60a0b6cb901a9d420c748f4dede149803dcf5a3d
rhead
  Thu Sep 22 19:41:51 2011 -0700
Simplified checkGbdbDiffs.csh so that it looks for missing files in all of /gbdb instead of a subset. This was prompted by a daily cron job error on an assembly with an entry in the dbDb table but no matching /gbdb directory. Removing getGbdbBeta.csh, as it was only called by checkGbdbDiffs.csh. Read more of my ramblings in Redmine #402.
diff --git src/utils/qa/checkGbdbDiffs.csh src/utils/qa/checkGbdbDiffs.csh
index a822e08..cbe4ae8 100755
--- src/utils/qa/checkGbdbDiffs.csh
+++ src/utils/qa/checkGbdbDiffs.csh
@@ -1,77 +1,75 @@
 #!/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 "  script to check for missing /gbdb files after reboot."
   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-genecats/qa/test-results/gbdb"
 set urlpath="http://genecats.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
+  ssh hgwbeta find /gbdb -type f -print | sort > $outpath/gbdb.all.$todayDate
 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
+