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authorArun Isaac2022-04-15 13:56:27 +0530
committerArun Isaac2022-04-15 13:56:27 +0530
commitd2b84265ad7068c6a22fa04f2820b80a0f481a78 (patch)
tree7a597c95a8dc9469dee1d8051508210ae1996ce3 /genenetwork-development.scm
downloadgn-machines-d2b84265ad7068c6a22fa04f2820b80a0f481a78.tar.gz
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+;;; genenetwork-machines --- Guix configuration for genenetwork machines
+;;; Copyright © 2022 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/>.
+
+(use-modules (gnu)
+ ((gn packages gemini) #:select (tissue))
+ ((gn packages genenetwork) #:select (genenetwork2 genenetwork3))
+ ((gn packages quality-control) #:select (sbcl-qc))
+ (gn services databases)
+ ((gnu packages admin) #:select (shepherd))
+ ((gnu packages base) #:select (gnu-make))
+ ((gnu packages bash) #:select (bash))
+ ((gnu packages bioinformatics) #:select (ccwl) #:prefix guix:)
+ ((gnu packages certs) #:select (nss-certs))
+ ((gnu packages check) #:select (python-pylint))
+ ((gnu packages ci) #:select (laminar))
+ ((gnu packages gnupg) #:select (guile-gcrypt))
+ ((gnu packages graphviz) #:select (graphviz))
+ ((gnu packages guile) #:select (guile-3.0 guile-zlib))
+ ((gnu packages guile-xyz) #:select (guile-dbd-mysql guile-dbi guile-libyaml))
+ ((gnu packages guile-xyz) #:select (guile-sparql) #:prefix guix:)
+ ((gnu packages haskell-apps) #:select (shellcheck))
+ ((gnu packages python-check) #:select (python-mypy))
+ ((gnu packages python-web) #:select (gunicorn))
+ ((gnu packages tls) #:select (openssl))
+ ((gnu packages version-control) #:select (git-minimal))
+ (gnu services ci)
+ (gnu services databases)
+ (gnu services shepherd)
+ (guix build-system gnu)
+ (guix git-download)
+ ((guix licenses) #:prefix license:)
+ (guix modules)
+ (guix packages)
+ (guix profiles)
+ (guix records)
+ (guix store)
+ (forge forge)
+ (forge laminar)
+ (forge utils)
+ (forge webhook)
+ (srfi srfi-1)
+ (ice-9 match))
+
+;; guix-daemon socket of the host shared inside the container
+(define %guix-daemon-uri
+ "/var/host-guix/daemon-socket/socket")
+
+(define (manifest-cons package onto-manifest)
+ "Return a manifest with PACKAGE and all packages in ONTO-MANIFEST."
+ (manifest (cons (package->manifest-entry package)
+ (manifest-entries onto-manifest))))
+
+(define (manifest-cons* . args)
+ "ARGS is of the form (PACKAGES ... ONTO-MANIFEST). Return a manifest
+with PACKAGES and all packages in ONTO-MANIFEST."
+ (let ((packages (drop-right args 1))
+ (onto-manifest (last args)))
+ (manifest (append (map package->manifest-entry packages)
+ (manifest-entries onto-manifest)))))
+
+(define (import-module? name)
+ "Return #t if NAME, a list of symbols, denotes a module that should
+be imported into G-expressions."
+ ;; Allow all guix-forge, genenetwork or guix modules.
+ (match name
+ (((or 'forge 'genenetwork) _ ...) #t)
+ (name (guix-module-name? name))))
+
+
+;;;
+;;; Development server configuration
+;;;
+
+;; A development server is a server that is automatically redeployed
+;; on every commit to its git repository. This is used by both the
+;; genenetwork2 and the genenetwork3 development servers. Here, we
+;; abstract out the details.
+
+(define-record-type* <development-server-configuration>
+ development-server-configuration make-development-server-configuration
+ development-server-configuration?
+ (name development-server-configuration-name)
+ (git-repository development-server-configuration-git-repository)
+ (git-branch development-server-configuration-git-branch)
+ (executable-path development-server-configuration-executable-path)
+ (runner development-server-configuration-runner)
+ (port development-server-configuration-port
+ (default 8080)))
+
+(define (development-server-redeploy config)
+ "Return a G-expression that provides a function redeploy which
+redeploys the development server specified by CONFIG, a
+<development-server-configuration> object."
+ (with-imported-modules (source-module-closure '((genenetwork development-helper)
+ (forge build git))
+ #:select? import-module?)
+ (with-extensions (list guile-gcrypt guile-zlib)
+ (with-packages (list git-minimal nss-certs)
+ #~(begin
+ (use-modules (genenetwork development-helper)
+ (forge build git)
+ (guix derivations)
+ (guix gexp)
+ (guix monads)
+ (guix store)
+ (guix utils)
+ (rnrs exceptions))
+
+ (define (redeploy)
+ (parameterize ((%daemon-socket-uri #$%guix-daemon-uri))
+ (switch-symlinks
+ #$(development-server-configuration-executable-path config)
+ (with-store store
+ (run-with-store store
+ (mlet* %store-monad ((latest-source
+ (latest-git-checkout
+ #$(string-append (development-server-configuration-name config)
+ "-checkout")
+ #$(development-server-configuration-git-repository config)
+ #:branch #$(development-server-configuration-git-branch config)))
+ (runner-drv
+ (gexp->script
+ #$(string-append (development-server-configuration-name config)
+ "-runner")
+ (#$(development-server-configuration-runner config)
+ latest-source)
+ #:guile (read-derivation-from-file
+ #$(raw-derivation-file
+ (with-store store
+ (package-derivation store guile-3.0)))))))
+ (mbegin %store-monad
+ (built-derivations (list runner-drv))
+ (return (derivation->output-path runner-drv))))))))))))))
+
+(define (development-server-activation config)
+ "Return a G-expression that runs the development server specified by
+CONFIG, a <development-server-configuration> object, on startup."
+ (let ((executable-path (development-server-configuration-executable-path config)))
+ #~(begin
+ (use-modules (guix build utils))
+
+ (mkdir-p #$(dirname executable-path))
+ (chown #$(dirname executable-path)
+ (passwd:uid (getpw "laminar"))
+ (passwd:gid (getpw "laminar")))
+ #$(development-server-redeploy config)
+ (redeploy))))
+
+
+;;;
+;;; genenetwork2
+;;;
+
+;; Path to genotype files required by genenetwork2
+(define %genotype-files
+ "/export/data/genenetwork/genotype_files")
+
+;; Port on which genenetwork3 is listening
+(define %genenetwork3-port
+ 9093)
+
+(define (genenetwork2-tests project test-command)
+ "Return a G-expression that runs TEST-COMMAND with genenetwork2
+source code. PROJECT is a <forge-project> object describing
+genenetwork2. TEST-COMMAND is a list of strings specifying the command
+to be executed."
+ (with-imported-modules '((guix build utils))
+ (with-packages (list bash coreutils git-minimal nss-certs)
+ #~(begin
+ (use-modules (guix build utils))
+
+ (define (hline)
+ "Print a horizontal line 50 '=' characters long."
+ (display (make-string 50 #\=))
+ (newline)
+ (force-output))
+
+ (invoke "git" "clone" "--depth" "1"
+ "--branch" #$(forge-project-repository-branch project)
+ #$(forge-project-repository project)
+ ".")
+ (hline)
+ (invoke "git" "log" "--max-count" "1")
+ (hline)
+ (setenv "SERVER_PORT" "8080")
+ (setenv "GN2_PROFILE"
+ #$(profile
+ (content (package->development-manifest genenetwork2))
+ (allow-collisions? #t)))
+ (setenv "GN_PROXY_URL" "http://genenetwork.org/gn3-proxy")
+ (setenv "GN3_LOCAL_URL" "http://localhost:9093")
+ (setenv "GENENETWORK_FILES" #$%genotype-files)
+ (setenv "HOME" "/tmp")
+ (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl")
+ (apply invoke '#$test-command)))))
+
+(define (genenetwork2-project config)
+ "Return a forge project describing genenetwork2. CONFIG is a
+<development-server-configuration> object describing genenetwork2."
+ (forge-project
+ (name "genenetwork2")
+ (repository (development-server-configuration-git-repository config))
+ (repository-branch (development-server-configuration-git-branch config))
+ (ci-jobs (list (forge-laminar-job
+ (name "genenetwork2")
+ (run (genenetwork2-tests
+ this-forge-project
+ (list "sh" "bin/genenetwork2" "./etc/default_settings.py"
+ "-c" "-m" "unittest" "-v")))
+ ;; If unit tests pass, redeploy genenetwork2.
+ (after #~(begin
+ (use-modules (guix build utils))
+ #$(development-server-redeploy config)
+ (when (string=? (getenv "RESULT") "success")
+ (redeploy)
+ ;; We cannot refer to sudo in the
+ ;; store since that sudo does not have
+ ;; the setuid bit set. See "(guix)
+ ;; Setuid Programs".
+ (invoke "/run/setuid-programs/sudo"
+ #$(file-append shepherd "/bin/herd")
+ "restart" "genenetwork2")
+ (invoke #$(file-append laminar "/bin/laminarc")
+ "queue" "genenetwork2-mechanical-rob")))))
+ (forge-laminar-job
+ (name "genenetwork2-mechanical-rob")
+ (run (genenetwork2-tests
+ this-forge-project
+ (list "sh" "bin/genenetwork2" "./etc/default_settings.py"
+ "-c" "../test/requests/test-website.py"
+ "--all" "http://localhost:9092")))
+ (trigger? #f))))
+ (ci-jobs-trigger 'webhook)))
+
+(define (genenetwork2-shepherd-service config)
+ "Return a shepherd service to run the genenetwork2 development
+server. CONFIG is a <development-server-configuration> object
+describing genenetwork2."
+ (shepherd-service
+ (documentation "Run GeneNetwork 2 development server.")
+ (provision '(genenetwork2))
+ ;; FIXME: The genenetwork2 service should depend on redis.
+ (requirement '(networking genenetwork3))
+ (modules '((gnu build shepherd)
+ (gnu system file-systems)))
+ (start
+ (with-imported-modules (source-module-closure '((gnu build shepherd)
+ (gnu system file-systems)))
+ #~(make-forkexec-constructor/container
+ (list #$(development-server-configuration-executable-path config)
+ "127.0.0.1" (number->string #$(development-server-configuration-port config)))
+ #:mappings (list (file-system-mapping
+ (source #$(development-server-configuration-executable-path config))
+ (target source))
+ (file-system-mapping
+ (source #$%genotype-files)
+ (target source))
+ (file-system-mapping
+ (source "/run/mysqld/mysqld.sock")
+ (target source)
+ (writable? #t)))
+ #:log-file "/var/log/genenetwork2.log")))
+ (stop #~(make-kill-destructor))))
+
+(define %default-genenetwork2-configuration
+ (development-server-configuration
+ (name "genenetwork2")
+ (git-repository "https://github.com/genenetwork/genenetwork2")
+ (git-branch "testing")
+ (executable-path "/laminar/bin/genenetwork2")
+ (runner (with-imported-modules (source-module-closure '((genenetwork development-helper))
+ #:select? import-module?)
+ #~(lambda (latest-gn2-source)
+ ((@@ (genenetwork development-helper) genenetwork2-runner-gexp)
+ latest-gn2-source
+ #$(profile
+ (content (package->development-manifest genenetwork2))
+ (allow-collisions? #t))
+ #$%genenetwork3-port
+ #$%genotype-files))))))
+
+(define genenetwork2-service-type
+ (service-type
+ (name 'genenetwork2)
+ (description "Run GeneNetwork 2 development server and CI.")
+ (extensions
+ (list (service-extension activation-service-type
+ development-server-activation)
+ (service-extension shepherd-root-service-type
+ (compose list genenetwork2-shepherd-service))
+ (service-extension forge-service-type
+ (compose list genenetwork2-project))))
+ (default-value %default-genenetwork2-configuration)))
+
+
+;;;
+;;; genenetwork3
+;;;
+
+(define (genenetwork3-tests tests-command manifest)
+ "Return a G-expression running TESTS-COMMAND in a profile described
+by MANIFEST with the latest git checkout of genenetwork3 as the
+current directory. TESTS-COMMAND is a list of strings specifying the
+command to be executed."
+ (with-imported-modules (source-module-closure '((genenetwork development-helper))
+ #:select? import-module?)
+ #~(lambda (genenetwork3-checkout)
+ ((@@ (genenetwork development-helper)
+ command-in-source-gexp)
+ genenetwork3-checkout
+ #$(profile
+ (content manifest)
+ (allow-collisions? #t))
+ '#$tests-command))))
+
+(define genenetwork3-unit-tests
+ (genenetwork3-tests (list "python3" "-m" "unittest")
+ (package->development-manifest genenetwork3)))
+
+(define genenetwork3-pylint
+ (with-imported-modules (source-module-closure '((genenetwork development-helper))
+ #:select? import-module?)
+ #~(lambda (genenetwork3-checkout)
+ ((@@ (genenetwork development-helper)
+ genenetwork3-lint-gexp)
+ genenetwork3-checkout
+ #$(profile
+ (content (manifest-cons* python-pylint shellcheck
+ (package->development-manifest genenetwork3)))
+ (allow-collisions? #t))))))
+
+(define genenetwork3-mypy
+ (genenetwork3-tests (list "mypy" ".")
+ (manifest-cons python-mypy
+ (package->development-manifest genenetwork3))))
+
+(define (genenetwork3-project config)
+ (forge-project
+ (name "genenetwork3")
+ (repository (development-server-configuration-git-repository config))
+ (repository-branch (development-server-configuration-git-branch config))
+ (ci-jobs (list (forge-laminar-job
+ (name "genenetwork3")
+ (run (derivation-job-gexp
+ this-forge-project
+ this-forge-laminar-job
+ genenetwork3-unit-tests
+ #:guix-daemon-uri %guix-daemon-uri))
+ ;; If unit tests pass, redeploy genenetwork3.
+ (after #~(begin
+ (use-modules (guix build utils))
+ #$(development-server-redeploy config)
+ (when (string=? (getenv "RESULT") "success")
+ (redeploy)
+ ;; We cannot refer to sudo in the
+ ;; store since that sudo does not have
+ ;; the setuid bit set. See "(guix)
+ ;; Setuid Programs".
+ (invoke "/run/setuid-programs/sudo"
+ #$(file-append shepherd "/bin/herd")
+ "restart" "genenetwork3")))))
+ (forge-laminar-job
+ (name "genenetwork3-pylint")
+ (run (derivation-job-gexp
+ this-forge-project
+ this-forge-laminar-job
+ genenetwork3-pylint
+ #:guix-daemon-uri %guix-daemon-uri)))
+ (forge-laminar-job
+ (name "genenetwork3-mypy")
+ (run (derivation-job-gexp
+ this-forge-project
+ this-forge-laminar-job
+ genenetwork3-mypy
+ #:guix-daemon-uri %guix-daemon-uri)))))
+ (ci-jobs-trigger 'webhook)))
+
+(define (genenetwork3-shepherd-service config)
+ (shepherd-service
+ (documentation "Run GeneNetwork 3.")
+ (provision '(genenetwork3))
+ (requirement '(networking))
+ (modules '((gnu build shepherd)
+ (gnu system file-systems)))
+ (start
+ (with-imported-modules (source-module-closure '((gnu build shepherd)
+ (gnu system file-systems)))
+ #~(make-forkexec-constructor/container
+ (list #$(development-server-configuration-executable-path config)
+ "127.0.0.1" #$(number->string (development-server-configuration-port config)))
+ #:mappings (list (file-system-mapping
+ (source #$(development-server-configuration-executable-path config))
+ (target source)))
+ #:log-file "/var/log/genenetwork3.log")))
+ (stop #~(make-kill-destructor))))
+
+(define %default-genenetwork3-configuration
+ (development-server-configuration
+ (name "genenetwork3")
+ (git-repository "https://github.com/genenetwork/genenetwork3")
+ (git-branch "main")
+ (executable-path "/laminar/bin/genenetwork3")
+ (runner (with-imported-modules (source-module-closure '((genenetwork development-helper))
+ #:select? import-module?)
+ #~(lambda (latest-gn3-source)
+ ((@@ (genenetwork development-helper) genenetwork3-runner-gexp)
+ latest-gn3-source
+ #$(profile
+ (content (manifest-cons gunicorn
+ (package->development-manifest genenetwork3)))
+ (allow-collisions? #t))))))))
+
+(define genenetwork3-service-type
+ (service-type
+ (name 'genenetwork3)
+ (description "Run GeneNetwork 3.")
+ (extensions
+ (list (service-extension activation-service-type
+ development-server-activation)
+ (service-extension shepherd-root-service-type
+ (compose list genenetwork3-shepherd-service))
+ (service-extension forge-service-type
+ (compose list genenetwork3-project))))
+ (default-value %default-genenetwork3-configuration)))
+
+
+;;;
+;;; qc
+;;;
+
+(define qc-tests
+ (with-imported-modules (cons '(guix build lisp-utils)
+ (source-module-closure '((genenetwork development-helper))
+ #:select? import-module?))
+ #~(lambda (source)
+ ((@@ (genenetwork development-helper)
+ asdf-test-gexp)
+ source
+ #$(profile
+ (content (package->development-manifest sbcl-qc))
+ (allow-collisions? #t))
+ "qc" (list "qc.asd")))))
+
+(define qc-project
+ (forge-project
+ (name "qc")
+ (repository "https://git.genenetwork.org/jgart/qc")
+ (ci-jobs (list (forge-laminar-job
+ (name "qc")
+ (run (derivation-job-gexp
+ this-forge-project
+ this-forge-laminar-job
+ qc-tests
+ #:guix-daemon-uri %guix-daemon-uri)))))
+ (ci-jobs-trigger 'webhook)))
+
+
+;;;
+;;; dump-genenetwork-database
+;;;
+
+;; Unreleased version of ccwl that is required by
+;; dump-genenetwork-database for its graphql library.
+(define ccwl
+ (let ((commit "02677a508b407779f5991a230341e016deb7f69b")
+ (revision "0"))
+ (package
+ (inherit guix:ccwl)
+ (name "ccwl")
+ (version (git-version (package-version guix:ccwl) revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/arunisaac/ccwl")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1kxry8y0pibl0x789jrzqkkh2s59ajyinfvrgvd00gkbqldih82r")))))))
+
+;; guile-sparql tests are broken. Disable them temporarily. The issue
+;; has been reported upstream at
+;; https://github.com/roelj/guile-sparql/issues/6
+(define guile-sparql
+ (package
+ (inherit guix:guile-sparql)
+ (arguments
+ `(#:tests? #f))))
+
+;; Temporarily package run64 here until it can be contributed to
+;; upstream Guix.
+(define run64
+ (package
+ (name "run64")
+ (version "0.1.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.systemreboot.net/run64")
+ (commit "a271723e3938b158aa6748e8befceb114b84c6df")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1kdx8h2x5a4cp8azzy1v2xgyb2153sakb1wbi2rj5ygkpmasygbm"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags (list (string-append "prefix=" %output))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure))))
+ (home-page "https://run64.systemreboot.net")
+ (synopsis "SRFI-64 test runner for Scheme")
+ (description "run64 is a SRFI-64 test runner for Scheme.")
+ (license license:gpl3+)))
+
+(define dump-genenetwork-database-tests
+ (with-imported-modules (source-module-closure '((genenetwork development-helper))
+ #:select? import-module?)
+ #~(lambda (source)
+ ((@@ (genenetwork development-helper)
+ command-in-source-gexp)
+ source
+ #$(profile
+ (content (packages->manifest
+ (list gnu-make guile-3.0 guile-dbi guile-dbd-mysql
+ ccwl graphviz guile-libyaml guile-sparql run64)))
+ (allow-collisions? #t))
+ (list "make" "check")))))
+
+(define dump-genenetwork-database-project
+ (forge-project
+ (name "dump-genenetwork-database")
+ (repository "https://git.genenetwork.org/arunisaac/dump-genenetwork-database")
+ (ci-jobs (list (forge-laminar-job
+ (name "dump-genenetwork-database")
+ (run (derivation-job-gexp
+ this-forge-project
+ this-forge-laminar-job
+ dump-genenetwork-database-tests
+ #:guix-daemon-uri %guix-daemon-uri)))))
+ (ci-jobs-trigger 'webhook)))
+
+
+;;;
+;;; gn-gemtext-threads
+;;;
+
+(define (gn-gemtext-threads-website project job)
+ (with-imported-modules '((guix utils))
+ #~(begin
+ (use-modules (guix utils))
+
+ (switch-symlinks #$(forge-project-website-directory project)
+ #$(derivation-job-gexp
+ project
+ job
+ (with-imported-modules (source-module-closure '((genenetwork development-helper))
+ #:select? import-module?)
+ #~(lambda (source-checkout)
+ ((@@ (genenetwork development-helper)
+ tissue-website-gexp)
+ source-checkout
+ #$(profile
+ (content (packages->manifest (list tissue)))
+ (allow-collisions? #t)))))
+ #:guix-daemon-uri %guix-daemon-uri
+ #:deep-clone? #t)))))
+
+(define gn-gemtext-threads-project
+ (forge-project
+ (name "gn-gemtext-threads")
+ (repository "https://github.com/genenetwork/gn-gemtext-threads/")
+ (website-directory "/srv/http/issues")
+ (ci-jobs (list (forge-laminar-job
+ (name "gn-gemtext-threads")
+ (run (gn-gemtext-threads-website
+ this-forge-project
+ this-forge-laminar-job)))))
+ ;; TODO: Also rebuild every night to handle update of stale issues.
+ (ci-jobs-trigger 'webhook)))
+
+
+;;;
+;;; operating-system definition
+;;;
+
+(operating-system
+ (host-name "genenetwork-development")
+ (timezone "UTC")
+ (locale "en_US.utf8")
+ (bootloader (bootloader-configuration
+ (bootloader grub-bootloader)
+ (targets (list "/dev/sdX"))))
+ (file-systems (cons (file-system
+ (device "root")
+ (mount-point "/")
+ (type "ext4"))
+ %base-file-systems))
+ (users %base-user-accounts)
+ (packages %base-packages)
+ (sudoers-file
+ (mixed-text-file "sudoers"
+ "@include " %sudoers-specification
+ ;; Permit the laminar user to restart genenetwork2
+ ;; and genenetwork3.
+ "\nlaminar ALL = NOPASSWD: "
+ (file-append shepherd "/bin/herd") " restart genenetwork2, "
+ (file-append shepherd "/bin/herd") " restart genenetwork3\n"))
+ (services (cons* (service forge-service-type
+ (forge-configuration
+ (projects (list qc-project
+ dump-genenetwork-database-project
+ gn-gemtext-threads-project))))
+ (service laminar-service-type
+ (laminar-configuration
+ (bind-http "localhost:9090")))
+ (service webhook-service-type
+ (webhook-configuration
+ (port 9091)))
+ (service redis-service-type)
+ (service virtuoso-service-type
+ (virtuoso-configuration
+ (server-port 8891)
+ (http-server-port 8892)))
+ (service genenetwork2-service-type
+ (development-server-configuration
+ (inherit %default-genenetwork2-configuration)
+ (port 9092)))
+ (service genenetwork3-service-type
+ (development-server-configuration
+ (inherit %default-genenetwork3-configuration)
+ (port %genenetwork3-port)))
+ %base-services)))