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I have hundreds of workspace files (FMW) and I would like to import and publish it to FME Server.

Can I do this automatically, not individually by FME Desktop?

If yes, please write me instruction how.

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You cannot publish multiple workspace at once in FME Desktop. But the FME Server API includes methods for publishing single workspaces or multiple workspaces. Please see here: https://docs.safe.com/fme/html/FME_REST/v2/apidoc/index.html#!/repositories/add_post_5

And some more detail here: http://playground.fmeserver.com/using-the-rest-api/workspaces/

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