Merge branch 'main' of github.com:genenetwork/genenetwork3

1 files changed, 120 insertions, 0 deletions

diff --git a/guix-system.scm b/guix-system.scm
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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)))