gn: genome browser tests good

2 files changed, 71 insertions, 35 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a8ebe68..58110a7 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -32,6 +32,7 @@
   #:use-module (gnu packages elf)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
@@ -1609,10 +1610,12 @@ multiple sequence alignment.")
                (substitute* (cons* "inc/cgi_build_rules.mk"
                                    (find-files "." "makefile"))
                   (("CGI_BIN\\}-\\$\\{USER") "CGI_BIN_USER"))
+
                ;; Force linking with freetype.
                (substitute* "inc/common.mk"
                  (("libpng-config --ldflags") "pkg-config --libs libpng freetype2")
                  (("libpng-config --I_opts") "pkg-config --cflags-only-I libpng freetype2"))
+
                ;; Force the trash location.
                (substitute* (cons*
                               "utils/qa/showTracks"
@@ -1620,12 +1623,11 @@ multiple sequence alignment.")
                               "hg/js/hgTracks.js"
                               (find-files "." "\\.c$"))
                  ;; This line is specifically needed as-is.
-                 (("\\.\\./trash") "/var/www/html/trash"))
+                 (("\\.\\./trash") "/var/cache/genome"))
 
                #t)))
          ;; Install happens during the 'build phase.
          ;; Install the website files too
-         ;; rsync -avzP rsync://hgdownload.cse.ucsc.edu/htdocs/ /var/www/html/
          (replace 'install
            (lambda _
              (invoke "make" "doc-install")
@@ -1639,15 +1641,13 @@ multiple sequence alignment.")
                      "include /var/lib/genome/hg.conf\n")))
                #t)))
          (add-after 'install 'create-symlink
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               ;; Some trash locations are hardcoded as "../trash"
-               ;(symlink "/var/www/html/trash"
-               ;         (string-append out "/trash"))
-               (symlink "../html"
-                        (string-append out "/htdocs"))
-               #t)))
-         )))
+           (lambda* (#:key inputs #:allow-other-keys)
+             (mkdir-p "htdocs")
+             ;; Fallback location for fonts.
+             (symlink (string-append (assoc-ref inputs "gs-fonts")
+                                     "/share/fonts/type1/ghostscript")
+                      "htdocs/urw-fonts")
+             #t)))))
     (inputs
      `(("freetype" ,freetype)
        ("libpng" ,libpng)
@@ -1658,7 +1658,8 @@ multiple sequence alignment.")
        ("python2" ,python-2)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)
+     `(("gs-fonts" ,gs-fonts)
+       ("pkg-config" ,pkg-config)
        ("python" ,python)
        ("rsync" ,rsync)    ; For installing js files from the source checkout
        ("tcl" ,tcl)
diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm
index 1a5b678..9da7535 100644
--- a/gn/services/genome-browser.scm
+++ b/gn/services/genome-browser.scm
@@ -4,6 +4,7 @@
 (define-module (gn services genome-browser))
 
 (use-modules (gnu)
+             (guix build utils)
              (guix packages)
              (gn packages bioinformatics))
 (use-service-modules
@@ -23,6 +24,7 @@
                    "db.user=readonly\n"
                    "db.password=access\n"
                    "db.trackDb=trackDb\n"
+                   "db.port=13306\n"
                    "gbdbLoc1=/gbdb/\n"
                    "gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/\n"
                    ;# To disable on-the-fly loading of mysql data, comment out these lines.
@@ -46,8 +48,7 @@
                    ;"hgc.psxyPath=/hive/data/outside/GMT4.3.1/bin/psxy"
                    ;"hgc.ps2rasterPath=""/bin/ps2raster"
                    "hgc.ghostscriptPath=" ghostscript "/bin/gs\n"   ; needed?
-                   "udc.cacheDir=/var/www/html/trash/udcCache\n"    ; default is /tmp/udcCache
-                   ))
+                   "udc.cacheDir=/var/cache/genome/udcCache\n"))    ; default is /tmp/udcCache
 
 (define %startup-script
   (mixed-text-file "create_databases.sh"
@@ -55,18 +56,37 @@
                    bash-minimal "/bin/sh " (package-source ucsc-genome-browser) "/src/product/ex.MySQLUserPerms.sh\n"
                    mariadb "/bin/mysql -e \"create database hgcentral;\" mysql\n"
                    mariadb "/bin/mysql hgcentral < hgcentral.sql\n"
-                   coreutils-minimal "/bin/mkdir -p /var/www/html/trash\n"
-                   coreutils-minimal "/bin/chown -R httpd:httpd /var/www\n"
-                   ))
+                   coreutils-minimal "/bin/mkdir -p /var/cache/genome\n"
+                   coreutils-minimal "/bin/chown -R httpd:httpd /var/www\n"))
+
+;; This might be useful as a one-off shepherd job.
+;(define %genome-activation-script
+;  #~(begin
+;      ;(unless (file-exists? "/var/lib/mysql/hgcentral")
+;      ;  (invoke #$(file-append wget "/bin/wget") "http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql" "-O" "/var/lib/mysql/hgcentral.sql")
+;      ;  ;(invoke "sh" #$(file-append (package-source ucsc-genome-browser) "/src/product/ex.MySQLUserPerms.sh"))
+;      ;  (invoke #$(file-append mariadb "/bin/mysql") "-e" "\"create database hgcentral;\"" "mysql")
+;      ;  (invoke #$(file-append mariadb "/bin/mysql") "hgcentral" "<" "/var/lib/mysql/hgcentral.sql"))
+;      (unless (file-exists? "/var/www/html/trash")
+;        (mkdir-p "/var/www/html/trash"))
+;      (unless (file-exists? "/var/cache/genome")
+;        (mkdir-p "/var/cache/genome"))
+;      (for-each (lambda (file)
+;                  (chown file (passwd:uid "httpd") (passwd:gid "httpd")))
+;                (append (find-files "/var/cache/genome" #:directories? #t)
+;                        (find-files "/var/www/html/trash" #:directories? #t)))
+;      (for-each (lambda (file)
+;                  (chown file (passwd:uid "mysql") (passwd:gid "mysql")))
+;                (find-files "/var/lib/mysql" #:directories? #t))))
+
+;(define %one-month-files
+;  (let ((%one-month (* 60 60 24 30)))
+;    (find-files "/var/cache/genome" (lambda (file stat)
+;                                      (> (stat:atime stat) %one-month)))))
 
 ;; TODO:
-;;  create 'daily clean' mcron scripts.
-;;  move /var/www/html/trash to /gbdb/trash?
-;;  Fix from main page:
-;;      hgVai
-;;      hgIntegrator
-;;  from 'more tools'
-;;      hgPhyloPlace
+;;  create 'daily clean' mcron scripts. Only needed in /var/cache/genome grows too large.
+;;  use rsync to make sure mouse genome data is kept up-to-date.
 
 (define ucsc-genome-browser-port 4321)
 
@@ -81,10 +101,12 @@
   (file-systems %base-file-systems)
   ;; No firmware for VMs
   (firmware '())
-  (packages (cons* mariadb  ; for create-db script
+  (packages (cons* mariadb  ; for create-db script, interacting with database if necessary
                    %base-packages))
   (services
-    (list (service mysql-service-type)
+    (list (service mysql-service-type
+                   (mysql-configuration
+                     (port 13306))) ; don't overlap with penguin2's mariadb
           (service special-files-service-type
                    `(("/root/create_hgcentral" ,%startup-script)
                      ("/var/lib/genome/hg.conf" ,%hg.conf)))
@@ -121,19 +143,27 @@
                              %default-httpd-modules))
                          (extra-config (list "\
 TypesConfig etc/httpd/mime.types
+# More logs for more debugging.
+LogFormat \"%h %l %u %t \\\"%r\\\" %>s %b\" common
+CustomLog /var/log/httpd/combined_log common
+#LogLevel debug
 # cgid.sock needs to be creatable, not in the store
 ScriptSock /var/run/cgid.sock
+#XBitHack needs to not be inside the VirtualHost block.
+XBitHack On
 # same as 'listen' above
 <VirtualHost *:" (number->string ucsc-genome-browser-port) ">
-  XBitHack On
   DocumentRoot " ucsc-genome-browser "/html
   Alias /bin " ucsc-genome-browser "/bin
   #Alias /cgi-bin " ucsc-genome-browser "/cgi-bin   # causes cgi scripts to fail to render
+  Alias /favicon.ico " ucsc-genome-browser "/html/faviconRR.ico
   Alias /htdocs " ucsc-genome-browser "/htdocs
-  #Alias /trash /var/www/html/trash # this is wrong
-  Alias /var/www/html/trash /var/www/html/trash
+  #Alias /htdocs " ucsc-genome-browser "/html
+  Alias /var/www/html/trash /var/cache/genome
+  Alias /var/cache/genome /var/cache/genome
   <Directory " ucsc-genome-browser "/html>
-    Options +Includes +FollowSymLinks +Indexes
+    Options +Includes
+    #Options +Includes +FollowSymLinks +Indexes
     AllowOverride None
     <IfModule mod_authz_host.c>
       Require all granted
@@ -144,13 +174,21 @@ ScriptSock /var/run/cgid.sock
   ScriptAlias /cgi-bin " ucsc-genome-browser "/cgi-bin
   <Directory " ucsc-genome-browser "/cgi-bin>
     AllowOverride None
-    Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch +Includes +FollowSymlinks
+    Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
+    #Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch +Includes +FollowSymlinks
     Order allow,deny
     #SetHandler cgi-script
     Require all granted
     Allow from all
   </Directory>
 
+  <Directory /var/cache/genome>
+    Options MultiViews
+    AllowOverride None
+    Order allow,deny
+    Allow from all
+  </Directory>
+  # Upstream default location, possibly expected by software
   <Directory /var/www/html/trash>
     Options MultiViews
     AllowOverride None
@@ -159,8 +197,5 @@ ScriptSock /var/run/cgid.sock
   </Directory>
 </VirtualHost>")))))))))
 
-;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genome-browser.scm --network --share=/path/to/gbdb=/gbdb
-;; ALSO need to share in the external database?
-;; Probably not, it falls back to http://hgdownload.soe.ucsc.edu/gbdb/
-;; Can skip the %startup-script dance if /var/lib/mysql is stored outside of the container, but might need /var/www/html/trash too then.
+;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genome-browser.scm --network --share=/export/efraimf/UCSC_Genome/gbdb=/gbdb --share=/export/efraimf/UCSC_Genome/var-lib-mysql=/var/lib/mysql --share=/export/efraimf/UCSC_Genome/var-cache-genome=/var/cache/genome --share=/export/efraimf/UCSC_Genome/var-cache-genome=/var/www/html/trash
 ;; xdg-open http://localhost:4321