You could do this within a custom shiro filter:
String principal = retrieveUser'sNameFromWherever();
PrincipalCollection principals = new SimplePrincipalCollection(principal,
"UUID-Realm");
WebSubject.Builder builder = new WebSubject.Builder(request, response);
builder.principals(principals).authenticated(true);
WebSubject webSubject = builder.buildWebSubject();
ThreadContext.bind(webSubject); 



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