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I need help getting started with Saml authentication. The scenario is we have a custom application that is authenticating users based on their windows auth (logging into their desktop via the domain). They want it to interface with a third party hr system using saml. I would like to know how to get started with this type of authentication without using adfs. How do we generate custom saml tokens in the request?

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Ok, so you dant want to use ADFS... The best way to do this is to use some application generating tokens and integrating with AD for the windows auth. Is the choice not to use ADFS due to economic reasons? If not use ADFS or some other application like Oracle Access Manager, OpenAM. If its about money have alook at Shiboleth.

If you really want to create custom SAML tokens using for example Java, have a look at OpenSAML. I have book on it here and a bunch of information on my blog