607f1da495428c8c0dff8245428cacb9ede44671 mspeir Thu Feb 2 10:09:50 2017 -0800 Add new check so that old contact file won't get deleted when it and the new contact file are different by more than 5 lines. Will throw an error if this is the case. refs #18316 diff --git src/utils/qa/getPubHubContact.sh src/utils/qa/getPubHubContact.sh index 460e78a..e905241 100755 --- src/utils/qa/getPubHubContact.sh +++ src/utils/qa/getPubHubContact.sh @@ -1,19 +1,19 @@ #!/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. # ################################ @@ -51,34 +51,35 @@ 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 + mv $contactFile $contactFile.old.temp 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/$label.hub.txt" @@ -87,31 +88,47 @@ # Extract email from hub.txt file we saved email=$(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" "$5}') + email=$(grep "$url" $contactFile.old.temp | 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)" + # 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