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My company is switching over to sharepoint and wants SSO in their other applications, amongst them a java EE application that i am developing. Is this possible? The login would have to be either directly connected to their windows login through their browser somehow, or clicking a link in sharepoint would need to somehow post login information to my page. The java EE application is currently using LDAP for authentication, connected to the same AD that sharepoint uses of course. The application is also available outside our companies network, so it's not an intranet.

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Yes this is possible.

One option is to use claims based authentication using SAML tokens, with the various applications trusting the same Secure Token Services (STS), which could be using your AD as a user database.

For how to do this with 2 sharepoint sites, with internal and external users see: http://msdn.microsoft.com/en-us/library/hh446525.aspx

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I will check this out when I get some budget for this development, so I won't accept your answer for a while, hope that's ok!
You say that this is for 2 sharepoint sites, but i asked for a java ee system.

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