#!/bin/bash
#
# Modified for BIRCH by Brian Fristensky
#
# Run cytoscape from a jar file
# This script is a UNIX-only (i.e. Linux, Mac OS, etc.) version
#-------------------------------------------------------------------------------

#============== Modified for BIRCH by BF ===================
# JAVA11_HOME should be set before running this script.
# The best place to do that is in $BIRCH/local/local.profile.source
# For testing purposes, you can uncomment the line below and
# modify it for the appropriate Java command on your system.
#JAVA11_HOME="/usr/lib/jvm/java-11-openjdk-11.0.14.0.9-1.el7_9.x86_64"

if [ ! -z "$JAVA11_HOME" ]
then
    JAVA_HOME="$JAVA11_HOME"
    export JAVA_HOME
    JVERSION=`$JAVA_HOME/bin/java -version 2>&1 | head -n 1 |cut -f2 -d'"' | cut -f1 -d'.'`
    
else
    JVERSION=`java -version 2>&1 | head -n 1 |cut -f2 -d'"' | cut -f1 -d'.'`
    JAVA_HOME=""
    export JAVA_HOME
fi
echo "JVERSION: "$JVERSION
echo "JAVA_HOME: "$JAVA_HOME

#===========================================================
if (( "$JVERSION" == "11" ))
then
     echo "running cytoscape"
    # First, see if help (-h, --help) or version (-v, --version) command line arguments
    # are specified. If so, display help or the current version and exit.

    CYTOSCAPE_VERSION="Cytoscape version: 3.9.1"

    if [[ $# > 0 ]]; then
	    if [ $1 == "-h" -o $1 == "--help" ]; then
		cat <<-EOF

	Cytoscape Command-line Arguments
	================================
	usage: cytoscape.{sh|bat} [OPTIONS]
	 -h,--help             Print this message.
	 -v,--version          Print the version number.
	 -s,--session <file>   Load a cytoscape session (.cys) file.
	 -N,--network <file>   Load a network file (any format).
	 -P,--props <file>     Load cytoscape properties file (Java properties
	                       format) or individual property: -P name=value.
	 -V,--vizmap <file>    Load vizmap properties file (Cytoscape VizMap
	                       format).
	 -S,--script <file>    Execute commands from script file.
	 -R,--rest <port>      Start a rest service.

	EOF
		    exit 0
	    fi

	    if [ $1 == "-v" -o $1 == "--version" ]; then
		    echo $CYTOSCAPE_VERSION
		    exit 0
	    fi
    fi

    DEBUG_PORT=12345

    #script_path="$(dirname -- $0)"
    script_path="$BIRCH/java/cytoscape"
   
    #if [ -h $0 ]; then
    #	    link="$(readlink $0)"
    #	    script_path="$(dirname -- $link)"
    #fi

    export JAVA_DEBUG_OPTS="-Xdebug -Xnoagent -Djava.compiler=NONE -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${DEBUG_PORT}"
    if [ `uname` = "Darwin" ]; then
	    CYTOSCAPE_MAC_OPTS="-Xdock:icon=$script_path/framework/cytoscape_logo_512.png -Xdock:name=Cytoscape"
	    export JAVAFX_DIR="mac"
    else
	    export JAVAFX_DIR="linux"
    fi

    #vm_options_path=$HOME/.cytoscape
    vm_options_path=$script_path

    # Attempt to generate Cytoscape.vmoptions if it doesn't exist!
    if [ ! -e "$vm_options_path/Cytoscape.vmoptions"  -a  -x "$script_path/gen_vmoptions.sh" ]; then
        "$script_path/gen_vmoptions.sh"
    fi

    export JAVA_OPTS=-Xms1550M\ -Xmx1550M
    if [ -r $vm_options_path/Cytoscape.vmoptions ]; then
		    JAVA_OPTS=`cat $vm_options_path/Cytoscape.vmoptions`
    else # Just use sensible defaults.
        echo '*** Missing Cytoscape.vmoptions, falling back to using defaults!'
		    # Initialize MAX_MEM to something reasonable
		    JAVA_OPTS=-Xms1550M\ -Xmx1550M
    fi

    # The Cytoscape home directory contains the "framework" directory
    # and this script.
    CYTOSCAPE_HOME_REL=$script_path
    CYTOSCAPE_HOME_ABS=`cd "$CYTOSCAPE_HOME_REL"; pwd`

    export KARAF_OPTS=-Dcytoscape.home="$CYTOSCAPE_HOME_ABS"\ "$CYTOSCAPE_MAC_OPTS"

    export KARAF_DATA="${HOME}/CytoscapeConfiguration/3/karaf_data"
    mkdir -p "${KARAF_DATA}/tmp"

    $script_path/framework/bin/karaf "$@"
else
    MESSAGE="Cytoscape requires Java11,and\nJAVA11_HOME must be set."
    TITLE="Dependencies"
    java -jar $BIRCH/script/OkayBox2.jar "$MESSAGE" "$TITLE"
    chooseviewer.py $BIRCH/public_html/birchadmin/dependencies/dependencies.html
fi