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;;; genenetwork-machines --- Guix configuration for genenetwork machines
;;; Copyright © 2024 jgart <jgart@dismail.de>
;;;
;;; This file is part of genenetwork-machines.
;;;
;;; genenetwork-machines is free software: you can redistribute it
;;; and/or modify it under the terms of the GNU General Public License
;;; as published by the Free Software Foundation, either version 3 of
;;; the License, or (at your option) any later version.
;;;
;;; genenetwork-machines is distributed in the hope that it will be
;;; useful, but WITHOUT ANY WARRANTY; without even the implied
;;; warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
;;; See the GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with genenetwork-machines. If not, see
;;; <https://www.gnu.org/licenses/>.
(define-module (genenetwork services genecup)
#:use-module (guix)
#:use-module (gnu)
#:use-module (guix git)
#:use-module (guix modules)
#:use-module (guix profiles)
#:use-module (guix records)
#:use-module (srfi srfi-1)
#:use-module (ice-9 match)
#:use-module (forge utils)
#:use-module (gn packages genecup)
#:use-module (gn packages mouse-longevity)
#:use-module (gn services rshiny)
#:use-module (gn packages machine-learning)
#:use-module (gnu packages certs)
#:use-module (gnu packages curl)
#:use-module (gn packages python)
#:use-module (gnu packages admin)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages compression)
#:use-module ((gnu packages python) #:select (python))
#:use-module (gnu packages python-xyz)
#:use-module (guix build python-build-system)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu services shepherd)
#:use-module (gnu packages python-science)
#:use-module (gnu packages machine-learning)
#:use-module ((gnu packages admin) #:select (shepherd))
#:export (genecup-configuration
genecup-configuration?
genecup-configuration-package
genecup-service-type))
(define-record-type* <genecup-configuration>
genecup-configuration make-genecup-configuration
genecup-configuration?
(package genecup-configuration-package ; <package>
(default genecup-latest-with-tensorflow-native)))
(define (genecup-activation config)
(match-record config <genecup-configuration>
(package)
(with-packages
(list python
python-nltk
nss-certs ; Needed for downloading data with nltk.downloader.
curl)
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils))
(let ((nltk-data "/var/cache/nltk_data/")
(data-dir "/export/ratspub/tmp"))
(unless (file-exists? nltk-data)
(begin
(mkdir-p nltk-data)
(chdir nltk-data)
(invoke #$(file-append python "/bin/python3") "-m" "nltk.downloader" "-d" nltk-data "punkt")))
(unless (file-exists? (string-append data-dir "/userspub.sqlite"))
(begin
(install-file #$(file-append package "/userspub.sqlite") data-dir)
(chmod (string-append data-dir "/userspub.sqlite") #o554)))))))))
(define genecup-shepherd-service
(match-lambda
(($ <genecup-configuration> package)
(with-imported-modules (source-module-closure
'((guix search-paths)
(gnu build shepherd)
(gnu system file-systems)))
(list (shepherd-service
(provision '(genecup))
(requirement '(networking))
(modules '((gnu build shepherd)
(gnu system file-systems)))
(start
#~(make-forkexec-constructor
(list #$(file-append package "/server.py"))
#:directory #$package
#:environment-variables
(list
"NLTK_DATA=/var/cache/nltk_data"
(string-append "EDIRECT_PUBMED_MASTER="
#$(file-append package "/minipubmed"))
(string-append "PERL_LWP_SSL_CA_FILE="
#$(file-append (profile (content (packages->manifest (list curl nss-certs))))
"/etc/ssl/certs/ca-certificates.crt")))
#:log-file "/var/log/genecup.log"))
(stop #~(make-kill-destructor))))))))
(define genecup-service-type
(service-type
(name 'genecup)
(extensions
(list
(service-extension activation-service-type
genecup-activation)
(service-extension shepherd-root-service-type
genecup-shepherd-service)))
(default-value (genecup-configuration))
(description
"Run a GeneCup Webserver.")))
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