9cea4ceb4ee3f5c28c3315f63f0c696e82f6a8d4
hiram
  Thu Aug 8 12:57:18 2024 -0700
adding the assemblyList table creation to the cron job refs #32596

diff --git src/hg/utils/otto/genArk/updateHgcentral.sh src/hg/utils/otto/genArk/updateHgcentral.sh
index 4670bdf..b15b071 100755
--- src/hg/utils/otto/genArk/updateHgcentral.sh
+++ src/hg/utils/otto/genArk/updateHgcentral.sh
@@ -1,123 +1,128 @@
 #!/bin/bash
 
 # *** Do not edit this file outside of the source tree. ***
 # This file is from source tree:
 #     kent/src/hg/utils/otto/genArk/updatgeHgcentral.sh
 # called by otto cron job in /hive/data/inside/GenArk/
 # and using the helper script:
 #     kent/src/hg/utils/otto/genArk/genArkListToSql.pl
 
 # exit on any error
 set -beEu -o pipefail
 
 function usage() {
   printf "usage: ./updateCentral.sh makeItSo\n" 1>&2
-  printf "updates hgcentral.genark with the latest hub list from hgdownload\n" 1>&2
+  printf "updates hgcentraltest.genark with the latest hub list from hgdownload\n" 1>&2
+  printf "and the hgcentraltest.assemblyList table from NCBI listings.\n" 1>&2
 }
 
 # check for an 'unbound' variable safely
 if [ -z "${1+x}" ]; then
   usage
   exit 255
 fi
 # something is in $1, verify is is 'makeItSo'
 if [ "xxx$1" != "xxxmakeItSo" ]; then
   usage
   exit 255
 fi
 
 cd /hive/data/inside/GenArk
 export DS=`date "+%F"`
 export YYYY=`date "+%Y"`
 export LC_NUMERIC=en_US
-export msgTo="hclawson@ucsc.edu"
-# export msgTo="hclawson@ucsc.edu,otto-group@ucsc.edu"
+export msgTo="hclawson@ucsc.edu,otto-group@ucsc.edu"
 export msgFile="/tmp/ottoGenArk.$$.txt"
 
 ###########################################################################
 ### helper functions
 ###########################################################################
 
 function msgToFrom() {
   printf "To: %s\n" "${msgTo}" > ${msgFile}
   printf "From: hiram@soe.ucsc.edu\n" >> ${msgFile}
 }
 
 function sendMsg() {
   cat $msgFile | /usr/sbin/sendmail -t -oi
   rm -f $msgFile
 }
 
 function oddRowCounts() {
   todayCount=$1
   mysqlCount=$2
   msgToFrom
-  printf "Subject: ALERT: hgcentral.genark update problem\n" >> ${msgFile}
+  printf "Subject: ALERT: hgcentraltest.genark update problem\n" >> ${msgFile}
   printf "\n" >> ${msgFile}
   printf "# puzzling, count in file %'d is not larger than the MySQL table %'d\n" "${todayCount}" "${mysqlCount}" >> ${msgFile}
   sendMsg
 }
 
 function updateIncorrect() {
   todayCount=$1
   mysqlCount=$2
   msgToFrom
-  printf "Subject: ALERT: hgcentral.genark update problem\n" >> ${msgFile}
+  printf "Subject: ALERT: hgcentraltest.genark update problem\n" >> ${msgFile}
   printf "\n" >> ${msgFile}
-  printf "# ERROR: hgcentral.genark table has been reloaded, but row count %'d is not larger than than previous MySQL table %'d\n" "${todayCount}" "${mysqlCount}" >> ${msgFile}
+  printf "# ERROR: hgcentraltest.genark table has been reloaded, but row count %'d is not larger than than previous MySQL table %'d\n" "${todayCount}" "${mysqlCount}" >> ${msgFile}
   sendMsg
 }
 
 function updateOK() {
   todayCount=$1
   mysqlCount=$2
   msgToFrom
-  printf "Subject: NOTE: hgcentral.genark has been updated\n" >> ${msgFile}
+  printf "Subject: NOTE: hgcentraltest.genark has been updated\n" >> ${msgFile}
   printf "\n" >> ${msgFile}
+  printf "# this message is from the otto cron job:\n" >> "${msgFile}"
+  printf "# 37 10 * * 2 /hive/data/inside/GenArk/updateHgcentral.sh makeItSo\n" >> "${msgFile}"
   printf "# today MySQL rowCount %'d vs. previous MySQL rowCount %'d\n" "${todayCount}" "${mysqlCount}" >> ${msgFile}
   sendMsg
 }
 
 ###########################################################################
 ### begin processing
 ###########################################################################
 
 # everything depends on this file from hgdownload
 rsync -a qateam@hgdownload:/mirrordata/hubs/UCSC_GI.assemblyHubList.txt ./list.${DS}
 
 #  see if it became newer than previous
 newSum=`grep -v "^#" list.${DS} | sort | md5sum | cut -d' ' -f1`
 prevSum=`grep -v "^#" previousList.txt | sort | md5sum | cut -d' ' -f1`
 
 if [ "${prevSum}" = "${newSum}" ]; then
   rm -f list.${DS}
   exit 0
 fi
 
 # save this new list in history
 mkdir -p history/${YYYY}
 cp -p list.${DS} history/${YYYY}
 countToday=`grep -v "^#" list.${DS} | wc -l`
 rowCount=`hgsql -N hgcentraltest -e 'select count(*) from genark;' | cat`
 
 if [ "${countToday}" -gt "${rowCount}" ]; then
 
   ./genArkListToSql.pl list.${DS} > genark.tsv
   hgsql hgcentraltest -e 'drop table genark;'
-  hgsql hgcentraltest < ~/kent/src/hg/lib/genark.sql
+  hgsql hgcentraltest < /hive/data/inside/GenArk/genark.sql
  hgsql hgcentraltest -e "LOAD DATA LOCAL INFILE 'genark.tsv' INTO TABLE genark;"
   newCount=`hgsql -N hgcentraltest -e 'select count(*) from genark;' | cat`
   if [ "${newCount}" -gt "${rowCount}" ]; then
     updateOK "${newCount}" "${rowCount}"
     rm -f previousList.txt
     mv list.${DS} previousList.txt
   else
     updateIncorrect "${newCount}" "${rowCount}"
     exit 255
   fi
 else
   oddRowCounts "${countToday}" "${rowCount}"
   exit 255
 fi
 
+### new assemblyList table in hgcentraltest 2024-08-08
+/hive/data/inside/GenArk/addAssemblyList.sh
+
 exit $?