src/utils/qa/checkMetaData.csh 1.14

Index: src/utils/qa/checkMetaData.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/checkMetaData.csh,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/utils/qa/checkMetaData.csh	7 Apr 2008 20:24:43 -0000	1.13
+++ src/utils/qa/checkMetaData.csh	20 Mar 2009 23:39:52 -0000	1.14
@@ -1,221 +1,221 @@
 #!/bin/tcsh
 
 ###############################################
 # 
 #  08-25-04
 #  Robert Kuhn
 # 
 #  checks the metadata for a new assembly.
 # 
 ###############################################
 
 set db=""
 set dbTrunc=""
 set metatables="dbDb blatServers defaultDb gdbPdb genomeClade liftOverChain"
 
 if ( $#argv < 1 || $#argv > 3 ) then
   # no command line args
   echo
   echo "  checks the metadata for a new assembly."
   echo
   echo "    usage:  database [machine1 machine2]"
   echo '        (defaults to dev and beta, or use "RR".)'
   echo
   exit
 else
   set db=$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 hgwbeta"
+set host2="-h hofbeta"
 
 # 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 hgwbeta"
+  set host1="-h hgofbeta"
 endif
 
 if ( $mach2 == "hgwbeta" ) then
   set centdb2="hgcentralbeta"
-  set host2="-h hgwbeta"
+  set host2="-h hgofbeta"
 endif
 
 
 if ( $mach1 == "RR" || $mach1 == "rr" ) then
   set centdb1="hgcentral"
   set host1="-h genome-centdb"
 endif
 
 if ( $mach2 == "RR" || $mach2 == "rr" ) then
   set centdb2="hgcentral"
   set host2="-h genome-centdb"
 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 genome-centdb"
   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 genome-centdb"
   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 gdbPdb
 set metatable="gdbPdb"
 
 hgsql $host1 -Ne 'SELECT * FROM gdbPdb WHERE genomeDb = "'$db'"' $centdb1 \
   > $metatable.$db.$out1 
 hgsql $host2 -Ne 'SELECT * FROM gdbPdb WHERE genomeDb = "'$db'"' $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`
 
 # pull out last word of the find, if in the format "G. species" 
 #    and use LIKE to query genomeClade.
 set secondWord=`echo $genome | gawk -F" " '{print $2}'`
 if ( $secondWord != "" ) then
   set genome=$secondWord
 endif
 
 set metatable="genomeClade"
 
 # get lookup for clade check
 # filter out "/" when it appears in genome name - to avoid e.g, Dog/Human
 hgsql $host1 -Ne 'SELECT * FROM genomeClade WHERE genome LIKE "%'$genome'"' \
   $centdb1 | grep -v "/" > $metatable.$db.$out1 
 hgsql $host2 -Ne 'SELECT * FROM genomeClade WHERE genome LIKE  "%'$genome'"' \
   $centdb2 | grep -v "/" > $metatable.$db.$out2
  
 set metatable=""
 
 # compare and  print results
 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