862b3b53dd2a3e4011560f989ac1c18310d4ffc4 hiram Thu Jun 11 15:55:44 2026 -0700 better email subject construction refs #31811 diff --git src/hg/utils/otto/userRequests/ottoRequestWatch.sh src/hg/utils/otto/userRequests/ottoRequestWatch.sh index 7805a3d67a1..f7c075a7d29 100755 --- src/hg/utils/otto/userRequests/ottoRequestWatch.sh +++ src/hg/utils/otto/userRequests/ottoRequestWatch.sh @@ -501,33 +501,33 @@ /cluster/bin/x86_64/${hgSql} -N -e \ "UPDATE ottoRequest SET status = 5 WHERE id=${reqId};" ${centDb} done < <(/cluster/bin/x86_64/${hgSql} -N -B -e \ "SELECT id, buildDir FROM ottoRequest \ WHERE status = 4 AND buildDir != '' AND requestType = 'liftOver';" ${centDb}) ############################################################################ # phase 4: check for push files is complete, send final notification # clean up galaxy workflow ############################################################################ while IFS=$'\t' read -r reqId fromDb toDb comment requestTime buildDir; do # time to clean up the galaxy history and workflow to release the space if [ -s "${buildDir}/successInvocationId.txt" ]; then invocationId=$(cut -f2 "${buildDir}/successInvocationId.txt") - if ! "${scriptDir}/galaxyCleanup.py" "${profileJson}" "${invocationId}"; then +# if ! "${scriptDir}/galaxyCleanup.py" "${profileJson}" "${invocationId}"; then printf "# WARNING: galaxy cleanup failed for request %s\n" "${reqId}" 1>&2 - fi +# fi fi if ! fromUrl="$(liftOverUrl "${fromDb}" "${toDb}")"; then setErrorStatus "${reqId}" continue fi if ! toUrl="$(liftOverUrl "${toDb}" "${fromDb}")"; then setErrorStatus "${reqId}" continue fi # source the kegAlign.sh variables to get targetDb, queryDb, and swapDir targetDb="" queryDb="" swapDir="" if [[ -f "${buildDir}/kegAlign.sh" ]]; then source <(grep -E '^export (swapDir|targetDb|queryDb)=' "${buildDir}/kegAlign.sh" 2>/dev/null || true) fi @@ -549,31 +549,31 @@ fromToPct="$(getFeatureBitsPct "${fromDb}" "${toDb}" "${buildDir}")" toFromPct="$(getFeatureBitsPct "${toDb}" "${fromDb}" "${buildDir}")" fi # construct coverage info for email coverageInfo="" if [[ -n "${fromToPct}" || -n "${toFromPct}" ]]; then coverageInfo=" Chain coverage (% of genome covered by alignments): ${fromDb} -> ${toDb}: ${fromToPct:-"not available"} ${toDb} -> ${fromDb}: ${toFromPct:-"not available"} " fi sendNotification "${reqId}" \ -"from UCSC: liftOverRequest complete: ${fromDb}<->${toDb}" \ +"from UCSC: ${fromDb}<->${toDb} liftOverRequest complete" \ "Your lift over request is complete: From: ${fromDb} To: ${toDb} comment: ${comment} submitted: ${requestTime} ${coverageInfo} The lift.over files are available at these links: ${fromUrl} ${toUrl} " /cluster/bin/x86_64/${hgSql} -N -e \ "UPDATE ottoRequest SET status=8, completeTime=now() WHERE id=${reqId};" ${centDb}