78a47c721e9903c1f1f879ebbcf7bef4a8038ee7 hiram Fri Feb 13 15:48:51 2026 -0800 properly test tracks on hgwdev from their /gbdb/genark hubs location refs #37109 diff --git src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh index 500650acb39..2bca4feffcf 100755 --- src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh +++ src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh @@ -39,56 +39,56 @@ elif [ "${subset}" == "mammals" ]; then minTrackCount=9 elif [ "${subset}" == "vertebrate" ]; then minTrackCount=11 elif [ "${subset}" == "archaea" ]; then minTrackCount=8 elif [ "${subset}" == "fungi" ]; then minTrackCount=10 elif [ "${subset}" == "viral" ]; then minTrackCount=6 fi # printf "# DBG subset '%s' min: %d\n" "${subset}" "${minTrackCount}" 1>&2 export dbHost="localhost" -export hubSource="hgdownload-test.gi.ucsc.edu" +export hubSource="/gbdb/genark" if [ "${host}" = "apibeta.soe.ucsc.edu" ]; then - hubSource="hgdownload.soe.ucsc.edu" + hubSource="https://hgdownload.soe.ucsc.edu/hubs" fi export totalTrackCount=0 for dirPath in `~/kent/src/hg/makeDb/doc/asmHubs/mkSendList.pl "${orderList}"` do ((doneCount=doneCount+1)) export genome=`basename $dirPath` case $genome in GC*) - trackCount=`curl -L "https://$host/list/tracks?genome=$genome;trackLeavesOnly=1;hubUrl=https://$hubSource/hubs/${dirPath}/hub.txt" \ + trackCount=`curl -L "https://$host/list/tracks?genome=$genome;trackLeavesOnly=1" \ 2> /dev/null | python -mjson.tool | egrep ": {$" \ | tr -d '"' | sed -e 's/^ \+//; s/ {//;' | xargs echo | wc -w` if [ "${trackCount}" -gt "${minTrackCount}" ]; then ((successCount=successCount+1)) printf "%03d\t%s\t%d tracks:\t" "${doneCount}" "${genome}" "${trackCount}" else printf "%03d\t%s\t%d (error <= %d) tracks:\t" "${doneCount}" "${genome}" "${trackCount}" "${minTrackCount}" fi totalTrackCount=`echo $totalTrackCount $trackCount | awk '{print $1+$2}'` - curl -L "https://$host/list/hubGenomes?hubUrl=https://$hubSource/hubs/${dirPath}/hub.txt" 2> /dev/null \ + curl -L "https://$host/list/hubGenomes?hubUrl=$hubSource/${dirPath}/hub.txt" 2> /dev/null \ | python -mjson.tool | egrep "organism\":|description\":" | sed -e "s/'/_/g;" \ | tr -d '"' | xargs echo \ | sed -e 's/genomes: //; s/description: //; s/organism: //; s/{ //g;' ;; *) db=`echo $genome | tr -d '_'` trackCount=`curl -L "https://$host/list/tracks?genome=$db;trackLeavesOnly=1" \ 2> /dev/null | python -mjson.tool | egrep ": {$" \ | egrep -v '"'$db'":' | tr -d '"' \ | sed -e 's/^ \+//; s/ {//;' | xargs echo | wc -w` if [ "${trackCount}" -gt "${minTrackCount}" ]; then ((successCount=successCount+1)) printf "%03d\t%s\t%d tracks:\t" "${doneCount}" "${db}" "${trackCount}" else printf "%03d\t%s\t%d (error < %d) tracks:\t" "${doneCount}" "${db}" "${trackCount}" "${minTrackCount}"