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authorArun Isaac2024-01-03 00:41:40 +0000
committerArun Isaac2024-01-03 00:41:40 +0000
commit32afafc93077e9d6d57354540967dfa1a42cb9b1 (patch)
treeebda4f598a062cb62bd27d3d4bac66bcd7fa3d64
parent69b7d4ea738ab6d0cd959a9cdd1101a4e600795d (diff)
downloadgn-machines-32afafc93077e9d6d57354540967dfa1a42cb9b1.tar.gz
Add GeneNetwork service.
* genenetwork/services/genenetwork.scm: New file.
-rw-r--r--genenetwork/services/genenetwork.scm266
1 files changed, 266 insertions, 0 deletions
diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm
new file mode 100644
index 0000000..966592d
--- /dev/null
+++ b/genenetwork/services/genenetwork.scm
@@ -0,0 +1,266 @@
+;;; genenetwork-machines --- Guix configuration for genenetwork machines
+;;; Copyright © 2024 Arun Isaac <arunisaac@systemreboot.net>
+;;;
+;;; 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/>.
+
+(define-module (genenetwork services genenetwork)
+ #:use-module ((gn packages genenetwork) #:select (genenetwork2 genenetwork3))
+ #:use-module ((gnu packages admin) #:select (shadow))
+ #:use-module (gnu services)
+ #:use-module (gnu services web)
+ #:use-module (gnu system file-systems)
+ #:use-module (gnu system shadow)
+ #:use-module (guix gexp)
+ #:use-module (guix profiles)
+ #:use-module (guix records)
+ #:use-module (forge environment)
+ #:use-module (forge nginx)
+ #:use-module (forge gunicorn)
+ #:use-module (forge socket)
+ #:use-module (srfi srfi-1)
+ #:use-module (ice-9 match)
+ #:export (genenetwork-service-type
+ genenetwork-configuration
+ genenetwork-configuration?
+ genenetwork-configuration-genenetwork2
+ genenetwork-configuration-genenetwork3
+ genenetwork-configuration-server-name
+ genenetwork-configuration-port
+ genenetwork-configuration-gn2-port
+ genenetwork-configuration-gn3-port
+ genenetwork-configuration-auth-db
+ genenetwork-configuration-xapian-db
+ genenetwork-configuration-genotype-files
+ genenetwork-configuration-sparql-endpoint
+ genenetwork-configuration-gn3-data-directory
+ genenetwork-configuration-gn2-secrets
+ genenetwork-configuration-gn3-secrets))
+
+(define-record-type* <genenetwork-configuration>
+ genenetwork-configuration make-genenetwork-configuration
+ genenetwork-configuration?
+ (genenetwork2 genenetwork-configuration-genenetwork2
+ (default genenetwork2))
+ (genenetwork3 genenetwork-configuration-genenetwork3
+ (default genenetwork3))
+ (server-name genenetwork-configuration-server-name
+ (default "genenetwork.org"))
+ (gn2-port genenetwork-configuration-gn2-port
+ (default 8082))
+ (gn3-port genenetwork-configuration-gn3-port
+ (default 8083))
+ (sql-uri genenetwork-configuration-sql-uri
+ (default "mysql://username:password@localhost/database"))
+ (auth-db genenetwork-configuration-auth-db
+ (default "/var/genenetwork/auth.db"))
+ (xapian-db genenetwork-configuration-xapian-db
+ (default "/var/genenetwork/xapian"))
+ (genotype-files genenetwork-configuration-genotype-files
+ (default "/var/genenetwork/genotype-files"))
+ (sparql-endpoint genenetwork-configuration-sparql-endpoint
+ (default "http://localhost:8081/sparql"))
+ (gn3-data-directory genenetwork-configuration-gn3-data-directory
+ (default "/var/genenetwork"))
+ (gn2-secrets genenetwork-configuration-gn2-secrets
+ (default "/etc/genenetwork/gn2-secrets.py"))
+ (gn3-secrets genenetwork-configuration-gn3-secrets
+ (default "/etc/genenetwork/gn3-secrets.py")))
+
+(define %genenetwork-accounts
+ (list (user-group
+ (name "genenetwork")
+ (system? #t))
+ (user-account
+ (name "genenetwork")
+ (group "genenetwork")
+ (system? #t)
+ (comment "GeneNetwork user")
+ (home-directory "/var/empty")
+ (shell (file-append shadow "/sbin/nologin")))))
+
+(define (genenetwork-activation config)
+ (match-record config <genenetwork-configuration>
+ (auth-db)
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils))
+
+ (for-each (lambda (file)
+ (chown file
+ (passwd:uid (getpw "genenetwork"))
+ (passwd:gid (getpw "genenetwork"))))
+ (find-files #$(dirname auth-db)
+ #:directories? #t))))))
+
+(define (configuration-file-gexp alist)
+ "Return a G-expression that constructs a configuration file of
+key-value pairs. @var{alist} is an association list mapping keys to
+their values. Keys must be strings. Values may be strings,
+G-expressions or numbers."
+ #~(begin
+ (use-modules (ice-9 match))
+
+ (call-with-output-file #$output
+ (lambda (port)
+ (for-each (match-lambda
+ ((key value)
+ (display key port)
+ (display " = " port)
+ (cond
+ ((number? value)
+ (display value port))
+ (else
+ (display "\"" port)
+ (display value port)
+ (display "\"" port)))
+ (newline port)))
+ '#$alist)))))
+
+(define (genenetwork-gunicorn-apps config)
+ "Return a list of gunicorn apps to run the genenetwork server
+described by @var{config}, a @code{<genenetwork-configuration>}
+object."
+ (match-record config <genenetwork-configuration>
+ (genenetwork2 genenetwork3 server-name gn2-port gn3-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn3-data-directory gn2-secrets gn3-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)))
+ (gn2-profile (profile
+ (content (package->development-manifest genenetwork2))
+ (allow-collisions? #t)))
+ (gn2-conf (computed-file "gn2.conf"
+ (configuration-file-gexp
+ `(("GEMMA_COMMAND" ,(file-append gn2-profile "/bin/gemma"))
+ ("GEMMA_WRAPPER_COMMAND" ,(file-append gn2-profile "/bin/gemma-wrapper"))
+ ("GENENETWORK_FILES" ,genotype-files)
+ ("GN2_SECRETS" ,gn2-secrets)
+ ("GN3_LOCAL_URL" ,(string-append "http://localhost:"
+ (number->string gn3-port)))
+ ("GN_SERVER_URL" ,(string-append "https://" server-name "/api3/"))
+ ("JS_GUIX_PATH" ,(file-append gn2-profile "/share/genenetwork2/javascript"))
+ ("PLINK_COMMAND" ,(file-append gn2-profile "/bin/plink2"))
+ ("SQL_URI" ,sql-uri)))))
+ (gn3-conf (computed-file "gn3.conf"
+ (configuration-file-gexp
+ `(("AUTH_DB" ,auth-db)
+ ("DATA_DIR" ,gn3-data-directory)
+ ("SPARQL_ENDPOINT" ,sparql-endpoint)
+ ("SQL_URI" ,sql-uri)
+ ("XAPIAN_DB_PATH" ,xapian-db))))))
+ (list (gunicorn-app
+ (name "genenetwork2")
+ (package genenetwork2)
+ (sockets (list (forge-ip-socket
+ (port gn2-port))))
+ (wsgi-app-module "gn2.wsgi")
+ (workers 20)
+ (environment-variables
+ (list (environment-variable
+ (name "GN2_PROFILE")
+ (value gn2-profile))
+ (environment-variable
+ (name "GN2_SETTINGS")
+ (value gn2-conf))
+ (environment-variable
+ (name "HOME")
+ (value "/tmp"))))
+ (mappings (list database-mapping
+ (file-system-mapping
+ (source genotype-files)
+ (target source))
+ (file-system-mapping
+ (source gn2-conf)
+ (target source))
+ (file-system-mapping
+ (source gn2-profile)
+ (target source))
+ (file-system-mapping
+ (source gn2-secrets)
+ (target source)))))
+ (gunicorn-app
+ (name "genenetwork3")
+ (package genenetwork3)
+ (sockets (list (forge-ip-socket
+ (port gn3-port))))
+ (wsgi-app-module "gn3.app:create_app()")
+ (workers 20)
+ (environment-variables
+ (list (environment-variable
+ (name "GN3_CONF")
+ (value gn3-conf))
+ (environment-variable
+ (name "GN3_SECRETS")
+ (value gn3-secrets))
+ (environment-variable
+ (name "HOME")
+ (value "/tmp"))))
+ (mappings (list database-mapping
+ (file-system-mapping
+ (source gn3-conf)
+ (target source))
+ (file-system-mapping
+ (source gn3-secrets)
+ (target source))
+ (file-system-mapping
+ (source gn3-data-directory)
+ (target source))
+ (file-system-mapping
+ (source xapian-db)
+ (target source))
+ (file-system-mapping
+ (source auth-db)
+ (target source)
+ (writable? #t)))))))))
+
+(define (genenetwork-nginx-server-block config)
+ "Return an @code{<nginx-server-configuration>} record specifying
+reverse proxy of the genenetwork service described by @var{config}, a
+@code{<genenetwork-configuration>} record."
+ (match-record config <genenetwork-configuration>
+ (server-name gn2-port gn3-port)
+ (nginx-server-configuration
+ (server-name (list server-name))
+ (locations
+ (list (nginx-location-configuration
+ (uri "/")
+ (body (list (string-append "proxy_pass http://localhost:"
+ (number->string gn2-port) ";")
+ "proxy_set_header Host $host;")))
+ (nginx-location-configuration
+ (uri "/api3/")
+ (body (list "rewrite /api3/(.*) /api/$1 break;"
+ (string-append "proxy_pass http://localhost:"
+ (number->string gn3-port) ";")
+ "proxy_set_header Host $host;"))))))))
+
+(define genenetwork-service-type
+ (service-type
+ (name 'genenetwork)
+ (description "Run GeneNetwork")
+ (extensions
+ (list (service-extension account-service-type
+ (const %genenetwork-accounts))
+ (service-extension activation-service-type
+ genenetwork-activation)
+ (service-extension gunicorn-service-type
+ genenetwork-gunicorn-apps)
+ (service-extension forge-nginx-service-type
+ (compose list genenetwork-nginx-server-block))))
+ (default-value (genenetwork-configuration))))