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You are right, if the application timestamp included in the event may be out of order (in relation to arrival time), then you should use the arrival time, that is, the system timestamp to derive time in CQL. This so because CQL does not support out-of-order events, otherwise a late event may invalidate a previously output event.
The simplest option would be to continue using system time-stamps, but if the application cannot cope with the fact that some of the output (number of trans) may be inconsistent in relation to the application time-stamp, then your approach of grouping by minute (single value) across a large enough window that would include all the events (even the late ones) for that 1-minute of application time should work.