Expose genotype files directory to uploader HEAD main

Expose the genotype files directory to the uploader, initially in
read-only mode.

1 files changed, 10 insertions, 3 deletions

diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm
index 868f00d..5c6b9f0 100644
--- a/genenetwork/services/genenetwork.scm
+++ b/genenetwork/services/genenetwork.scm
@@ -157,6 +157,8 @@
                               (default "/var/genenetwork/sqlite/gn-uploader"))
   (gn-tmpdir gn-uploader-configuration-gn-tmpdir
              (default "/opt/gn/tmp"))
+  (genotype-files-directory gn-uploader-configuration-genotype-files-directory
+                            (default "/var/genenetwork/genotype-files"))
   (log-level gn-uploader-configuration-log-level
              (default 'warning)
              (sanitize sanitize-log-level)))
@@ -768,7 +770,7 @@ a @code{<genenetwork-configuration>} record."
 
 (define (gn-uploader-gunicorn-app config)
   (match-record config <gn-uploader-configuration>
-    (gn-uploader sql-uri port data-directory secrets log-level auth-server-url gn2-server-url sessions-dir sqlite-databases-directory gn-tmpdir)
+    (gn-uploader sql-uri port data-directory secrets log-level auth-server-url gn2-server-url sessions-dir sqlite-databases-directory gn-tmpdir genotype-files-directory)
     ;; If we mapped only the mysqld.sock socket file, it would break
     ;; when the external mysqld server is restarted.
     (let* ((database-mapping (file-system-mapping
@@ -786,7 +788,8 @@ a @code{<genenetwork-configuration>} record."
                                                ("AUTH_SERVER_URL" ,auth-server-url)
                                                ("GN2_SERVER_URL" ,gn2-server-url)
                                                ("SESSION_FILESYSTEM_CACHE_PATH" ,sessions-dir)
-                                               ("ASYNCHRONOUS_JOBS_SQLITE_DB" ,(string-append sqlite-databases-directory "/background-jobs.db"))))))
+                                               ("ASYNCHRONOUS_JOBS_SQLITE_DB" ,(string-append sqlite-databases-directory "/background-jobs.db"))
+                                               ("GENOTYPE_FILES_DIRECTORY" ,genotype-files-directory)))))
            (gn-uploader-profile (profile
                                  (content (package->development-manifest gn-uploader))
                                  (allow-collisions? #t)))
@@ -841,7 +844,11 @@ a @code{<genenetwork-configuration>} record."
                              (file-system-mapping
                               (source gn-uploader-tmpdir)
                               (target source)
-                              (writable? #t))))
+                              (writable? #t))
+                             (file-system-mapping
+                              (source genotype-files-directory)
+                              (target source)
+                              (writable? #f))))
              (extra-cli-arguments
               (list "--log-level"
                     (string-upcase (symbol->string log-level)))))))))