From bafa701d22078351f4c1210ddca2a4ab397f32ab Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 28 Mar 2025 04:48:07 +0000 Subject: Make dirs-allowed a list of directories. * genenetwork-development.scm (operating-system)[services]{virtuoso-service-type}: Make dirs-allowed a list of directories. --- genenetwork-development.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genenetwork-development.scm b/genenetwork-development.scm index 50d72a5..ad45898 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -1372,7 +1372,7 @@ gn-auth." (number-of-buffers 4000000) (maximum-dirty-buffers 3000000) (server-port 9081) - (dirs-allowed "/var/lib/data") + (dirs-allowed (list "/var/lib/data")) (http-server-port %virtuoso-sparql-port))) (service genenetwork-service-type (genenetwork-configuration -- cgit 1.4.1 From 3fa821115a00867f8f9aecc454839232cbf500d2 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 28 Mar 2025 04:49:00 +0000 Subject: Update tissue configuration in line with guix-forge update. guix-forge has introduced a breaking change in tissue configuration. Update configuration. * genenetwork-development.scm (operating-system)[services]{tissue-service-type}: Update tissue configuration. --- genenetwork-development.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/genenetwork-development.scm b/genenetwork-development.scm index ad45898..f841255 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -1399,8 +1399,12 @@ gn-auth." (hosts (list (tissue-host (name "issues.genenetwork.org") - (user "laminar") - (upstream-repository "https://github.com/genenetwork/gn-gemtext-threads")))))) + (projects (list (tissue-project + (name "issues.genenetwork.org") + (user "laminar") + (base-path "/") + (upstream-repository + "https://github.com/genenetwork/gn-gemtext-threads"))))))))) (service forge-nginx-service-type (forge-nginx-configuration (http-listen (forge-ip-socket -- cgit 1.4.1 From 44875e5f08339763ec60f2aa492251c789e36d80 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 2 Apr 2025 12:39:05 -0500 Subject: public-sparql: Separate instance dir from data directories The "allowed" directories are directories other than the instance directory, which virtuoso can access to load data. --- public-sparql-deploy.sh | 1 + public-sparql.scm | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/public-sparql-deploy.sh b/public-sparql-deploy.sh index bc4348d..0359dc6 100755 --- a/public-sparql-deploy.sh +++ b/public-sparql-deploy.sh @@ -26,6 +26,7 @@ container_script=$(guix system container \ --share=/export/guix-containers/public-sparql/tmp=/tmp \ --share=/export/guix-containers/public-sparql/var/log=/var/log \ --share=/export/guix-containers/public-sparql/var/lib/acme=/var/lib/acme \ + --share=/export2/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso \ public-sparql.scm) echo $container_script diff --git a/public-sparql.scm b/public-sparql.scm index 4f5ad13..6fbf75c 100644 --- a/public-sparql.scm +++ b/public-sparql.scm @@ -56,7 +56,7 @@ SPARQL endpoint is listening on." (server-port %virtuoso-port) (http-server-port %sparql-port) (number-of-buffers 4000000) - (dirs-allowed (list "/var/lib/virtuoso")) + (dirs-allowed (list "/export/data/virtuoso")) (maximum-dirty-buffers 3000000) (database-file "/var/lib/virtuoso/public-virtuoso.db") (transaction-file "/var/lib/virtuoso/public-virtuoso.trx"))) -- cgit 1.4.1 From a5e43e8a2f53d18283e2c6c2cd080131cb93b3e2 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 2 Apr 2025 12:59:51 -0500 Subject: public-sparql: use the /export2 disk. --- public-sparql-deploy.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/public-sparql-deploy.sh b/public-sparql-deploy.sh index 0359dc6..4ecacc6 100755 --- a/public-sparql-deploy.sh +++ b/public-sparql-deploy.sh @@ -22,10 +22,10 @@ container_script=$(guix system container \ --network \ --verbosity=3 \ - --share=/export/guix-containers/public-sparql/var/lib/virtuoso=/var/lib/virtuoso \ - --share=/export/guix-containers/public-sparql/tmp=/tmp \ - --share=/export/guix-containers/public-sparql/var/log=/var/log \ - --share=/export/guix-containers/public-sparql/var/lib/acme=/var/lib/acme \ + --share=/export2/guix-containers/public-sparql/var/lib/virtuoso=/var/lib/virtuoso \ + --share=/export2/guix-containers/public-sparql/tmp=/tmp \ + --share=/export2/guix-containers/public-sparql/var/log=/var/log \ + --share=/export2/guix-containers/public-sparql/var/lib/acme=/var/lib/acme \ --share=/export2/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso \ public-sparql.scm) -- cgit 1.4.1 From 01bf00c060f00af089bb8cd57ff7eeb966c0afab Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 3 Apr 2025 12:26:07 -0500 Subject: ACME: Allow acme service to restart nginx with no sudo password --- public-sparql.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/public-sparql.scm b/public-sparql.scm index 6fbf75c..4603cec 100644 --- a/public-sparql.scm +++ b/public-sparql.scm @@ -20,6 +20,7 @@ (use-modules (gnu) (gn services databases) (gnu services web) + ((gnu packages admin) #:select (shepherd)) (forge nginx) (forge socket)) @@ -50,6 +51,10 @@ SPARQL endpoint is listening on." (targets (list "/dev/sdX")))) (file-systems %base-file-systems) (users %base-user-accounts) + (sudoers-file + (mixed-text-file "sudoers" + "@include " %sudoers-specification + "\nacme ALL = NOPASSWD: " (file-append shepherd "/bin/herd") " restart nginx\n")) (packages %base-packages) (services (cons* (service virtuoso-service-type (virtuoso-configuration -- cgit 1.4.1 From 5058a3e359084741200dab7e4051bc3cd848e945 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Wed, 14 May 2025 11:42:41 -0500 Subject: Update filesystem shares for "public-sparql" container. --- public-sparql-deploy.sh | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/public-sparql-deploy.sh b/public-sparql-deploy.sh index 4ecacc6..bd8b938 100755 --- a/public-sparql-deploy.sh +++ b/public-sparql-deploy.sh @@ -22,11 +22,11 @@ container_script=$(guix system container \ --network \ --verbosity=3 \ - --share=/export2/guix-containers/public-sparql/var/lib/virtuoso=/var/lib/virtuoso \ - --share=/export2/guix-containers/public-sparql/tmp=/tmp \ - --share=/export2/guix-containers/public-sparql/var/log=/var/log \ - --share=/export2/guix-containers/public-sparql/var/lib/acme=/var/lib/acme \ - --share=/export2/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso \ + --share=/export/guix-containers/public-sparql/var/lib/virtuoso=/var/lib/virtuoso \ + --share=/export/guix-containers/public-sparql/tmp=/tmp \ + --share=/export/guix-containers/public-sparql/var/log=/var/log \ + --share=/export/guix-containers/public-sparql/var/lib/acme=/var/lib/acme \ + --share=/export/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso \ public-sparql.scm) echo $container_script -- cgit 1.4.1 From be2defaee9fdb09317c8639c3a104643434bd78d Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 15 May 2025 10:58:11 -0500 Subject: Production: Update filesystem paths from `/export2/*` to `/export/*` --- production-deploy.sh | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/production-deploy.sh b/production-deploy.sh index a88fcb8..43ebe3b 100755 --- a/production-deploy.sh +++ b/production-deploy.sh @@ -26,21 +26,21 @@ container_script=$(guix system container \ --network \ --load-path=. \ --verbosity=3 \ - --share=/export2/guix-containers/genenetwork/var/genenetwork=/var/genenetwork \ - --share=/export2/guix-containers/genenetwork/var/lib/acme=/var/lib/acme \ - --share=/export2/guix-containers/genenetwork/var/lib/redis=/var/lib/redis \ - --share=/export2/guix-containers/genenetwork/var/lib/virtuoso=/var/lib/virtuoso \ - --share=/export2/guix-containers/genenetwork/var/log=/var/log \ - --share=/export2/guix-containers/genenetwork/etc/genenetwork=/etc/genenetwork \ - --share=/export2/guix-containers/genenetwork/var/lib/xapian=/var/lib/xapian \ - --share=/export2/guix-containers/genenetwork/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite \ - --share=/export2/guix-containers/genenetwork/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa \ + --share=/export/guix-containers/genenetwork/var/genenetwork=/var/genenetwork \ + --share=/export/guix-containers/genenetwork/var/lib/acme=/var/lib/acme \ + --share=/export/guix-containers/genenetwork/var/lib/redis=/var/lib/redis \ + --share=/export/guix-containers/genenetwork/var/lib/virtuoso=/var/lib/virtuoso \ + --share=/export/guix-containers/genenetwork/var/log=/var/log \ + --share=/export/guix-containers/genenetwork/etc/genenetwork=/etc/genenetwork \ + --share=/export/guix-containers/genenetwork/var/lib/xapian=/var/lib/xapian \ + --share=/export/guix-containers/genenetwork/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite \ + --share=/export/guix-containers/genenetwork/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa \ --share=/var/run/mysqld=/run/mysqld \ --share=/export/data/gn-docs/ \ - --share=/export2/guix-containers/genenetwork/tmp=/opt/gn/tmp \ - --expose=/export2/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso/ \ - --share=/export2/guix-containers/genenetwork/var/lib/gn-docs=/export/data/gn-docs \ - --share=/export2/guix-containers/genenetwork/var/genenetwork/sessions=/var/genenetwork/sessions \ + --share=/export/guix-containers/genenetwork/tmp=/opt/gn/tmp \ + --expose=/export/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso/ \ + --share=/export/guix-containers/genenetwork/var/lib/gn-docs=/export/data/gn-docs \ + --share=/export/guix-containers/genenetwork/var/genenetwork/sessions=/var/genenetwork/sessions \ production.scm) echo $container_script -- cgit 1.4.1 From a227787297447d0fa3869debb11aaaadeec594f5 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Sun, 18 May 2025 16:02:12 -0500 Subject: Production: bind the gn-docs repository to the container. --- production-deploy.sh | 2 +- production.scm | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/production-deploy.sh b/production-deploy.sh index 43ebe3b..1be4167 100755 --- a/production-deploy.sh +++ b/production-deploy.sh @@ -36,7 +36,7 @@ container_script=$(guix system container \ --share=/export/guix-containers/genenetwork/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite \ --share=/export/guix-containers/genenetwork/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa \ --share=/var/run/mysqld=/run/mysqld \ - --share=/export/data/gn-docs/ \ + --share=/export/guix-containers/genenetwork/var/lib/gn-docs.git=/var/lib/gn-docs.git \ --share=/export/guix-containers/genenetwork/tmp=/opt/gn/tmp \ --expose=/export/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso/ \ --share=/export/guix-containers/genenetwork/var/lib/gn-docs=/export/data/gn-docs \ diff --git a/production.scm b/production.scm index 9e629f0..d64f8d1 100644 --- a/production.scm +++ b/production.scm @@ -88,5 +88,6 @@ (llm-db-path "/var/lib/genenetwork-gnqa/llm.db") (gn3-alias-server-port 9800) (gn-tmpdir "/opt/gn/tmp") + (gn-doc-git-checkout "/var/lib/gn-docs.git") (log-level 'debug))) %base-services))) -- cgit 1.4.1 From f3fb72711690bbe42f266d8c54e654aa747d2de4 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 2 May 2025 13:06:59 -0500 Subject: Provide common host directory for sqlite databases. --- genenetwork/services/genenetwork.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index a403f21..3289576 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -150,6 +150,8 @@ (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))) @@ -684,7 +686,7 @@ a @code{} record." (define (gn-uploader-activation config) (match-record config - (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 +697,8 @@ a @code{} record." (passwd:gid (getpw "gunicorn-gn-uploader")))) (append (list #$secrets) (find-files #$sessions-dir + #:directories? #t) + (find-files #$sqlite-databases-directory #:directories? #t))) ;; Set owner-only permissions on secrets files. (for-each (lambda (file) -- cgit 1.4.1 From a5ae96d721a7109b0de8d161f4c1a1185524771b Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 15 May 2025 11:03:33 -0500 Subject: Production: Reorganise filesystem paths for sqlite databases. --- production-deploy.sh | 4 ++-- production.scm | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/production-deploy.sh b/production-deploy.sh index 1be4167..ae858d9 100755 --- a/production-deploy.sh +++ b/production-deploy.sh @@ -33,8 +33,8 @@ container_script=$(guix system container \ --share=/export/guix-containers/genenetwork/var/log=/var/log \ --share=/export/guix-containers/genenetwork/etc/genenetwork=/etc/genenetwork \ --share=/export/guix-containers/genenetwork/var/lib/xapian=/var/lib/xapian \ - --share=/export/guix-containers/genenetwork/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite \ - --share=/export/guix-containers/genenetwork/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa \ + --share=/export/guix-containers/genenetwork/var/lib/genenetwork/sqlite/gn-auth=/var/lib/genenetwork/sqlite/gn-auth \ + --share=/export/guix-containers/genenetwork/var/lib/genenetwork/sqlite/genenetwork3=/var/lib/genenetwork/sqlite/genenetwork3 \ --share=/var/run/mysqld=/run/mysqld \ --share=/export/guix-containers/genenetwork/var/lib/gn-docs.git=/var/lib/gn-docs.git \ --share=/export/guix-containers/genenetwork/tmp=/opt/gn/tmp \ diff --git a/production.scm b/production.scm index d64f8d1..8c162e5 100644 --- a/production.scm +++ b/production.scm @@ -84,8 +84,8 @@ (gn2-secrets "/etc/genenetwork/genenetwork2") (gn3-secrets "/etc/genenetwork/genenetwork3/gn3-secrets.py") (gn-auth-secrets "/etc/genenetwork/gn-auth") - (auth-db "/var/lib/genenetwork-sqlite/auth.db") - (llm-db-path "/var/lib/genenetwork-gnqa/llm.db") + (auth-db "/var/lib/genenetwork/sqlite/gn-auth/auth.db") + (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") -- cgit 1.4.1 From d428cf321395c76314e43fd6e1ff858426373ff2 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 2 May 2025 13:07:46 -0500 Subject: Define setting for the asynchronous/background jobs sqlite db. --- genenetwork/services/genenetwork.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index 3289576..fb5a41a 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -715,7 +715,7 @@ a @code{} record." (define (gn-uploader-gunicorn-app config) (match-record config - (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 @@ -730,7 +730,8 @@ a @code{} 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))) @@ -775,6 +776,10 @@ a @code{} 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" -- cgit 1.4.1 From 80d9931b9bf2795790322a408023edbd25f8a213 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 12 Jun 2025 10:01:45 -0500 Subject: Increase timeout value for gn-auth and gn-uploader. --- genenetwork/services/genenetwork.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index fb5a41a..80b6c3c 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -536,6 +536,7 @@ 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") @@ -743,6 +744,7 @@ a @code{} record." (port port)))) (wsgi-app-module "scripts.qcapp_wsgi:app") (workers 20) + (timeout 1200) (environment-variables (list (environment-variable (name "UPLOADER_CONF") -- cgit 1.4.1 From ad19c44b0809375b1bc5c8ccce71910e2f838e1c Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 30 Jun 2025 10:59:21 -0500 Subject: Add uploader service to production container. --- production-deploy.sh | 2 ++ production.scm | 12 ++++++++++++ 2 files changed, 14 insertions(+) diff --git a/production-deploy.sh b/production-deploy.sh index ae858d9..7cd1cc7 100755 --- a/production-deploy.sh +++ b/production-deploy.sh @@ -41,6 +41,8 @@ container_script=$(guix system container \ --expose=/export/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso/ \ --share=/export/guix-containers/genenetwork/var/lib/gn-docs=/export/data/gn-docs \ --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 \ production.scm) echo $container_script diff --git a/production.scm b/production.scm index 8c162e5..ffa75da 100644 --- a/production.scm +++ b/production.scm @@ -90,4 +90,16 @@ (gn-tmpdir "/opt/gn/tmp") (gn-doc-git-checkout "/var/lib/gn-docs.git") (log-level 'debug))) + (service gn-uploader-service-type + (gn-uploader-configuration + (server-name "uploader.genenetwork.org") + (port 9897) + (secrets "/etc/genenetwork/gn-uploader/gn-uploader-secrets.py") + (sql-uri + "mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock&charset=utf8") + (data-directory "/var/lib/genenetwork/uploader/data") + (auth-server-url "https://auth.genenetwork.org/") + (gn2-server-url "https://genenetwork.org") + (sqlite-databases-directory "/var/lib/genenetwork/sqlite/gn-uploader") + (log-level 'debug))) %base-services))) -- cgit 1.4.1 From 7a8e68ae4697723a8b66959c250ccd2463d6d0f8 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 19 Jul 2025 12:12:23 +0200 Subject: README: note on docs --- README.org | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.org b/README.org index 892ab23..e4985da 100644 --- a/README.org +++ b/README.org @@ -3,7 +3,11 @@ containers. The git repo lives at https://git.genenetwork.org/gn-machines/ -* GeneNetwork development container +For philosophy and (KISS) incremental development containers, see: + +=> https://issues.genenetwork.org/topics/systems/debug-and-developing-code-with-genenetwork-system-container + +* GeneNetwork development container (aka CI/CD) The GeneNetwork development container is currently run on /tux02/. It runs continuous integration and continuous deployment services for @@ -31,6 +35,7 @@ To build and install the container, you will need the guix-bioinformatics channel. Once guix-bioinformatics is pulled and available, on /tux01/, run #+begin_src shell + $ ./virtuoso-deploy.sh #+end_src -- cgit 1.4.1 From d018b17794d2079f853e245e7a00df1a78b0105c Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 21 Jul 2025 08:41:06 +0200 Subject: Set GN_GUILE_SERVER_URL for dev container (aka GN4) --- genenetwork/services/genenetwork.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index 80b6c3c..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 @@ -372,6 +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")) @@ -388,6 +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) @@ -616,7 +621,7 @@ a @code{} 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)) -- cgit 1.4.1