30e9677ddc4349e1f54dec3d406d7c229502c2ae
lrnassar
  Tue Nov 16 16:09:06 2021 -0800
Fixing up discrepancies between hive and tree for otto, refs #28331

diff --git src/hg/utils/otto/grcIncident/runUpdate.sh src/hg/utils/otto/grcIncident/runUpdate.sh
index f94d308..75e9d0f 100755
--- src/hg/utils/otto/grcIncident/runUpdate.sh
+++ src/hg/utils/otto/grcIncident/runUpdate.sh
@@ -1,112 +1,112 @@
 #!/bin/sh
 
 # set -beEu -o pipefail
 
 export TOP="/hive/data/outside/grc/incidentDb"
 export ECHO="/bin/echo -e"
-export failMail="hiram@soe.ucsc.edu"
+export failMail="hiram@soe.ucsc.edu,lrnassar@ucsc.edu"
 
 
 if [[ $# == 0 || "$1" != "makeItSo" ]]; then
   printf "To: $failMail\nFrom: $failMail\nSubject: ALERT: GRC Incident update\n\nERROR: ${TOP}/runUpdate.sh is being run without the argument: makeItSo\n" | /usr/sbin/sendmail -t -oi
 # echo "ERROR: ${TOP}/runUpdate.sh is being run without the argument: makeItSo" \
 #	| mail -s "ALERT: GRC Incident update" ${failMail} \
 #	    > /dev/null 2> /dev/null
     ${ECHO} "usage: runUpdate.sh makeItSo"
     ${ECHO} "this script needs the argument: makeItSo"
     ${ECHO} "to make it run.  It will update the GRC incident database"
     ${ECHO} "tracks in the working directory:"
     ${ECHO} "${TOP}"
     ${ECHO} "activity logs can be found in:"
     ${ECHO} "${TOP}/*/*.log.YYYY-mm-dd"
     exit 255
 fi
 
 # echo "WARN: ${TOP}/runUpdate.sh is disabled" \
 # 	| mail -s "ALERT: GRC Incident update" ${failMail} \
 # 	    > /dev/null 2> /dev/null
 # exit $?
 
 cd ${TOP}
 
 export DS=`date "+%Y-%m-%d"`
 export YM=`date "+%Y/%m"`
 
 for D in GRCh37 GRCh38 GRCm38 Zv9 MGSCv37 GRCz10 GRCz11 Gallus_gallus-5.0 GRCg6a
 do
   mkdir -p ${D}/log/${YM}
 done
 
 ./grcUpdate.sh GRCh38 hg38 GRCh38.p12_issues human/GRC/Issue_Mapping \
   > GRCh38/log/${YM}/${DS}.txt 2>&1
 
 ./grcUpdate.sh GRCh37 hg19 GRCh37.p13_issues human/GRC/Issue_Mapping \
   > GRCh37/log/${YM}/${DS}.txt 2>&1
 
 ./grcUpdate.sh GRCm38 mm10 GRCm38.p6_issues mouse/GRC/Issue_Mapping \
   > GRCm38/log/${YM}/${DS}.txt 2>&1
 
 ./grcUpdate.sh Zv9 danRer7 Zv9_issues zebrafish/GRC/Issue_Mapping \
   > Zv9/log/${YM}/${DS}.txt 2>&1
 
 ./grcUpdate.sh MGSCv37 mm9 MGSCv37_issues mouse/GRC/Issue_Mapping \
   > MGSCv37/log/${YM}/${DS}.txt 2>&1
 
 ./grcUpdate.sh GRCz10 danRer10 GRCz10_issues zebrafish/GRC/Issue_Mapping \
   > GRCz10/log/${YM}/${DS}.txt 2>&1
 
 ./grcUpdate.sh GRCz11 danRer11 GRCz11_issues zebrafish/GRC/Issue_Mapping \
   > GRCz11/log/${YM}/${DS}.txt 2>&1
 
 ./grcUpdate.sh GRCg6a galGal6 GRCg6a_issues chicken/GRC/Issue_Mapping \
   > GRCg6a/log/${YM}/${DS}.txt 2>&1
 
 ./grcUpdate.sh Gallus_gallus-5.0 galGal5 Gallus_gallus-5.0_issues \
     chicken/GRC/Issue_Mapping > Gallus_gallus-5.0/log/${YM}/${DS}.txt 2>&1
 
 WC=`tail --quiet --lines=1 ${TOP}/GRCg6a/log/${YM}/${DS}.txt ${TOP}/GRCh37/log/${YM}/${DS}.txt ${TOP}/GRCh38/log/${YM}/${DS}.txt ${TOP}/GRCm38/log/${YM}/${DS}.txt ${TOP}/GRCz10/log/${YM}/${DS}.txt ${TOP}/GRCz11/log/${YM}/${DS}.txt ${TOP}/Gallus_gallus-5.0/log/${YM}/${DS}.txt ${TOP}/MGSCv37/log/${YM}/${DS}.txt ${TOP}/Zv9/log/${YM}/${DS}.txt | grep SUCCESS | wc -l`
 if [ "${WC}" -ne 9 ]; then
     ${ECHO} "incidentDb/runUpdate.sh failing" 1>&2
     ${ECHO} "WC: ${WC} <- should be nine" 1>&2
     exit 255
 fi
 
 if [ 0 = 1 ]; then
 # GRCg6a/log/2019/09/2019-09-03.txt  GRCz11/log/2019/09/2019-09-03.txt
 # GRCh37/log/2019/09/2019-09-03.txt  Gallus_gallus-5.0/log/2019/09/2019-09-03.txt
 # GRCh38/log/2019/09/2019-09-03.txt  MGSCv37/log/2019/09/2019-09-03.txt
 # GRCm38/log/2019/09/2019-09-03.txt  Zv9/log/2019/09/2019-09-03.txt
 # GRCz10/log/2019/09/2019-09-03.txt
 
 ### disabled ###
 export update="/hive/data/outside/grc/incidentDb/update.sh"
 mkdir -p ${TOP}/human
 cd ${TOP}/human
 # ${update} human hg19 Hg19 GRCh37 > human.hg19.log.${DS} 2>&1
 # ${update} human hg38 Hg38 GRCh38 > human.hg38.log.${DS} 2>&1
 mkdir -p ${TOP}/mouse
 cd ${TOP}/mouse
 ${update} mouse mm9 Mm9 MGSCv37 > mouse.mm9.log.${DS} 2>&1
 ${update} mouse mm10 Mm10 GRCm38 > mouse.mm10.log.${DS} 2>&1
 mkdir -p ${TOP}/zebrafish
 cd ${TOP}/zebrafish
 ${update} zebrafish danRer7 DanRer7 Zv9 > zebrafish.log.${DS} 2>&1
 cd "${TOP}"
 # ./verifyTransfer.sh Hg19 Mm9 DanRer7
 ./verifyTransfer.sh Mm9 DanRer7
 if [ $? -ne 0 ]; then
     ${ECHO} "incidentDb/runUpdate.sh failing verifyTransfer.sh" 1>&2
     exit 255
 fi
 
 WC=`tail --quiet --lines=1 ${TOP}/mouse/mouse.mm9.log.${DS} ${TOP}/mouse/mouse.mm10.log.${DS} ${TOP}/zebrafish/zebrafish.log.${DS} | grep SUCCESS | wc -l`
 if [ "${WC}" -ne 3 ]; then
     ${ECHO} "incidentDb/runUpdate.sh failing" 1>&2
     ${ECHO} "WC: ${WC}" 1>&2
     exit 255
 fi
 
 ### disabled ###
 fi