Index: src/utils/qa/compareTrackDbFast.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/compareTrackDbFast.csh,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/utils/qa/compareTrackDbFast.csh	24 Mar 2009 19:10:44 -0000	1.6
+++ src/utils/qa/compareTrackDbFast.csh	11 Apr 2009 00:37:02 -0000	1.7
@@ -1,142 +1,143 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 if ($#argv < 3 || $#argv > 4) then
  echo ""
  echo "  compares trackDb on two machines."
  echo "  optionally compares another field instead of tableName."
  echo "  uses MySQL query for speed, not WGET."
  echo "  uses public mysql machine for RR queries."
  echo
  echo "    usage: machine1 machine2 database [field] (defaults to tableName)"
  echo ""
  exit 1
 endif
 
 #set machine1 = "hgwdev"
 #set machine1 = "hgwbeta"
 #set machine2 = "hgw1"
 
 set machine1 = $argv[1]
 set machine2 = $argv[2]
 set db = $argv[3]
 set cent=""
 set host=""
 
 # check validity of machine name and existence of db on the machine
 foreach machine ( $machine1 $machine2 )
   checkMachineName.csh $machine
   if ( $status ) then
     echo ${0}:
     $0
     exit 1
   endif
   if ( $machine == "hgwdev" ) then
     set cent="test"
     set host=""
   else
     if ( $machine == "hgwbeta" ) then
       set cent="beta"
-      set host="-h hgwbeta"
+      set host="-h $sqlbeta"
     else
       set cent=""
       set host="-h genome-centdb"
     endif
   endif
   hgsql -N $host -e "SELECT name FROM dbDb" hgcentral$cent | grep "$db" >& /dev/null
   if ( $status ) then
     echo
     echo "  database $db is not found on $machine"
     echo
     echo ${0}:
     $0
     exit 1
   endif
   
 end
 
 set table = "trackDb"
 set field = "tableName"
 
 if ( $#argv == 4 ) then
   # check if valid field -- checks on dev"
   set field = $argv[4]
   hgsql -t -e "DESC $table" $db | grep -w $field > /dev/null
   if ( $status ) then
     echo
     echo "  $field is not a valid field for $table"
     echo
     echo ${0}:
     $0
     exit 1
   endif
 endif
 
 # check individual html longBlobs one at a time and make pretty output
 # using list of tracks from beta
 # for html and settings fields, using public mysql server 
 # -- not RR node-specific
 set pubMySqlFlag=0
 set tableRow=""
 if ( $field == "html" || $field == "settings" ) then
   rm -f $machine1.$db.$table
   rm -f $machine2.$db.$table
-  set tracks=`hgsql -N -h hgwbeta -e "SELECT tableName FROM trackDb" $db`
+  set tracks=`hgsql -N -h $sqlbeta -e "SELECT tableName FROM trackDb" $db`
   foreach row ( $tracks )
     set tableRow=$row
     foreach machX ( $machine1 $machine2 )
       if ( $machX == "hgwbeta" ) then
-        hgsql -h hgwbeta -e 'SELECT '$field' FROM trackDb \
+        hgsql -h $sqlbeta -e 'SELECT '$field' FROM trackDb \
           WHERE tableName = "'$tableRow'"' $db > $machX.$db.$table.$field
       else
         set pubMySqlFlag=1
         mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
           -e 'SELECT '$field' FROM trackDb \
           WHERE tableName = "'$tableRow'"' $db > $machX.$db.$table.$field
       endif
       cat $machX.$db.$table.$field | perl -pw -e "s/\\n/\n/g" \
           | sed -e "s/^/${tableRow} \| /" >> $machX.$db.$table
       rm -f $machX.$db.$table.$field
     end
   end
 
 else
 
   foreach mach ( $machine1 $machine2 )
     rm -f $mach.$db.$table 
     if ( $mach == "hgwbeta" ) then
-      hgsql -h hgwbeta -e 'SELECT '$field' FROM trackDb' $db \
+      hgsql -h $sqlbeta -e 'SELECT '$field' FROM trackDb' $db \
          > $mach.$db.$table
     else
       set pubMySqlFlag=1
       mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
         -e "SELECT $field FROM trackDb"  $db > $mach.$db.$table
     endif
   end
 endif
 
 # DO NOT CHANGE this output, unless you want to change all of the following, too:
 # compareTrackDbs.csh
 # compareTrackDbAll.csh
 # trackDbGlobal.csh
   
 echo
 echo "---------------------------------------------------------------"
 echo 
 # if the line begins with a digit, substitute a newline at the beginning
 # | perl -pw -e "s/^(\d)/\nx/"
 diff $machine1.$db.$table $machine2.$db.$table | sed -e "/^[0123456789]/s/^/\n/" >& $db.temp
 if ( $status ) then
   echo "\n$db.$table.$field : Differences exist between $machine1 and $machine2 \n"
   if ( $pubMySqlFlag == 1 ) then
     echo "(RR fields taken from public MySql server, not individual machine)"
   endif
   cat $db.temp
   echo
 else
   echo "\n$db.$table.$field : No differences between $machine1 and $machine2 \n"
 endif
 
 # clean up
 rm -f $machine1.$db.$table 
 rm -f $machine2.$db.$table 
 rm -f $db.temp 

