b26ad6e7a08036ee13cd05598e81dbf5111be67d
hiram
  Tue Jul 22 13:22:29 2025 -0700
minimum allowed tracks on bacteria lowered and more categories allow scientific name to come through as the "common name" in the browser for odd categories of archaea and bacteria refs #29545

diff --git src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
index 20d68a3248d..2bc6683a355 100755
--- src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
+++ src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
@@ -1,104 +1,104 @@
 #!/bin/bash
 
 # set -beEu -o pipefail
 
 if [ $# -ne 2 ]; then
   printf "usage: ./verifyOnDownload.sh <host> <subset.orderList.tsv>\n" 1>&2
   printf "where <host> is something like:\n" 1>&2
   printf "api-test.gi.ucsc.edu - to use the hgwdev server\n" 1>&2
   printf "apibeta.soe.ucsc.edu - to use the hgwbeta server\n" 1>&2
   exit 255
 fi
 
 #  printf "usage: ./verifyOnDownload.sh <GCF/012/345/678/GCF_012345678.nn>\n" 1>&2
 #	${toolsDir}/mkSendList.pl ${orderList} | while read F; do \
 #	  ${toolsDir}/verifyOnDownload.sh $$F < /dev/null; done
 
 export host=$1
 export orderList=$2
 export successCount=0
 export doneCount=0
 export fileName=`basename $orderList`
 export subset=${fileName%.orderList.tsv}
 
 export minTrackCount=11
 if [ "${subset}" == "invertebrate" ]; then
   minTrackCount=9
 elif [ "${subset}" == "brc" ]; then
   minTrackCount=6
 elif [ "${subset}" == "bacteria" ]; then
-  minTrackCount=8
+  minTrackCount=7
 elif [ "${subset}" == "legacy" ]; then
   minTrackCount=8
 elif [ "${subset}" == "plants" ]; then
   minTrackCount=10
 elif [ "${subset}" == "birds" ]; then
   minTrackCount=11
 elif [ "${subset}" == "fish" ]; then
   minTrackCount=11
 elif [ "${subset}" == "mammals" ]; then
   minTrackCount=9
 elif [ "${subset}" == "vertebrate" ]; then
   minTrackCount=11
 elif [ "${subset}" == "archaea" ]; then
   minTrackCount=9
 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"
 if [ "${host}" = "apibeta.soe.ucsc.edu" ]; then
   hubSource="hgdownload.soe.ucsc.edu"
 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/${dirPath}/hub.txt" \
       2> /dev/null | python -mjson.tool | egrep ": {$" \
        | 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 \
      | 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}"
   fi
   totalTrackCount=`echo $totalTrackCount $trackCount | awk '{print $1+$2}'`
 hgsql -N -e "select organism,description,\",\",scientificName from dbDb where name=\"$db\";" hgcentraltest | tr "'" '_' | xargs echo | sed -e 's/ ,/,/;'
        ;;
   esac
 
 done
 export failCount=`echo $doneCount $successCount | awk '{printf "%d", $1-$2}'`
 export DS=`date "+%F %T"`
 printf "# checked %3d hubs, %3d success, %3d fail, total tracks: %d, %s\n" "${doneCount}" "${successCount}" "${failCount}" "${totalTrackCount}" "${DS}"