105b90ada7157b6cc8cdc005c86322c6711fee76
cath
  Tue Jan 10 14:38:50 2017 -0800
Specifying usage stmnt for hgwbeta instead of beta, no RM

diff --git src/utils/qa/checkMetaData.csh src/utils/qa/checkMetaData.csh
index b055b3e..84f298b 100755
--- src/utils/qa/checkMetaData.csh
+++ src/utils/qa/checkMetaData.csh
@@ -1,206 +1,206 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 ###############################################
 # 
 #  08-25-04
 #  Robert Kuhn
 # 
 #  checks the metadata for a new assembly.
 # 
 ###############################################
 
 set db=""
 set dbTrunc=""
 set metatables="dbDb blatServers defaultDb genomeClade liftOverChain"
 
 if ( $#argv < 1 || $#argv > 3 ) then
   # no command line args
   echo
   echo "  checks the metadata for a new assembly."
   echo
   echo "    usage:  database [machine1 machine2]"
-  echo '        (defaults to dev and beta, or use "RR".)'
+  echo '        (defaults to dev and beta, or use "hgwbeta RR".)'
   echo
   exit
 else
   set db=$argv[1]
   set dbTrunc=`echo $db | sed -e "s/[0-9]*//"`
 endif
 
 # set defaults
 set mach1="hgwdev"
 set mach2="hgwbeta"
 set centdb1="hgcentraltest"
 set centdb2="hgcentralbeta"
 set host1=""
 set host2="-h $sqlbeta"
 
 # check if asssembly database exits on dev.
 set orgCheck=`hgsql -N -e 'SELECT COUNT(*) FROM dbDb WHERE name = "'$db'"' \
   hgcentraltest`
 if ( $orgCheck == 0 ) then
   echo
   echo "  $db is not a valid genome database."
   echo
   exit
 endif
 
 # set machines, if given on command line.
 if ( $#argv == 2 ) then
   echo "\n  please use two machine names.\n"
   echo "${0}:"
   $0
   exit 1
 endif
 
 if ( $#argv == 3 ) then
   set mach1=$argv[2]
   set mach2=$argv[3]
 endif
 
 # set machines to dev where needed
 if ( $mach1 == "hgwdev" ) then
   set centdb1="hgcentraltest"
   set host1=""
 endif
 
 if ( $mach2 == "hgwdev" ) then
   set centdb2="hgcentraltest"
   set host2=""
 endif
 
 # set machines to beta where needed
 if ( $mach1 == "hgwbeta" ) then
   set centdb1="hgcentralbeta"
   set host1="-h $sqlbeta"
 endif
 
 if ( $mach2 == "hgwbeta" ) then
   set centdb2="hgcentralbeta"
   set host2="-h $sqlbeta"
 endif
 
 
 if ( $mach1 == "RR" || $mach1 == "rr" ) then
   set centdb1="hgcentral"
   set host1="-h $sqlrr"
 endif
 
 if ( $mach2 == "RR" || $mach2 == "rr" ) then
   set centdb2="hgcentral"
   set host2="-h $sqlrr"
 endif
 
 # set machines to RR where needed if hgw# format used
 set covered="hgwdev hgwbeta rr RR"
 
 echo $covered | grep -wq "$mach1"
 if ( $status ) then
   checkMachineName.csh $mach1
   if ( $status ) then
     exit 1
   else
     set centdb1="hgcentral"
     set host1="-h $sqlrr"
   endif
 endif
  
 echo $covered | grep -wq "$mach2" 
 if ( $status ) then
   checkMachineName.csh $mach2
   if ( $status ) then
     exit 1
   else
     set centdb2="hgcentral"
     set host2="-h $sqlrr"
   endif
 endif
 
 # echo
 # echo "host1 = $host1"
 # echo "centdb1= $centdb1"
 # echo
 # echo "host2 = $host2"
 # echo "centdb2= $centdb2"
 echo
 
 # make file extention for output
 set out1=`echo $centdb1 | sed -e "s/-h //"`
 set out2=`echo $centdb2 | sed -e "s/-h //"`
 
 # echo "out1 = $out1"
 # echo "out2 = $out2"
 
 # ----------------------------------------------------
 # compare metadata
 
 echo "database = $db"
 echo
 
 # check dbDb
 set metatable="dbDb"
 
 hgsql $host1 -Ne 'SELECT * FROM dbDb WHERE name = "'$db'"' $centdb1 \
   > $metatable.$db.$out1 
 hgsql $host2 -Ne 'SELECT * FROM dbDb WHERE name = "'$db'"' $centdb2  \
   > $metatable.$db.$out2
 
 
 # check blatServers
 set metatable="blatServers"
 
 hgsql $host1 -Ne 'SELECT * FROM blatServers WHERE db = "'$db'"' $centdb1 | sort \
   > $metatable.$db.$out1 
 hgsql $host2 -Ne 'SELECT * FROM blatServers WHERE db = "'$db'"' $centdb2 | sort \
   > $metatable.$db.$out2 
 
 
 # check defaultDb 
 set metatable="defaultDb"
 
 hgsql $host1 -Ne 'SELECT * FROM defaultDb WHERE name LIKE "'$dbTrunc'%"' \
    $centdb1 > $metatable.$db.$out1 
 hgsql $host2 -Ne 'SELECT * FROM defaultDb WHERE name LIKE "'$dbTrunc'%"' \
    $centdb2 > $metatable.$db.$out2 
 
 
 # check liftOverChain
 set metatable="liftOverChain"
 
 hgsql $host1 -Ne 'SELECT * FROM liftOverChain WHERE fromDb = "'$db'" \
   or toDb = "'$db'"' $centdb1 | sort \
   > $metatable.$db.$out1
 hgsql $host2 -Ne 'SELECT * FROM liftOverChain WHERE fromDb = "'$db'" \
   or toDb = "'$db'"' $centdb2 | sort \
   > $metatable.$db.$out2
 
 
 # check genomeClade
 # get genome name for the assembly to query genomeClade table.
 
 set genome=`hgsql -N -e 'SELECT genome FROM dbDb WHERE name = "'$db'"' \
   hgcentraltest`
 
 set metatable="genomeClade"
 
 # get lookup for clade check
 hgsql $host1 -Ne "SELECT * FROM genomeClade WHERE genome='$genome'" \
   $centdb1 | sort > $metatable.$db.$out1 
 hgsql $host2 -Ne "SELECT * FROM genomeClade WHERE genome='$genome'" \
   $centdb2 | sort > $metatable.$db.$out2
  
 set metatable=""
 
 # compare and  print results
 # should replace with commTiro.csh, but for now simply sorting genomeClade above
 foreach table ( `echo $metatables` )
   comm -23 $table.$db.$out1 $table.$db.$out2 > $table.$db.${out1}Only
   comm -13 $table.$db.$out1 $table.$db.$out2 > $table.$db.${out2}Only
   comm -12 $table.$db.$out1 $table.$db.$out2 > $table.$db.common
   wc -l $table.$db.${out1}Only $table.$db.${out2}Only $table.$db.common \
     | gawk '{ printf("%3d %-45s\n", $1, $2) }' \
     | grep -v "total"
   echo
 end