5adcf6bc2904690de7b7b30a83ec8a7a0996abe9
galt
Tue Aug 21 00:01:25 2018 -0700
changing cse subdomain to soe
diff --git src/utils/qa/trackDbGlobal.csh src/utils/qa/trackDbGlobal.csh
index a5512a6..9486e84 100755
--- src/utils/qa/trackDbGlobal.csh
+++ src/utils/qa/trackDbGlobal.csh
@@ -1,141 +1,141 @@
#!/bin/tcsh
source `which qaConfig.csh`
#######################
#
# 01-23-05
# checks all databases on beta and compares trackDbs.
#
# Robert Kuhn
#
#######################
set machine="hgw1"
set today=""
set dropdir=""
set dirs=""
set diffs=0
set outfile=""
set summaryFile=""
set comment=0
set archived=0
set mode="fast"
if ( $#argv < 1 || $#argv > 2 ) then
echo
echo " checks all databases on RR and compares trackDbs."
echo
echo " usage: RRmachine [realTime | fast]"
echo " - defaults to fast which uses genome-mysql instead of wget"
echo " - uses fast for settings and html fields, even in realTime"
echo " - overwrites file in dev/qa/test-results/trackDb "
echo " if used twice the same day."
echo
exit 1
else
set machine=$argv[1]
endif
if ( $#argv == 2 ) then
set mode="$argv[2]"
if ( $mode == "realTime" ) then
set mode = ""
else
if ( $mode != "fast" ) then
echo '\n mode not "realTime" or "fast"\n'
echo "${0}:"
$0
exit 1
endif
endif
endif
checkMachineName.csh $machine
if ( $status ) then
echo "${0}:"
$0
exit 1
endif
set dbs=`getAssemblies.csh chromInfo hgwbeta \
| egrep -v "getting|found" | egrep "."`
if ( $status ) then
echo $dbs
exit 1
endif
# set file paths and URLs
set today=`date +%Y-%m-%d`
# set today="2005-01-23"
set dirPath="/usr/local/apache/htdocs-genecats/qa/test-results/trackDb"
-set urlPath="http://genecats.cse.ucsc.edu/qa/test-results/trackDb"
+set urlPath="http://genecats.soe.ucsc.edu/qa/test-results/trackDb"
# remove dirs from same month last year
set dropdir=`getMonthLastYear.csh go`
set dirs=`ls -l $dirPath | grep $dropdir | grep ^d | awk '{print $9}'`
foreach dir ( $dirs )
rm -r $dirPath/$dir
end
# make new dir for today's output
mkdir -p $dirPath/$today
set summaryFile=$dirPath/$today/index.html
set summaryUrl=$urlPath/$today/index.html
rm -f $summaryFile
echo "trackDb Diffs $today\n \
\n" >! $summaryFile
echo "db diffs"
echo "-------------"
foreach db ( $dbs )
set todaysPath="$dirPath/$today"
set dbSummaryOut="$db.$machine.trackDbAll"
set dbHtmlOut="$db.$machine.htmlOut"
set outfile="$todaysPath/$dbSummaryOut"
set htmlfile="$todaysPath/$dbHtmlOut"
set active=`hgsql -h $sqlrr -N -e 'SELECT active FROM dbDb \
WHERE name = "'$db'"' hgcentral`
if ( 0 == $active ) then
set comment="staged"
set archived=`hgsql -h $sqlrr -N -e 'SELECT active FROM dbDbArch \
WHERE name = "'$db'"' hgcentral`
if ( 1 == $archived ) then
set comment="archived\n"
endif
echo $db $comment | gawk '{printf "%7s %-10s", $1, $2}'
echo
echo $db $comment | gawk '{printf "%7s %-10s", $1, $2}' >> $summaryFile
echo "\n\n\n" >> $summaryFile
continue
endif
compareTrackDbAll.csh $db hgwbeta $machine $mode >& $outfile
if ( $status ) then
echo "$db dbDbErr" | gawk '{printf "%7s %3s", $1, $2}'
echo
echo ''$db' dbDbErr \n\n' \
>> $summaryFile
else
set diffs=`cat $outfile | egrep " Diff|The diff" | wc -l`
echo "$db $diffs" | gawk '{printf "%7s %2d", $1, $2}'
echo
if ( $diffs == 0 ) then
echo "$db number of diffs:" >> $summaryFile
# rm -f $outfile
else
echo ''$db' number of diffs:' \
>> $summaryFile
tail $outfile | grep "Differences exist in html field" > /dev/null
if (! $status ) then
echo 'html field' >> $summaryFile
endif
endif
echo " $diffs\n" >> $summaryFile
endif
# get output again for html field for display purposes
compareTrackDbFast.csh hgwbeta $machine $db html >& $htmlfile
end
echo "\n
" >> $summaryFile
echo $summaryUrl
exit 0