makefile
+--- 3184,3189 ----
+***************
+*** 3236,3245 ****
+  	docsrc/stylesheets/Makefile
+  	docsrc/xmlsource/Makefile
+  	libsrc/Dk/Makefile
+- 	libsrc/JDBCDriverType4/Makefile
+- 	libsrc/JDBCDriverType4/testsuite_4.0/Makefile
+- 	libsrc/JDBCDriverType4/virtuoso/jdbc/Makefile
+- 	libsrc/JDBCDriverType4/virtuoso/Makefile
+  	libsrc/langfunc/Makefile
+  	libsrc/odbcsdk/Makefile
+  	libsrc/plugin/Makefile
+--- 3225,3230 ----
+*** a-virtuoso-opensource-7.2.7/libsrc/Makefile.am	1970-01-01 01:00:01.000000000 +0100
+--- b-virtuoso-opensource-7.2.7/libsrc/Makefile.am	2022-05-27 12:30:12.658593011 +0200
+***************
+*** 19,25 ****
+  #  
+  #  
+  
+! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new JDBCDriverType4
+  
+  noinst_HEADERS = Dk.h libutil.h
+  
+--- 19,25 ----
+  #  
+  #  
+  
+! SUBDIRS = util zlib odbcsdk Dk Thread langfunc Wi plugin Tidy Xml.new
+  
+  noinst_HEADERS = Dk.h libutil.h
+  
-- 
2.36.1