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>

3 files changed, 239 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 $host;")))))))))
+
+(define gn-uploader-service-type
+  (service-type
+   (name 'gn-uploader)
+   (description "GeneNetwork data uploader service.")
+   (extensions
+    (list (service-extension activation-service-type
+                             gn-uploader-activation)
+          (service-extension gunicorn-service-type
+                             gn-uploader-gunicorn-app)
+          (service-extension forge-nginx-service-type
+                             gn-uploader-nginx-server-block)))
+   (default-value (genenetwork-configuration))))
diff --git a/uploader-deploy.sh b/uploader-deploy.sh
new file mode 100755
index 0000000..77a91e6
--- /dev/null
+++ b/uploader-deploy.sh
@@ -0,0 +1,60 @@
+#! /bin/bash -e
+
+# genenetwork-machines --- Guix configuration for genenetwork machines
+# Copyright © 2022, 2024 Arun Isaac <arunisaac@systemreboot.net>
+# Copyright © 2022, 2024 Frederick M. Muriithi <fredmanglis@gmail.com>
+#
+# This file is part of genenetwork-machines.
+#
+# genenetwork-machines is free software: you can redistribute it
+# and/or modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation, either version 3 of
+# the License, or (at your option) any later version.
+#
+# genenetwork-machines is distributed in the hope that it will be
+# useful, but WITHOUT ANY WARRANTY; without even the implied warranty
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with genenetwork-machines.  If not, see
+# <https://www.gnu.org/licenses/>.
+
+# Build and install genenetwork production container on tux02.
+
+SCRIPTARGS=("$@")
+
+MODULEARGS=()
+if [ "${#SCRIPTARGS[@]}" -gt 0 ]
+then
+    echo "===== Auxilliary module load paths ====="
+    for path in "${SCRIPTARGS[@]}"
+    do
+	echo "-L ${path}"
+	MODULEARGS+=("-L" "${path}")
+    done
+    echo "===== END: Auxilliary module load paths ====="
+fi
+
+container_script=$(guix system container \
+			"${MODULEARGS[@]}" \
+                        --network \
+                        --load-path=. \
+                        --verbosity=3 \
+                        --share=/export2/guix-containers/genenetwork/uploader/var/genenetwork=/var/genenetwork \
+                        --share=/export2/guix-containers/genenetwork/uploader/var/lib/acme=/var/lib/acme \
+                        --share=/export2/guix-containers/genenetwork/uploader/var/lib/mysql=/var/lib/mysql \
+                        --share=/export2/guix-containers/genenetwork/uploader/var/lib/virtuoso=/var/lib/virtuoso \
+                        --share=/export2/guix-containers/genenetwork/uploader/var/log=/var/log \
+                        --share=/export2/guix-containers/genenetwork/uploader/etc/genenetwork=/etc/genenetwork \
+                        --expose=/export/data/uploader/genenetwork-xapian=/export/data/genenetwork-xapian \
+                        --share=/export/data/uploader/genenetwork-sqlite=/export/data/genenetwork-sqlite \
+                        --expose=/export/data/genenetwork/genotype_files=/export/data/genenetwork/genotype_files \
+                        --expose=/export/data/uploader/genenetwork3 \
+                        --expose=/export/data/uploader/gn-uploader \
+                        --share=/var/run/mysqld3307=/run/mysqld \
+                        uploader.scm)
+
+echo "${container_script}"
+sudo ln --force --symbolic "${container_script}" /usr/local/bin/genenetwork-uploader-container
+sudo ln --force --symbolic /usr/local/bin/genenetwork-uploader-container /var/guix/gcroots
diff --git a/uploader.scm b/uploader.scm
new file mode 100644
index 0000000..9491a22
--- /dev/null
+++ b/uploader.scm
@@ -0,0 +1,76 @@
+;;; genenetwork-machines --- Guix configuration for genenetwork machines
+;;; Copyright © 2022–2024 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2022–2024 Frederick M. Muriithi <fredmanglis@gmail.com>
+;;;
+;;; 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/>.
+
+(use-modules (gnu)
+             (genenetwork services genenetwork)
+             ((gnu packages admin) #:select (shepherd))
+             (gn services databases)
+             (gn packages genenetwork)
+             (gnu services databases)
+             (forge acme)
+             (forge nginx)
+             (forge socket))
+
+(operating-system
+  (host-name "genenetwork-uploader")
+  (timezone "UTC")
+  (locale "en_US.utf8")
+  (bootloader (bootloader-configuration
+               (bootloader grub-bootloader)
+               (targets (list "/dev/sdX"))))
+  (file-systems %base-file-systems)
+  (users %base-user-accounts)
+  (sudoers-file
+   (mixed-text-file "sudoers"
+                    "@include " %sudoers-specification
+                    "\nacme ALL = NOPASSWD: " (file-append shepherd "/bin/herd") " restart nginx\n"))
+  (packages %base-packages)
+  (services (cons* (service forge-nginx-service-type
+                            (forge-nginx-configuration
+                             (http-listen (forge-ip-socket
+                                           (ip "0.0.0.0")
+                                           (port 10890)))
+                             (https-listen (forge-ip-socket
+                                            (ip "0.0.0.0")
+                                            (port 10891)))))
+                   (service acme-service-type
+                            (acme-configuration
+                             (email "arunisaac@systemreboot.net")))
+                   (service genenetwork-service-type
+                            (genenetwork-configuration
+                             (genenetwork2 genenetwork2)
+                             (server-name "staging.genenetwork.org")
+                             (gn-auth-server-name "staging-auth.genenetwork.org")
+                             (gn2-port 10894)
+                             (gn3-port 10895)
+                             (gn-auth-port 10896)
+                             (sql-uri "mysql://webqtlout:webqtlout@127.0.0.1:3307/db_webqtl")
+                             (auth-db "/export/data/genenetwork-sqlite/auth.db")
+                             (xapian-db "/export/data/genenetwork-xapian")
+                             (genotype-files "/export/data/genenetwork/genotype_files")
+                             (sparql-endpoint "http://localhost:10892/sparql")
+                             (gn3-data-directory "/export/data/uploader/genenetwork3")))
+                   (service gn-uploader-service-type
+                            (gn-uploader-configuration
+                             (server-name "staging-uploader.genenetwork.org")
+                             (port 10897)
+                             (sql-uri "mysql://webqtlout:webqtlout@127.0.0.1:3307/db_webqtl")
+                             (data-directory "/export/data/uploader/gn-uploader")))
+                   %base-services)))