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(use-modules (gnu)
(gn services databases)
(gnu packages admin)
(gnu services shepherd)
(guix derivations)
(guix monads)
(guix profiles)
(guix search-paths)
(guix records)
(guix store)
(ice-9 match))
(define genenetwork3
(load "guix.scm"))
(define (packages->profile packages)
"Return profile with PACKAGES."
(with-store store
(run-with-store store
(mlet* %store-monad ((prof-drv (profile-derivation
(packages->manifest packages)))
(profile -> (derivation->output-path prof-drv)))
(mbegin %store-monad
(built-derivations (list prof-drv))
(return profile))))))
(define (packages->environment-variables packages)
"Return environment variables of a profile with PACKAGES. Return value is an
association list mapping the names of environment variables to their values."
(map (match-lambda
((search-path . value)
(cons (search-path-specification-variable search-path)
value)))
(profile-search-paths (packages->profile packages))))
(define (packages->profile-environment packages)
"Return environment of a profile with PACKAGES. Return value is a
list of environment variables suitable as input to the environ
function."
(map (match-lambda
((search-path . value)
(string-append (search-path-specification-variable search-path)
"=" value)))
(profile-search-paths (packages->profile packages))))
(define-record-type* <genenetwork3-configuration>
genenetwork3-configuration make-genenetwork3-configuration
genenetwork3-configuration?
(package genenetwork3-configuration-package
(default genenetwork3))
(port genenetwork3-configuration-port
(default 5000)))
(define %genenetwork3-accounts
(list (user-group (name "genenetwork3")
(system? #t))
(user-account
(name "genenetwork3")
(group "genenetwork3")
(system? #t)
(comment "GeneNetwork 3 user")
(home-directory "/var/empty")
(shell (file-append shadow "/sbin/nologin")))))
;; FIXME: Factorize this service into two. We should have a gunicorn
;; service that is extended by the genenetwork service. This way, the
;; app is better decoupled from the deployment.
(define genenetwork3-shepherd-service
(match-lambda
(($ <genenetwork3-configuration> package port)
(shepherd-service
(documentation "Run GeneNetwork 3.")
(provision '(genenetwork3))
(requirement '(networking virtuoso))
(start #~(begin
;; Reference the profile.
#$(packages->profile (list package))
;; Start the gunicorn process.
(make-forkexec-constructor
(list #$(file-append gunicorn "/bin/gunicorn")
"-b" #$(string-append "127.0.0.1:" (number->string port))
"gn3.app:create_app()")
#:user "genenetwork3"
#:group "genenetwork3"
#:environment-variables
'#$(packages->profile-environment (list package)))))
(stop #~(make-kill-destructor))))))
(define genenetwork3-service-type
(service-type
(name 'genenetwork3)
(description "Run GeneNetwork 3.")
(extensions
(list (service-extension account-service-type
(const %genenetwork3-accounts))
(service-extension shepherd-root-service-type
(compose list genenetwork3-shepherd-service))))
(default-value (genenetwork3-configuration))))
(operating-system
(host-name "genenetwork3")
(timezone "UTC")
(locale "en_US.utf8")
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(targets (list "/dev/sdX"))))
(file-systems (cons (file-system
(device "root")
(mount-point "/")
(type "ext4"))
%base-file-systems))
(users %base-user-accounts)
(packages %base-packages)
(services (cons* (service virtuoso-service-type
(virtuoso-configuration
(http-server-port 8891)))
(service genenetwork3-service-type
(genenetwork3-configuration
(port 5000)))
%base-services)))
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