SAML Custom User Provisioning + WebServiceUser

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Hi,   I implemented SAML + Custom User Provisioning and it works perfectly. Now, I would like to use custom authentication for our Published Web Services in such a way that the user coming in the http header is passed to the IdP to be authenticated and eventually gets created as a System.User(with WebServiceUser = true) if passes my Custom User Provisioning conditions. How do I do that? SAML seems to work only through browser + the /sso/ handler. For sure I'm missing something. Thanks!
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