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authorFrederick Muriuki Muriithi2024-10-28 16:26:52 -0500
committerArun Isaac2024-10-29 22:39:44 +0000
commit55ccfdffeed950ca8a8549b5985e13eb136f6aa6 (patch)
treef6adde5af3e4ab736fdc03771e33a6ec3d276131
parent7a0b349a6cfaa723e4c111b32bd8c61fc156e6e7 (diff)
downloadgn-machines-55ccfdffeed950ca8a8549b5985e13eb136f6aa6.tar.gz
Add llm-db-path field to genenetwork configuration..
*
genenetwork/services/genenetwork.scm (<genenetwork-configuration>)[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 <arunisaac@systemreboot.net>
-rw-r--r--genenetwork/services/genenetwork.scm11
1 files 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{<genenetwork-configuration>}
 object."
   (match-record config <genenetwork-configuration>
-    (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"