# ------------------------------------------------------------
#            PLANT ONTOLOGY HTTPD CONFIGURATION FILE
# ------------------------------------------------------------
DocumentRoot /data/www/plantontology/plantontology/html/

LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-agent}i\"" combined
CustomLog /data/www/plantontology/plantontology/logs/transfer_log combined

TransferLog  /data/www/plantontology/plantontology/logs/access_log
ErrorLog     /data/www/plantontology/plantontology/logs/error_log

Include /data/www/plantontology/plantontology/conf/local.conf

Alias   /icons        /usr/local/apache/icons
Alias   /logs         /data/www/plantontology/plantontology/logs
Alias	/images		/data/www/plantontology/plantontology/html/images

##RewriteEngine On
##RewriteLog /data/www/plantontology/logs/rewrite_log 
##RewriteBase /amigo/
##RewriteRule /amigo/$ /amigo/go.cgi
##RewriteRule /amigo/$ /amigo/go.cgi[type=application/x-httpd-cgi]

RewriteEngine On
RewriteCond %{REQUEST_URI} !^/(download/database)
RewriteCond %{REQUEST_URI} !^/(owlfiles)
RewriteRule ^(.*)/$ $1/index.html

<IfModule mod_perl.c>

   PerlRequire /data/www/plantontology/plantontology/conf/perl.startup

   <Location />
       PerlSetVar   NavConf     /data/www/plantontology/plantontology/conf/navbar.conf
       PerlSetVar   Stylesheet  /stylesheets/plantontology.css
#       PerlSetVar   Background  /images/netbkgnd.gif
       PerlSetVar   Bgcolor     white
       PerlSetVar   Banner      /images/poc_banner.gif
       PerlSetVar   Logo        /images/poc_logo.gif
       PerlSetVar   Footer      /data/www/plantontology/plantontology/conf/footer.html
   </Location>

   <Directory /data/www/plantontology/plantontology/html/images>
	SetHandler	default-handler
   </Directory>

   <Directory /data/www/plantontology/plantontology/html/amigo_user_guide/images>
	SetHandler	default-handler
   </Directory>

   <Directory /data/www/plantontology/plantontology/html/download/database>
	SetHandler	None
	Options Indexes FollowSymLinks
	Allow from all
   </Directory>

   <Directory /data/www/plantontology/plantontology/html/services>
	SetHandler	None
	Options Indexes FollowSymLinks
	Allow from all
   </Directory>

   <Directory /data/www/plantontology/plantontology/html/owlfiles>
	SetHandler	None
	Options Indexes FollowSymLinks
	Allow from all
   </Directory>

   <Directory /data/www/plantontology/plantontology/html/docs/presentations/tutorials>
	SetHandler	None
	Options Indexes FollowSymLinks
	Allow from all
   </Directory>

   <Directory /data/www/plantontology/plantontology/html/docs/development/pdfs>
	SetHandler	None
	Options Indexes FollowSymLinks
	Allow from all
   </Directory>

   <Directory /data/www/plantontology/plantontology/html/docs/dbxref>
	SetHandler	None
	Options Indexes FollowSymLinks
	Allow from all
   </Directory>

   <Directory /data/www/plantontology/plantontology/html>
	       SetHandler   perl-script
	       PerlHandler  Apache::PlantOntology
   </Directory>


   <Directory /data/www/plantontology/plantontology/cgi-perl>
       SetHandler     perl-script
       PerlHandler    ModPerl::Registry
       PerlSetVar     AceBrowserRoot /plantontology
       PerlSendHeader On
       Options        +ExecCGI
   </Directory>

   Alias     /db/ /data/www/plantontology/plantontology/cgi-perl/

   ##########################
   # AmiGO NEW VERSION
   #########################

   ScriptAlias /amigo/go.cgi /data/www/plantontology/po_amigo/cgi-bin/plantontology/go.cgi

   Alias  /amigo/docs/ /data/www/plantontology/po_amigo/docs/amigo/
   ### NOTICE!!! Uncomment this line when switching to the new AmiGO, otherwise the 'show def' will not show!!!
   Alias /amigo/ /data/www/plantontology/po_amigo/docs/amigo/

   <Directory  /data/www/plantontology/po_amigo/cgi-bin>
       PerlHandler ModPerl::Registry
       Options ExecCGI FollowSymLinks
       PerlSetEnv GO_ROOT /data/www/plantontology/po_amigo/go-cvs/go-dev
       DirectoryIndex go.cgi
       ErrorDocument 404  /amigo/go.cgi
   </Directory>

   ###########
   ## OLD AmiGO ##
   ###########

#   ScriptAlias /amigo/go.cgi /usr/local/amigo/cgi-bin/plantontology/go.cgi
   ScriptAlias /amigo_old/go.cgi /usr/local/amigo/cgi-bin/plantontology/go.cgi

#   Alias  /amigo/docs/ /usr/local/amigo/docs/
   Alias  /amigo_old/docs/ /usr/local/amigo/docs/
#   Alias  /gost/docs/ /usr/local/amigo/go-cvs/go-dev/amigo/gost/docs/

   <Directory  /usr/local/amigo/cgi-bin>
       PerlHandler ModPerl::Registry
       Options ExecCGI FollowSymLinks
       PerlSetEnv GO_ROOT /usr/local/amigo/go-cvs-developers/go-dev
       DirectoryIndex go.cgi
       ErrorDocument 404  /amigo/go.cgi
   </Directory>

   #If I was smart I could do this with mod_rewrite,   -Steve
   <Location /amigo/>
       #Directory/data/www/plantontology/html/amigo>
       DirectoryIndex go.cgi
       ErrorDocument 404  /amigo/go.cgi
   </Location>

#   <Directory /usr/local/amigo/docs/user_guide/>
#       SetHandler   perl-script
#       PerlHandler  Apache::PlantOntology
#   </Directory>

#   <Location /amigo/user_guide>
#      DirectoryIndex index.html
#   </Location>
  

   ##########
   ## GOst ##
   ##########

#    <Directory /usr/local/amigo/go-cvs/go-dev/amigo/gost/cgi-bin> 
#        Options ExecCGI FollowSymLinks
#        PerlSetEnv GO_ROOT /usr/local/amigo/go-cvs/go-dev
#    </Directory>

#   ScriptAlias /gost/gost.cgi /usr/local/amigo/cgi-bin/POst/gost.cgi

</IfModule>