01f8a6872a8d3679c29e63adac60c59f6a86c0c9
hiram
  Fri Jun 12 15:14:45 2026 -0700
correctly reloading assemblyList table with new indexes and no interference with the running system

diff --git src/hg/utils/otto/genArk/addAssemblyList.sh src/hg/utils/otto/genArk/addAssemblyList.sh
index acc44bdf499..df615e88a07 100755
--- src/hg/utils/otto/genArk/addAssemblyList.sh
+++ src/hg/utils/otto/genArk/addAssemblyList.sh
@@ -5,33 +5,40 @@
 
 cd /hive/data/inside/GenArk
 
 export YYYY=`date "+%Y"`
 export DS=`date "+%F"`
 export dayOfMonth=`date "+%d" |  sed -e 's/^0//;'`
 
 mkdir -p history/${YYYY}
 
 time (./assemblyList.py dbDb.clade.year.acc.tsv) > history/${YYYY}/asmList${DS}.log 2>&1
 
 rm -f beforeSort.prio
 mv assemblyList.tsv beforeSort.asmList
 sort -k2,2n beforeSort.asmList > assemblyList.tsv
 
-hgsql hgcentraltest -e 'DROP TABLE IF EXISTS assemblyList;'
-hgsql hgcentraltest < /hive/data/inside/GenArk/assemblyList.sql
-hgsql hgcentraltest -e "LOAD DATA LOCAL INFILE 'assemblyList.tsv' INTO TABLE assemblyList;"
+rm -f aLT.sql
+sed -e 's/CREATE TABLE assemblyList/CREATE TABLE assemblyListTemp/;' \
+    /cluster/home/otto/kent/src/hg/lib/assemblyList.sql \
+     > aLT.sql
+hgsql hgcentraltest -e 'DROP TABLE IF EXISTS assemblyListTemp;'
+hgsql hgcentraltest < aLT.sql
+rm -f aLT.sql
+hgsql hgcentraltest -e "LOAD DATA LOCAL INFILE 'assemblyList.tsv' INTO TABLE assemblyListTemp;"
+hgsql hgcentraltest \
+ -e 'DROP TABLE assemblyList; RENAME TABLE assemblyListTemp TO assemblyList;'
 
 hgsql hgcentraltest -e 'select count(*) from assemblyList;' >> history/${YYYY}/asmList${DS}.log 2>&1
 
 sort genark.tsv | join -t$'\t' - <(sort assemblyList.tsv | cut -f1-2,6) \
   | sort -t$'\t' -k7n > newGenark.tsv
 
 hgsql hgcentraltest -e 'DROP TABLE IF EXISTS genark;'
 hgsql hgcentraltest < /hive/data/inside/GenArk/newGenark.sql
 hgsql hgcentraltest -e "LOAD DATA LOCAL INFILE 'newGenark.tsv' INTO TABLE genark;"
 
 hgsql hgcentraltest -e 'SELECT COUNT(*) FROM genark;' >> history/${YYYY}/asmList${DS}.log 2>&1
 
 # once a month (in the first week) archive the assemblyList.tsv
 if [ "${dayOfMonth}" -lt 8 ]; then
   mkdir -p history/${YYYY}