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(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
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