An upload and update procedure will allow a project administrator to select upload from the administration section. This will create a backup of the local IBDB and block write access to the local IBDB until after the update. A copy of the backup will be sent to the central crop administrator who will upload the local data to the central (including project users for first time uploads), clean out the local database and create a new central installer and a local database installer for the project. The Workbench administrator will download and install the new central, and the project administrator will download and install the new local.
I don't think we can assume sufficient connectivity to assume that the process will be automatic. I also believe that making it automatic is the responsibility of the implementing institution, and a number of solutions might be used. Having said that we are under pressure from the donor (who doesn't understand the technical or cultural problems involved) to develop and automatic solution to this problem. My first cut would be to see if we can use the shared dataspace on the IBPortal to facilitate this. So each workbench project would have a data directory in the iPlant dataspace with a sub-directory for backups, and one for uploads. The upload directory would be shared with the crop curator which might be automatically notified when an upload is delivered. After uploading the data, a new central is published to the crop link on the portal and a cleaned local is delivered to a download subdirectory of the dataspace. Now I am not sure if the workbench could detect that a new central is available, and even a new local for a particular project and then initiate the update.
The idea is that all communication (data, services and community) is to pass through the IBPortal, but again some institutes may want to develop their own infrastructure. I think if we work to integrate to the portal we at least offer a solution to the lowest common denominator.