src/utils/qa/getPubHubContact.sh 51b0e05f3807e351efb2ff9a4870946175121722

51b0e05f3807e351efb2ff9a4870946175121722
mspeir
  Wed Dec 21 10:00:55 2016 -0800
Adding usage message and ability to specify output directory per Jonathan's suggestion. Also setting qaConfig and other standard stuff at the top of the script. refs #18316

diff --git src/utils/qa/getPubHubContact.sh src/utils/qa/getPubHubContact.sh
index 3a97a2a..a07fbff 100755
--- src/utils/qa/getPubHubContact.sh
+++ src/utils/qa/getPubHubContact.sh
@@ -1,20 +1,70 @@
 #!/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
+	runScript="$1"
+	base="$2"
+fi
+
+#If no user provided base location, then assume it's being run on dev and output to default loc.
+if [[ "$base" == "" ]]
+then
 	base="/usr/local/apache/htdocs-genecats/qa/test-results/publicHubContactInfo"
-contactFile="$base/publicHubContact.html"
+fi
 
+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
@@ -38,15 +88,20 @@
 			# 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