b62da609cf70688466da60372a361df5488c75e6 mspeir Thu Jan 5 10:40:21 2017 -0800 Adding check to see if user-supplied directory exists before accepting it. Also adding command that checks to see of there is a hubFiles directory in the supplied directory and creates it if it doesn't exist. refs #18603 #18316 diff --git src/utils/qa/getPubHubContact.sh src/utils/qa/getPubHubContact.sh index a07fbff..460e78a 100755 --- src/utils/qa/getPubHubContact.sh +++ src/utils/qa/getPubHubContact.sh @@ -1,107 +1,117 @@ #!/bin/bash # quit if something within the script fails 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 fi # Make header for html file echo -e " <!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\"> " >> $contactFile while read url label do # Save hub shortLabel as a file so we can use it in a filename later label=$(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 | awk '{print $4" "$5}') fi fi # Create hyperlinks to hub.txt files hubLink="<a href=\"$url\" target=\"_blank\">$label</a>" # Write contact email + hubUrl to file echo -e "$hubLink $email<br>" >> $contactFile done<<<"$(hgsql -h genome-centdb -Ne "select hubUrl,shortLabel from hubPublic" hgcentral)" else echo -e "Error: \"$1\" is not a valid input. Please see the usage message.\n\n" echo -e $usage exit 1 fi