crawl

#!/bin/bash

start_time=$(date +%s)
SCRIPT_DIRECTORY=`dirname $0`

hput() {
    eval "$1""$2"='$3'
}

hget() {
    eval echo '${'"$1$2"'#hash}'
}


hput COMMANDS chado2es org.genedb.crawl.elasticsearch.index.sql.IncrementalSQLIndexBuilder
hput COMMANDS das2es org.genedb.crawl.elasticsearch.index.das.DASIndexBuilder
hput COMMANDS das2file org.genedb.crawl.elasticsearch.index.das.DASFileBuilder
hput COMMANDS gff2es org.genedb.crawl.elasticsearch.index.gff.GFFIndexBuilder
hput COMMANDS org2es org.genedb.crawl.elasticsearch.index.json.OrganismIndexBuilder
hput COMMANDS ref2es org.genedb.crawl.elasticsearch.index.json.ReferenceIndexBuilder
hput COMMANDS cv2es org.genedb.crawl.elasticsearch.index.cv.CvIndexBuilder
hput COMMANDS hazelcast org.genedb.crawl.hazelcast.HazelcastService

usage() {
	usage_string="crawl ["
	sep=""
	for i in $(compgen -A variable COMMANDS); 
	do 
		key=${i/COMMANDS/}
		usage_string=$usage_string$sep$key
		sep="|" 
	done 
	usage_string=$usage_string"] [OPTIONS]"
	echo $usage_string
	exit 1
}


# this is the classpath location in the project folder
CP1="$SCRIPT_DIRECTORY/build/libs/"
# this is the expected classpath location in an installed folder
CP2="$SCRIPT_DIRECTORY/../lib/"

if [[ -z $CRAWL_CLASSPATH ]]
then
	if [ -d $CP1 ]; then
		export CRAWL_CLASSPATH="$CP1/*"
	elif [ -d "$CP2" ]; then
		export CRAWL_CLASSPATH="$CP2/*"
	else
		echo "Could not find a crawl library in $CP1 or $CP1, and no CRAWL_CLASSPATH has been set. Aborting." 
	fi
fi

if [[ -z $CRAWL_JAVA_SETTINGS ]]
then
    export CRAWL_JAVA_SETTINGS="-Xmx2000m"
fi

if [ $# -lt 1 ]; then
	usage
fi

COMMAND=$1
shift

JAVA_ENTRY_POINT=`hget COMMANDS $COMMAND`

if [[ ${#JAVA_ENTRY_POINT} -lt 1 ]]
then
	usage
fi

if [[ -z $JAVA_HOME ]]
then
    export JAVA='java'
else
    export JAVA="$JAVA_HOME/bin/java"
fi

# echo $JAVA

# the java.net.preferIPv4Stack must be set to true, or else Hazelcast 
# instances may not be able to see it (it is also set in the Hazelcast 
# example wrapper scripts)
$JAVA $CRAWL_JAVA_SETTINGS -Djava.net.preferIPv4Stack=true -cp "$CRAWL_CLASSPATH" $JAVA_ENTRY_POINT "$@"

finish_time=$(date +%s)
echo "Time duration: $((finish_time - start_time)) secs."