src/utils/qa/compareTrackDbAll.csh 1.22

Index: src/utils/qa/compareTrackDbAll.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/compareTrackDbAll.csh,v
retrieving revision 1.21
retrieving revision 1.22
diff -b -B -U 1000000 -r1.21 -r1.22
--- src/utils/qa/compareTrackDbAll.csh	6 May 2009 17:33:18 -0000	1.21
+++ src/utils/qa/compareTrackDbAll.csh	8 Jun 2009 22:58:07 -0000	1.22
@@ -1,131 +1,131 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 
 ###############################################
 #  09-16-04
 #  Robert Kuhn
 #
 #  Checks all fields (except html) in trackDb
 ###############################################
 
 if ($#argv < 1 || $#argv > 4) then
   echo ""
   echo "  checks all fields in trackDb"
   echo
   echo "    usage: database [machine1] [machine2] [mode] "
   echo
   echo "      (defaults to hgw1 and hgwbeta)"
   echo "      mode = (fast | verbose | fastVerbose) "
   echo "       - verbose is for html field - defaults to terse"
-  echo "       - fast = (mysql-genome) - defaults to realTime (WGET)"
+  echo "       - fast = (genome-mysql) - defaults to realTime (WGET)"
   echo 
   exit 1
 endif
 
 #set machine1 = "hgwdev"
 set machine1 = "hgw1"
 set machine2 = "hgwbeta"
 set inputMode=""
 set mode="terse"
 set mode2="realTime"
 
 set db = $argv[1]
 if ( $#argv > 2 ) then
   set machine1 = $argv[2]
   set machine2 = $argv[3]
 endif
 
 if ( $#argv == 2 ) then
   set inputMode = $argv[2]
 endif
 
 if ( $#argv == 4 ) then
   set inputMode = $argv[4]
 endif
 
 # confirm that choice of mode is acceptable
 if (! ( $inputMode == "fast" || $inputMode == "fastVerbose" \
         || $inputMode == "verbose" || $inputMode == "" )) then
     echo
     echo "  mode ($inputMode) not acceptable.\n"
     echo "${0}:"
     $0
     exit 1
   endif
 endif
 
 if ( $inputMode == "verbose" || $inputMode == "fastVerbose" ) then
   set mode = "verbose" 
 endif
 
 if ( $inputMode == "fast" || $inputMode == "fastVerbose" ) then
   set mode2 = "fast" 
 endif
 
 foreach mach ( $machine1 $machine2 )
   checkMachineName.csh $mach
   if ( $status ) then
     echo "${0}:"
     $0
     exit 1
   endif
 end
 
 set table = "trackDb"
 set fields=`hgsql -N -e "DESC $table" $db | gawk '{print $1}' | grep -vw "html"`
 if ( $status ) then
   echo  
   echo "  query failed.  check database name."
   echo  
   exit 1
 endif
 
 
 foreach field ( $fields )
   if ( $mode2 == "fast" || $field == "settings" ) then
     # echo "\n mode2 = $mode2"
     # echo "field  = $field"
     compareTrackDbFast.csh $machine1 $machine2 $db $field
     if ( $status ) then
       exit 1
     endif
     echo "  not real time for $field for RR results."
   else
     # echo "\n mode2 = $mode2"
     # echo "field  = $field"
     compareTrackDbs.csh $machine1 $machine2 $db $field
     if ( $status ) then
       exit 1
     endif
   endif
 end
 
 set field="html"
 if ( $mode == "terse" ) then
   # expecting one of these two types of output from compareTrackDbFast.csh:
   # hg17.trackDb.html : Differences exist between hgw1 and hgwbeta
   # hg17.trackDb.html : No differences between hgw1 and hgw2
 
   set diffLine=`compareTrackDbFast.csh $machine1 $machine2 $db $field \
      | grep -i differences`
   echo $diffLine | grep "exist between $machine1" > /dev/null 
   if ( $status ) then  # errStatus of 1 says there are no diffs
   # DO NOT CHANGE this output, unless you want to change trackDbGlobal parsing, too.
     echo
     echo "  No differences in $field field"
     echo
   else
     echo
     echo "  Differences exist in $field field"
     echo
   endif
 else
   # mode is verbose: spew results to stdout 
   echo
   compareTrackDbFast.csh $machine1 $machine2 $db $field 
   echo "  not real time for $field for RR results."
   echo
 endif
 
 exit 0