src/utils/qa/checkGbdbDiffs.csh 1.7

Index: src/utils/qa/checkGbdbDiffs.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/checkGbdbDiffs.csh,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/utils/qa/checkGbdbDiffs.csh	17 Sep 2007 23:41:41 -0000	1.6
+++ src/utils/qa/checkGbdbDiffs.csh	11 Apr 2009 00:37:01 -0000	1.7
@@ -1,76 +1,77 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 ####################
 #  06-20-05 Bob Kuhn
 #
 #  Script to check /gbdb files that might have been lost after reboot.
 #
 ####################
 
 set filePath=""
 set db=""
 set errFlag=0
 set mode=""
 set debug="true"
 set debug="false"
 
 if ($#argv != 1) then
   echo
   echo "  script to check for most /gbdb files missing after reboot."
   echo "    checks assemblies and hgFixed."
   echo "    checks for missing files on hgnfs1."
   echo "    uses existing list of /gbdb files - in dev:qa/test-results."
   echo "    ignores scaffolds, axtNetDp1, ci1, zoo, /sacCer1/sam."
   echo
   echo '      usage:  go|override'
   echo '        where "override" regenerates the file for today'
   echo
   exit
 endif
 
 set mode=$argv[1]
 
 if ($mode != "go" && $mode != "override") then
   echo '\n  the only way to run this is to use "go" or "override" \
        on the command line.'
   echo "\n${0}:"
   $0
   exit 0
 endif
 
 set todayDate=`date +%Y%m%d`
 set outpath="/usr/local/apache/htdocs/qa/test-results/gbdb"
 set urlpath="http://hgwdev.cse.ucsc.edu/qa/test-results/gbdb"
 
 # get the two files to compare or create if none for today
 if ($mode == "override" ) then
   rm -f $outpath/gbdb.all.$todayDate
 endif
 
 if (! -e $outpath/gbdb.all.$todayDate) then
   getGbdbBeta.csh all > /dev/null
 endif
 
 set twoFiles=`ls -ltr $outpath | grep all | tail -2 | awk '{print $NF}'`
 set file1=`echo $twoFiles | awk '{print $1}'`
 set file2=`echo $twoFiles | awk '{print $2}'`
 echo "files: $file1 $file2\n" > $outpath/gbdbDiff.$todayDate
 diff $outpath/$file1 $outpath/$file2 >> $outpath/gbdbDiff.$todayDate
 if ( $status ) then
   set lost=`grep "<" $outpath/gbdbDiff.$todayDate | wc -l`
   set  new=`grep ">" $outpath/gbdbDiff.$todayDate | wc -l`
   echo
   echo "  $lost files lost"
   echo "  $new new files"
   echo " see: $urlpath/gbdbDiff.$todayDate"
   echo
 else
   rm -f $outpath/gbdbDiff.$todayDate
   echo "\n  files match: $file1 $file2\n"
 endif
 
 # remove files a year old
 set lastYear=`getMonthLastYear.csh go | sed "s/-//"`
 rm -f $outpath/gbdb*${lastYear}*
 
 exit