diff options
Diffstat (limited to 'genenetwork')
| -rw-r--r-- | genenetwork/services/genecup.scm | 121 | ||||
| -rw-r--r-- | genenetwork/services/genenetwork.scm | 33 | ||||
| -rw-r--r-- | genenetwork/services/mouse-longevity.scm | 33 |
3 files changed, 186 insertions, 1 deletions
diff --git a/genenetwork/services/genecup.scm b/genenetwork/services/genecup.scm new file mode 100644 index 0000000..6ee2812 --- /dev/null +++ b/genenetwork/services/genecup.scm @@ -0,0 +1,121 @@ +;;; genenetwork-machines --- Guix configuration for genenetwork machines +;;; Copyright © 2024 jgart <jgart@dismail.de> +;;; +;;; 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 genecup) + #:use-module (guix) + #:use-module (gnu) + #:use-module (guix git) + #:use-module (guix modules) + #:use-module (guix profiles) + #:use-module (guix records) + #:use-module (srfi srfi-1) + #:use-module (ice-9 match) + #:use-module (forge utils) + #:use-module (gn packages genecup) + #:use-module (gn packages mouse-longevity) + #:use-module (gn services rshiny) + #:use-module (gn packages machine-learning) + #:use-module (gnu packages certs) + #:use-module (gnu packages curl) + #:use-module (gn packages python) + #:use-module (gnu packages admin) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages compression) + #:use-module ((gnu packages python) #:select (python)) + #:use-module (gnu packages python-xyz) + #:use-module (guix build python-build-system) + #:use-module (gnu packages python-crypto) + #:use-module (gnu packages python-web) + #:use-module (gnu services shepherd) + #:use-module (gnu packages python-science) + #:use-module (gnu packages machine-learning) + #:use-module ((gnu packages admin) #:select (shepherd)) + #:export (genecup-configuration + genecup-configuration? + genecup-configuration-package + genecup-service-type)) + +(define-record-type* <genecup-configuration> + genecup-configuration make-genecup-configuration + genecup-configuration? + (package genecup-configuration-package ; <package> + (default genecup-latest-with-tensorflow-native))) + +(define (genecup-activation config) + (match-record config <genecup-configuration> + (package) + (with-packages + (list python + python-nltk + nss-certs ; Needed for downloading data with nltk.downloader. + curl) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + (let ((nltk-data "/var/cache/nltk_data/") + (data-dir "/export/ratspub/tmp")) + (unless (file-exists? nltk-data) + (begin + (mkdir-p nltk-data) + (chdir nltk-data) + (invoke #$(file-append python "/bin/python3") "-m" "nltk.downloader" "-d" nltk-data "punkt"))) + (unless (file-exists? (string-append data-dir "/userspub.sqlite")) + (begin + (install-file #$(file-append package "/userspub.sqlite") data-dir) + (chmod (string-append data-dir "/userspub.sqlite") #o554))))))))) + +(define genecup-shepherd-service + (match-lambda + (($ <genecup-configuration> package) + (with-imported-modules (source-module-closure + '((guix search-paths) + (gnu build shepherd) + (gnu system file-systems))) + (list (shepherd-service + (provision '(genecup)) + (requirement '(networking)) + (modules '((gnu build shepherd) + (gnu system file-systems))) + (start + #~(make-forkexec-constructor + (list #$(file-append package "/server.py")) + #:directory #$package + #:environment-variables + (list + "NLTK_DATA=/var/cache/nltk_data" + (string-append "EDIRECT_PUBMED_MASTER=" + #$(file-append package "/minipubmed")) + (string-append "PERL_LWP_SSL_CA_FILE=" + #$(file-append (profile (content (packages->manifest (list curl nss-certs)))) + "/etc/ssl/certs/ca-certificates.crt"))) + #:log-file "/var/log/genecup.log")) + (stop #~(make-kill-destructor)))))))) + +(define genecup-service-type + (service-type + (name 'genecup) + (extensions + (list + (service-extension activation-service-type + genecup-activation) + (service-extension shepherd-root-service-type + genecup-shepherd-service))) + (default-value (genecup-configuration)) + (description + "Run a GeneCup Webserver."))) diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index 99e78b9..60fe718 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -285,6 +285,33 @@ "gn2.scripts.sample_count" #$sql-uri))))) +(define (make-non-human-data-public-cron-gexp config) + (match-record config <genenetwork-configuration> + (gn-auth sql-uri auth-db) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + + (setenv "PYTHONPATH" + (string-append + #$(file-append gn-auth + "/lib/python" + (python-version (package-version python)) + "/site-packages") + ":" + #$(profile + (content (package->development-manifest gn-auth)) + (allow-collisions? #t)) + "/lib/python" + #$(python-version (package-version python)) + "/site-packages")) + + (invoke #$(file-append python "/bin/python3") + "-m" + "scripts.batch_assign_data_to_default_admin" + #$auth-db + #$sql-uri))))) + (define (genenetwork-activation config) (match-record config <genenetwork-configuration> (gn2-secrets gn3-secrets gn-auth-secrets auth-db llm-db-path genotype-files gn-tmpdir gn-doc-git-checkout gn2-sessions-dir) @@ -650,7 +677,11 @@ a @code{<genenetwork-configuration>} record." #:user "root") #~(job '(next-minute-from (next-hour) '(17)) ;17th minute of every hour #$(program-file "samples-count-script-gexp" - (samples-count-script-gexp config))))) + (samples-count-script-gexp config))) + #~(job '(next-minute (range 0 60 15)) + #$(program-file "make-non-human-data-public-cron-gexp" + (make-non-human-data-public-cron-gexp config)) + #:user "gunicorn-gn-auth"))) (define (gn-guile-gexp gn-guile-port gn-guile-pkg) (with-imported-modules '((guix build utils)) diff --git a/genenetwork/services/mouse-longevity.scm b/genenetwork/services/mouse-longevity.scm new file mode 100644 index 0000000..c9b977d --- /dev/null +++ b/genenetwork/services/mouse-longevity.scm @@ -0,0 +1,33 @@ +;;; genenetwork-machines --- Guix configuration for genenetwork machines +;;; Copyright © 2024 jgart <jgart@dismail.de> +;;; +;;; 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 mouse-longevity) + #:use-module (gn packages genecup) + #:use-module (gn packages mouse-longevity) + #:use-module (gn services rshiny) + #:use-module (gnu services) + #:export (mouse-longevity-service)) + +(define* (mouse-longevity-service #:optional (package mouse-longevity-app)) + (simple-service 'mouse-longevity + rshiny-service-type + (list + (rshiny-configuration + (package package) + (binary "mouse-longevity-app"))))) |