diff options
| -rw-r--r-- | genenetwork-development.scm | 86 |
1 files changed, 38 insertions, 48 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm index f0db2b7..a015154 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -1,6 +1,8 @@ ;;; genenetwork-machines --- Guix configuration for genenetwork machines ;;; Copyright © 2022–2024 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2022–2024 Frederick Muriuki Muriithi <fredmanglis@gmail.com> +;;; Copyright © 2024 Munyoki Kilyungi <me@bonfacemunyoki.com> +;;; Copyright © 2024 John Nduli <rookie101@jnduli.co.ke> ;;; ;;; This file is part of genenetwork-machines. ;;; @@ -248,8 +250,10 @@ genenetwork3 source from the latest commit of @var{project}." (lambda () ;; Build xapian index. (setenv "PYTHONPATH" (getcwd)) - (invoke "./scripts/index-genenetwork" xapian-build-directory - "mysql://webqtlout:webqtlout@localhost/db_webqtl") + (invoke "./scripts/index-genenetwork" "create-xapian-index" + xapian-build-directory + "mysql://webqtlout:webqtlout@localhost/db_webqtl" + "http://localhost:9082/sparql") ;; Stop genenetwork3, replace old xapian index and ;; start genenetwork3. (dynamic-wind @@ -264,54 +268,40 @@ genenetwork3 source from the latest commit of @var{project}." ;; G-expression that is configured in cron to trigger a rebuild of the ;; xapian index (define build-xapian-index-cron-gexp - (with-extensions (list guile-dsv guile-lib guile-xapian) - (with-imported-modules '((guix build utils)) + (with-imported-modules '((guix build utils)) + (with-manifest + (manifest-cons* git-minimal nss-certs + (package->development-manifest genenetwork3)) #~(begin (use-modules (guix build utils) - (dsv) - (xapian wrap) - (xapian xapian) - (ice-9 match) - (ice-9 popen) - (srfi srfi-26) - (srfi srfi-71) - (rnrs io ports)) - - ;; guile-dbi does not support guile 3. So, we shell out to - ;; mysql instead. - (define (mysql-table-checksums user password database tables) - "Return list of checksums for @var{tables} in MySQL -@var{database}. Authenticate with @var{user} and @var{password}." - (let ((from to pids (pipeline `((#$(file-append mariadb "/bin/mysql") - "--batch" - ,(string-append "--user=" user) - ,(string-append "--password=" password) - ,database))))) - (put-string to (string-append "CHECKSUM TABLES " - (string-join tables ",") - ";")) - (close to) - (match (dsv->scm from #\tab) - ((header (tables checksums) ...) - (close from) - checksums)))) - - (call-with-database #$%xapian-directory - (lambda (db) - (let ((tables (string-split (Database-get-metadata db "tables") - #\space)) - (checksums (map string->number - (string-split (Database-get-metadata db "checksums") - #\space)))) - ;; Trigger xapian index rebuild when table checksums - ;; in the index do not match with the SQL database and - ;; there is no running build job. - (unless (or (equal? (mysql-table-checksums "webqtlout" "webqtlout" "db_webqtl" tables) - checksums) - (file-exists? (string-append #$%xapian-directory "/build"))) - (setenv "LAMINAR_REASON" "Nightly xapian index rebuild") - (invoke #$(file-append laminar "/bin/laminarc") - "queue" "genenetwork3-build-xapian-index"))))))))) + (srfi srfi-26)) + + (define (call-with-temporary-directory proc) + (let ((tmp-dir (mkdtemp "/tmp/xapian-index-cron.XXXXXX"))) + (dynamic-wind + (const #t) + (cut proc tmp-dir) + (cut delete-file-recursively tmp-dir)))) + + (call-with-temporary-directory + (lambda (gn3-dir) + (invoke "git" "clone" "--depth" "1" + "https://github.com/genenetwork/genenetwork3.git" + gn3-dir) + (setenv "PYTHONPATH" gn3-dir) + ;; Only trigger a laminar build when the data is modified. + (when + (and + (not (file-exists? (string-append #$%xapian-directory "/build"))) + (zero? (status:exit-val + (system* (string-append gn3-dir "/scripts/index-genenetwork") + "is-data-modified" + #$%xapian-directory + "mysql://webqtlout:webqtlout@localhost/db_webqtl" + "http://localhost:9082/sparql")))) + (setenv "LAMINAR_REASON" "Nightly xapian index rebuild") + (invoke #$(file-append laminar "/bin/laminarc") + "queue" "genenetwork3-build-xapian-index")))))))) (define (genenetwork-projects config) "Return forge projects for genenetwork described by CONFIG, a |