In JIRA 4.1, you can use the JIRA RPC Services, but I would recommend to you to upgrade your JIRA version so you can use the REST API instead, which is a much more powerful tool to interact with JIRA.
Cheers!
Teilor
JIRA4 already has a SOAP service that exposes the progressWorkflowAction function. See https://docs.atlassian.com/rpc-jira-plugin/4.4/com/atlassian/jira/rpc/soap/JiraSoapService.html#progressWorkflowAction%28java.lang.String,%20java.lang.String,%20java.lang.String,%20com.atlassian.jira.rpc.soap.beans.RemoteFieldValue[]%29
You will find examples of this if you search in Answers.
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