afab2f8e49e5855e3531b34ffc95ea348cedc05b
mspeir
  Wed Jan 29 11:24:03 2020 -0800
Fixing issue with head -1 after the ls causing pipefail. The pipefail trigger was causing the script to exit early and produce no results. The awk command after ls shouldn't have this issue. Also simplifying the method for finding the name of the previous log file. refs #24811

diff --git src/utils/qa/qaAutoTrack.sh src/utils/qa/qaAutoTrack.sh
index 19ecebf..4b31b1d 100755
--- src/utils/qa/qaAutoTrack.sh
+++ src/utils/qa/qaAutoTrack.sh
@@ -199,69 +199,67 @@
 if [[ "$newLogDir" != "" ]]
 then
 	# Set logDir if newLogDir is provided
 	logDir="$newLogDir"
 fi
 if [[ $overwriteLogUrl == true ]]
 then
 	# Overwrite url if option is set
 	logUrl=$logDir
 fi
 
 # set currLogFile
 currLogFile="$db.$tableName.$currDate.$currTime.txt"
 
 # set info for prevLog
-prevLogDate=$(ls -Lt $logDir | sed -n /$db.$tableName/p | head -1 | awk -F . '{print $3}')
-prevLogTime=$(ls -Lt $logDir | sed -n /$db.$tableName/p | head -1 | awk -F . '{print $4}')
+prevLogFile=$(ls -Lt $logDir | sed -n /$db.$tableName/p | awk '(NR==1)')
 
 #initialize output string
 output="\n$db\n"
 
-if [ -e $logDir/$db.$tableName.$prevLogDate.$prevLogTime.txt ]
+if [[ $prevLogFile != "" ]]
 then
-	prevLogFile="$logDir/$db.$tableName.$prevLogDate.$prevLogTime.txt"
+	prevLogFile="$logDir/$prevLogFile"
 fi
 
 # Set tooOld for different tables
 if  [[ "$tableName" == "clinvar" ]]
 then
 	tooOld=$(date -d "$currDate - 2 months" +%F)
 elif [[ "$tableName" == "grcIndcidentDb" ]]
 then
 	tooOld=$(date -d "$currDate - 6 months" +%F)
 else
 	tooOld=$(date -d "$currDate - 1 month" +%F)
 fi
 
 # Run tests for different tracks 
 if [[ $bigBedMode == "on" ]]
 then
 	# ClinVar has muliple tables
 	if [[ $tableName == "clinvar" ]]
 	then
 		for tbl in clinvarMain clinvarCnv
 		do
 			# Get file name from beta
 			fileName=$(hgsql -Ne "SELECT * FROM $tbl LIMIT 1" $db)
 			# Get table update time from beta
 			tblDate=$(ssh qateam@hgwbeta "date -d '$(stat -Lc '%y' $fileName)' +%F' '%T")
 			MYTEMPFILE=$(mktemp --tmpdir tmp.XXXXXXXXXX.bed)
 			# featureBits doesn't work with bigBeds, need to turn into bed first
 			ssh qateam@hgwbeta "/usr/local/apache/cgi-bin/utils/bigBedToBed $fileName stdout" > $MYTEMPFILE
 			tblCov=$(featureBits -countGaps $db $MYTEMPFILE 2>&1)
-
 			outputCovDiff "$prevLogFile" "$tblCov" "$tbl" "$tblDate"
 			# Check for issues with table
 			checkForIssues "$tblDate" "$tooOld" "$tbl" "$percentDiff"
 
 			rm -f $MYTEMPFILE
 		done
 	# Tests for all other bigBed based autopushed tracks (assuming they don't use remote bigBed files)
 	else
 		fileName=$(hgsql -Ne "SELECT * FROM $tableName LIMIT 1" $db)
 		# Get table update time from beta
 		tblDate=$(ssh qateam@hgwbeta "date -d '$(stat -Lc '%y' $fileName)' +%F' '%T")
 		MYTEMPFILE=$(mktemp --tmpdir tmp.XXXXXXXXXX.bed)
 		# featureBits doesn't work with bigBeds, need to turn into bed first
 		ssh qateam@hgwbeta "/usr/local/apache/cgi-bin/utils/bigBedToBed $fileName stdout" > $MYTEMPFILE
 		tblCov=$(featureBits -countGaps $db $MYTEMPFILE 2>&1)