92a5d7bbd9c296362f89607d37df5ae238c28825 mspeir Thu Feb 2 10:11:24 2017 -0800 accidentally commented out set line in previous commit, no redmine diff --git src/utils/qa/getPubHubContact.sh src/utils/qa/getPubHubContact.sh index e905241..3428016 100755 --- src/utils/qa/getPubHubContact.sh +++ src/utils/qa/getPubHubContact.sh @@ -1,134 +1,134 @@ #!/bin/bash # quit if something within the script fails -#set -beEu -o pipefail +set -beEu -o pipefail source `which qaConfig.bash` umask 002 ################################ # # 12-20-2016 # Matthew Speir # # getPubHubInfo.sh # Collects contact information for # hubs listed in hgcentral.hubPublic. # Outputs contact information to HTML- # formatted file. # ################################ usage=""" Collect contact information for hubs in hgcentral.hubPublic on the RR. Places all contact information into an HTML-formatted page.\nDefault output location:\n /usr/local/apache/htdocs-genecats/qa/test-results/publicHubContactInfo\n\n `basename $0` go [outputLocation]\n\n\ outputLocation is a path to the directory where output should be placed. If not set, script assumes default location above.\n """ runScript="" base="" # Print usage statement if (( $# < 1 )) || (( $# > 2 )) then echo -e $usage exit 1 elif (( $# == 1 )) then runScript=$1 elif (( $# == 2 )) then # Check if outputLocation exists if [[ -d $2 ]] then runScript="$1" base="$2" else echo -e "Sorry, directory \"$2\" does not exist. Check spelling or create this directory and try again.\n" exit 1 fi fi # If no user provided base location, then assume it's being run on dev and output to default loc. if [[ "$base" == "" ]] then base="/usr/local/apache/htdocs-genecats/qa/test-results/publicHubContactInfo" fi # Create "hubFiles" directory in base if it doesn't exist mkdir -p $base/hubFiles if [[ "$runScript" == "go" ]] then contactFile="$base/publicHubContact.html" # Check if old contact file exists and if it does move it to archive file if [ -e $contactFile ] then mv $contactFile $contactFile.old.temp fi # Make header for html file echo -e " " >> $contactFile while read url label do # Save hub shortLabel as a file so we can use it in a filename later label=$(echo $label | sed -e 's/ /_/g') # Make name for hub.txt output file that includes hub shortLabel hubFile="$base/hubFiles/$label.hub.txt" wget -t 5 -O $hubFile $url &> /dev/null # Extract email from hub.txt file we saved email=$(egrep "^email" $hubFile) # If email is empty, then wget failed or hub is down if [[ $email == "" ]] then # Attempt to get hub.txt file w/ curl curl --retry 5 $url -o $hubFile &> /dev/null # Extract email from hub.txt file we saved email=$(grep "^email" $hubFile) # If email is still empty, hub is likely down and # we want to use the last email we have as contact email if [[ $email == "" ]] && [ -e $contactFile.old ] then email=$(grep "$url" $contactFile.old.temp | awk '{print $4" "$5}') fi fi # Create hyperlinks to hub.txt files hubLink="$label" # Write contact email + hubUrl to file echo -e "$hubLink $email
" >> $contactFile done<<<"$(hgsql -h genome-centdb -Ne "select hubUrl,shortLabel from hubPublic" hgcentral)" # Get line counts for current/old contact info files lineCountNew=$(wc -l $contactFile | cut -d " " -f 1) lineCountOld=$(wc -l $contactFile.old.temp | cut -d " " -f 1) lineDiff=$(expr $lineCountNew - $lineCountOld) # find absolute value of line diff absLineDiff=$([ $lineDiff -lt 0 ] && echo $((-$lineDiff)) || echo $lineDiff) # Check if line diff is >5 lines if [ $(echo "$absLineDiff >= 5" | bc) -ne 0 ] then echo "Error: New contact file seems to be missing many entries from old file." echo " Something may have failed while running. Try running again to" echo " see if that helps." exit 1 else mv $contactFile.old.temp $contactFile.old fi else echo -e "Error: \"$1\" is not a valid input. Please see the usage message.\n\n" echo -e $usage exit 1 fi