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

[Efraim Flashner <efraim@flashner.co.il>]

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On Fri, May 27, 2022 at 12:47:18PM +0200, Roel Janssen wrote:
> 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 <roel@gnu.org> 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 <roel@gnu.org>
> 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")))))

how about
(for-each delete-file-recursively
  (list "libsrc/JDBCDriverType4"
        "binsrc/hibernate"
        ...))

>      (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")))

This would probably be better as (replace 'bootstrap

>           ;; 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))

That's more than I expected!

>      (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 <roel@gnu.org>
> +*** 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
> 


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Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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