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authorArun Isaac2023-01-18 18:09:29 +0000
committerArun Isaac2023-01-18 18:09:29 +0000
commit676c578ffe2d35197542f636eb21bae4a75d0057 (patch)
tree39831aaac333c9c0e2409cc2dec3e8985db78dbc
parent442ec2370efa2dfb5f9c0405c167964bcc2478a4 (diff)
downloadgn-machines-676c578ffe2d35197542f636eb21bae4a75d0057.tar.gz
Add data directory to genenetwork configuration.
* genenetwork-development.scm (<genenetwork-configuration>)[data-directory]: New field. (genenetwork3-cd-gexp): Set DATA_DIR in settings file. (genenetwork-shepherd-services): Map data directory into container. (operating-system)[services]: Set data-directory of genenetwork service to /export/data/genenetwork. * genenetwork-development-deploy.sh: Expose entire data directory /export/data/genenetwork instead of the contained genotype files directory.
-rwxr-xr-xgenenetwork-development-deploy.sh3
-rw-r--r--genenetwork-development.scm11
2 files changed, 10 insertions, 4 deletions
diff --git a/genenetwork-development-deploy.sh b/genenetwork-development-deploy.sh
index ee3d12e..b7f469d 100755
--- a/genenetwork-development-deploy.sh
+++ b/genenetwork-development-deploy.sh
@@ -29,8 +29,7 @@ container_script=$(guix system container --network \
--share=/export2/guix-containers/genenetwork-development/var/lib/tissue=/var/lib/tissue \
--share=/export2/guix-containers/genenetwork-development/var/lib/virtuoso=/var/lib/virtuoso \
--share=/export2/guix-containers/genenetwork-development/var/log/cd=/var/log/cd \
- --expose=/export/data/genenetwork/genotype_files \
- --share=/export/data/genenetwork/xapian \
+ --expose=/export/data/genenetwork \
--share=/export/data/genenetwork-xapian \
--share=/export/genenetwork-database-dump \
--share=/var/run/mysqld/mysqld.sock=/run/mysqld/mysqld.sock \
diff --git a/genenetwork-development.scm b/genenetwork-development.scm
index 3c34ccc..638d2c9 100644
--- a/genenetwork-development.scm
+++ b/genenetwork-development.scm
@@ -113,6 +113,8 @@ be imported into G-expressions."
(default "/var/genenetwork/genotype-files"))
(sparql-endpoint genenetwork-configuration-sparql-endpoint
(default "http://localhost:8081/sparql"))
+ (data-directory genenetwork-data-directory
+ (default "/var/genenetwork"))
(xapian-db-path genenetwork-xapian-db-path
(default "/var/genenetwork/xapian")))
@@ -384,7 +386,7 @@ server described by CONFIG, a <genenetwork-configuration> object."
"Return a G-expression that runs the latest genenetwork3 development
server described by CONFIG, a <genenetwork-configuration> object."
(match-record config <genenetwork-configuration>
- (gn3-repository gn3-port sparql-endpoint xapian-db-path)
+ (gn3-repository gn3-port sparql-endpoint data-directory xapian-db-path)
(with-manifest (package->development-manifest genenetwork3)
(with-packages (list git-minimal nss-certs)
(with-imported-modules '((guix build utils))
@@ -409,6 +411,7 @@ server described by CONFIG, a <genenetwork-configuration> object."
(setenv "GN3_CONF"
#$(mixed-text-file "gn3.conf"
"SPARQL_ENDPOINT=\"" sparql-endpoint "\"\n"
+ "DATA_DIR=\"" data-directory "\"\n"
"XAPIAN_DB_PATH=\"" xapian-db-path "\"\n"))
(setenv "HOME" "/tmp")
;; Run genenetwork3.
@@ -422,7 +425,7 @@ server described by CONFIG, a <genenetwork-configuration> object."
"Return shepherd services to run the genenetwork development server
described by CONFIG, a <genenetwork-configuration> object."
(match-record config <genenetwork-configuration>
- (gn2-port gn3-port genotype-files xapian-db-path)
+ (gn2-port gn3-port genotype-files data-directory xapian-db-path)
(list (shepherd-service
(documentation "Run GeneNetwork 2 development server.")
(provision '(genenetwork2))
@@ -460,6 +463,9 @@ described by CONFIG, a <genenetwork-configuration> object."
(target source)
(writable? #t))
(file-system-mapping
+ (source data-directory)
+ (target source))
+ (file-system-mapping
(source xapian-db-path)
(target source)))
#:namespaces (delq 'net %namespaces))
@@ -938,6 +944,7 @@ reverse proxy tissue."
(sparql-endpoint (string-append "http://localhost:"
(number->string %virtuoso-sparql-port)
"/sparql"))
+ (data-directory "/export/data/genenetwork")
(xapian-db-path %xapian-directory)))
(simple-service 'set-build-directory-permissions
activation-service-type