diff options
| author | Arun Isaac | 2022-09-26 13:21:25 +0530 |
|---|---|---|
| committer | Arun Isaac | 2022-09-26 13:37:41 +0530 |
| commit | bbdd74d2def319f53e40aab3a5e1dc50e5cc2388 (patch) | |
| tree | 17de183da768c759493b0c66ac8bcd70f62eb3a4 | |
| parent | 3b7ac978875648171b485bed992b8976dc3d5e3e (diff) | |
| download | gn-machines-bbdd74d2def319f53e40aab3a5e1dc50e5cc2388.tar.gz | |
Set up xapian search index for genenetwork2 CD.
* genenetwork-development.scm (%xapian-db-path): New variable.
(genenetwork2-shepherd-service)[start]: Share %xapian-db-path with the
container.
(%default-genenetwork2-configuration)[runner]: Pass %xapian-db-path to
CD runner.
* genenetwork/development-helper.scm (genenetwork2-runner-gexp):
Accept xapian-db-path argument and set XAPIAN_DB_PATH environment
variable.
* genenetwork-development-deploy.sh: Expose
/export/data/genenetwork/xapian in the container.
| -rwxr-xr-x | genenetwork-development-deploy.sh | 1 | ||||
| -rw-r--r-- | genenetwork-development.scm | 10 | ||||
| -rw-r--r-- | genenetwork/development-helper.scm | 6 |
3 files changed, 14 insertions, 3 deletions
diff --git a/genenetwork-development-deploy.sh b/genenetwork-development-deploy.sh index ad9f795..4391bb8 100755 --- a/genenetwork-development-deploy.sh +++ b/genenetwork-development-deploy.sh @@ -30,6 +30,7 @@ container_script=$(guix system container --network \ --share=/var/guix-containers/genenetwork-development/var/lib/virtuoso=/var/lib/virtuoso \ --share=/var/guix-containers/genenetwork-development/var/log/cd=/var/log/cd \ --expose=/export/data/genenetwork/genotype_files \ + --expose=/export/data/genenetwork/xapian \ --share=/export/genenetwork-database-dump \ --share=/var/run/mysqld/mysqld.sock=/run/mysqld/mysqld.sock \ genenetwork-development.scm) diff --git a/genenetwork-development.scm b/genenetwork-development.scm index 2de0ff4..852711f 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -177,6 +177,10 @@ CONFIG, a <development-server-configuration> object, on startup." (define %genotype-files "/export/data/genenetwork/genotype_files") +;; Path to the xapian search index used by genenetwork2 +(define %xapian-db-path + "/export/data/genenetwork/xapian") + ;; Port on which genenetwork2 is listening (define %genenetwork2-port 9092) @@ -284,6 +288,9 @@ describing genenetwork2." (source #$%genotype-files) (target source)) (file-system-mapping + (source #$%xapian-db-path) + (target source)) + (file-system-mapping (source "/run/mysqld/mysqld.sock") (target source) (writable? #t))) @@ -305,7 +312,8 @@ describing genenetwork2." (content (package->development-manifest genenetwork2)) (allow-collisions? #t)) #$%genenetwork3-port - #$%genotype-files)))))) + #$%genotype-files + #$%xapian-db-path)))))) (define %genenetwork-accounts (list (user-group diff --git a/genenetwork/development-helper.scm b/genenetwork/development-helper.scm index 7899630..353bf1a 100644 --- a/genenetwork/development-helper.scm +++ b/genenetwork/development-helper.scm @@ -101,13 +101,14 @@ with genenetwork3 dependencies." (invoke "pylint" "gn3")) (mkdir-p #$output))))) -(define (genenetwork2-runner-gexp genenetwork2-source profile gn3-port genotype-files) +(define (genenetwork2-runner-gexp genenetwork2-source profile gn3-port + genotype-files xapian-db-path) "Return a G-expression that runs the genenetwork2 server for GENENETWORK2-SOURCE in PROFILE. GENENETWORK2-SOURCE is a checkout of the genenetwork2 source code. PROFILE is a profile with genenetwork2 dependencies. GN3-PORT is the port on which a local instance of genenetwork3 is listening. GENOTYPE-FILES is the path to genotype -files." +files. XAPIAN-DB-PATH is the path to the xapian search index." (with-imported-modules '((guix build utils)) (with-profile profile #~(begin @@ -128,6 +129,7 @@ files." (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl") (setenv "HOME" "/tmp") (setenv "NO_REDIS" "no-redis") + (setenv "XAPIAN_DB_PATH" #$xapian-db-path) (invoke "sh" "bin/genenetwork2"))))))) (define (genenetwork3-runner-gexp genenetwork3-source profile) |