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What is the SiteMinder application server? There seems to be very little documentation on what this is.

The follow-up question would be, do I need to set up JBoss / WebLogic / WebSphere.

I am using a 32 bit Windows XP.

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Web findings:

The SiteMinder Application Server Agent protects resources on Java application servers that follow the Java 2 Enterprise Edition standard. These resources can be Java servlets, JavaServer Pages (JSPs), and Enterprise JavaBeans (EJBs).

When a user requests a resource from an application server, the Agent intercepts the request and determines whether the resource is protected by SiteMinder. The SiteMinder Application Server Agent consists of two components: Java servlet Agent — a collection of servlets that communicates with the Policy Server via the SiteMinder Agent API. EJB Agent — a component that integrates with the application server and communicates with the Policy Server like the servlet Agent. The EJB Agent protects only EJBs. In the absence of an Application Server Agent, you can use a Web Agent to protect application server resources; however, the Application Server Agent can protect resources at a more fine-grained level than a Web Agent.

The original document is here.
And you can find other SiteMinder documents here.

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