(define-module (gn services genenetwork))

(use-modules (gnu)
             (ice-9 match)
             (past packages python)
             (past packages web)
             (gn packages genenetwork)
             (gn packages python24))
(use-service-modules web)

(define %default-httpd22-modules
  (map (match-lambda
         ((name file)
          (httpd-module
           (name name)
           (file file))))
       '(("authn_file_module" "modules/mod_authn_file.so")
         ("authn_dbm_module" "modules/mod_authn_dbm.so")
         ("authn_anon_module" "modules/mod_authn_anon.so")
         ("authn_dbd_module" "modules/mod_authn_dbd.so")
         ("authn_default_module" "modules/mod_authn_default.so")
         ("authz_host_module" "modules/mod_authz_host.so")
         ("authz_groupfile_module" "modules/mod_authz_groupfile.so")
         ("authz_user_module" "modules/mod_authz_user.so")
         ("authz_dbm_module" "modules/mod_authz_dbm.so")
         ("authz_owner_module" "modules/mod_authz_owner.so")
         ("authz_default_module" "modules/mod_authz_default.so")
         ("auth_basic_module" "modules/mod_auth_basic.so")
         ("auth_digest_module" "modules/mod_auth_digest.so")
         ("dbd_module" "modules/mod_dbd.so")
         ("dumpio_module" "modules/mod_dumpio.so")
         ("reqtimeout_module" "modules/mod_reqtimeout.so")
         ("ext_filter_module" "modules/mod_ext_filter.so")
         ("include_module" "modules/mod_include.so")
         ("filter_module" "modules/mod_filter.so")
         ("substitute_module" "modules/mod_substitute.so")
         ("log_config_module" "modules/mod_log_config.so")
         ("logio_module" "modules/mod_logio.so")
         ("env_module" "modules/mod_env.so")
         ("mime_magic_module" "modules/mod_mime_magic.so")
         ("expires_module" "modules/mod_expires.so")
         ("headers_module" "modules/mod_headers.so")
         ("ident_module" "modules/mod_ident.so")
         ("setenvif_module" "modules/mod_setenvif.so")
         ("version_module" "modules/mod_version.so")
         ("ssl_module" "modules/mod_ssl.so")
         ("mime_module" "modules/mod_mime.so")
         ("dav_module" "modules/mod_dav.so")
         ("status_module" "modules/mod_status.so")
         ("autoindex_module" "modules/mod_autoindex.so")
         ("asis_module" "modules/mod_asis.so")
         ("info_module" "modules/mod_info.so")
         ("cgi_module" "modules/mod_cgi.so")
         ("dav_fs_module" "modules/mod_dav_fs.so")
         ("vhost_alias_module" "modules/mod_vhost_alias.so")
         ("negotiation_module" "modules/mod_negotiation.so")
         ("dir_module" "modules/mod_dir.so")
         ("imagemap_module" "modules/mod_imagemap.so")
         ("actions_module" "modules/mod_actions.so")
         ("speling_module" "modules/mod_speling.so")
         ("userdir_module" "modules/mod_userdir.so")
         ("alias_module" "modules/mod_alias.so")
         ("rewrite_module" "modules/mod_rewrite.so"))))

(operating-system
  (host-name "genenetwork")
  (timezone "Etc/UTC")
  (locale "en_US.utf8")

  (bootloader (bootloader-configuration
               (bootloader grub-bootloader)
               (target "does-not-matter")))
  (file-systems %base-file-systems)
  ;; No firmware for VMs
  (firmware '())

  (packages (cons* python-2.4
                   python24-htmlgen-GN1
                   python24-json-GN1
                   python24-mysqlclient ; MySQLdb
                   python24-numarray
                   python24-piddle
                   python24-pp
                   python24-pyx
                   python24-pyxlwriter
                   python24-qtlreaper
                   python24-rpy2
                   python24-svg-GN1
                   %base-packages))

  (services (list (service special-files-service-type
                           ;; The genotypes folder doesn't have it's shebangs patched.
                           `(("/usr/bin/python" ,(file-append python-2.4 "/bin/python"))))
                  (service httpd-service-type
                           (httpd-configuration
                             ;; Must be a httpd-2.2 variant.
                             (package httpd22-with-mod-python)
                             (config
                               (httpd-config-file
                                 (server-name "gn1-test.genenetwork.org")
                                 ;; Defaults to httpd, should be same as 'package' above.
                                 (server-root httpd22-with-mod-python)
                                 (user "nobody")
                                 (group "root")
                                 ;; Only while debugging
                                 (pid-file "/tmp/httpd-genenetwork1")
                                 (error-log "/tmp/httpd-genenetwork1-error-log")
                                 (listen '("8042"))
                                 (modules (cons*
                                            (httpd-module
                                              (name "python_module")
                                              (file "modules/mod_python.so"))
                                            %default-httpd22-modules))
                                 (extra-config (list "\
TypesConfig " httpd22-with-mod-python "/etc/httpd/mime.types
DefaultType application/octet-stream
# DocumentRoot MUST NOT be in the PythonPath. Because genenetwork1 must be in PythonPath we leave the document-root keyword above unset.
PythonPath \"sys.path+['/run/current-system/profile/lib/python2.4', '/run/current-system/profile/lib/python2.4/site-packages', '" genenetwork1 "/web/webqtl']\"
# same as 'listen' above
NameVirtualHost *:8042
<VirtualHost *:8042>
  DocumentRoot "genenetwork1 "/web
</VirtualHost>
<Directory " genenetwork1 "/web/webqtl>
  PythonOption session FileSession
  #what is the difference between these two?
  #AddHandler mod_python .py
  SetHandler python-program
  #publisher has more debug information
  PythonHandler " genenetwork1 "/web/webqtl/main.py
  #PythonHandler mod_python.publisher
  #PythonHandler mod_python.cgihandler
  # only while debugging:
  PythonDebug On
</Directory>
# only while debugging:
<Location /mpinfo>
  SetHandler python-program
  PythonHandler mod_python.testhandler
</Location>")))))))))

;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genenetwork.scm --network --expose=/gnshare/gn/web/genotypes
;; xdg-open http://localhost:8042