You have a Glassfish server.

You are a Drupal developer.

You want to run Drupal in Glassfish. More importantly, you want to have it use clean urls because without that capability, all of your urls look like this: /index.php?foo/bar/baz. Which sucks, of course.

Let's set aside for the moment the desirability of running PHP in a Java application container for the moment¹, and jump right to the meat of this geeky post. Here's how I got some of the clean url functionality you'd normally get from Apache's mod_rewrite, or using either mod_rewrite or Lua in lighttpd.

I'm assuming you've already got Glassfish installed, so from there:

1. Get a copy of Quercus, Caucho's Java implementation of PHP 5. I downloaded the version 3.2.1 .war file.
2. Unzip the .war:²
   

   jar -xvf quercus-3.2.1.war

3. Get a copy of Url Rewrite Filter. I used version 3.2.0 (beta), but 2.6 should work also.
   

   > cd quercus-3.2.1
   > wget http://urlrewritefilter.googlecode.com/files/urlrewritefilter-3.2.0-src.zip
   > unzip urlrewritefilter-3.2.0-src.zip

4. Get Drupal. I used the latest 6.x version.:
   

   > cd ../
   > wget http://ftp.drupal.org/files/projects/drupal-6.10.tar.gz
   > tar zxvf drupal-6.10.tar.gz
    
   Copy Drupal files to the quercus docroot
   > cp -r drupal-6.10/* quercus-3.2.1/

5. Configure Url Rewrite Filter. This is where it gets a little sketchy. Drupal comes prepackaged with a .htaccess file, which sets up the mod_rewrite rules for Apache:
   

   # Rewrite current-style URLs of the form 'index.php?q=x'.
   RewriteCond %{REQUEST_FILENAME} !-f
   RewriteCond %{REQUEST_FILENAME} !-d
   RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]

   
   Unfortunately, Url Rewrite Filter doesn't support the REQUEST_FILENAME directive (yet). So I've put in some hacks to at least get clean urls working. I don't pretend that this is production-ready, but it gets it working for basic testing. If anyone has input, I'd welcome it. Anyway, in the WEB-INF/web.xml file, the following directives need to be added:
   

   <filter>
     <filter-name>UrlRewriteFilter</filter-name>
     <filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
   </filter>
   <filter-mapping>
     <filter-name>UrlRewriteFilter</filter-name>
     <url-pattern>/*</url-pattern>
   </filter-mapping>

   
   This should go before the <servlet></servlet> section.

   Next, create WEB-INF/urlrewrite.xml:
   

   <?xml version="1.0" encoding="utf-8"?>
   <!DOCTYPE urlrewrite
   PUBLIC "-//tuckey.org//DTD UrlRewrite 2.6//EN"
   "http://tuckey.org/res/dtds/urlrewrite2.6.dtd">
   <urlrewrite>
     <rule>
       <note>
         Prevent rewriting of specific files. Definitely not
         the best way to do this.
       </note>
       <from>^/(.*)(css|js|png|jpg|gif)$</from>
       <to>/$1$2</to>
     </rule>
     <rule>
       <note>
         Prevent rewriting of files in the files directory
       </note>
       <from>^/(.*)/files/(.*)$</from>
       <to>/$1/files/$2</to>
     </rule>
     <rule>
       <note>
         Do the Drupaly stuff
       </note>
       <from>^/(.*)$</from>
       <to>/index.php?q=$1</to>
     </rule>
   </urlrewrite>

6. Re-zip your directory back into a .war file to deploy onto the app server:
   

   >jar -cvf quercus-3.2.1.war quercus-3.2.1/*

7. Deploy to Glassfish through the admin console, or from the auto-deploy directory. Note that you should set your context-root to / to run Drupal at the root of the app server.
8. Oh yeah, you'll probably want to connect to a database too, right? In the admin panel, go to Resources > JDBC > Connection Pools and create a new Connection Pool. Let's call it mysqlpool.

   Set Datasource Classname to com.mysql.jdbc.jdbc2.optional.MysqlConnectionPoolDataSource.

   Plug in the following Additional Parameters for your Drupal DB:
   

   password
   user
   databaseName
   portNumber
   serverName

That should be about it.