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I am not aware of any way to pass an x.509 cert to SAP via JCO. The x.509 standard provides a single-sign mechanism, such that any system which generates a legitimate certificate can provide external authentication to SAP. The only way, currently, to use x.509 certs to offer SSO is through SAP ITS. ITS can accept an x.509 then generate an SAP logon ticket to represent that user back to SAP. If anyone out there knows how to use JCo to provide this same functionality, please let me know!
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