From 688ae928d748676ba95a3ec9cfffea9e4bd9eba8 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 28 Oct 2022 16:20:47 +0530 Subject: 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. --- genenetwork/development-helper.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) (limited to 'genenetwork') 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" -- cgit v1.2.3