diff options
Diffstat (limited to 'genenetwork/services/genenetwork.scm')
| -rw-r--r-- | genenetwork/services/genenetwork.scm | 44 |
1 files changed, 37 insertions, 7 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) |