setup_taxomachine.sh

# TODO: record output to log file

JAVAFLAGS="-Xms4G -Xmx16G"
HELPTEXT="usage:\nsetup_taxomachine.sh <options>\n\t[--clean-db]\n\t[--setup-db]\n\t[--download-ott]\n\t[--setup-neo4j]\n\t[--restart-neo4j]\n\t[--force]\n\t[--update-from-git]\n\t[--recompile-standalone]\n\t[--recompile-plugin]\n\t[-ott-version <2.8draft3>]\n\t[-prefix <path>]\n\n"

while [ $# -gt 0 ]; do
	case "$1" in
		--clean-db) CLEANDB=true;;
		--setup-db) SETUP_DB=true;;
		--download-ott) DOWNLOAD_OTT=true;;
		--setup-neo4j) SETUP_NEO4J=true;;
		--restart-neo4j) RESTART_NEO4J=true;;
#		--test) TEST=true;;
		--force) FORCE=true;;
		--recompile-standalone) RECOMPILE=true;;
		--recompile-plugin) RECOMPILE_PLUGIN=true;;
		-ott-version) shift; VERSION="$1";;
		-prefix) shift; PFSET=true; PREFIX="$1";;
		--help) printf "$HELPTEXT"; exit 0;;
		*) printf "\nunrecognized argument: $1.\n"; printf "$HELPTEXT"; exit 1;
	esac
	shift
done

JAVA=java
#if [ $TEST ]; then
#	printf "\njust testing. java commands will be printed instead of executed\n"
#	$JAVA="java"
#fi

if [ ! $VERSION ]; then
	VERSION="ott2.6"
	printf "\nwill attempt to use $VERSION\n"
fi

# assume we are running this from within the taxomachine directory
TAXOMACHINE_HOME=$(pwd)

if [ ! $PFSET ]; then
	PREFIX="../"
	if [ ! $FORCE ]; then
		printf "\nprefix is not set. the default prefix $PREFIX will be used. continue? y/n:"
		while [ true ]; do
			read RESP
			case "$RESP" in
				n) exit;;
				y) break;;
				*) printf "unrecognized input. uze ^C to exit script";;
			esac
		done
	fi
fi

if [ ! -d $PREFIX ]; then
	mkdir $PREFIX
fi
cd $PREFIX
PREFIX=$(pwd)
printf "\nworking at prefix $PREFIX\n"

JARSDIR="$PREFIX/jars"
#if [ ! -d $JARSDIR ]; then
    mkdir $JARSDIR
#fi

OTT_SOURCENAME=$VERSION
OTT_DOWNLOADDIR=$PREFIX"/data"
if [ ! -d $OTT_DOWNLOADDIR ]; then
	mkdir $
fi

if [ $DOWNLOAD_OTT ]; then

	printf "\ntaxonomy $VERSION will be downloaded\n"
	printf "installing $VERSION taxonomy at: $OTT_DOWNLOADDIR\n"

	# removing existing copy
	cd $OTT_DOWNLOADDIR
	rm -Rf $VERSION $VERSION.tgz

	# download and decompress ott
	wget "http://files.opentreeoflife.org/ott/$VERSION.tgz"
	tar -xvf $VERSION.tgz
	mv ott $VERSION # doesn't work with nonstandard releases of ott (like aster)
	
fi 

OTT_SOURCEDIR="$OTT_DOWNLOADDIR/$VERSION"
if [ ! -d $OTT_SOURCEDIR ]; then
	printf "\ncan\'t find $OTT_SOURCEDIR. use --download-ott to download a copy\n"
	exit
fi
printf "\nusing $VERSION taxonomy at: $OTT_SOURCEDIR\n"

OTT_TAXONOMY=$OTT_SOURCEDIR"/taxonomy.tsv"
OTT_SYNONYMS=$OTT_SOURCEDIR"/synonyms.tsv"
OTT_DEPRECATED=$OTT_SOURCEDIR"/deprecated.tsv"

# download taxomachine
#TAXOMACHINE_HOME=$PREFIX"/taxomachine"
#if [ ! -d $TAXOMACHINE_HOME ]; then
#	printf "\ninstalling taxomachine at: $TAXOMACHINE_HOME\n"
#	git clone http://github.com/OpenTreeOfLife/taxomachine.git
#fi
printf "\nusing taxomachine at: $TAXOMACHINE_HOME\n"

# pull from the git repo and remove the binary if updating is turned on
TAXOMACHINE_JAR="taxomachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar"
TAXOMACHINE_COMPILE_LOCATION="$TAXOMACHINE_HOME/target/$TAXOMACHINE_JAR"
TAXOMACHINE_INSTALL_LOCATION="$JARSDIR/$TAXOMACHINE_JAR"

# just remove the binary if we want recompile
if [ $RECOMPILE ]; then
	rm -f $TAXOMACHINE_INSTALL_LOCATION
fi

# compile taxomachine if necessary
if [ ! -f $TAXOMACHINE_INSTALL_LOCATION ]; then
	cd $TAXOMACHINE_HOME
	sh compile_standalone.sh
	mv $TAXOMACHINE_COMPILE_LOCATION $TAXOMACHINE_INSTALL_LOCATION
fi

TAXOMACHINE_COMMAND="$JAVA $JAVAFLAGS -jar $TAXOMACHINE_INSTALL_LOCATION "

#TAXOMACHINE_COMMAND="$JAVA $JAVAFLAGS -jar $TAXOMACHINE_INSTALL_LOCATION \"\$@\""
#TAXOMACHINE_START_SCRIPT="~/phylo/bin/taxomachine"
#INSTALL_START_SCRIPT=true
#if [ -f $TAXOMACHINE_START_SCRIPT ]; then
#    if cat $TAXOMACHINE_START_SCRIPT | grep '$TAXOMACHINE_COMMAND' ; then
#        INSTALL_START_SCRIPT=false
#    fi
#fi

#if [ $INSTALL_START_SCRIPT = true ]; then
#    echo $TAXOMACHINE_COMMAND > $TAXOMACHINE_START_SCRIPT
#    chmod +x $TAXOMACHINE_START_SCRIPT
#fi

#if [ ! -f $TAXOMACHINE_START_SCRIPT ]; then
#    printf "\nthe taxomachine start script could not be installed. do you need to sudo? quitting\n"
#    exit
#fi

# prepare for dealing with the neo4j server if necessary
TAXO_NEO4J_HOME="$PREFIX/neo4j-taxomachine"
TAXO_NEO4J_DAEMON="$TAXO_NEO4J_HOME/bin/neo4j"

# download neo4j if necessary
if [ ! -d $TAXO_NEO4J_HOME ]; then
    cd "$HOME/Downloads"
    wget "http://neo4j.com/artifact.php?name=neo4j-community-1.9.8-unix.tar.gz"
    tar -xvf "neo4j-community-1.9.8-unix.tar.gz"
    tar -xvf "artifact.php?name=neo4j-community-1.9.8-unix.tar.gz"  # this seems to be what happens for travis ci
    printf "\ninstalling neo4j instance for taxomachine at: $TAXO_NEO4J_HOME\n"
    mv neo4j-community-1.9.8 $TAXO_NEO4J_HOME
fi

# clean the db if necessary
TAXOMACHINE_DB="$OTT_DOWNLOADDIR/$VERSION.db"
if [ $CLEANDB ]; then
    if [ -f $TAXO_NEO_DAEMON ]; then
        printf "\nattempting to shut down the neo4j server\n"
        $TAXO_NEO4J_DAEMON stop
    fi
	printf "\nremoving the existing database at: $TAXOMACHINE_DB\n"
	rm -Rf $TAXOMACHINE_DB
fi

# load taxonomy and make the indexes
if [ $SETUP_DB ]; then

	# require explicit instructions to remove existing db
	if [ -d $TAXOMACHINE_DB ]; then
		printf "\ndatabase at $TAXOMACHINE_DB already exists. to rebuild it, use --clean-db --setup-db\n"
		exit
	fi

	$TAXOMACHINE_COMMAND loadtaxsyn $OTT_SOURCENAME $OTT_TAXONOMY $OTT_SYNONYMS $TAXOMACHINE_DB	
	$TAXOMACHINE_COMMAND makecontexts $TAXOMACHINE_DB
	$TAXOMACHINE_COMMAND makegenusindexes $TAXOMACHINE_DB
    $TAXOMACHINE_COMMAND adddeprecated $OTT_DEPRECATED $TAXOMACHINE_DB

fi

# start the server
if [ $SETUP_NEO4J ]; then
    
    # point the server at the taxomachine db location
    TAXOMACHINE_DB_ASSIGNMENT="org.neo4j.server.database.location=$TAXOMACHINE_DB"
    COMMENT="###############################################################\n# location for taxomachine db, original location settings are in original file"
    SERVER_PROPERTIES="$TAXO_NEO4J_HOME/conf/neo4j-server.properties"
    
    if cat $SERVER_PROPERTIES | grep -q $TAXOMACHINE_DB_ASSIGNMENT ; then
        printf "\nServer set correctly to use db at $TAXOMACHINE_DB\n"
    else
        printf "\nServer config will be changed to use db at $TAXOMACHINE_DB\n"

        ORIG_SERVER_PROPERTIES="$SERVER_PROPERTIES.original"
        mv "$SERVER_PROPERTIES" "$ORIG_SERVER_PROPERTIES"
        printf "$COMMENT\n$TAXOMACHINE_DB_ASSIGNMENT\n\n" > "$SERVER_PROPERTIES"
        grep -v "org.neo4j.server.database.location" "$ORIG_SERVER_PROPERTIES" >> "$SERVER_PROPERTIES"
    fi
fi

printf "\nusing neo4j instance for taxomachine at: $TAXO_NEO4J_HOME\n"

# install the plugin if necessary
PLUGIN="taxomachine-neo4j-plugins-0.0.1-SNAPSHOT.jar"
PLUGIN_INSTALL_LOCATION="$TAXO_NEO4J_HOME/plugins/"$PLUGIN

# just remove the binary if we want recompile
if [ $RECOMPILE_PLUGIN ]; then
    rm -f $PLUGIN_INSTALL_LOCATION
fi

# recompile if the plugin is not there    
if [[ -d $TAXO_NEO4J_HOME && ! -f $PLUGIN_INSTALL_LOCATION ]]; then
    cd $TAXOMACHINE_HOME	
    sh compile_server_plugins.sh
    PLUGIN_COMPILE_LOCATION="$TAXOMACHINE_HOME/target/$PLUGIN"
    mv "$PLUGIN_COMPILE_LOCATION" "$PLUGIN_INSTALL_LOCATION"
fi

if [ $RESTART_NEO4J ]; then
    $TAXO_NEO4J_DAEMON restart
fi