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;;; genenetwork-machines --- Guix configuration for genenetwork machines
;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; 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 development-helper)
#:use-module (ice-9 match)
#:use-module (guix gexp)
#:use-module (guix profiles)
#:use-module (guix search-paths)
#:use-module (forge build utils))
(define (command-in-source-gexp source profile command)
"Return a G-expression that runs COMMAND in PROFILE and with SOURCE
as the current directory. SOURCE and PROFILE are store items. COMMAND
is a list of strings specifying the command to be executed."
(with-imported-modules '((guix build utils))
(with-profile profile
#~(begin
(use-modules (rnrs exceptions)
(guix build utils))
(chdir #$source)
(guard (condition ((invoke-error? condition)
(format (current-error-port)
"`~a~{ ~a~}' failed with exit status ~a~%"
(invoke-error-program condition)
(invoke-error-arguments condition)
(invoke-error-exit-status condition))
(exit #f)))
(apply invoke '#$command))
(mkdir-p #$output)))))
(define (asdf-test-gexp source profile system asd-files)
"Return a G-expression that tests SYSTEM using asdf after loading
ASD-FILES. SOURCE is the source code under test. PROFILE is a profile
with all necessary dependencies. SOURCE and PROFILE are both store
items."
(with-imported-modules '((guix build lisp-utils)
(guix build utils))
(with-profile profile
#~(begin
(use-modules (guix build lisp-utils)
(guix build utils))
(chdir #$source)
(setenv "HOME" "/tmp")
(parameterize ((%lisp "sbcl")
(%lisp-type "sbcl"))
(test-system #$system '#$asd-files #f))
(mkdir-p #$output)))))
(define (genenetwork3-lint-gexp genenetwork3-source profile)
"Return a G-expression that runs GeneNetwork3 lint tests in PROFILE
with GENENETWORK3-SOURCE as the current directory. GENENETWORK3-SOURCE
is a checkout of the genenetwork3 source code. PROFILE is a profile
with genenetwork3 dependencies."
(with-imported-modules '((guix build utils))
(with-profile profile
#~(begin
(use-modules (rnrs exceptions)
(srfi srfi-26)
(ice-9 rdelim)
(guix build utils))
(define (shell-script? filename stat-obj)
(and (eq? (stat:type stat-obj) 'regular)
(call-with-input-file filename
(lambda (port)
(let ((first-line (read-line port)))
(and (not (eof-object? first-line))
(> (string-length first-line) 2)
(string=? (string-take first-line 2) "#!")
(or (string-contains first-line "/bin/sh")
(string-contains first-line "/bin/bash"))))))))
(chdir #$genenetwork3-source)
(guard (condition ((invoke-error? condition)
(format (current-error-port)
"`~a~{ ~a~}' failed with exit status ~a~%"
(invoke-error-program condition)
(invoke-error-arguments condition)
(invoke-error-exit-status condition))
(exit #f)))
(for-each (cut invoke "shellcheck" <>)
(find-files "." shell-script?))
(invoke "pylint" "gn3"))
(mkdir-p #$output)))))
(define (genenetwork2-runner-gexp genenetwork2-source profile gn3-port genotype-files)
"Return a G-expression that runs the genenetwork2 server for
GENENETWORK2-SOURCE in PROFILE. GENENETWORK2-SOURCE is a checkout of
the genenetwork2 source code. PROFILE is a profile with genenetwork2
dependencies. GN3-PORT is the port on which a local instance of
genenetwork3 is listening. GENOTYPE-FILES is the path to genotype
files."
(with-imported-modules '((guix build utils))
(with-profile profile
#~(begin
(use-modules (guix build utils)
(ice-9 match))
(chdir #$genenetwork2-source)
(match (command-line)
((_ ip port)
(setenv "SERVER_PORT" port)
(setenv "GN2_PROFILE" #$profile)
(setenv "GN_PROXY_URL" "http://genenetwork.org/gn3-proxy/")
(setenv "GN_SERVER_URL" "https://gn3dev.genenetwork.org/")
(setenv "GN3_LOCAL_URL"
(string-append "http://localhost:"
(number->string #$gn3-port)))
(setenv "GENENETWORK_FILES" #$genotype-files)
(setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl")
(setenv "HOME" "/tmp")
(setenv "NO_REDIS" "no-redis")
(invoke "sh" "bin/genenetwork2")))))))
(define (genenetwork3-runner-gexp genenetwork3-source profile)
"Return a G-expression that runs the genenetwork3 server for
GENENETWORK3-SOURCE in PROFILE. GENENETWORK3-SOURCE is a checkout of
the genenetwork3 source code. PROFILE is a profile with genenetwork3
dependencies."
(with-imported-modules '((guix build utils))
(with-profile profile
#~(begin
(use-modules (guix build utils)
(ice-9 match))
(chdir #$genenetwork3-source)
(match (command-line)
((_ ip port)
(invoke "gunicorn"
"-b" (string-append ip ":" port)
"gn3.app:create_app()")))))))
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