diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/services/genenetwork.scm | 104 | ||||
| -rw-r--r-- | gn/services/gn1-httpd-config.scm | 106 |
2 files changed, 110 insertions, 100 deletions
diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm index db3f55d..c00c808 100644 --- a/gn/services/genenetwork.scm +++ b/gn/services/genenetwork.scm @@ -1,67 +1,13 @@ (define-module (gn services genenetwork)) (use-modules (gnu) - (ice-9 match) (past packages python) (past packages web) (gn packages genenetwork) - (gn packages python24)) + (gn packages python24) + (gn services gn1-httpd-config)) (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") @@ -80,7 +26,7 @@ python24-mysqlclient ; MySQLdb python24-numarray python24-piddle - python24-parallel + python24-pp-GN1 ; not python24-parallel, we need an older version python24-pyx python24-pyxlwriter python24-qtlreaper @@ -95,49 +41,7 @@ (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>"))))))))) + (config GN1-httpd-config)))))) ;; 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 diff --git a/gn/services/gn1-httpd-config.scm b/gn/services/gn1-httpd-config.scm new file mode 100644 index 0000000..e62f027 --- /dev/null +++ b/gn/services/gn1-httpd-config.scm @@ -0,0 +1,106 @@ +(define-module (gn services gn1-httpd-config) + #:export (%default-httpd22-modules + GN1-httpd-config)) + +(use-modules (gnu) + (ice-9 match) + (gn packages genenetwork) + (past packages web)) +(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")))) + +(define GN1-httpd-config + (httpd-config-file + (server-name "gn1-test.genenetwork.org") + ;; Defaults to httpd, should be same as 'package' above to launch service. + (server-root httpd22-with-mod-python) + (user "nobody") + (group "root") + (pid-file "/tmp/guix-gn1/httpd-genenetwork1.pid") + (error-log "/tmp/guix-gn1/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/webqtl +</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>")))) |