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sorry if i misunderstood something.

I have a bunch of similar questions:

are there ways to create new SSS target application programmatically?

are there ways to add user(or user mapping) in SSS programmatically?

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SSS, lol im a bit slow with abriviations ;) – ali Sharepoint Mar 19 '13 at 16:10
oh, yeah, I'm sorry. "Add user in SSS programmatically" that is right. – Popov Sergei Mar 20 '13 at 6:41
up vote 1 down vote accepted

Doing what you ask is essentially re-writing the Central Administration functionality. Managing Target Applications cannot be done from a content web application - it requires permissions to the configuration database.

If you want to automate the creation of target applications, I recommend starting with this Secure Store PowerShell script:

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