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When you look at the General tab of a sequence, all Compilation options are stored as a comma separated list in a job property called jobSeqCodeGenOpts. Each check box corresponds to a named value in the comma separated list:

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For example, jobs with Add checkpoints so sequence is restartable on failure and Automatically handle activities that fail will have a jobSeqCodeGenOpts value of handleaborts,checkpoints. Putting all this together, a simple compliance rule for ensuring all sequences must have checkpoints enabled would look something like this:

Job Sequence is Restartable.qjb.grm

// In file "Job Sequence Is Restartable.qjb.grm"
if (item.properties.jobSeqCodeGenOpts.contains("checkpoints") == false) {
   compliance.failure("Sequence is not restartable on failure")
   return
}