Add gn-uploader service.

* genenetwork/services/genenetwork.scm (<gn-uploader-configuration>):
New type.
(gn-uploader-activation, gn-uploader-gunicorn-app,
gn-uploader-nginx-server-block): New functions.
(gn-uploader-service-type): New variable.
* uploader.scm, uploader-deploy.sh: New files.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>

1 files changed, 103 insertions, 2 deletions

diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm
index cdb7ff4..0382d01 100644
--- a/genenetwork/services/genenetwork.scm
+++ b/genenetwork/services/genenetwork.scm
@@ -1,5 +1,6 @@
 ;;; genenetwork-machines --- Guix configuration for genenetwork machines
 ;;; Copyright © 2024 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2024 Frederick M. Muriithi <fredmanglis@gmail.com>
 ;;;
 ;;; This file is part of genenetwork-machines.
 ;;;
@@ -18,7 +19,7 @@
 ;;; <https://www.gnu.org/licenses/>.
 
 (define-module (genenetwork services genenetwork)
-  #:use-module ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth))
+  #:use-module ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth gn-uploader))
   #:use-module ((gnu packages admin) #:select (shadow))
   #:use-module (gnu services)
   #:use-module (gnu services web)
@@ -48,7 +49,13 @@
             genenetwork-configuration-sparql-endpoint
             genenetwork-configuration-gn3-data-directory
             genenetwork-configuration-gn2-secrets
-            genenetwork-configuration-gn3-secrets))
+            genenetwork-configuration-gn3-secrets
+            gn-uploader-service-type
+            gn-uploader-configuration
+            gn-uploader-configuration?
+            gn-uploader-configuration-server-name
+            gn-uploader-configuration-port
+            gn-uploader-configuration-secrets))
 
 (define-record-type* <genenetwork-configuration>
   genenetwork-configuration make-genenetwork-configuration
@@ -88,6 +95,22 @@
   (gn-auth-secrets genenetwork-configuration-gn-auth-secrets
                    (default "/etc/genenetwork/gn-auth-secrets.py")))
 
+(define-record-type* <gn-uploader-configuration>
+  gn-uploader-configuration make-gn-uploader-configuration
+  gn-uploader-configuration?
+  (gn-uploader gn-uploader-configuration-gn-uploader
+               (default gn-uploader))
+  (server-name gn-uploader-server-name
+               (default "upload.genenetwork.org"))
+  (port gn-uploader-configuration-port
+        (default 8085))
+  (sql-uri gn-uploader-configuration-sql-uri
+           (default "mysql://username:password@localhost/database"))
+  (data-directory gn-uploader-configuration-data-directory
+                  (default "/var/genenetwork"))
+  (secrets gn-uploader-configuration-secrets
+           (default "/etc/genenetwork/gn-uploader-secrets.py")))
+
 (define %genenetwork-accounts
   (list (user-group
          (name "genenetwork")
@@ -334,3 +357,81 @@ a @code{<genenetwork-configuration>} record."
           (service-extension forge-nginx-service-type
                              genenetwork-nginx-server-blocks)))
    (default-value (genenetwork-configuration))))
+
+(define (gn-uploader-activation config)
+  (match-record config <gn-uploader-configuration>
+    (secrets)
+    (with-imported-modules '((guix build utils))
+      #~(begin
+          (use-modules (guix build utils))
+          ;; Let service user own their own secrets files.
+          (chown #$secrets
+                 (passwd:uid (getpw "gunicorn-gn-uploader"))
+                 (passwd:gid (getpw "gunicorn-gn-uploader")))
+          ;; Set owner-only permissions on secrets files.
+          (for-each (lambda (file)
+                      (chmod file #o600))
+                    (list #$secrets))))))
+
+(define (gn-uploader-gunicorn-app config)
+  (match-record config <gn-uploader-configuration>
+    (gn-uploader sql-uri port data-directory secrets)
+    ;; If we mapped only the mysqld.sock socket file, it would break
+    ;; when the external mysqld server is restarted.
+    (let ((database-mapping (file-system-mapping
+                             (source "/run/mysqld")
+                             (target source)
+                             (writable? #t)))
+          (gn-uploader-conf (computed-file "gn-uploader.conf"
+                                           (configuration-file-gexp
+                                            `(("QCAPP_SECRETS" ,secrets)
+                                              ("SQL_URI" ,sql-uri))))))
+      (list (gunicorn-app
+             (name "gn-uploader")
+             (package gn-uploader)
+             (sockets (list (forge-ip-socket
+                             (port port))))
+             (wsgi-app-module "qc_app:create_app()")
+             (workers 20)
+             (environment-variables
+              (list (environment-variable
+                     (name "QCAPP_CONF")
+                     (value gn-uploader-conf))
+                    (environment-variable
+                     (name "HOME")
+                     (value "/tmp"))))
+             (mappings (list database-mapping
+                             (file-system-mapping
+                              (source gn-uploader-conf)
+                              (target source))
+                             (file-system-mapping
+                              (source secrets)
+                              (target source))
+                             (file-system-mapping
+                              (source data-directory)
+                              (target source)))))))))
+
+(define (gn-uploader-nginx-server-block config)
+  (match-record config <gn-uploader-configuration>
+   (server-name port)
+    (list (nginx-server-configuration
+           (server-name (list server-name))
+           (locations
+            (list (nginx-location-configuration
+                   (uri "/")
+                   (body (list (string-append "proxy_pass http://localhost:"
+                                              (number->string port) ";")
+                               "proxy_set_header Host $host;")))))))))
+
+(define gn-uploader-service-type
+  (service-type
+   (name 'gn-uploader)
+   (description "GeneNetwork data uploader service.")
+   (extensions
+    (list (service-extension activation-service-type
+                             gn-uploader-activation)
+          (service-extension gunicorn-service-type
+                             gn-uploader-gunicorn-app)
+          (service-extension forge-nginx-service-type
+                             gn-uploader-nginx-server-block)))
+   (default-value (genenetwork-configuration))))