#!/bin/bash
# It is preferable to place lphybeast inside the BEAST2 bin folder

if [ -z "$BEAST" ]; then
	## resolve links - $0 may be a link to application
	PRG="$0"

	# need this for relative symlinks
	while [ -h "$PRG" ] ; do
	    ls=`ls -ld "$PRG"`
	    link=`expr "$ls" : '.*-> \(.*\)$'`
	    if expr "$link" : '/.*' > /dev/null; then
		PRG="$link"
	    else
		PRG="`dirname "$PRG"`/$link"
	    fi
	done

	# make it fully qualified
	saveddir=`pwd`
	BEAST0=`dirname "$PRG"`/..
	BEAST=`cd "$BEAST0" && pwd`
	cd "$saveddir"
fi

if [ -n "$BEAST" ]; then
  # if not empty
  BEAST_LIB="$BEAST/lib"
else
  echo "Error: cannot locate the BEAST 2 folder ! $BEAST"
  exit 1
fi

if [ -d "$BEAST"/jre ]; then
  # use Zulu JRE in the BEAST directory if it exists
  JAVA="$BEAST"/jre/bin/java
elif [ -n "$JAVA_HOME" ]; then
  # else use $JAVA_HOME
  JAVA="$JAVA_HOME"/bin/java
else
  # else
  JAVA=java
fi
# print Java version
echo $("$JAVA" -version)

# use BEAGLE_LIB if it is not empty
if [ -n "$BEAGLE_LIB" ]; then
	if [ -n "$BEAST_EXTRA_LIBS" ]; then
		BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
	else
		BEAST_EXTRA_LIBS="$BEAGLE_LIB"
	fi
fi

# Explicitly add /usr/local/lib to library search path to ensure
# beast continues to find beagle when installed here.  (This is
# necessary due to known problems with certain JREs.)
if [ -z "$LD_LIBRARY_PATH" ]; then
    export LD_LIBRARY_PATH=/usr/local/lib
else
    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":/usr/local/lib
fi

### $LPHY_LIB must be provided

if [ -z "$LPHY_LIB" ]; then
  # if $LPHY_LIB does not exist, detect the OS
  if [[ "$OSTYPE" == "linux-gnu"* ]]; then
      echo "Guessing LPHY_LIB on Linux ..."
      # set working dir to ~
      OS_PREFIX="$HOME"

  elif [[ "$OSTYPE" == "darwin"* ]]; then
      echo "Guessing LPHY_LIB on macOS ..."
      OS_PREFIX="/Applications"

#  elif [[ "$OSTYPE" == "cygwin" ]]; then
#      echo "Running on Cygwin (Windows)"
#  elif [[ "$OSTYPE" == "msys" ]]; then
#      echo "Running on MSYS (Windows)"
#  elif [[ "$OSTYPE" == "win32" ]]; then
#      echo "Running on Windows"

  else
      echo "Cannot guess the LPhy library path LPHY_LIB in unknown OS: $OSTYPE !"
      echo "Please set it as your environment variable."
      echo "Get help from https://linguaphylo.github.io/setup"
      exit 1
  fi

  # if multiple LPhy installed, sort the search result to get the latest version, usually last line
  LPHY_DIR=$(find "$OS_PREFIX" -maxdepth 1 -type d -name 'lphy*studio-1*' | sort | tail -1)
  # Guess LPHY_LIB
  LPHY_LIB="$LPHY_DIR/lib"
fi
# set to specific path in script
#LPHY_LIB="/Applications/BEAST 2.7.5/lphystudio-1.4.3/lib"

if [ ! -d "$LPHY_LIB" ]; then
  echo "Error: Invalid LPhy library path : $LPHY_LIB !"
  echo "Please set an existing LPhy library path to LPHY_LIB as your environment variable."
  echo "Get help from https://linguaphylo.github.io/setup"
  exit 1
fi
echo "BEAST_LIB = $BEAST_LIB"
echo "BEAST_EXTRA_LIBS = $BEAST_EXTRA_LIBS"
echo "LPHY_LIB = $LPHY_LIB"
echo ""

# test if there is any lphy*.jar
JAR_FILES=$(ls "$LPHY_LIB"/lphy*.jar)
if [ -z "$JAR_FILES" ]; then
  echo "Error: No core jar files found in $LPHY_LIB !"
  echo "Please install LPhy properly. Get help from https://linguaphylo.github.io/setup"
  exit 1
fi

# must set -Dpicocli.disable.closures=true using picocli:4.7.0
# otherwise it will throw otherwise java.lang.NoClassDefFoundError: groovy.lang.Closure
ARG="-Xms256m -Xmx60g -Dpicocli.disable.closures=true -Dlauncher.wait.for.exit=true -Duser.language=en"
if [ -n "$BEAST_EXTRA_LIBS" ]; then
  "$JAVA" $ARG -Djava.library.path="$BEAST_EXTRA_LIBS" -cp "$BEAST_LIB/launcher.jar:$LPHY_LIB/*" beast.pkgmgmt.launcher.AppLauncherLauncher lphybeast $*
else
  "$JAVA" $ARG -cp "$BEAST_LIB/launcher.jar:$LPHY_LIB/*" beast.pkgmgmt.launcher.AppLauncherLauncher lphybeast $*
fi