diff options
| -rw-r--r-- | genenetwork-development.scm | 64 |
1 files changed, 56 insertions, 8 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm index 62394f3..7415885 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -31,11 +31,12 @@ ((gnu packages check) #:select (python-pylint)) ((gnu packages ci) #:select (laminar)) ((gnu packages compression) #:select (gzip)) - ((gnu packages databases) #:select (virtuoso-ose)) + ((gnu packages databases) #:select (mariadb virtuoso-ose)) ((gnu packages gnupg) #:select (guile-gcrypt)) ((gnu packages graphviz) #:select (graphviz)) ((gnu packages guile) #:select (guile-3.0 guile-git guile-zlib)) - ((gnu packages guile-xyz) #:select (guile-dbd-mysql guile-dbi guile-hashing guile-ini guile-lib guile-libyaml guile-smc)) + ((gnu packages guile-xyz) #:select (guile-dbd-mysql guile-dbi guile-dsv guile-hashing + guile-ini guile-lib guile-libyaml guile-smc guile-xapian)) ((gnu packages guile-xyz) #:select (guile-sparql) #:prefix guix:) ((gnu packages haskell-apps) #:select (shellcheck)) ((gnu packages python-check) #:select (python-mypy)) @@ -293,6 +294,58 @@ genenetwork3 source from the latest commit of @var{project}." (cut invoke #$sudo #$(file-append shepherd "/bin/herd") "start" "genenetwork3"))) (cut delete-file-recursively xapian-build-directory))))))) +;; 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)) + #~(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"))))))))) + (define (genenetwork-projects config) "Return forge projects for genenetwork described by CONFIG, a <genenetwork-configuration> object." @@ -1125,12 +1178,7 @@ gn-auth." (mcron-configuration (jobs (list #~(job '(next-day) #$(program-file "build-xapian-index-cron" - (with-imported-modules '((guix build utils)) - #~(begin - (use-modules (guix build utils)) - (setenv "LAMINAR_REASON" "Nightly xapian index rebuild") - (invoke #$(file-append laminar "/bin/laminarc") - "queue" "genenetwork3-build-xapian-index")))) + build-xapian-index-cron-gexp) #:user "laminar"))))) (simple-service 'install-laminar-template activation-service-type |