CVR seq date file had blank seq dates for some samples. This was occurring with samples from the AZ / Sophia cohorts.
Cause
Once a sample was in the CVR clinical sample file, its seq date would never get updated even if it was pulled again from the queue. This is because even though the queue contains the correct date, the value would get overwritten by a subsequent call to processSeqDateFile which backfills the old value from seq_date.txt.
Solution
This PR updates the code so that the JSON seq date is pulled after the existing one. This way, the value is only backfilled for pre-existing samples that do not have an incoming update from the CVR queue.
Problem
CVR seq date file had blank seq dates for some samples. This was occurring with samples from the AZ / Sophia cohorts.
Cause
Once a sample was in the CVR clinical sample file, its seq date would never get updated even if it was pulled again from the queue. This is because even though the queue contains the correct date, the value would get overwritten by a subsequent call to
processSeqDateFilewhich backfills the old value fromseq_date.txt.Solution
This PR updates the code so that the JSON seq date is pulled after the existing one. This way, the value is only backfilled for pre-existing samples that do not have an incoming update from the CVR queue.
/cc @averyniceday @callachennault @sheridancbio