diff options
| -rwxr-xr-x | genenetwork-development-deploy.sh | 3 | ||||
| -rw-r--r-- | genenetwork-development.scm | 66 |
2 files changed, 63 insertions, 6 deletions
diff --git a/genenetwork-development-deploy.sh b/genenetwork-development-deploy.sh index ac5acd5..93d5987 100755 --- a/genenetwork-development-deploy.sh +++ b/genenetwork-development-deploy.sh @@ -29,7 +29,8 @@ container_script=$(guix system container --network \ --share=/export2/guix-containers/genenetwork-development/var/lib/tissue=/var/lib/tissue \ --share=/export2/guix-containers/genenetwork-development/var/lib/virtuoso=/var/lib/virtuoso \ --share=/export2/guix-containers/genenetwork-development/var/log/cd=/var/log/cd \ - --expose=/export/data/genenetwork \ + --expose=/export/data/genenetwork/genotype_files \ + --share=/export/data/genenetwork/xapian \ --share=/export/genenetwork-database-dump \ --share=/var/run/mysqld/mysqld.sock=/run/mysqld/mysqld.sock \ genenetwork-development.scm) diff --git a/genenetwork-development.scm b/genenetwork-development.scm index 8176d0d..88dca36 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -45,6 +45,7 @@ ((gnu packages version-control) #:select (git-minimal)) (gnu services ci) (gnu services databases) + (gnu services mcron) (gnu services shepherd) (gnu services web) (gnu system file-systems) @@ -207,6 +208,42 @@ command to be executed." (manifest-cons python-mypy (package->development-manifest genenetwork3)))) +(define %xapian-directory + "/export/data/genenetwork/xapian") + +(define (build-xapian-index-gexp project) + "Return a G-expression that builds and installs a Xapian index using +genenetwork3 source from the latest commit of @var{project}." + (with-imported-modules '((guix build utils)) + (with-manifest (manifest-cons* git-minimal nss-certs + (package->development-manifest genenetwork3)) + #~(begin + (use-modules (guix build utils) + (srfi srfi-26)) + + (invoke "git" "clone" "--depth" "1" + #$(forge-project-repository project) + ".") + (let ((xapian-directory #$%xapian-directory) + (xapian-build-directory (string-append #$%xapian-directory + "/build"))) + (dynamic-wind + (cut mkdir xapian-build-directory) + (lambda () + ;; Build xapian index. + (setenv "PYTHONPATH" (getcwd)) + (invoke "./scripts/index-genenetwork" xapian-build-directory) + ;; Stop genenetwork3, replace old xapian index and + ;; start genenetwork3. + (dynamic-wind + (cut invoke #$sudo #$(file-append shepherd "/bin/herd") "stop" "genenetwork3") + (lambda () + (for-each (lambda (file) + (rename-file file (string-append xapian-directory "/" (basename file)))) + (find-files xapian-build-directory))) + (cut invoke #$sudo #$(file-append shepherd "/bin/herd") "start" "genenetwork3"))) + (cut delete-file-recursively xapian-build-directory))))))) + (define (genenetwork-projects config) "Return forge projects for genenetwork described by CONFIG, a <genenetwork-configuration> object." @@ -275,7 +312,11 @@ command to be executed." this-forge-project this-forge-laminar-job genenetwork3-mypy - #:guix-daemon-uri %guix-daemon-uri))))) + #:guix-daemon-uri %guix-daemon-uri))) + (forge-laminar-job + (name "genenetwork3-build-xapian-index") + (run (build-xapian-index-gexp this-forge-project)) + (trigger? #f)))) (ci-jobs-trigger 'webhook))))) (define (genenetwork2-cd-gexp config) @@ -795,6 +836,8 @@ reverse proxy tissue." ;; and genenetwork3. "\nlaminar ALL = NOPASSWD: " (file-append shepherd "/bin/herd") " restart genenetwork2, " + (file-append shepherd "/bin/herd") " start genenetwork3, " + (file-append shepherd "/bin/herd") " stop genenetwork3, " (file-append shepherd "/bin/herd") " restart genenetwork3\n")) (services (cons* (service forge-service-type (forge-configuration @@ -805,6 +848,17 @@ reverse proxy tissue." (laminar-configuration (title "GeneNetwork CI") (bind-http "localhost:9089"))) + (service mcron-service-type + (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")))) + #:user "laminar"))))) (simple-service 'install-laminar-template activation-service-type (install-laminar-template-gexp @@ -829,8 +883,8 @@ reverse proxy tissue." (sparql-endpoint (string-append "http://localhost:" (number->string %virtuoso-sparql-port) "/sparql")) - (xapian-db-path "/export/data/genenetwork/xapian"))) - (simple-service 'set-dump-genenetwork-database-export-directory-permissions + (xapian-db-path %xapian-directory))) + (simple-service 'set-build-directory-permissions activation-service-type (with-imported-modules '((guix build utils)) #~(begin @@ -840,8 +894,10 @@ reverse proxy tissue." (chown file (passwd:uid (getpw "laminar")) (passwd:gid (getpw "laminar")))) - (find-files #$%dump-genenetwork-database-export-directory - #:directories? #t))))) + (append (find-files #$%xapian-directory + #:directories? #t) + (find-files #$%dump-genenetwork-database-export-directory + #:directories? #t)))))) (service tissue-service-type (tissue-configuration (hosts |