#!/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.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 $url &> /dev/null || true
# Extract email from hub.txt file we saved
email=$(egrep "^email" $hubFile) || true
# 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 $hubFile &> /dev/null || true
# Extract email from hub.txt file we saved
email=$(grep "^email" $hubFile) || true
# 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" "$5}') || true
fi
fi
# Create hyperlinks to hub.txt files
hubLink="$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