2da75463c55d14a61c509128ba82733f39e0c784
hiram
  Thu Sep 17 12:04:16 2026 -0700
correctly detect count difference in dev,beta and hgw1 listings no redmine

diff --git src/hg/utils/otto/genArk/whatIsNew.sh src/hg/utils/otto/genArk/whatIsNew.sh
index beadc85b3b7..0f534a6efee 100755
--- src/hg/utils/otto/genArk/whatIsNew.sh
+++ src/hg/utils/otto/genArk/whatIsNew.sh
@@ -1,103 +1,103 @@
 #!/bin/bash
 #############################################################################
 ###  this script lives in the source tree at:
 ###      kent/src/hg/utils/otto/genArk/whatIsNew.sh
 ###  edit that copy instead of the in-use copy at:
 ###      /hive/data/inside/GenArk/pushRR/whatIsNew.sh
 #############################################################################
 
 export TOP="/hive/data/inside/GenArk/pushRR"
 
 cd "${TOP}"
 
 export doNotCount="public.hub.txt|beta.hub.txt|alpha.hub.txt|user.hub.txt|hub.txt|/contrib/"
 
 export devCount=`zegrep -c -v "${doNotCount}" dev.todayList.gz`
 export betaCount=`zegrep -c -v "${doNotCount}" hgwbeta.todayList.gz`
 export hgw1Count=`zegrep -c -v "${doNotCount}" hgw1.todayList.gz`
 
 printf "### excluding the files:\n\t${doNotCount}\nin these counts.\n"
 
 printf "### count of files on hgwdev: ${devCount}, beta: ${betaCount} and hgw1: ${hgw1Count}\n"
 
 
 printf "### count of common files between beta and hgwdev,\nnot counting /contrib/ or the hub.txt files:\n"
 zegrep -v "${doNotCount}" dev.todayList.gz | cut -f2 | sort \
   | join -t$'\t' - <(zegrep -v "${doNotCount}" hgwbeta.todayList.gz | cut -f2 | sort) | wc -l
 
 printf "### count of files unique to beta compared to hgwdev,\nnot counting /contrib/ or the hub.txt files:\n"
 zegrep -v "${doNotCount}" dev.todayList.gz | cut -f2 | sort \
   | join -v2 -t$'\t' - <(zegrep -v "${doNotCount}" hgwbeta.todayList.gz | cut -f2 | sort) | wc -l
 zegrep -v "${doNotCount}" dev.todayList.gz | cut -f2 | sort \
   | join -v2 -t$'\t' - <(zegrep -v "${doNotCount}" hgwbeta.todayList.gz | cut -f2 | sort) > uniq.beta.not.hgwdev.list
 zegrep -v "${doNotCount}" dev.todayList.gz | cut -f2 | sort \
   | join -v1 -t$'\t' - <(zegrep -v "${doNotCount}" hgwbeta.todayList.gz | cut -f2 | sort) > uniq.hgwdev.not.beta.list
 
 printf "### count of common files between hgw1 and hgwbeta,\nnot counting /contrib/ or the hub.txt files:\n"
 
 zegrep -v "${doNotCount}" hgwbeta.todayList.gz | cut -f2 | sort \
   | join -t$'\t' - <(zegrep -v "${doNotCount}" hgw1.todayList.gz | cut -f2 | sort) | wc -l
 
 # what new needs to get from hgwdev go beta
 rm -f new.files.ready.to.beta.txt
 touch new.files.ready.to.beta.txt
-if [ "${devCount}" -gt "${betaCount}" ]; then
+if [ "${devCount}" -ne "${betaCount}" ]; then
    export newFiles=`echo ${devCount} ${betaCount} | awk '{printf "%d", $1-$2}'`
    printf "### ${newFiles} new files to go out from hgwdev to beta not /contrib/\n"
    zegrep -v "${doNotCount}" dev.todayList.gz | cut -f2 | sort \
      | join -v1 -t$'\t' - <(zegrep -v "${doNotCount}" hgwbeta.todayList.gz | cut -f2 | sort) | sort -u > new.files.ready.to.beta.txt
    head -3 new.files.ready.to.beta.txt
    printf " . . .\n"
    tail -3 new.files.ready.to.beta.txt
 fi
 
 printf "### files with different time stamps hgwdev to hgwbeta:\n"
 
 rm -f new.beta.timeStamps.txt
 zegrep -v "${doNotCount}" dev.todayList.gz | sort -k2 \
   | join -t$'\t' -1 2 -2 2 - <(zegrep -v "${doNotCount}" hgwbeta.todayList.gz | sort -k2) | awk -F$'\t' '$2 != $3' | cut -f1 | sort -u > new.beta.timeStamps.txt
 
 if [ -s "new.beta.timeStamps.txt" ]; then
   head -3 new.beta.timeStamps.txt
   printf " . . .\n"
   tail -3 new.beta.timeStamps.txt
 fi
 
 # accumulate list for cluster-admin cron job rsync
 #   from hgwbeta out to RR machines
 rm -f rsync.gbdb.toRR.fileList.txt
 rm -f rsync.gbdb.genark.fileList.txt
 
 rm -f new.files.ready.to.go.txt
 touch new.files.ready.to.go.txt
-if [ "${betaCount}" -gt "${hgw1Count}" ]; then
+if [ "${betaCount}" -ne "${hgw1Count}" ]; then
    export newFiles=`echo ${betaCount} ${hgw1Count} | awk '{printf "%d", $1-$2}'`
    printf "### ${newFiles} new files to go out from beta to the RR not /contrib/\n"
    zegrep -v "${doNotCount}" hgwbeta.todayList.gz | cut -f2 | sort \
      | join -v1 -t$'\t' - <(zegrep -v "${doNotCount}" hgw1.todayList.gz | cut -f2 | sort) | sort -u > new.files.ready.to.go.txt
    head -3 new.files.ready.to.go.txt
    printf " . . .\n"
    tail -3 new.files.ready.to.go.txt
    touch rsync.gbdb.genark.fileList.txt rsync.gbdb.toRR.fileList.txt
    cat new.files.ready.to.go.txt >> rsync.gbdb.genark.fileList.txt
    sed -e 's#^#genark/#;'  new.files.ready.to.go.txt >> rsync.gbdb.toRR.fileList.txt
 fi
 
 printf "### files with different time stamps:\n"
 
 rm -f new.timeStamps.txt
 zegrep -v "${doNotCount}" hgwbeta.todayList.gz | sort -k2 \
   | join -t$'\t' -1 2 -2 2 - <(zegrep -v "${doNotCount}" hgw1.todayList.gz | sort -k2) | awk -F$'\t' '$2 != $3' | cut -f1 | sort -u > new.timeStamps.txt
 
 if [ -s "new.timeStamps.txt" ]; then
   head new.timeStamps.txt
   touch rsync.gbdb.genark.fileList.txt rsync.gbdb.toRR.fileList.txt
   cat new.timeStamps.txt >> rsync.gbdb.genark.fileList.txt
   sed -e 's#^#genark/#;'  new.timeStamps.txt >> rsync.gbdb.toRR.fileList.txt
 fi
 
 ./quickLiftNew.sh
 ./liftOverNew.sh
 ./loopDetect.sh
 
 exit $?