diff options
| -rw-r--r-- | genenetwork-development.scm | 11 | ||||
| -rw-r--r-- | genenetwork/development-helper.scm | 14 |
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" |