fb895c82bef394408aff9fa5ce3008daa4cee6e3
mspeir
  Wed Jul 31 12:16:46 2019 -0700
Fixed an issue with qaAutoTrack not properly checking date for grcIncidentDb tracks. Bumped up tooOld date for grcIncidentDb tracks to 6 months since updates seem to come infrequently from GRC. Fixed issue with runQaAutoTrack not deleting old log files. Added checks for grcIncidentDb track on danRer10 and galGal5. Removed check for danRer7 as GRC site does not seem to have data for this assembly anymore. no redmine

diff --git src/utils/qa/runQaAutoTrack.sh src/utils/qa/runQaAutoTrack.sh
index 6fde56f..e80f394 100755
--- src/utils/qa/runQaAutoTrack.sh
+++ src/utils/qa/runQaAutoTrack.sh
@@ -1,117 +1,118 @@
 #!/bin/bash
 # quit if something within the script fails
 set -beEu -o pipefail
 source `which qaConfig.bash`
 umask 002
 
 ################################
 #
 #  01-13-2017
 #  Matthew Speir
 #
 #  runQaAutoTrack.sh
 #  Runs script bin/qaAutoTrack.sh for 
 #  various autopushed tracks
 #
 #  Runs day after track is supposed
 #  to be updated for most tracks
 #
 ################################
 
 # Set current day of the week
 # Needed to determine which tracks to test
 dayOfWeek=$(date +%A)
 # Set date used to delete logs older than this. 
 # Currently set to 6mo ago
 logTooOld=$(date --date="-6 months" +%F)
 # Where qaAutoTrack is placing the results
 logDir=""
 
 usage="""
 Runs script qaAutoTrack.sh for various autopushed tracks.\nWill
 remove log files older than six months from log directory\nfor
 qaAutoTrack.sh. Log directory defaults to\n
 /usr/local/apache/htdocs-genecats/qa/test-results/qaAutoTrackLogs
 \n\n
 usage:`basename $0` go logDirectory
 \n\nlogDirectory is directory where output files are being placed\nby
 qaAutoTrack.sh if it's different that the default listed above.\n
 """
 # Print really basic usage statement
 if (( $# < 1 )) || (( $# > 2 ))
 then
 	echo -e $usage
 	exit 1
 elif (( $# == 1 ))
 then
         runScript=$1
 elif (( $# == 2 ))
 then
 	# Check if logDirectory exists
 	if [ -d $2 ]
 	then
         	runScript="$1"
 		logDir="$2"
 	else
 		echo -e "Sorry, directory \"$2\" does not exist. "
 		echo -e "Check spelling or create this directory and try again.\n"
 		exit 1
 	fi
 fi
 
 if [[ $logDir == "" ]]
 then
 	logDir="/usr/local/apache/htdocs-genecats/qa/test-results/qaAutoTrackLogs"
 fi
 
 # Print usage statement if the supplied argument isn't "go"
 if [[ $runScript != "go" ]]
 then
 	echo -e $usage
 	exit 1
 # Run qaAutoTrack.sh for different tracks depending on the day of the week
 else
 	if [ -e  "$logDir/*.txt" ]
 	then
-		# Identify log files that are greater than 6 months old
-		# $1, $2, $3, and $4 are the db, table, date, and time respectively
+		# Identify log files that are greater than 6 months old.
+		# $1, $2, $3, and $4 are the db, table, date, and time respectively.
+		# $5 is the file extension (txt).
 		oldLogFiles=$(ls $logDir/*.txt | awk -v ymdOld=$logTooOld -F'.' '$3 <= ymdOld {print $1"."$2"."$3"."$4"."$5}')
 		# Remove these old log files
 		# Prevents log file directory from becoming overstuffed with files
 		for file in $(echo $oldLogFiles)
 		do
-			rm $file.txt
+			rm $file
 		done
 	fi
 
 	if [[ $dayOfWeek == "Monday" ]]
 	then
 		qaAutoTrack.sh hg19 isca 
 		qaAutoTrack.sh hg38 isca 
 		qaAutoTrack.sh hg19 decipher 
 		qaAutoTrack.sh hg19 geneReviews 
 		qaAutoTrack.sh hg38 geneReviews 
 	elif [[ $dayOfWeek == "Tuesday" ]]
 	then
 		qaAutoTrack.sh hg18 lovd 
 		qaAutoTrack.sh hg19 gwasCatalog 
 		qaAutoTrack.sh hg38 gwasCatalog 
 	elif [[ $dayOfWeek == "Wednesday" ]]
 	then
-
-		qaAutoTrack.sh -b danRer7 grcIncidentDb
+		qaAutoTrack.sh -b danRer10 grcIncidentDb
+		qaAutoTrack.sh -b galGal5 grcIncidentDb
 		qaAutoTrack.sh -b hg19 grcIncidentDb
 		qaAutoTrack.sh -b hg38 grcIncidentDb
 		qaAutoTrack.sh -b mm9 grcIncidentDb
 		qaAutoTrack.sh -b mm10 grcIncidentDb
 	elif [[ $dayOfWeek == "Thursday" ]]
 	then
 		qaAutoTrack.sh hg19 omim 
 		qaAutoTrack.sh hg38 omim 
 		qaAutoTrack.sh -b hg19 clinvar
 		qaAutoTrack.sh -b hg38 clinvar
 	elif [[ $dayOfWeek == "Friday" ]]
 	then
 		qaAutoTrack.sh hg38 refGene
 	fi
 fi