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authorFrederick Muriuki Muriithi2024-03-08 04:27:21 +0300
committerArun Isaac2024-03-25 23:47:57 +0000
commit081e2865c3354415fbcb186e562060d6ac2885f1 (patch)
treec8f22fb0ef90b9a8240e1593dca646d5ba6591f9 /genenetwork
parentaf7480a6fe3469b29723d0013926f17dd426e012 (diff)
downloadgn-machines-081e2865c3354415fbcb186e562060d6ac2885f1.tar.gz
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>
Diffstat (limited to 'genenetwork')
-rw-r--r--genenetwork/services/genenetwork.scm105
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))))