8a0a3fdc82e2a1362e24e91a2f5de0ee9c1931fe
hiram
  Thu Oct 21 11:17:30 2021 -0700
scripts for the GRC Incident otto job no redmine

diff --git src/hg/utils/otto/grcIncident/runUpdate.sh src/hg/utils/otto/grcIncident/runUpdate.sh
new file mode 100755
index 0000000..f94d308
--- /dev/null
+++ src/hg/utils/otto/grcIncident/runUpdate.sh
@@ -0,0 +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"
+
+
+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
+
+