There are many different ways to connect to SAP R/3. Your choice depends largely on the type of application you are building. If you are looking to support transparent system to non-SAP system commication, then using the XML document standards of Business Connector (BC) is the tool for you. BC allows you to chain together multiple RFC/BAPI calls in what is termed a pipeline into which you map inbound XML fields using the BC browser.If you need to provide realtime, client based communication (from a Web page), then JCo is the right connector for you. JCo is a highly optimized Java Native Interface (JNI) that provides quick connectivity into the RFC/BAPI layer.
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