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(define-module (gn packages guile)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix gexp)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system guile)
#:use-module (guix build-system gnu)
#:use-module ((gnu packages autotools) #:select (libltdl autoconf automake libtool))
#:use-module ((gnu packages databases) #:select (mariadb))
#:use-module ((gnu packages compression) #:select (zlib))
#:use-module ((gnu packages perl) #:select (perl))
#:use-module ((gnu packages texinfo) #:select (texinfo))
#:use-module (guix utils)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages package-management)
#:use-module ((gnu packages bash) #:select (bash-minimal))
#:use-module ((gnu packages bioinformatics) #:select (gemma))
#:use-module ((gnu packages certs) #:select (nss-certs))
#:use-module ((gnu packages guile) #:select (guile-json-4 guile-3.0 guile-2.2 guile-readline))
#:use-module ((gnu packages guile-xyz) #:select (guile-dbi guile-dbd-mysql guile-fibers guile-redis guile-hashing guile-commonmark))
#:use-module ((gnu packages parallel) #:select (parallel))
#:use-module ((gnu packages perl) #:select (perl))
#:use-module ((gnu packages tls) #:select (guile-gnutls openssl)))
(define %default-gnu-imported-modules
(if (defined? '%default-gnu-imported-modules)
%default-gnu-imported-modules
'((guix build gnu-build-system)
(guix build utils)
(guix build gremlin)
(guix elf))))
;; Lifted from:
;; https://lists.gnu.org/archive/html/artanis/2023-03/txtNk7zz7rJAN.txt
(define-public guile3-dbi
(package
(name "guile3-dbi")
(version "2.1.8")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/opencog/guile-dbi")
(commit (string-append "guile-dbi-" version))))
(file-name (git-file-name name version))
(sha256
(base32
"123m4j82bi60s1v95pjh4djb7bh6zdwmljbpyg7zq8ni2gyal7lw"))))
(build-system gnu-build-system)
(arguments
`(#:modules (((guix build guile-build-system)
#:select (target-guile-effective-version))
,@%gnu-build-system-modules)
#:imported-modules ((guix build guile-build-system)
,@%gnu-build-system-modules)
#:configure-flags
(list (string-append
"--with-guile-site-dir=" %output "/share/guile/site/"
(target-guile-effective-version (assoc-ref %build-inputs "guile"))))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
;; The upstream Git repository contains all the code, so change
;; to the directory specific to guile-dbi.
(chdir "guile-dbi")))
(add-after 'install 'patch-extension-path
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(dbi.scm (string-append out "/share/guile/site/"
(target-guile-effective-version
(assoc-ref inputs "guile"))
"/dbi/dbi.scm"))
(ext (string-append out "/lib/libguile-dbi")))
(substitute* dbi.scm (("libguile-dbi") ext))))))))
(inputs
(list libltdl))
(native-inputs
(list autoconf automake libtool perl texinfo guile-3.0))
(synopsis "Guile database abstraction layer")
(home-page "https://github.com/opencog/guile-dbi")
(description
"guile-dbi is a library for Guile that provides a convenient interface to
SQL databases. Database programming with guile-dbi is generic in that the same
programming interface is presented regardless of which database system is used.
It currently supports MySQL, Postgres and SQLite3.")
(license license:gpl2+)
(native-search-paths
(list (search-path-specification
(variable "GUILE_DBD_PATH")
(files '("lib")))))))
(define-public guile3-dbd-mysql
(package
(inherit guile3-dbi)
(name "guile3-dbd-mysql")
(arguments
(substitute-keyword-arguments (package-arguments guile3-dbi)
((#:phases phases)
`(modify-phases ,phases
(replace 'chdir
(lambda _
;; The upstream Git repository contains all the code, so change
;; to the directory specific to guile-dbd-mysql.
(chdir "guile-dbd-mysql")))
(add-after 'chdir 'patch-src
(lambda _
(substitute* "configure.ac"
(("mariadbclient") "mariadb"))
(substitute* "src/guile-dbd-mysql.c"
(("<mariadb/") "<mysql/"))))
(delete 'patch-extension-path)))))
(inputs
(modify-inputs (package-inputs guile3-dbi)
(prepend `(,mariadb "dev")
`(,mariadb "lib")
zlib)))
(native-inputs
(modify-inputs (package-native-inputs guile3-dbi)
(prepend guile3-dbi ; only required for headers
)))
(synopsis "Guile DBI driver for MySQL")
(description "@code{guile-dbi} is a library for Guile that provides a
convenient interface to SQL databases. This package implements the interface
for MySQL.")
(license license:gpl2+)))
(define-public gn-guile
(let ((commit "7af301caa7d8a5f01e7e3be007e4ba53dc482eee")
(revision "0"))
(package
(name "gn-guile")
(version (git-version "4.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://git.genenetwork.org/gn-guile/")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
(base32
"0j6nf9k5rdanx5r74dw1rcw7rvyjhzvsv1l5s86jkgkhvrpbb82c"))))
(build-system guile-build-system)
(propagated-inputs
(list guile-3.0 guile3-dbi guile3-dbd-mysql guile-fibers guile-gnutls guile-readline
guile-commonmark guile-redis openssl nss-certs gemma parallel guile-hashing
guile-json-4))
(arguments
(list
#:phases
#~(modify-phases %standard-phases
;; When using the guile-build-system, guild doesn't
;; correctly set the GUILE_LOAD_PATH for the various guile
;; packages in the build phase leading to build failures.
(add-before 'build 'augment-GUILE_LOAD_PATH
(lambda* (#:key outputs #:allow-other-keys)
(let* ((guile-version (target-guile-effective-version)))
;; guild uses this: "\\.(scm|sls)$" regexp to try and
;; compile all scm files in this repository. We don't
;; need to compile guix.scm and manifest.scm.
(delete-file "guix.scm")
(setenv "GUILE_LOAD_PATH"
(string-append
(format
#f "~{~a:~}"
(map (lambda (package)
(format #f "~a/share/guile/site/~a"
package guile-version))
(list #$guile3-dbi #$guile-fibers #$guile-commonmark #$guile-json-4 #$guile-hashing)))
#$(getenv "GUILE_LOAD_PATH")))))))))
(home-page "https://git.genenetwork.com/gn-guile")
(synopsis "Next generation GN code in guile")
(description "Use of guile.")
(license license:gpl3))))
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