src/utils/qa/getAssemblies.csh 1.23

Index: src/utils/qa/getAssemblies.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/getAssemblies.csh,v
retrieving revision 1.22
retrieving revision 1.23
diff -b -B -U 1000000 -r1.22 -r1.23
--- src/utils/qa/getAssemblies.csh	13 Apr 2009 19:38:19 -0000	1.22
+++ src/utils/qa/getAssemblies.csh	22 Jan 2010 21:17:19 -0000	1.23
@@ -1,233 +1,233 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 #######################
 #
 #  04-19-04
 #  gets the names of all databases that contain a given table
 #
 #######################
 
 set tablename=""
 set machine="hgwbeta"
 set host="-h $sqlbeta"
 set found=0
 set dbs=""
 set rr="false"
 set dumpDate=""
 set quiet=1
 
+set debug=true
+set debug=false
+
 if ( "$HOST" != "hgwdev" ) then
  echo "\n error: you must run this script on dev!\n"
  exit 1
 endif
 
 if ($#argv < 1 || $#argv > 3) then
   echo
   echo "  gets the names of all databases that contain a given table."
   echo "  will accept the MySQL wildcard, %, but not on RR machines"
   echo "  note: not real-time on RR.  uses nightly TABLE STATUS dump."
   echo
   echo "    usage:  tablename [machine] [verbose] - defaults to beta"
   echo '              "verbose" prints list of assemblies checked'
   echo
   exit
 else
   set tablename=$argv[1]
 endif
 
-set debug=0
-
 # assign command line arguments
 
-set argNum=$#argv
-if ( $argv[$argNum] == "verbose" ) then
+if ( $argv[$#argv] == "verbose" ) then
   set quiet=0
 endif
 
 if (($#argv > 1 && $quiet == 1) || $#argv == 3 ) then
   set machine="$argv[2]"
   if ($argv[2] == "hgwdev") then
     set host=""
   endif
 else
 endif
 
 
-if ($debug == 1) then
-  echo "tablename = $tablename"
-  echo "machine   = $machine"
-  echo "host      = $host"
-  echo "found     = $found"
-  echo "dbs       = $dbs"
-  echo "rr        = $rr"
-  echo "quiet     = $quiet"
-  echo "dumpDate  = $dumpDate"
-  echo
-endif
-
 # check machine validity
 checkMachineName.csh $machine
-
 if ( $status ) then
   echo "${0}:"
   $0
   exit 1
 endif
 
+
 # -------------------------------------------------
 # get all databases
 
 if ($machine == hgwdev || $machine == hgwbeta) then
   set dbs=`hgsql -N $host -e "SHOW DATABASES"`
 else
   set host=""
   set dumpDate=`getRRdatabases.csh $machine | grep "last dump" \
      | gawk '{print $NF}'`
-  set dbs=`getRRdatabases.csh $machine | grep -v "last dump"`
-  set checkMach=`echo $dbs | grep "is not a valid"`
+  set dbs=`getRRdatabases.csh $machine | egrep -v "inform|last dump"`
+  echo $dbs | grep "is not a valid" > /dev/null
   if ( $status == 0 ) then
-    echo "  $dbs"
     echo
     exit 1
   endif
 endif
 
+if ( $debug == "true" ) then
+  echo "tablename = $tablename"
+  echo "machine   = $machine"
+  echo "host      = $host"
+  echo "found     = $found"
+  echo "dbs       = $dbs"
+  echo "rr        = $rr"
+  echo "quiet     = $quiet"
+  echo "dumpDate  = $dumpDate"
+  echo
+endif
+
 # -------------------------------------------------
 # get all assemblies containing $tablename
 
 echo
 echo "getting all assemblies containing $tablename from $machine"
 
 set chrom=""
 set isSplit=""
 set isChromInfo=0
 set splitlist=""
 set notSplitlist=""
 if ( $machine == hgwdev || $machine == hgwbeta ) then
   foreach db ( $dbs )
     if ( $quiet == 0 ) then
       echo "checking "$db
     endif
     # check for chromInfo table
     set isChromInfo=`hgsql -N $host -e 'SHOW TABLES' $db | grep "chromInfo" \
        | wc -l`
 
     # check if split table
     if ( $isChromInfo > 0 ) then
       set chrom=`hgsql -N $host -e 'SELECT chrom FROM chromInfo LIMIT 1' $db`
       set isSplit=`hgsql -N $host -e 'SHOW TABLES LIKE "'${chrom}_$tablename'"' \
         $db | wc -l`
       # echo "  split = $isSplit"
       if ( $isSplit != 0 ) then
         set splitlist=`echo "$splitlist $db"`
       endif
     endif
     # if no chromInfo or if table not split
     set found=`hgsql -N $host -e 'SHOW TABLES LIKE "'$tablename'"' $db | wc -l`
     if ( $found > 0 ) then
       set notSplitlist=`echo "$notSplitlist $db"`
     endif
   end
 else   # not dev or beta
   set rr="true"
   echo $tablename | grep "%" > /dev/null
   if (! $status ) then
     echo "sorry, wildcard not supported for RR machines at this time\n"
     exit 1
   endif
   foreach db ( $dbs )
     if ( $quiet == 0 ) then
       echo "checking "$db
     endif
     # check for chromInfo table on dev 
-    set isChromInfo=1
     hgsql -N $host -e 'SHOW TABLES' $db | grep "chromInfo" > /dev/null
     if ( $status ) then
       set isChromInfo=0
+    else
+      set isChromInfo=1
     endif
     if ( $isChromInfo == 1 ) then
       set chrom=`hgsql -N $host -e 'SELECT chrom FROM chromInfo LIMIT 1' $db` 
       # check if split table (on dev)
       set isSplit=`hgsql -N $host -e 'SHOW TABLES LIKE "'${chrom}_$tablename'"' \
         $db | wc -l`
       if ( $isSplit == 1 ) then
         set found=`getRRtables.csh $machine $db | grep -w "${chrom}_$tablename" \
           | wc -l`
         if ( $found == 1 ) then
           set splitlist=`echo "$splitlist $db"`
         endif
       endif
     endif
     # if no chromInfo or if table not split
     set found=`getRRtables.csh $machine $db | grep -w "$tablename" \
       | wc -l`
     if ( $found == 1 ) then
       set notSplitlist=`echo "$notSplitlist $db"`
     endif
     set isChromInfo=""
   end # end foreach db
 endif # end if if/else dev, beta
 echo 
 
 # report databases found
 set ok=""
 
 #check for wildcard and print tables, too, if so
 echo $tablename | grep -v % > /dev/null
 set isWildcard=$status
 if ( $isWildcard == 0 ) then
   if ( `echo $notSplitlist | awk '{print $1}'` != "" ) then
     set ok=1
     echo "$tablename found in:\n"
     echo $notSplitlist | sed -e "s/ /\n/g"
     echo
   endif
   if ( `echo $splitlist | awk '{print $1}'` != "" ) then
     set ok=1
     echo "split_$tablename found in:\n"
     echo $splitlist | sed -e "s/ /\n/g"
   endif
 else
   # get tablenames for wildcards
   # unsplit first
   if ( `echo $notSplitlist | awk '{print $1}'` != "" ) then
     set ok=1
     echo "$tablename found in:\n"
     foreach db ( $notSplitlist )
       set list=`hgsql -N $host -e 'SHOW TABLES LIKE "'$tablename'"' $db`
       echo $db
         foreach table ( $list )
           echo $table | awk '{printf("   %-65s\n", $1)}'
         end
       echo
     end
     echo
   endif
 
   # split 
   if ( `echo $splitlist | awk '{print $1}'` != "" ) then
     set ok=1
     echo "split_$tablename found in:\n"
     foreach db ( $splitlist )
       set chrom=`hgsql -N $host -e 'SELECT chrom FROM chromInfo LIMIT 1' $db`
       set list=`hgsql -N $host -e 'SHOW TABLES LIKE "'${chrom}_$tablename'"' $db`
       echo $db
         foreach table ( $list )
           echo $table | awk '{printf("   %-65s\n", $1)}'
         end
       echo
     end
     echo
   endif
 endif
 
 if ( $ok != 1 ) then
   echo "neither $tablename nor split_$tablename are found on $machine"
 endif
 
 if ( $rr == "true" ) then
   echo "  as of last TABLE STATUS dump, $dumpDate"
   echo 
 endif
 echo