3a6f7a2ceb39e56238f5a5d3ffa8c40a6d39f14e
hiram
  Tue Aug 11 13:14:09 2026 -0700
better organization of the asmAlias update procedure refs #31811

diff --git src/hg/utils/otto/genArk/asmAlias/runUpdate.sh src/hg/utils/otto/genArk/asmAlias/runUpdate.sh
index ad9a6232021..2676b1e2b53 100755
--- src/hg/utils/otto/genArk/asmAlias/runUpdate.sh
+++ src/hg/utils/otto/genArk/asmAlias/runUpdate.sh
@@ -1,60 +1,60 @@
 #!/bin/bash
 
 # fail on any failed command
 set -eEu -o pipefail
 
 export TOP="/hive/data/inside/GenArk/asmAlias"
 
 cd "${TOP}"
 
 eval "$(date "+YMD=%F Y=%Y M=%m DS=%F_%T")"
 export YMD Y M DS
 
 export db="hgcentraltest"
 export logDir="${TOP}/log/${Y}/${M}"
 mkdir -p "${logDir}"
 export logFile="${logDir}/${DS}.txt"
 export prevAliasTsv="${logDir}/${YMD}.asmAlias.tsv.gz"
 export updateTsv="${logDir}/update.${YMD}.tsv"
 
 # do not overwrite this copy if it was already done today
 if [ ! -s "${prevAliasTsv}" ]; then
   hgsql -N -e 'select * from asmAlias;' "${db}" \
     | gzip -c > "${prevAliasTsv}"
 fi
 
-printf "### cwd: %s\n" "`pwd -P`" >> "${logFile}"
+printf "### cwd: %s\n" "$(pwd -P)" >> "${logFile}"
 printf "### logFile: log/${Y}/${M}/${DS}.txt.gz\n" >> "${logFile}"
 printf "####### running the update command:\n" >> "${logFile}"
 printf "time (./asmAliasUpdate.py -o update.${YMD}.tsv > update.${DS}.out 2> update.${DS}.err) >> logFile\n" >> "${logFile}"
 
 time (./asmAliasUpdate.py -o "${updateTsv}" > ${logDir}/update.${DS}.out 2> ${logDir}/update.${DS}.err) >> "${logFile}" 2>&1
 
 # watch for any new types of errors
 unexpected=$(egrep -v "OBSOLETE|UPDATE|NEW ALIAS|NOTE" "${logDir}/update.${DS}.err" \
     | egrep -v "ing to browser=[a-z]" \
       | egrep -v "are not case-independent|skipping" \
         | grep ERROR || true)
 if [ -n "${unexpected}" ]; then
     printf '%s\n' "${unexpected}" 1>&2
     echo "unexpected ERROR lines found, aborting before load" 1>&2
     exit 1
 fi
 
 hgLoadSqlTab "${db}" asmAliasUpdate ${TOP}/asmAlias.sql \
    "${updateTsv}" >> "${logFile}" 2>&1
 
 gzip -f "${updateTsv}"
 hgsql "${db}" -e 'DROP TABLE IF EXISTS asmAliasPrev;' >> "${logFile}" 2>&1
 hgsql "${db}" -e "RENAME TABLE asmAlias TO asmAliasPrev, asmAliasUpdate TO asmAlias;" >> "${logFile}" 2>&1
 
 printf "previous asmAlias size:\n" >> "${logFile}" 2>&1
 hgsql -t "${db}" -e 'select count(*) from asmAliasPrev;' >> "${logFile}" 2>&1
 printf "updated asmAlias size:\n" >> "${logFile}" 2>&1
 hgsql -t "${db}" -e 'select count(*) from asmAlias;' >> "${logFile}" 2>&1
 gzip -f "${logFile}" "${logDir}/update.${DS}.out" "${logDir}/update.${DS}.err"
 
 printf "##############################################\n" 1>&2
 printf "### asmAlias update change log ${DS}\n" 1>&2
 zcat "${logFile}.gz" 1>&2
 printf "##############################################\n" 1>&2