Define new container for gn2-fred* domains.production-container

3 files changed, 134 insertions, 3 deletions

diff --git a/fred-production-deploy.sh b/fred-production-deploy.sh
new file mode 100755
index 0000000..498c4a8
--- /dev/null
+++ b/fred-production-deploy.sh
@@ -0,0 +1,44 @@
+#! /bin/sh -e
+
+# genenetwork-machines --- Guix configuration for genenetwork machines
+# Copyright © 2022, 2024 Arun Isaac <arunisaac@systemreboot.net>
+# Copyright © 2024 Frederick Muriuki Muriithin <fredmanglis@protonmail.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.
+
+container_script=$(guix \
+                       system container \
+                       --network \
+                       --load-path=. \
+                       --verbosity=3 \
+                       --share=/export2/guix-containers/fred-production/var/genenetwork=/var/genenetwork \
+                       --share=/export2/guix-containers/fred-production/var/lib/acme=/var/lib/acme \
+                       --share=/export2/guix-containers/fred-production/var/lib/redis=/var/lib/redis \
+                       --share=/export/mysql/database=/var/lib/mysql \
+                       --share=/home/zas1024/guix-containers/var/lib/virtuoso=/var/lib/virtuoso \
+                       --share=/export2/guix-containers/fred-production/var/log=/var/log \
+                       --share=/export2/guix-containers/fred-production/etc/genenetwork=/etc/genenetwork \
+                       --share=/export2/guix-containers/fred-production/var/lib/xapian=/var/lib/xapian \
+                       --share=/export2/guix-containers/fred-production/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite \
+                       --share=/var/run/mysqld=/run/mysqld \
+                       fred-production.scm)
+
+echo $container_script
+sudo ln --force --symbolic $container_script /usr/local/bin/genenetwork-fred-container
+sudo ln --force --symbolic /usr/local/bin/genenetwork-fred-container /var/guix/gcroots
diff --git a/fred-production.scm b/fred-production.scm
new file mode 100644
index 0000000..42dcb05
--- /dev/null
+++ b/fred-production.scm
@@ -0,0 +1,85 @@
+;;; genenetwork-machines --- Guix configuration for genenetwork machines
+;;; Copyright © 2022–2024 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2024 Frederick Muriuki Muriithi <fredmanglis@protonmail.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)
+             (gnu services databases)
+             (forge acme)
+             (forge nginx)
+             (forge socket))
+
+(operating-system
+  (host-name "genenetwork-fred-production")
+  (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 mysql-service-type
+                            (mysql-configuration
+                             (auto-upgrade? #f)))
+                   (service virtuoso-service-type
+                            (virtuoso-configuration
+                             (server-port 9892)
+                             (http-server-port 9893)))
+                   (service forge-nginx-service-type
+                            (forge-nginx-configuration
+                             (http-listen (forge-ip-socket
+                                           (ip "0.0.0.0")
+                                           (port 9890)))
+                             (https-listen (forge-ip-socket
+                                            (ip "0.0.0.0")
+                                            (port 9891)))))
+                   (service acme-service-type
+                            (acme-configuration
+                             (email "arunisaac@systemreboot.net")))
+                   (service redis-service-type
+                            ;; Added since Tux04 has no redis running
+                            ;; on port 6379
+                            (redis-configuration
+                             (bind "127.0.0.1")
+                             (port 6379)
+                             (working-directory "/var/lib/redis")))
+                   (service genenetwork-service-type
+                            (genenetwork-configuration
+                             (server-name "gn2-fred.genenetwork.org")
+                             (gn-auth-server-name "gn2-fred-auth.genenetwork.org")
+                             (gn2-port 9894)
+                             (gn3-port 9895)
+                             (gn-auth-port 9896)
+                             (sql-uri "mysql://webqtlout:webqtlout@localhost/db_webqtl")
+                             (xapian-db "/var/lib/xapian")
+                             (sparql-endpoint "http://localhost:9893/sparql")
+                             (gn3-data-directory "/var/genenetwork/data/genenetwork3")
+                             (gn2-secrets "/etc/genenetwork/genenetwork2")
+                             (gn3-secrets "/etc/genenetwork/genenetwork3/gn3-secrets.py")
+                             (gn-auth-secrets "/etc/genenetwork/gn-auth")
+                             (auth-db "/var/lib/genenetwork-sqlite/auth.db")
+                             (log-level "DEBUG")))
+                   %base-services)))
diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm
index 9808ce5..e5d75ae 100644
--- a/genenetwork/services/genenetwork.scm
+++ b/genenetwork/services/genenetwork.scm
@@ -102,7 +102,8 @@
   (gn3-secrets genenetwork-configuration-gn3-secrets
                (default "/etc/genenetwork/gn3-secrets.py"))
   (gn-auth-secrets genenetwork-configuration-gn-auth-secrets
-                   (default "/etc/genenetwork")))
+                   (default "/etc/genenetwork"))
+  (log-level gn-uploader-log-level (default "WARNING")))
 
 (define-record-type* <gn-uploader-configuration>
   gn-uploader-configuration make-gn-uploader-configuration
@@ -304,7 +305,7 @@ G-expressions or numbers."
 described by @var{config}, a @code{<genenetwork-configuration>}
 object."
   (match-record config <genenetwork-configuration>
-    (genenetwork2 genenetwork3 gn-auth server-name gn-auth-server-name gn2-port gn3-port gn-auth-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn-sourcecode-directory gn3-data-directory gn2-secrets gn3-secrets gn-auth-secrets)
+    (genenetwork2 genenetwork3 gn-auth server-name gn-auth-server-name gn2-port gn3-port gn-auth-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn-sourcecode-directory gn3-data-directory gn2-secrets gn3-secrets gn-auth-secrets log-level)
     ;; 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
@@ -385,7 +386,8 @@ object."
                              (file-system-mapping
                               (source gn2-secrets)
                               (target source)
-                              (writable? #t)))))
+                              (writable? #t))))
+             (extra-cli-arguments (list "--log-level" log-level)))
             (gunicorn-app
              (name "genenetwork3")
              (package genenetwork3)