d7d1c06cce94bfb5abced6d45f2f6ad3e2dbd2db
hiram
  Wed Dec 29 12:47:26 2021 -0800
updated scripts to tolerate database assemblies in the listings no redmine

diff --git src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
index bf03807..45a8e30 100755
--- src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
+++ src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
@@ -7,49 +7,58 @@
   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 dbHost="localhost"
 export hubSource="hgdownload-test.gi.ucsc.edu"
 if [ "${host}" = "apibeta.soe.ucsc.edu" ]; then
   hubSource="hgdownload.soe.ucsc.edu"
 fi
 
 for dirPath in `~/kent/src/hg/makeDb/doc/asmHubs/mkSendList.pl "${orderList}"`
 do
   ((doneCount=doneCount+1))
 
   export genome=`basename $dirPath`
 
-#   hubCount=`wget -O- https://hgdownload.soe.ucsc.edu/hubs/${dirPath}/hub.txt 2> /dev/null | wc -l`
-# if [ "${hubCount}" -lt 200 ]; then
-#   printf "%d\t%s\tWARNING\n" "${hubCount}" "${dirPath}"
-# fi
-# else
-#  printf "%d\t%s/hub.txt line count\n" "${hubCount}" "${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 [ "${trackCount}" -gt 14 ]; then
     ((successCount=successCount+1))
   fi
   printf "%03d\t%s\t%d tracks:\t" "${doneCount}" "${genome}" "${trackCount}"
   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;'
-# fi
+       ;;
+     *)
+       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 14 ]; then
+    ((successCount=successCount+1))
+  fi
+  printf "%03d\t%s\t%d tracks:\t" "${doneCount}" "${db}" "${trackCount}"
+hgsql -N -e "select organism,description,\",\",scientificName from dbDb where name=\"$db\";" hgcentraltest | tr "'" '_' | xargs echo | sed -e 's/ ,/,/;'
+       ;;
+  esac
 
 done
 export failCount=`echo $doneCount $successCount | awk '{printf "%d", $1-$2}'`
 printf "# checked %3d hubs, %3d success, %3d fail\n" "${doneCount}" "${successCount}" "${failCount}"