From 55ccfdffeed950ca8a8549b5985e13eb136f6aa6 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Mon, 28 Oct 2024 16:26:52 -0500 Subject: Add llm-db-path field to genenetwork configuration.. * genenetwork/services/genenetwork.scm ()[llm-db-path]: New field. (genenetwork-gunicorn-apps): Set LLM_DB_PATH in gn3.conf. Mount LLM database into the container. Signed-off-by: Arun Isaac --- genenetwork/services/genenetwork.scm | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm index 9024d54..91b53f4 100644 --- a/genenetwork/services/genenetwork.scm +++ b/genenetwork/services/genenetwork.scm @@ -91,6 +91,8 @@ (default "mysql://username:password@localhost/database")) (auth-db genenetwork-configuration-auth-db (default "/var/genenetwork/auth.db")) + (llm-db-path genenetwork-configuration-llm-db-path + (default "/var/genenetwork/llm.db")) (xapian-db genenetwork-configuration-xapian-db (default "/var/genenetwork/xapian")) (genotype-files genenetwork-configuration-genotype-files @@ -293,7 +295,7 @@ G-expressions or numbers." described by @var{config}, a @code{} object." (match-record config - (genenetwork2 genenetwork3 gn-auth server-name gn-auth-server-name gn2-port gn3-port gn-auth-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn-sourcecode-directory gn3-data-directory gn2-secrets gn3-secrets gn-auth-secrets log-level) + (genenetwork2 genenetwork3 gn-auth server-name gn-auth-server-name gn2-port gn3-port gn-auth-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn-sourcecode-directory gn3-data-directory gn2-secrets gn3-secrets gn-auth-secrets llm-db-path log-level) ;; 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 @@ -326,7 +328,8 @@ object." ("SQL_URI" ,sql-uri) ("XAPIAN_DB_PATH" ,xapian-db) ("GENOTYPE_FILES" ,genotype-files) - ("REAPER_COMMAND" ,(file-append gn2-profile "/bin/qtlreaper")))))) + ("REAPER_COMMAND" ,(file-append gn2-profile "/bin/qtlreaper")) + ("LLM_DB_PATH" ,llm-db-path))))) (gn-auth-conf (computed-file "gn-auth.conf" (configuration-file-gexp `(("GN_AUTH_SECRETS" ,(string-append gn-auth-secrets "/gn-auth-secrets.py")) @@ -429,6 +432,10 @@ object." (file-system-mapping (source auth-db) (target source) + (writable? #t)) + (file-system-mapping + (source llm-db-path) + (target source) (writable? #t)))) (extra-cli-arguments (list "--log-level" -- cgit v1.2.3