src/utils/qa/doGenbankTests 1.8

Index: src/utils/qa/doGenbankTests
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/doGenbankTests,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 4 -r1.7 -r1.8
--- src/utils/qa/doGenbankTests	22 Apr 2009 03:30:47 -0000	1.7
+++ src/utils/qa/doGenbankTests	14 May 2009 01:03:15 -0000	1.8
@@ -8,10 +8,9 @@
 #  Note: this script assumes the kent source tree is checked out in ~/kent/src
 # 
 ###############################################################################
 
-tableExists()
-{
+tableExists() {
   local db=$1 table=$2
   local res=$(hgsql -Ne "show tables like '$table'" $db)
   if [ -z "$res" ]
   then
@@ -20,10 +19,9 @@
     return 0
   fi
 }
 
-databaseExists()
-{
+databaseExists() {
   local db=$1
   local res=$(hgsql -Ne "show databases like '$db'")
   if [ -z "$res" ]
   then
@@ -32,14 +30,26 @@
     return 0
   fi
 }
 
-getShortLabel()
-{
+selectShortLabel() {
   local db=$1 table=$2
   hgsql -NBe "select shortLabel from trackDb where tableName='$table'" $db
 }
 
+getShortLabel() {
+  local db=$1 table=$2
+  local res=$(selectShortLabel $db $table)
+  if [ -z "$res" -a "$table" = "all_mrna" ] 
+  then
+    res=$(selectShortLabel $db mrna)
+  elif [ -z "$res" -a "$table" = "all_est" ] 
+  then
+    res=$(selectShortLabel $db est)
+  fi
+  echo $res
+}
+
 allOk=yes
 
 # check host, set path to genbank table list
 if [ "$HOST" != hgwdev -a "$HOST" != hgwbeta ]
@@ -83,9 +93,9 @@
 echo -e "The following GenBank tracks are present in this assembly:\n"
 for table in refGene xenoRefGene mgcFullMrna orfeomeMrna \
              all_mrna intronEst all_est xenoMrna xenoEst
 do
-  tableExists $db && getShortLabel $db $table
+  tableExists $db $table && getShortLabel $db $table
 done
 echo
 
 # run genePredChecks and pslChecks
@@ -134,13 +144,13 @@
 echo
 
 # run gbSanity
 filename=${db}.sanity.$(date +%m.%d.%Y-%R%p)
-echo -e "--> Running gbSanity, and putting output in:\n"
+echo -e "--> Running gbSanity, and putting output in:"
 echo -e "${HOST}:$sanityPath/misc/$filename"
 # need to run in a subshell, since gbSanity wants to be run from this dir
 (cd $sanityPath && bin/x86_64/gbSanity $db >& misc/$filename) || allOk=no
-echo -e "\nHere is the last line of that file:\n"
+echo -e "Here is the last line of that file:\n"
 tail -1 $sanityPath/misc/$filename
 echo -e "\nIf there are any errors here, consult Mark Diekhans.\n"
 
 # run featureBits