diff options
Diffstat (limited to 'genenetwork')
| -rw-r--r-- | genenetwork/services/genenetwork.scm | 24 |
1 files changed, 20 insertions, 4 deletions
diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index a403f21..65e8e22 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -57,6 +57,7 @@ genenetwork-configuration-port ; external port genenetwork-configuration-gn2-port ; internal port genenetwork-configuration-gn3-port ; internal port + genenetwork-configuration-gn-guile-port ; aka gn4 internal port (may be external) genenetwork-configuration-auth-db ; RW auth DB genenetwork-configuration-xapian-db ; RO search index, unless you want to regenerate inside VM genenetwork-configuration-genotype-files ; RO genotype files @@ -150,6 +151,8 @@ (default "https://genenetwork.org")) (sessions-dir gn-uploader-sessions-dir (default "/var/genenetwork/sessions/gn-uploader")) + (sqlite-databases-directory gn-uploader-sqlite-databases-directory + (default "/var/genenetwork/sqlite/gn-uploader")) (log-level gn-uploader-configuration-log-level (default 'warning) (sanitize sanitize-log-level))) @@ -370,6 +373,8 @@ object." ("GENENETWORK_FILES" ,genotype-files) ("GN3_LOCAL_URL" ,(string-append "http://localhost:" (number->string gn3-port))) + ("GN_GUILE_SERVER_URL" ,(string-append "http://localhost:" ; AKA GN4 + (number->string gn-guile-port) "/" )) ("GN_SERVER_URL" ,(string-append "https://" server-name "/api3/")) ("AUTH_SERVER_URL" ,(string-append "https://" gn-auth-server-name "/")) ("JS_GUIX_PATH" ,(file-append gn2-profile "/share/genenetwork2/javascript")) @@ -386,6 +391,8 @@ object." (configuration-file-gexp `(("AUTH_DB" ,auth-db) ("AUTH_SERVER_URL" ,(string-append "https://" gn-auth-server-name "/")) + ("GN_GUILE_SERVER_URL" ,(string-append "http://localhost:" ; AKA GN4 + (number->string gn-guile-port) "/")) ("DATA_DIR" ,gn3-data-directory) ("SOURCE_DIR" ,gn-sourcecode-directory) ("SPARQL_ENDPOINT" ,sparql-endpoint) @@ -534,6 +541,7 @@ object." (port gn-auth-port)))) (wsgi-app-module "gn_auth:create_app()") (workers 20) + (timeout 1200) (environment-variables (list (environment-variable (name "GN_AUTH_CONF") @@ -613,7 +621,7 @@ a @code{<genenetwork-configuration>} record." (build-xapian-index-cron-gexp config)) #:user "root"))) -(define (gn-guile-gexp gn-guile-port) +(define (gn-guile-gexp gn-guile-port) (with-imported-modules '((guix build utils)) #~(begin (use-modules (guix build utils)) @@ -684,7 +692,7 @@ a @code{<genenetwork-configuration>} record." (define (gn-uploader-activation config) (match-record config <gn-uploader-configuration> - (secrets data-directory sessions-dir) + (secrets data-directory sessions-dir sqlite-databases-directory) (with-imported-modules '((guix build utils)) #~(begin (use-modules (guix build utils)) @@ -695,6 +703,8 @@ a @code{<genenetwork-configuration>} record." (passwd:gid (getpw "gunicorn-gn-uploader")))) (append (list #$secrets) (find-files #$sessions-dir + #:directories? #t) + (find-files #$sqlite-databases-directory #:directories? #t))) ;; Set owner-only permissions on secrets files. (for-each (lambda (file) @@ -711,7 +721,7 @@ a @code{<genenetwork-configuration>} record." (define (gn-uploader-gunicorn-app config) (match-record config <gn-uploader-configuration> - (gn-uploader sql-uri port data-directory secrets log-level auth-server-url gn2-server-url sessions-dir) + (gn-uploader sql-uri port data-directory secrets log-level auth-server-url gn2-server-url sessions-dir sqlite-databases-directory) ;; If we mapped only the mysqld.sock socket file, it would break ;; when the external mysqld server is restarted. (let* ((database-mapping (file-system-mapping @@ -726,7 +736,8 @@ a @code{<genenetwork-configuration>} record." "/uploads")) ("AUTH_SERVER_URL" ,auth-server-url) ("GN2_SERVER_URL" ,gn2-server-url) - ("SESSION_FILESYSTEM_CACHE_PATH" ,sessions-dir))))) + ("SESSION_FILESYSTEM_CACHE_PATH" ,sessions-dir) + ("ASYNCHRONOUS_JOBS_SQLITE_DB" ,(string-append sqlite-databases-directory "/background-jobs.db")))))) (gn-uploader-profile (profile (content (package->development-manifest gn-uploader)) (allow-collisions? #t))) @@ -738,6 +749,7 @@ a @code{<genenetwork-configuration>} record." (port port)))) (wsgi-app-module "scripts.qcapp_wsgi:app") (workers 20) + (timeout 1200) (environment-variables (list (environment-variable (name "UPLOADER_CONF") @@ -771,6 +783,10 @@ a @code{<genenetwork-configuration>} record." (file-system-mapping (source sessions-dir) (target source) + (writable? #t)) + (file-system-mapping + (source sqlite-databases-directory) + (target source) (writable? #t)))) (extra-cli-arguments (list "--log-level" |