Add guix configuration for the LLM instance.

* qa-gn-deploy.sh: New file.
* qa-gn.scm: New file.

Co-authored-by: Alexander_Kabui <alexanderkabua@gmail.com>
Co-authored-by: John Nduli <rookie101@jnduli.co.ke>

2 files changed, 182 insertions, 0 deletions

diff --git a/qa-gn-deploy.sh b/qa-gn-deploy.sh
new file mode 100755
index 0000000..42904b7
--- /dev/null
+++ b/qa-gn-deploy.sh
@@ -0,0 +1,63 @@
+#! /bin/bash -e
+
+# qa-deploy.sh --- Guix configuration for genenetwork machines LLM
+# instance
+
+# Copyright © 2024 Munyoki Kilyungi <me@bonfacemunyoki.com>
+# Copyright © 2024 Alexander Kabui <alexanderkabua@gmail.com>
+# Copyright © 2024 John Nduli <rookie101@jnduli.co.ke>
+#
+# This file is part of genenetwork-machines.
+#
+# This program 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.
+
+# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
+
+# Build and install qa 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/gn-qa/var/genenetwork=/var/genenetwork \
+                        --share=/export2/guix-containers/genenetwork/gn-qa/var/lib/acme=/var/lib/acme \
+                        --share=/export2/guix-containers/genenetwork/gn-qa/var/lib/mysql=/var/lib/mysql \
+                        --share=/export2/guix-containers/genenetwork/gn-qa/var/lib/virtuoso=/var/lib/virtuoso \
+                        --share=/export2/guix-containers/genenetwork/gn-qa/var/log=/var/log \
+			--share=/export2/guix-containers/genenetwork/gn-qa/var/ssl=/var/ssl \
+                        --share=/export2/guix-containers/genenetwork/gn-qa/etc/genenetwork=/etc/genenetwork \
+                        --expose=/export/data/genenetwork-xapian/=/export/data/genenetwork-xapian \
+                        --share=/export/data/gn-qa/genenetwork-sqlite=/export/data/genenetwork-sqlite \
+                        --expose=/export/data/genenetwork/genotype_files=/export/data/genenetwork/genotype_files \
+			--share=/export/data/gn-qa/genenetwork3=/export/data/genenetwork3 \
+                        --share=/export/data/gn-qa/gn-uploader \
+                        --share=/var/run/mysqld3307=/run/mysqld \
+                        qa-gn.scm)
+
+echo "${container_script}"
+sudo ln --force --symbolic "${container_script}" /usr/local/bin/gn-qa-container
+sudo ln --force --symbolic /usr/local/bin/gn-qa-container /var/guix/gcroots
diff --git a/qa-gn.scm b/qa-gn.scm
new file mode 100644
index 0000000..5c2b281
--- /dev/null
+++ b/qa-gn.scm
@@ -0,0 +1,119 @@
+;;; qa-gn.scm ---
+;;; Copyright © 2024 Munyoki Kilyungi <me@bonfacemunyoki.com>
+;;; Copyright © 2024 Alexander Kabui <alexanderkabua@gmail.com>
+;;; Copyright © 2024 John Nduli <rookie101@jnduli.co.ke>
+;;;
+;;; This file is part of genenetwork-machines.
+;;;
+;;; This program 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.
+;;;
+;;; This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
+
+(use-modules (gnu)
+	     ((gnu packages admin) #:select (shepherd))
+	     ((gnu packages certs) #:select (nss-certs))
+	     (gnu services databases)
+	     (gnu build linux-container)
+	     (genenetwork services genenetwork)
+	     (gn services databases)
+	     (guix packages)
+	     (guix download)
+	     (guix git)
+	     (guix git-download)
+	     (guix build-system python)
+	     ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth))
+	     (forge acme)
+	     (forge nginx)
+	     (forge socket))
+
+
+
+(operating-system
+  (host-name "qa-gn")
+  (timezone "UTC")
+  (locale "en_US.utf8")
+  (bootloader (bootloader-configuration
+	       (bootloader grub-bootloader)
+	       (targets (list "/dev/sdX"))))
+  (file-systems %base-file-systems)
+  (sudoers-file
+   (mixed-text-file "sudoers"
+		    "@include " %sudoers-specification
+		    "\nacme ALL = NOPASSWD: "
+		    (file-append shepherd "/bin/herd")
+		    " restart nginx\n"))
+  (packages (cons (specification->package "nss-certs") %base-packages))
+  (services
+   (cons*
+    (service genenetwork-service-type
+	     (genenetwork-configuration
+	      ;; Use the latest stable version of GN2/3 with the most
+	      ;; recent LLM code.
+	      (genenetwork2 (package
+			      (inherit genenetwork2)
+			      (name "genenetwork2")
+			      (version "0")
+			      (source
+			       (git-checkout
+				(branch "feature/gnqa-system")
+				(url "https://github.com/genenetwork/genenetwork2.git")))))
+	      (genenetwork3 (package
+			      (inherit genenetwork3)
+			      (name "genenetwork3")
+			      (version "0")
+			      (source
+			       (git-checkout
+				(branch "feature/gnqa-api")
+				(url "https://github.com/genenetwork/genenetwork3.git")))))
+	      (gn-auth (package
+			 (inherit gn-auth)
+			 (source
+			  (origin
+			    (method git-fetch)
+			    (uri (git-reference
+				  (url "https://git.genenetwork.org/gn-auth")
+				  (commit "de4a7f6bfa870a0e5fc4b1f381cb452ab1250210")))
+			    (hash
+			     (content-hash
+			      (base32
+			       "0dxanpgwgjil3g0qlkar7gg8znm9dpizcwkgbyvj0h44qnv1346k")))))
+			 (propagated-inputs
+			  (modify-inputs (package-propagated-inputs genenetwork3)
+			    (append nss-certs)))
+			 (arguments
+			  `(#:tests? #f))))
+	      (server-name "qa.genenetwork.org")
+	      (gn-auth-server-name "qa-auth.genenetwork.org")
+	      ;; XXX: We probably need to use the production server
+	      ;; for this
+	      (gn2-port 10904)
+	      (gn3-port 10905)
+	      (gn-auth-port 10906)
+	      (sql-uri "mysql://webqtlout:webqtlout@127.0.0.1:3307/db_webqtl")
+	      (auth-db "/export/data/genenetwork-sqlite/auth-qa.db")
+	      (xapian-db "/export/data/genenetwork-xapian")
+	      (genotype-files "/export/data/genenetwork/genotype_files")
+	      (sparql-endpoint "http://localhost:9082/sparql")
+	      (gn3-data-directory "/export/data/genenetwork3")
+	      (llm-db "/export/data/genenetwork-sqlite/llm-qa.db")))
+    (service forge-nginx-service-type
+	     (forge-nginx-configuration
+	      (http-listen (forge-ip-socket
+			    (ip "0.0.0.0")
+			    (port 10907)))
+	      (https-listen (forge-ip-socket
+			     (ip "0.0.0.0")
+			     (port 10908)))))
+    (service acme-service-type
+             (acme-configuration
+              (email "arunisaac@systemreboot.net")))
+    %base-services)))