src/utils/qa/checkGbdb.csh 1.6

Index: src/utils/qa/checkGbdb.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/checkGbdb.csh,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/utils/qa/checkGbdb.csh	20 Mar 2009 23:46:19 -0000	1.5
+++ src/utils/qa/checkGbdb.csh	24 Mar 2009 19:10:43 -0000	1.6
@@ -1,116 +1,116 @@
 #!/bin/tcsh
 
 ####################
 #  07-09-04 Bob Kuhn
 #
 #  Script to check for /gbdb sync
 #
 ####################
 
 set filePath=""
 set db=""
 set errFlag=0
 set debug="true"
 set debug="false"
 
 if ($#argv != 1) then
   echo
   echo "  script to check for /gbdb sync."
   echo "    checks only active assemblies."
   echo "    ignores scaffolds unless a db that uses them is specified."
   echo "    ignores: description genbank axtNetDp1 ci1 zoo."
   echo
   echo '      usage:  database or path (will use "all")'
   echo
   exit
 else
   set filePath=$argv[1]
   set outpath=`echo $filePath | sed -e 's/\//./'`
   set db=`echo $filePath | sed -e 's/\/.*//'`
 endif
 
 set output=$outpath.gbdb.out
 set output2=$outpath.gbdb.list
 
 rm -f $output
 rm -f $output2
 
 # get assembly list from beta
-hgsql -h hgofbeta -N -e "SELECT name FROM dbDb" hgcentralbeta \
+hgsql -h hgwbeta -N -e "SELECT name FROM dbDb" hgcentralbeta \
    | sort | grep -v ci1 | grep -v zoo  > xxAssembliesxx
 echo "all" >> xxAssembliesxx
 
 # error checking for db name on command line
 set dbFlag=0
 foreach assembly (`cat xxAssembliesxx`)
   # echo $assembly
   if ($db == "$assembly") then
     set dbFlag=1
     break
   endif
 end
 
 if ($dbFlag == "0") then
   echo '\n'$db' is not an active assembly. try another assembly name, or "all"'
   echo
   exit
 endif
 
 # get the files from beta
 rm -f xxDirlistxx
 if ($db == "all") then
   foreach assembly (`cat xxAssembliesxx | grep -v "all"`)
     ssh hgwbeta find /gbdb/$assembly -type f -print | grep -vi Scaffold \
          | grep -v description | grep -v genbank \
          | grep -v axtNetDp1   >> xxDirlistxx
   end
   echo "no assemblies with scaffolds are checked\n" >> $output
 else
   if (-e /gbdb/$filePath) then
     ssh hgwbeta find /gbdb/$filePath -type f -print \
          | grep -v description > xxDirlistxx
   else
     echo "\ndirectory /gbdb/$filePath does not exist\n"
     exit
   endif
 endif
 
 
 # compare the files from beta on dev
 set errFlag=0
 foreach file (`cat xxDirlistxx`)
   # echo $file
   if (-e $file) then
     set dev=`ls -ogL $file`
   else
     set dev=""
   endif
   set beta=`ssh hgwbeta ls -og $file`
   if ("$dev" != "$beta") then
     echo $dev >> $output2
     set errFlag=1
     echo ". $dev" >> $output
     echo ". $beta" >> $output
     echo "-------------------------" >> $output
   endif
 
   if ($debug == "true") then
     echo $file
     echo "dev  = $dev"
     echo "beta = $beta"
     echo "-------------------------"
     echo
   endif
 end
 
 # output only if problem is found
 if ($errFlag == "1") then
   cat $output 
 else
   echo "\n  all /gbdb files match on dev and hgnfs1 for $db.\n"
   rm -f $output
 endif
 
 # clean up
 rm -f xxDirlistxx
 rm -f xxAssembliesxx