diff options
| -rw-r--r-- | genenetwork/services/genenetwork.scm | 41 | ||||
| -rw-r--r-- | guix/gn-machines/genenetwork.scm | 40 | ||||
| -rw-r--r-- | production.scm | 4 | ||||
| -rw-r--r-- | public-sparql.scm | 4 |
4 files changed, 70 insertions, 19 deletions
diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index 5c6b9f0..dd49be1 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -289,6 +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 + #$sql-uri))))) + (define (genenetwork-activation config) (match-record config <genenetwork-configuration> (gn2-secrets gn3-secrets gn-auth-secrets auth-db llm-db-path genotype-files gn-tmpdir gn-doc-git-checkout gn2-sessions-dir) @@ -450,7 +477,7 @@ object." (sockets (list (forge-ip-socket (port gn2-port)))) (wsgi-app-module "gn2.wsgi") - (workers 20) + (workers 10) (timeout 1200) (environment-variables (list (environment-variable @@ -509,7 +536,7 @@ object." (sockets (list (forge-ip-socket (port gn3-port)))) (wsgi-app-module "gn3.app:create_app()") - (workers 20) + (workers 10) ;; gunicorn's default 30 second timeout is insufficient ;; for Fahamu AI endpoints and results in worker timeout ;; errors. @@ -572,7 +599,7 @@ object." (sockets (list (forge-ip-socket (port gn-auth-port)))) (wsgi-app-module "gn_auth:create_app()") - (workers 20) + (workers 10) (timeout 1200) (environment-variables (list (environment-variable @@ -654,7 +681,11 @@ a @code{<genenetwork-configuration>} record." #:user "root") #~(job '(next-minute-from (next-hour) '(17)) ;17th minute of every hour #$(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)) @@ -800,7 +831,7 @@ a @code{<genenetwork-configuration>} record." (sockets (list (forge-ip-socket (port port)))) (wsgi-app-module "scripts.qcapp_wsgi:app") - (workers 20) + (workers 10) (timeout 1200) (environment-variables (list (environment-variable diff --git a/guix/gn-machines/genenetwork.scm b/guix/gn-machines/genenetwork.scm index 36b3abe..74be3c1 100644 --- a/guix/gn-machines/genenetwork.scm +++ b/guix/gn-machines/genenetwork.scm @@ -2,11 +2,14 @@ #:use-module ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth gn-uploader gn-libs) #:prefix gn:) + #:use-module((gn packages guile) + #:select (gn-guile) + #:prefix gng:) #:use-module (guix git-download) #:use-module (guix packages)) (define-public genenetwork2 - (let ((commit "bde8bde1732cc042e96819bfdfd17a004b92d06f") + (let ((commit "905cacdc33a054b463d3b98c2adcd882dc3573fe") (revision "4")) (package (inherit gn:genenetwork2) @@ -20,14 +23,14 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "05yslcqykvxiddlhdvfmjpmrm36149zxr7mjwq0pyhm6fg5dgzqp")))) + "0vjsfihj94g1cxivkvmfnixjpmmn3wsciiiry2zkqjnzb3yryy2x")))) (propagated-inputs (modify-inputs (package-propagated-inputs gn:genenetwork2) (replace "gn-libs" gn-libs) (replace "genenetwork3" genenetwork3)))))) (define-public genenetwork3 - (let ((commit "810dbf22e6e921681dc187f37658c5f9874f12d7") + (let ((commit "34a6b37b312b2e2e92324683ec47046b6ab63fe4") (revision "5")) (package (inherit gn:genenetwork3) @@ -42,13 +45,13 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1jjv4fdjsilcjad8lpqpx2d3qaq90ygv6hcrq8di2wb63998xcvb")))) + "1mz71kc4icgcj8mjpnipbyfv3nvyrdmqdzpjy1nd3j2f9zjxypz0")))) (propagated-inputs (modify-inputs (package-propagated-inputs gn:genenetwork3) (replace "gn-libs" gn-libs)))))) (define-public gn-auth - (let ((commit "5823b0aaa411748bd361d23ad6eb07c2a3604dbf") + (let ((commit "bd0f453033327a392afa3194538db5d2be22969e") (revision "1")) (package (inherit gn:gn-auth) @@ -64,13 +67,13 @@ (hash (content-hash (base32 - "01c4diaw560ki51zssygl0738a9wj60hk47w7vd2dsfwnjmcilq4"))))) + "0iamdg2xbj4f5z0qd8z8jildmq2scr10s547fn2k4rac2xm0yn59"))))) (propagated-inputs (modify-inputs (package-propagated-inputs gn:gn-auth) (replace "gn-libs" gn-libs)))))) (define-public gn-uploader - (let ((commit "9514647b70fe90a709b2881e50871a6e15f1236e") + (let ((commit "e4db73ebd5daf7cf4e228fb0f2b70e02db046e31") (revision "0")) (package (inherit gn:gn-uploader) @@ -85,13 +88,13 @@ (hash (content-hash (base32 - "1gdn60vb4jk63akffkmbmgi7lil6bv8fqksdn1v2bww1z9rmiydl"))))) + "1x0h4czkkd0lv63yg95yrz65h9s1rbrfccx1sr988zp17v82s4hj"))))) (propagated-inputs (modify-inputs (package-propagated-inputs gn:gn-uploader) (replace "gn-libs" gn-libs)))))) (define-public gn-libs - (let ((commit "ef71bf1f5a1af847492ea58282511d728a837630") + (let ((commit "9bc82972ad971dac4eb604923b9a6df51d4411ff") (revision "03")) (package (inherit gn:gn-libs) @@ -105,4 +108,21 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "03i1kj7jbmlkjs61a9fb4j3s78p4d5lmd8lqnfsv42wxwwyvsm8p"))))))) + "00xfz6wqqkik7ck5yszd6nhh9s0g870lssyclaz9j6kvw2p12a0n"))))))) + +(define-public gn-guile + (let ((commit "454244b774ece37f04f146c74353ea4ec35d43e1") + (revision "0")) + (package + (inherit gng:gn-guile) + (name "gn-guile") + (version (git-version "4.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.genenetwork.org/gn-guile/") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "1n1zjpwfksq8bf42d7xr7lnblgsbqc0yszkbid253s943fyxzhfn"))))))) diff --git a/production.scm b/production.scm index bfd9e48..6339b66 100644 --- a/production.scm +++ b/production.scm @@ -49,8 +49,8 @@ (server-port 9892) (http-server-port 9893) (dirs-allowed (list "/export/data/virtuoso")) - (number-of-buffers 4000000) - (maximum-dirty-buffers 3000000) + (number-of-buffers 680000) + (maximum-dirty-buffers 500000) (database-file "/var/lib/virtuoso/genenetwork-virtuoso.db") (transaction-file "/var/lib/virtuoso/genenetwork-virtuoso.trx"))) (service forge-nginx-service-type diff --git a/public-sparql.scm b/public-sparql.scm index edfcd87..87ef843 100644 --- a/public-sparql.scm +++ b/public-sparql.scm @@ -60,9 +60,9 @@ SPARQL endpoint is listening on." (virtuoso-configuration (server-port %virtuoso-port) (http-server-port %sparql-port) - (number-of-buffers 4000000) + (number-of-buffers 680000) + (maximum-dirty-buffers 500000) (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") (error-log-file "/var/lib/public-virtuoso-errors.log") |