8 files changed, 84 insertions, 40 deletions
diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm
index f1a1c88..3b39f6c 100644
--- a/genenetwork/services/genenetwork.scm
+++ b/genenetwork/services/genenetwork.scm
@@ -119,6 +119,10 @@
                  (default 8091))
   (gn-doc-git-checkout genenetwork-configuration-gn-doc-git-checkout
                        (default "/export/data/gn-docs"))
+  (gn-virtuoso-ttl-directory genenetwork-configuration-gn-virtuoso-ttl-directory
+                             (default "/export/data/virtuoso/ttl"))
+  (gn-tmpdir genenetwork-configuration-gn-tmpdir
+             (default "/opt/gn/tmp"))
   (log-level genenetwork-configuration-log-level
              (default 'warning)
              (sanitize sanitize-log-level)))
@@ -170,6 +174,8 @@
          (genenetwork3 (genenetwork-configuration-genenetwork3 config))
          (xapian-directory (genenetwork-configuration-xapian-db config))
          (sparql-endpoint (genenetwork-configuration-sparql-endpoint config))
+         (virtuoso-ttl-directory
+          (genenetwork-configuration-gn-virtuoso-ttl-directory config))
          (xapian-build-directory (string-append xapian-directory "/build"))
          (herd (file-append shepherd "/bin/herd"))
          (index-genenetwork (file-append genenetwork3 "/bin/index-genenetwork"))
@@ -203,7 +209,9 @@
                                                   "is-data-modified"
                                                   #$xapian-directory
                                                   #$sql-uri
-                                                  #$sparql-endpoint))))
+                                                  #$sparql-endpoint
+                                                  "--virtuoso-ttl-directory"
+                                                  #$virtuoso-ttl-directory))))
             (dynamic-wind
               (const #t)
               ;; build the index
@@ -212,7 +220,9 @@
                         "create-xapian-index"
                         #$xapian-build-directory
                         #$sql-uri
-                        #$sparql-endpoint)
+                        #$sparql-endpoint
+                        "--virtuoso-ttl-directory"
+                        #$virtuoso-ttl-directory)
                 (dynamic-wind
                   ;; stop GN3: Here there is magic!!!
                   ;;     The name `gunicorn-genenetwork' is magical. It is not set
@@ -242,7 +252,7 @@
 
 (define (genenetwork-activation config)
   (match-record config <genenetwork-configuration>
-    (gn2-secrets gn3-secrets gn-auth-secrets auth-db llm-db-path)
+    (gn2-secrets gn3-secrets gn-auth-secrets auth-db llm-db-path genotype-files gn-tmpdir gn-doc-git-checkout)
     (with-imported-modules '((guix build utils))
       #~(begin
           (use-modules (guix build utils))
@@ -262,6 +272,8 @@
                              (passwd:uid (getpw "gunicorn-genenetwork2"))
                              (passwd:gid (getpw "gunicorn-genenetwork2"))))
                     (append (list #$gn2-secrets)
+                            (find-files #$genotype-files
+                                        #:directories? #t)
                             (find-files #$gn2-secrets
                                         #:directories? #t)))
           (for-each (lambda (file)
@@ -278,7 +290,31 @@
                             (find-files #$gn2-secrets
                                         #:directories? #f)
                             (find-files #$gn-auth-secrets
-                                        #:directories? #f)))))))
+                                        #:directories? #f)))
+          ;; Make sub-directories for various apps under gn-tmpdir and assign
+          ;; appropriate permissions
+          (for-each (match-lambda
+                      ((subdir user)
+                       (let ((full-path
+                              (string-append #$gn-tmpdir "/" subdir)))
+                         (unless (file-exists? full-path)
+                           (mkdir full-path #o755))
+                         (for-each (lambda (file)
+                                     (chown file
+                                            (passwd:uid (getpw user))
+                                            (passwd:gid (getpw user))))
+                                   (find-files full-path
+                                               #:directories? #t)))))
+                    '(("gn2-tmpdir" "gunicorn-genenetwork2")
+                      ("gn3-tmpdir" "gunicorn-genenetwork3")))
+
+          ;; setup correct ownership for gn-docs
+          (for-each (lambda (file)
+                      (chown file
+                             (passwd:uid (getpw "genenetwork"))
+                             (passwd:gid (getpw "genenetwork"))))
+                    (find-files #$gn-doc-git-checkout
+                                #:directories? #t))))))
 
 (define (configuration-file-gexp alist)
   "Return a G-expression that constructs a configuration file of
@@ -309,7 +345,7 @@ G-expressions or numbers."
 described by @var{config}, a @code{<genenetwork-configuration>}
 object."
   (match-record config <genenetwork-configuration>
-    (genenetwork2 genenetwork3 gn-auth server-name gn-auth-server-name gn2-port gn3-port gn-auth-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn-sourcecode-directory gn3-data-directory gn2-secrets gn3-secrets gn-auth-secrets llm-db-path log-level)
+    (genenetwork2 genenetwork3 gn-auth server-name gn-auth-server-name gn2-port gn3-port gn-auth-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn-sourcecode-directory gn3-data-directory gn2-secrets gn3-secrets gn-auth-secrets llm-db-path gn-tmpdir log-level)
     ;; 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
@@ -358,9 +394,9 @@ object."
                                         (configuration-file-gexp
                                          `(("GN_AUTH_SECRETS" ,(string-append gn-auth-secrets "/gn-auth-secrets.py"))
                                            ("AUTH_DB" ,auth-db)
-                                           ("SQL_URI" ,sql-uri)
-                                           ("CLIENTS_SSL_PUBLIC_KEYS_DIR" ,(string-append gn-auth-secrets "/clients-public-keys"))
-                                           ("SSL_PRIVATE_KEY" ,(string-append gn-auth-secrets "/gn-auth-ssl-private-key.pem")))))))
+                                           ("SQL_URI" ,sql-uri)))))
+           (gn2-tmpdir (string-append gn-tmpdir "/gn2-tmpdir"))
+           (gn3-tmpdir (string-append gn-tmpdir "/gn3-tmpdir")))
       (list (gunicorn-app
              (name "genenetwork2")
              (package genenetwork2)
@@ -375,7 +411,7 @@ object."
                      (value gn2-profile))
                     (environment-variable
                      (name "TMPDIR")
-                     (value "/tmp"))
+                     (value gn2-tmpdir))
                     (environment-variable
                      (name "GN2_SETTINGS")
                      (value gn2-conf))
@@ -388,13 +424,17 @@ object."
              (mappings (list database-mapping
                              (file-system-mapping
                               (source genotype-files)
-                              (target source))
+                              (target source)
+                              (writable? #t))
                              (file-system-mapping
                               (source gn-sourcecode-directory)
                               (target source))
-                             (file-system-mapping ; GN2 and GN3 need to share TMPDIR
-                              (source "/tmp")
-                              (target "/tmp")
+                             (file-system-mapping ; GN2 and GN3 need to communicate via TMPDIR
+                              (source gn-tmpdir)
+                              (target source))
+                             (file-system-mapping
+                              (source gn2-tmpdir)
+                              (target source)
                               (writable? #t))
                              (file-system-mapping
                               (source gn2-conf)
@@ -429,7 +469,7 @@ object."
                      (value gn3-conf))
                     (environment-variable
                      (name "TMPDIR")
-                     (value "/tmp"))
+                     (value gn3-tmpdir))
                     (environment-variable
                      (name "GN3_SECRETS")
                      (value gn3-secrets))
@@ -455,9 +495,12 @@ object."
                              (file-system-mapping
                               (source gn3-data-directory)
                               (target source))    ; Rqtl usese this
-                             (file-system-mapping ; GN2 and GN3 need to share TMPDIR
-                              (source "/tmp")
-                              (target "/tmp")
+                             (file-system-mapping ; GN2 and GN3 need to communicate via TMPDIR
+                              (source gn-tmpdir)
+                              (target source))
+                             (file-system-mapping
+                              (source gn3-tmpdir)
+                              (target source)
                               (writable? #t))
                              (file-system-mapping
                               (source xapian-db)
diff --git a/production-deploy.sh b/production-deploy.sh
index bd95814..6de5ebe 100755
--- a/production-deploy.sh
+++ b/production-deploy.sh
@@ -26,19 +26,20 @@ container_script=$(guix system container \
                         --network \
                         --load-path=. \
                         --verbosity=3 \
-                        --share=/export2/guix-containers/genenetwork/var/genenetwork=/var/genenetwork \
-                        --share=/export2/guix-containers/genenetwork/var/lib/acme=/var/lib/acme \
-                        --share=/export2/guix-containers/genenetwork/var/lib/redis=/var/lib/redis \
-                        --share=/export/mysql/database=/var/lib/mysql \
-                        --share=/export2/guix-containers/genenetwork/var/lib/virtuoso=/var/lib/virtuoso \
-                        --share=/export2/guix-containers/genenetwork/var/log=/var/log \
-                        --share=/export2/guix-containers/genenetwork/etc/genenetwork=/etc/genenetwork \
-                        --share=/export2/guix-containers/genenetwork/var/lib/xapian=/var/lib/xapian \
-                        --share=/export2/guix-containers/genenetwork/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite \
-                        --share=/export2/guix-containers/genenetwork/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa \
+                        --share=/export/guix-containers/genenetwork/var/genenetwork=/var/genenetwork \
+                        --share=/export/guix-containers/genenetwork/var/lib/acme=/var/lib/acme \
+                        --share=/export/guix-containers/genenetwork/var/lib/redis=/var/lib/redis \
+                        --share=/export/guix-containers/genenetwork/var/lib/virtuoso=/var/lib/virtuoso \
+                        --share=/export/guix-containers/genenetwork/var/log=/var/log \
+                        --share=/export/guix-containers/genenetwork/etc/genenetwork=/etc/genenetwork \
+                        --share=/export/guix-containers/genenetwork/var/lib/xapian=/var/lib/xapian \
+                        --share=/export/guix-containers/genenetwork/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite \
+                        --share=/export/guix-containers/genenetwork/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa \
                         --share=/var/run/mysqld=/run/mysqld \
 			--share=/export/data/gn-docs/ \
-                        --share=/export2/guix-containers/genenetwork/tmp=/tmp \
+                        --share=/export/guix-containers/genenetwork/tmp=/opt/gn/tmp \
+                        --expose=/export/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso/ \
+                        --share=/export/guix-containers/genenetwork/var/lib/gn-docs=/export/data/gn-docs \
                         production.scm)
 
 echo $container_script
diff --git a/production.scm b/production.scm
index dfa4f3d..9e629f0 100644
--- a/production.scm
+++ b/production.scm
@@ -44,14 +44,11 @@
                     "@include " %sudoers-specification
                     "\nacme ALL = NOPASSWD: " (file-append shepherd "/bin/herd") " restart nginx\n"))
   (packages %base-packages)
-  (services (cons* (service mysql-service-type
-                            (mysql-configuration
-                             (auto-upgrade? #f)))
-                   (service virtuoso-service-type
+  (services (cons* (service virtuoso-service-type
                             (virtuoso-configuration
                              (server-port 9892)
                              (http-server-port 9893)
-                             (dirs-allowed "/var/lib/virtuoso")
+                             (dirs-allowed (list "/export/data/virtuoso"))
                              (number-of-buffers 4000000)
                              (maximum-dirty-buffers 3000000)
                              (database-file "/var/lib/virtuoso/genenetwork-virtuoso.db")
@@ -90,5 +87,6 @@
                              (auth-db "/var/lib/genenetwork-sqlite/auth.db")
                              (llm-db-path "/var/lib/genenetwork-gnqa/llm.db")
                              (gn3-alias-server-port 9800)
+                             (gn-tmpdir "/opt/gn/tmp")
                              (log-level 'debug)))
                    %base-services)))
diff --git a/public-sparql-deploy.sh b/public-sparql-deploy.sh
index bee9abf..bc4348d 100755
--- a/public-sparql-deploy.sh
+++ b/public-sparql-deploy.sh
@@ -22,10 +22,10 @@
 container_script=$(guix system container \
                         --network \
                         --verbosity=3 \
-                        --share=/export2/guix-containers/public-sparql/var/lib/virtuoso=/var/lib/virtuoso \
-			--share=/export2/guix-containers/public-sparql/tmp=/tmp \
-			--share=/export2/guix-containers/public-sparql/var/log=/var/log \
-			--share=/export2/guix-containers/public-sparql/var/lib/acme=/var/lib/acme \
+                        --share=/export/guix-containers/public-sparql/var/lib/virtuoso=/var/lib/virtuoso \
+			--share=/export/guix-containers/public-sparql/tmp=/tmp \
+			--share=/export/guix-containers/public-sparql/var/log=/var/log \
+			--share=/export/guix-containers/public-sparql/var/lib/acme=/var/lib/acme \
                         public-sparql.scm)
 
 echo $container_script
diff --git a/public-sparql.scm b/public-sparql.scm
index f6efb15..4f5ad13 100644
--- a/public-sparql.scm
+++ b/public-sparql.scm
@@ -56,7 +56,7 @@ SPARQL endpoint is listening on."
                              (server-port %virtuoso-port)
                              (http-server-port %sparql-port)
 			     (number-of-buffers 4000000)
-			     (dirs-allowed "/var/lib/virtuoso")
+			     (dirs-allowed (list "/var/lib/virtuoso"))
 			     (maximum-dirty-buffers 3000000)
                              (database-file "/var/lib/virtuoso/public-virtuoso.db")
                              (transaction-file "/var/lib/virtuoso/public-virtuoso.trx")))
diff --git a/uploader.scm b/uploader.scm
index 3cbe53f..551a2c2 100644
--- a/uploader.scm
+++ b/uploader.scm
@@ -81,7 +81,8 @@
                              (server-name "staging-uploader.genenetwork.org")
                              (port 10897)
                              (secrets "/etc/genenetwork/gn-uploader/gn-uploader-secrets.py")
-                             (sql-uri "mysql://webqtlout:webqtlout@127.0.0.1:3307/db_webqtl")
+                             (sql-uri
+                              "mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock&charset=utf8")
                              (data-directory "/export/data/uploader/gn-uploader")
                              (log-level 'debug)
                              (auth-server-url "https://staging-auth.genenetwork.org/")
diff --git a/virtuoso-deploy.sh b/virtuoso-deploy.sh
index 0414a65..0dd2509 100755
--- a/virtuoso-deploy.sh
+++ b/virtuoso-deploy.sh
@@ -25,6 +25,7 @@ container_script=$(guix system container \
                         --network \
                         --verbosity=3 \
                         --share=/export2/guix-containers/virtuoso/var/lib/virtuoso=/var/lib/virtuoso \
+                        --share=/export2/guix-containers/genenetwork/data/virtuoso=/export/data/virtuoso \
                         virtuoso.scm)
 
 echo $container_script
diff --git a/virtuoso.scm b/virtuoso.scm
index edcd575..3272f41 100644
--- a/virtuoso.scm
+++ b/virtuoso.scm
@@ -34,5 +34,5 @@
                            (virtuoso-configuration
                             (server-port 8891)
                             (http-server-port 8892)
-                            (dirs-allowed "/var/lib/virtuoso")))
+                            (dirs-allowed (list "/export/data/virtuoso"))))
                   %base-services)))