From f4f92b60aba85cf74cb3c38e95daa4e740e6afe4 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 17 Mar 2025 11:40:30 -0500
Subject: uploader-container: Abstract away paths in the container.

Break the implicit connection between the paths on the host system
with the paths inside the container. This allows the operating-system
definition to define its own paths, regardless of what is on the host.

The builder script will explicitly do the mapping between host
directories and container paths.

We also collect all uploader-related directories under the host path
`/export2/guix-containers/uploader` to make maintenance easier.
---
 uploader-deploy.sh | 13 +++++--------
 uploader.scm       |  7 +++----
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/uploader-deploy.sh b/uploader-deploy.sh
index 58bb9ec..a8d0913 100755
--- a/uploader-deploy.sh
+++ b/uploader-deploy.sh
@@ -43,23 +43,20 @@ container_script=$(guix system container \
                         --verbosity=3 \
                         --share=/export2/guix-containers/uploader/var/genenetwork=/var/genenetwork \
                         --share=/export2/guix-containers/uploader/var/lib/acme=/var/lib/acme \
-                        --share=/export2/guix-containers/uploader/var/lib/mysql=/var/lib/mysql \
+                        --share=/export2/guix-containers/uploader/var/lib/redis=/var/lib/redis \
                         --share=/export2/guix-containers/uploader/var/lib/virtuoso=/var/lib/virtuoso \
                         --share=/export2/guix-containers/uploader/var/log=/var/log \
                         --share=/export2/guix-containers/uploader/etc/genenetwork=/etc/genenetwork \
-                        --share=/export/data/uploader/genenetwork-xapian=/export/data/genenetwork-xapian \
-                        --share=/export/data/uploader/genenetwork-sqlite=/export/data/genenetwork-sqlite \
-                        --expose=/export/data/uploader/genotype_files=/export/data/genenetwork/genotype_files \
-                        --expose=/export/data/uploader/genenetwork3 \
-                        --share=/export/data/uploader/gn-uploader \
-                        --share=/var/run/mysqld3307=/run/mysqld \
-                        --share=/export/data/uploader/genenetwork-gnqa=/var/lib/genenetwork-gnqa \
+                        --share=/export2/guix-containers/uploader/var/lib/genenetwork-xapian=/var/lib/xapian \
+                        --share=/export2/guix-containers/uploader/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite \
+                        --share=/export2/guix-containers/uploader/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa \
                         --share=/var/run/mysqld3307=/run/mysqld \
 			--share=/export/data/gn-docs \
                         --share=/export2/guix-containers/uploader/tmp=/opt/gn/tmp \
                         --expose=/export2/guix-containers/uploader/data/virtuoso=/export/data/virtuoso/ \
                         --share=/export2/guix-containers/uploader/var/lib/gn-docs=/export/data/gn-docs \
                         --share=/export2/guix-containers/uploader/var/genenetwork/sessions=/var/genenetwork/sessions \
+                        --share=/export/data/uploader/gn-uploader \
                         uploader.scm)
 
 echo "${container_script}"
diff --git a/uploader.scm b/uploader.scm
index de46f90..5064426 100644
--- a/uploader.scm
+++ b/uploader.scm
@@ -62,11 +62,10 @@
                              (gn-auth-port 10896)
                              (sql-uri
                               "mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock&charset=utf8")
-                             (auth-db "/export/data/genenetwork-sqlite/auth.db")
-                             (xapian-db "/export/data/genenetwork-xapian")
-                             (genotype-files "/export/data/genenetwork/genotype_files")
+                             (auth-db "/var/lib/genenetwork-sqlite/auth.db")
+                             (xapian-db "/var/lib/xapian")
                              (sparql-endpoint "http://localhost:10893/sparql")
-                             (gn3-data-directory "/export/data/uploader/genenetwork3")
+                             (gn3-data-directory "/var/genenetwork/data/genenetwork3")
                              (gn2-secrets "/etc/genenetwork/genenetwork2")
                              (gn3-secrets "/etc/genenetwork/genenetwork3/gn3-secrets.py")
                              (gn-auth-secrets "/etc/genenetwork/gn-auth")
-- 
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