Customizing existing Alerts or creating a new alert based on existing

We have implemented availability groups extensively in our new environment and we have some issues with alerting that is getting in the way of real alerts that we need to address. For example we have jobs reporting failure that are actually not real failures. We have setup 2 copies of our jobs, one on each node. In our case all jobs run from the primary server. We have a step in each job that checks for primary. If it finds that the job is trying to run from the secondary node it will execute SP_STOP_JOB <job name>. This goes into the status as "not successful". SQL Monitor alerts us to this. It is troublesome. I would like to implement either one of the below proposed changes to help us resolve this.
Edit the current Job Failed alert to not send an alert if the job failed on step 1, CheckPrimary.
Disable the built in Job Failed alert and create a custom one that has this check in it.

Can we do either one of those things?
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