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authorArun Isaac2022-10-28 16:20:47 +0530
committerArun Isaac2022-10-28 19:10:43 +0530
commit688ae928d748676ba95a3ec9cfffea9e4bd9eba8 (patch)
treef3e366867ec7f2d75fa65c6d3e99218bfde54618
parent44e7437ba602e732f40781ef76c0065e3bcef7b6 (diff)
downloadgn-machines-688ae928d748676ba95a3ec9cfffea9e4bd9eba8.tar.gz
Expose xapian index to genenetwork3 instead of genenetwork2.
* genenetwork-development.scm (genenetwork2-shepherd-service): Do not expose xapian index. (genenetwork3-shepherd-service): Expose xapian index. * genenetwork/development-helper.scm (genenetwork2-runner-gexp): Do not accept xapian index argument. (genenetwork3-runner-gexp): Accept config file argument.
-rw-r--r--genenetwork-development.scm11
-rw-r--r--genenetwork/development-helper.scm14
2 files changed, 14 insertions, 11 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm
index e345c59..4fb7c46 100644
--- a/genenetwork-development.scm
+++ b/genenetwork-development.scm
@@ -299,9 +299,6 @@ 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))
@@ -328,8 +325,7 @@ describing genenetwork2."
(content (package->development-manifest genenetwork2))
(allow-collisions? #t))
#$%genenetwork3-port
- #$%genotype-files
- #$%xapian-db-path))))))
+ #$%genotype-files))))))
(define %genenetwork-accounts
(list (user-group
@@ -460,6 +456,9 @@ command to be executed."
(source "/run/mysqld/mysqld.sock")
(target source)
(writable? #t))
+ (file-system-mapping
+ (source %xapian-db-path)
+ (target source))
%store-mapping)
#:namespaces (delq 'net %namespaces))
"127.0.0.1" #$(number->string (development-server-configuration-port config)))
@@ -479,6 +478,8 @@ command to be executed."
#~(lambda (latest-gn3-source)
((@@ (genenetwork development-helper) genenetwork3-runner-gexp)
latest-gn3-source
+ #$(mixed-text-file "gn3.conf"
+ "XAPIAN_DB_PATH=\"" %xapian-db-path "\"\n")
#$(profile
(content (manifest-cons gunicorn
(package->development-manifest genenetwork3)))
diff --git a/genenetwork/development-helper.scm b/genenetwork/development-helper.scm
index bbb5d6e..9bf737d 100644
--- a/genenetwork/development-helper.scm
+++ b/genenetwork/development-helper.scm
@@ -103,13 +103,13 @@ with genenetwork3 dependencies."
(mkdir-p #$output)))))
(define (genenetwork2-runner-gexp genenetwork2-source profile gn3-port
- genotype-files xapian-db-path)
+ genotype-files)
"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. XAPIAN-DB-PATH is the path to the xapian search index."
+files."
(with-imported-modules '((guix build utils))
(with-profile profile
#~(begin
@@ -130,15 +130,15 @@ files. XAPIAN-DB-PATH is the path to the xapian search index."
(setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl")
(setenv "HOME" "/tmp")
(setenv "NO_REDIS" "no-redis")
- (setenv "XAPIAN_DB_PATH" #$xapian-db-path)
(setenv "RUST_BACKTRACE" "1")
(invoke "sh" "bin/genenetwork2" "etc/default_settings.py" "-gunicorn-prod")))))))
-(define (genenetwork3-runner-gexp genenetwork3-source profile)
+(define (genenetwork3-runner-gexp genenetwork3-source config-file profile)
"Return a G-expression that runs the genenetwork3 server for
GENENETWORK3-SOURCE in PROFILE. GENENETWORK3-SOURCE is a checkout of
-the genenetwork3 source code. PROFILE is a profile with genenetwork3
-dependencies."
+the genenetwork3 source code. CONFIG-FILE is a file containing
+configuration settings for genenetwork3. PROFILE is a profile with
+genenetwork3 dependencies."
(with-imported-modules '((guix build utils))
(with-profile profile
#~(begin
@@ -146,6 +146,8 @@ dependencies."
(ice-9 match))
(chdir #$genenetwork3-source)
+ (setenv "GN3_CONF" #$config-file)
+ (setenv "HOME" "/tmp")
(match (command-line)
((_ ip port)
(invoke "gunicorn"