55fcac8a40acd4e41d0bcdff1c878f7214a58d6d hiram Sun May 3 13:20:45 2026 -0700 should be cron quiet now on no error conditions refs #31811 diff --git src/hg/utils/otto/userRequests/ottoRequestWatch.sh src/hg/utils/otto/userRequests/ottoRequestWatch.sh index 2d9fe3f6c56..ad67f1b6422 100755 --- src/hg/utils/otto/userRequests/ottoRequestWatch.sh +++ src/hg/utils/otto/userRequests/ottoRequestWatch.sh @@ -210,37 +210,37 @@ mkdir -p "${gbdbLiftOverDir}" "${gbdbQuickLiftDir}" rm -f "${gbdbLiftOverDir}/${over}" rm -f "${gbdbQuickLiftDir}/${quick}.bb" rm -f "${gbdbQuickLiftDir}/${quick}.link.bb" ln -s "${quickBb}" "${gbdbQuickLiftDir}/${quick}.bb" ln -s "${quickLinkBb}" "${gbdbQuickLiftDir}/${quick}.link.bb" ln -s "${liftOverDir}/${over}" "${gbdbLiftOverDir}/${over}" chainPath="${gbdbLiftOverDir}/${over}" quickPath="${gbdbQuickLiftDir}/${quick}.bb" fi # register both rows in hgcentraltest if ! /cluster/bin/x86_64/hgAddLiftOverChain -minMatch=0.1 -multiple \ - -path="${chainPath}" "${tDb}" "${qDb}"; then + -path="${chainPath}" "${tDb}" "${qDb}" > /dev/null 2>&1; then printf "ERROR: installLinks: hgAddLiftOverChain failed for %s -> %s\n" \ "${tDb}" "${qDb}" 1>&2 return 1 fi if ! "${HOME}/kent/src/hg/utils/automation/addQuickLift.py" \ - "${tDb}" "${qDb}" "${quickPath}"; then + "${tDb}" "${qDb}" "${quickPath}" > /dev/null 2>&1; then printf "ERROR: installLinks: addQuickLift.py failed for %s -> %s\n" \ "${tDb}" "${qDb}" 1>&2 return 1 fi return 0 } ############################################################################## ############################################################################## ### refresh Galaxy queue status snapshot for ottoRequestView.cgi ############################################################################## export galaxyStatusFile="/data/apache/trash/ottoRequestGalaxyStatus.json" export profileJson="${HOME}/.planemo/profiles/vgp/planemo_profile_options.json" gsTmp=$(mktemp "${galaxyStatusFile}.XXXXXX") if timeout 45 "${scriptDir}/galaxyStatus.py" "${profileJson}" > "${gsTmp}" 2>/dev/null; then @@ -314,38 +314,38 @@ export swapWork="$(basename "${swapDir}")" export doTdb="`dirname ${trackData}`/doTrackDb.bash" export swapTdb="`dirname ${swapData}`/doTrackDb.bash" if [ ! -x "${doTdb}" ]; then printf "ERROR: can not find %s\n" "${doTdb}" 1>&2 setErrorStatus "${reqId}" continue fi if [ ! -x "${swapTdb}" ]; then printf "ERROR: can not find %s\n" "${swapTdb}" 1>&2 setErrorStatus "${reqId}" continue fi rm -f "${trackData}/lastz.${queryDb}" ln -s "${workDir}" "${trackData}/lastz.${queryDb}" - if ! ${doTdb} 1>&2; then + if ! ${doTdb} > /dev/null 2>&1; then printf "ERROR: %s failed\n" "${doTdb}" 1>&2 setErrorStatus "${reqId}" continue fi rm -f "${swapData}/lastz.${targetDb}" ln -s "${swapWork}" "${swapData}/lastz.${targetDb}" - if ! ${swapTdb} 1>&2; then + if ! ${swapTdb} > /dev/null 2>&1; then printf "ERROR: %s failed\n" "${swapTdb}" 1>&2 setErrorStatus "${reqId}" continue fi # install liftOver and quickLift symlinks + register in hgcentraltest, # for both directions if ! installLinks "${targetDb}" "${queryDb}" "${buildDir}"; then setErrorStatus "${reqId}" continue fi if ! installLinks "${queryDb}" "${targetDb}" "${swapDir}"; then setErrorStatus "${reqId}" continue fi