diff options
Diffstat (limited to 'genenetwork/services/genenetwork.scm')
| -rw-r--r-- | genenetwork/services/genenetwork.scm | 60 |
1 files changed, 54 insertions, 6 deletions
diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index 9ba6213..2091c2c 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -20,7 +20,7 @@ ;;; <https://www.gnu.org/licenses/>. (define-module (genenetwork services genenetwork) - #:use-module ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth gn-uploader)) + #:use-module ((gn-machines genenetwork) #:select (genenetwork2 genenetwork3 gn-auth gn-uploader)) #:use-module ((gn packages guile) #:select (gn-guile)) #:use-module (gnu build linux-container) #:use-module ((gnu packages web) #:select (nginx)) @@ -155,6 +155,10 @@ (default "/var/genenetwork/sessions/gn-uploader")) (sqlite-databases-directory gn-uploader-sqlite-databases-directory (default "/var/genenetwork/sqlite/gn-uploader")) + (gn-tmpdir gn-uploader-configuration-gn-tmpdir + (default "/opt/gn/tmp")) + (genotype-files-directory gn-uploader-configuration-genotype-files-directory + (default "/var/genenetwork/genotype-files")) (log-level gn-uploader-configuration-log-level (default 'warning) (sanitize sanitize-log-level))) @@ -285,6 +289,33 @@ "gn2.scripts.sample_count" #$sql-uri))))) +(define (make-non-human-data-public-cron-gexp config) + (match-record config <genenetwork-configuration> + (gn-auth sql-uri auth-db) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + + (setenv "PYTHONPATH" + (string-append + #$(file-append gn-auth + "/lib/python" + (python-version (package-version python)) + "/site-packages") + ":" + #$(profile + (content (package->development-manifest gn-auth)) + (allow-collisions? #t)) + "/lib/python" + #$(python-version (package-version python)) + "/site-packages")) + + (invoke #$(file-append python "/bin/python3") + "-m" + "scripts.batch_assign_data_to_default_admin" + #$auth-db + #$sql-uri))))) + (define (genenetwork-activation config) (match-record config <genenetwork-configuration> (gn2-secrets gn3-secrets gn-auth-secrets auth-db llm-db-path genotype-files gn-tmpdir gn-doc-git-checkout gn2-sessions-dir) @@ -650,7 +681,11 @@ a @code{<genenetwork-configuration>} record." #:user "root") #~(job '(next-minute-from (next-hour) '(17)) ;17th minute of every hour #$(program-file "samples-count-script-gexp" - (samples-count-script-gexp config))))) + (samples-count-script-gexp config))) + #~(job '(next-minute (range 0 60 15)) + #$(program-file "make-non-human-data-public-cron-gexp" + (make-non-human-data-public-cron-gexp config)) + #:user "gunicorn-gn-auth"))) (define (gn-guile-gexp gn-guile-port gn-guile-pkg bare-repo) (with-imported-modules '((guix build utils)) @@ -735,7 +770,7 @@ a @code{<genenetwork-configuration>} record." (define (gn-uploader-activation config) (match-record config <gn-uploader-configuration> - (secrets data-directory sessions-dir sqlite-databases-directory) + (secrets data-directory sessions-dir sqlite-databases-directory gn-tmpdir) (with-imported-modules '((guix build utils)) #~(begin (use-modules (guix build utils)) @@ -760,27 +795,32 @@ a @code{<genenetwork-configuration>} record." (passwd:gid (getpw "gunicorn-gn-uploader")))) (append (list #$data-directory) (find-files #$data-directory + #:directories? #t) + (find-files #$(string-append gn-tmpdir "/gn-uploader-tmpdir") #:directories? #t))))))) (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 sqlite-databases-directory) + (gn-uploader sql-uri port data-directory secrets log-level auth-server-url gn2-server-url sessions-dir sqlite-databases-directory gn-tmpdir genotype-files-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 (source "/run/mysqld") (target source) (writable? #t))) + (gn-uploader-tmpdir (string-append gn-tmpdir "/gn-uploader-tmpdir")) (gn-uploader-conf (computed-file "gn-uploader.conf" (configuration-file-gexp `(("UPLOADER_SECRETS" ,secrets) ("SQL_URI" ,sql-uri) ("UPLOAD_FOLDER" ,(string-append data-directory "/uploads")) + ("TEMPORARY_DIRECTORY" ,gn-uploader-tmpdir) ("AUTH_SERVER_URL" ,auth-server-url) ("GN2_SERVER_URL" ,gn2-server-url) ("SESSION_FILESYSTEM_CACHE_PATH" ,sessions-dir) - ("ASYNCHRONOUS_JOBS_SQLITE_DB" ,(string-append sqlite-databases-directory "/background-jobs.db")))))) + ("ASYNCHRONOUS_JOBS_SQLITE_DB" ,(string-append sqlite-databases-directory "/background-jobs.db")) + ("GENOTYPE_FILES_DIRECTORY" ,genotype-files-directory))))) (gn-uploader-profile (profile (content (package->development-manifest gn-uploader)) (allow-collisions? #t))) @@ -831,7 +871,15 @@ a @code{<genenetwork-configuration>} record." (file-system-mapping (source sqlite-databases-directory) (target source) - (writable? #t)))) + (writable? #t)) + (file-system-mapping + (source gn-uploader-tmpdir) + (target source) + (writable? #t)) + (file-system-mapping + (source genotype-files-directory) + (target source) + (writable? #f)))) (extra-cli-arguments (list "--log-level" (string-upcase (symbol->string log-level))))))))) |