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.scm        | 11 ++++++-----
 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
@@ -298,9 +298,6 @@ describing genenetwork2."
                                        (file-system-mapping
                                         (source %genotype-files)
                                         (target source))
-                                       (file-system-mapping
-                                        (source %xapian-db-path)
-                                        (target source))
                                        (file-system-mapping
                                         (source "/run/mysqld/mysqld.sock")
                                         (target source)
@@ -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"
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