Atef, you haven't quite got the workflow for Server and data sources figured out yet.
Data sources can only be created in Tableau Desktop. You then publish those data sources to Tableau Server for use and management.
So, create a workbook and connect to MongoDB using the MongoDB BI connector. Set up your joins and any calculated fields, hierarchies and so on that you want, and save the workbook with NO vizzes, just the data source.
Then, right-click on the data source name in the Data tab of the workbook and select "Publish to server..." from the pop-up menu. Log into the Server, pick your project and publish the data source. Now you can manage the data source in Server (e.g., set a refresh schedule, assign permissions, etc.), and users can select that data source to use in the creation of their own workbooks.
Does that help?