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I can check user in active directory, if he exist then I give him permission to open app window, but what if an application has many levels of permission? Do I create special groups of permission in active direcotry and check if user belongs to one of them? . Can application log in automaticaly, or there is always need to enter password?

A: 

Active Directory can fulfill two related but seperate functions for an application: Authorization and Authentication.

Authentication is validating that the person using your application is a valid user. If you have the user's credentials (i.e. the application prompts the user for their username and password), you can authenticate them against AD by attempting a connection using their username/password.

Authorization is what lets you determine the level of permissions a particular user has in your application. Active Directory groups are a relatively straightforward and flexible way to implement the various permissions levels. Typically, I will create very fine-grained permissions groups that represent each securable action users can perform in the application (i.e. CanDeleteWidgets, CanAddWidgets, CanEditWidgets ). Then create functional or role groups where you place the users for that role (i.e. Managers, Coordinators, Technicians, etc). Finally, you just nest the role groups into the permissions groups so if, for example, the business requirement is that Managers can delete widgets, you would add the Managers group as a member of the CanDeleteWidgets group. While this may seem more complex, it makes it extremely simple to respond to changing business security requirements (i.e. "Technicians need to be able to delete widgets" - Piece of cake. Add the Technicians role group to the CanDeleteWidgets permissions group and you're done).

As far as logging in automatically, yes, there are a number of ways you can automatically log in a user. For winforms apps, you should just be able to grab the currently logged in user and use that. For web apps, if you can use integrated authentication, you end up with the same thing. Your web server will handle the authentication piece and send over the DOMAIN\USERNAME of the user in a server header variable.

David Archer
your answer is very helpful and complete.