diff options
| -rw-r--r-- | genenetwork/services/genenetwork.scm | 44 | ||||
| -rwxr-xr-x | production-deploy.sh | 1 | ||||
| -rw-r--r-- | production.scm | 2 | ||||
| -rw-r--r-- | public-sparql.scm | 4 | ||||
| -rw-r--r-- | test-r-container.scm | 111 |
5 files changed, 153 insertions, 9 deletions
diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index 4aa35b9..99e78b9 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -259,6 +259,32 @@ (chmod file #o644)) (find-files #$xapian-directory))))))))) +(define (samples-count-script-gexp config) + (match-record config <genenetwork-configuration> + (genenetwork2 sql-uri) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + + (setenv "PYTHONPATH" + (string-append + #$(file-append genenetwork2 + "/lib/python" + (python-version (package-version python)) + "/site-packages") + ":" + #$(profile + (content (package->development-manifest genenetwork2)) + (allow-collisions? #t)) + "/lib/python" + #$(python-version (package-version python)) + "/site-packages")) + + (invoke #$(file-append python "/bin/python3") + "-m" + "gn2.scripts.sample_count" + #$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) @@ -562,9 +588,9 @@ object." (source gn-auth-conf) (target source)) (file-system-mapping - (source auth-db) - (target source) - (writable? #t)) + (source (dirname auth-db)) + (target source) + (writable? #t)) (file-system-mapping (source gn-auth-secrets) (target source) @@ -621,7 +647,10 @@ a @code{<genenetwork-configuration>} record." (list #~(job '(next-hour) #$(program-file "build-xapian-index-cron-gexp" (build-xapian-index-cron-gexp config)) - #:user "root"))) + #:user "root") + #~(job '(next-minute-from (next-hour) '(17)) ;17th minute of every hour + #$(program-file "samples-count-script-gexp" + (samples-count-script-gexp config))))) (define (gn-guile-gexp gn-guile-port gn-guile-pkg) (with-imported-modules '((guix build utils)) @@ -715,7 +744,7 @@ a @code{<genenetwork-configuration>} record." (chown file (passwd:uid (getpw "gunicorn-gn-uploader")) (passwd:gid (getpw "gunicorn-gn-uploader")))) - (append (list #$secrets) + (append (list #$(dirname secrets)) (find-files #$sessions-dir #:directories? #t) (find-files #$sqlite-databases-directory @@ -782,8 +811,9 @@ a @code{<genenetwork-configuration>} record." (source gn-uploader-conf) (target source)) (file-system-mapping - (source secrets) - (target source)) + (source (dirname secrets)) + (target source) + (writable? #t)) (file-system-mapping (source data-directory) (target source) diff --git a/production-deploy.sh b/production-deploy.sh index 7cd1cc7..c8e30fe 100755 --- a/production-deploy.sh +++ b/production-deploy.sh @@ -43,6 +43,7 @@ container_script=$(guix system container \ --share=/export/guix-containers/genenetwork/var/genenetwork/sessions=/var/genenetwork/sessions \ --share=/export/guix-containers/genenetwork/var/lib/genenetwork/uploader=/var/lib/genenetwork/uploader \ --share=/export/guix-containers/genenetwork/var/lib/genenetwork/sqlite/gn-uploader=/var/lib/genenetwork/sqlite/gn-uploader \ + --share=/export/guix-containers/genenetwork/var/lib/genenetwork/gn-guile=/var/lib/genenetwork/gn-guile \ production.scm) echo $container_script diff --git a/production.scm b/production.scm index ffa75da..bfd9e48 100644 --- a/production.scm +++ b/production.scm @@ -88,7 +88,7 @@ (llm-db-path "/var/lib/genenetwork/sqlite/genenetwork3/llm.db") (gn3-alias-server-port 9800) (gn-tmpdir "/opt/gn/tmp") - (gn-doc-git-checkout "/var/lib/gn-docs.git") + (gn-doc-git-checkout "/var/lib/genenetwork/gn-guile/gn-docs.git") (log-level 'debug))) (service gn-uploader-service-type (gn-uploader-configuration diff --git a/public-sparql.scm b/public-sparql.scm index 4603cec..edfcd87 100644 --- a/public-sparql.scm +++ b/public-sparql.scm @@ -64,7 +64,9 @@ SPARQL endpoint is listening on." (dirs-allowed (list "/export/data/virtuoso")) (maximum-dirty-buffers 3000000) (database-file "/var/lib/virtuoso/public-virtuoso.db") - (transaction-file "/var/lib/virtuoso/public-virtuoso.trx"))) + (transaction-file "/var/lib/virtuoso/public-virtuoso.trx") + (error-log-file "/var/lib/public-virtuoso-errors.log") + (syslog "1"))) (service forge-nginx-service-type (forge-nginx-configuration (http-listen (forge-ip-socket diff --git a/test-r-container.scm b/test-r-container.scm new file mode 100644 index 0000000..3167574 --- /dev/null +++ b/test-r-container.scm @@ -0,0 +1,111 @@ +(use-modules (guix) + (gnu) + (guix git) + (guix modules) + (guix profiles) + (guix records) + (guix packages) + (guix git-download) + (guix build-system trivial) + (gnu services dbus) + (gnu services networking) + (gnu services ssh) + (gnu services web) + (gnu services certbot) + (gnu services docker) + (gnu services desktop) + (gnu services shepherd) + (gnu packages admin) + (gnu packages statistics) + (gnu packages cran) + (gnu packages curl) + (gnu packages lsof) + (srfi srfi-1) + (ice-9 match) + (genenetwork services mouse-longevity) + (gn services rshiny) + (gn packages mouse-longevity) + (forge acme) + (forge nginx) + (forge socket) + (gnu services)) + +(define %nginx-configuration + (nginx-configuration + (server-blocks + (list + ;; Redirect domains that don't explicitly support HTTP (below) to HTTPS. + (nginx-server-configuration + (listen '("8080"))) + + ;; Domains that still explicitly support plain HTTP. + (nginx-server-configuration + (listen '("80")) + (server-name '("longevity-explorer.genenetwork.org")) + (locations + (list + (nginx-location-configuration + (uri "/") + (body (list "proxy_pass http://127.0.0.1:3979;"))))) + (raw-content + (list + "proxy_set_header Host $host;" + "proxy_set_header X-Real-IP $remote_addr;" + "proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;" + "proxy_set_header X-Forwarded-Proto $scheme;"))))))) + +(operating-system + (host-name "testing-genenetwork-services") + (keyboard-layout (keyboard-layout "us")) + (kernel-arguments + (cons* "console=ttyS0,115200" "console=tty0" + %default-kernel-arguments)) + (bootloader (bootloader-configuration (bootloader grub-bootloader))) + (issue "This is a GeneNetwork container. Welcome!\n") + (file-systems %base-file-systems) + (sudoers-file + (mixed-text-file "sudoers" + "@include " %sudoers-specification + "\nacme ALL = NOPASSWD: " (file-append shepherd "/bin/herd") " restart nginx\n")) + (packages (cons* lsof curl %base-packages)) + (services + (cons* + (service dhcp-client-service-type) + (service dbus-root-service-type) + (service polkit-service-type) + (service forge-nginx-service-type + (forge-nginx-configuration + (http-listen (forge-ip-socket + (ip "127.0.0.1") + (port "8080"))) + (https-listen (forge-ip-socket + (ip "127.0.0.1") + (port "8443"))) + (server-blocks + (list + (nginx-server-configuration + (server-name '("longevity-explorer.genenetwork.org")) + (locations + (list (nginx-location-configuration + (uri "/") + (body (list "proxy_pass http://localhost:3979;" + "proxy_set_header Host $host;")))))))))) + (service acme-service-type + (acme-configuration + (email "jgart@dismail.de") + (acme-url %letsencrypt-staging-url))) + ;; (service certbot-service-type + ;; (certbot-configuration + ;; (email "jgart@dismail.de") + ;; (certificates + ;; (list + ;; (certificate-configuration + ;; (domains '("longevity-explorer.genenetwork.org" + ;; "www.longevity-explorer.genenetwork.org"))))))) + ;; (mouse-longevity-service ) + (service rshiny-service-type + (rshiny-configuration + (package mouse-longevity-app) + (binary "mouse-longevity-app"))) + ;; (service nginx-service-type %nginx-configuration) + %base-services))) |