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Project-Level Message Handlers: These are installed in an application directory per Engine and and aren't supported by MettleCI so should be deployed manually.
Job-Level Message Handlers: There is a MettleCI plugin to support their deployment only. While MettleCI deploys Job-Level Message Handler files from a Project's Git repository, it doesn't offer native check-in and deletion functions for them (as they are not “DataStage assets”, see Why do Data Migrators suggest switching away from The Problem With Message Handlers? for more information) so they must be managed via command line Git.
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Both the 'Root ISX directory' and 'Root message handler directory' fields must contain the following text: datastage.
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These techniques steps will let you manage and deploy your Job-Level Message Handlers. We suggest that where possible you migrate away from using message handlers as discussed in Why do Data Migrators suggest switching away from Message Handlers?