bidmat

#!/bin/bash
# export JAVA_HOME="" # Set here if not set in environment
# set CUDA_HOME=""   # set if desired, otherwise defaults to /usr/local/cuda
# note CUDA_PATH="" # Should be set to the latest toolkit in Windows
# Change these if needed
MEMSIZE="-Xmx14G"
BIDMAT_ROOT="${BASH_SOURCE[0]}"
if [ ! `uname` = "Darwin" ]; then
  BIDMAT_ROOT=`readlink -f "${BIDMAT_ROOT}"`
else
  while [ -L "${BIDMAT_ROOT}" ]; do
    BIDMAT_ROOT=`readlink "${BIDMAT_ROOT}"`
  done
fi
BIDMAT_ROOT=`dirname "$BIDMAT_ROOT"`
pushd "${BIDMAT_ROOT}" > /dev/null
BIDMAT_ROOT=`pwd -P`
BIDMAT_ROOT0="$( echo ${BIDMAT_ROOT} | sed 's+^/cygdrive/\(.\)+\1:+' )"
BIDMAT_ROOT="$( echo ${BIDMAT_ROOT0} | sed 's+^/mnt/\(.\)+\1:+' )"
LIBDIR=${BIDMAT_ROOT}/lib

LOGGING_CONF="${BIDMAT_ROOT}/conf/logging.conf"
if [ -e "${LOGGING_CONF}" ]; then
    LOG_OPTS="-Djava.util.logging.config.file=${LOGGING_CONF}"
else
    LOG_OPTS=""
fi
export JAVA_OPTS="${MEMSIZE} -Xms128M -Dfile.encoding=UTF-8 ${LOG_OPTS} ${JAVA_OPTS}" # Set as much memory as possible

BIDMAT_VERSION=`echo target/BIDMat-*.jar | sed 's/.*BIDMat-//' | sed 's/\.jar//'`

OSS=`uname -a`
if [ "$ARCH" = "" ]; then
    ARCH=`arch`
fi
if [[ "$OSS" == Darwin* ]] ; then
    if [[ "$OSS" == *x86_64 ]] ; then
	ARCH="x86_64"
    fi
    OSS="apple"
    JUPYTER_DIR="${HOME}/Library/Jupyter"
elif [[ "$OSS" == Linux* ]] ; then
    WSL=`cat /proc/version | grep 'Microsoft'`
    if [ ! "$WSL" = "" ]; then
	OSS="WSL"
    else
	OSS="linux"
    fi
    JUPYTER_DIR="${HOME}/.local/share/jupyter"
elif [[ "$OSS" == CYGWIN* ]] ; then
    if [[ "$OSS" == *WOW* ]] ; then
        ARCH="x86_64"
    fi
    OSS="windows"
    JUPYTER_DIR=`echo $APPDATA | sed 's_\\\\_/_g' | sed 's_^\([A-Z]\):_/cygdrive/\1_'`
    JUPYTER_DIR="${JUPYTER_DIR}/jupyter"
else
    echo "OS not supported" $OSS
    exit 1
fi

if [ "$OSS" = "windows" ]; then
    if [ ! "${JAVA_HOME}" = "" ]; then
        JAVA_HOME=`${BIDMAT_ROOT}/shortpath.bat "${JAVA_HOME}"`
        JAVA_HOME=`echo ${JAVA_HOME} | tr -d '\r'`
	    export JAVA_HOME=`echo ${JAVA_HOME} | sed 's_\\\\_/_g'`/bin
    fi
fi

cd lib
BIDMAT_JARS=`echo *.jar`
BIDMAT_LIBS="${BIDMAT_ROOT}/target/BIDMat-${BIDMAT_VERSION}.jar"
for lib in ${BIDMAT_JARS}; do
    BIDMAT_LIBS="${BIDMAT_LIBS};${LIBDIR}/${lib}"
done
popd  > /dev/null

TOOL_LIBS="${JAVA_HOME}/lib/tools.jar"
ALL_LIBS="${TOOL_LIBS};${BIDMAT_LIBS}"

if [ "$OSS" = "windows" ]; then
    if [ ! "${CUDA_PATH}" = "" ]; then
	    NEWPATH=`${BIDMAT_ROOT}/shortpath.bat "${CUDA_PATH}"`
	    NEWPATH=`echo $NEWPATH | sed 's_\\\\_/_g'`/bin
    fi
elif [ ! "$OSS" = "WSL" ]; then
    ALL_LIBS=`echo "${ALL_LIBS}" | sed 's/;/:/g'`
fi

if [ "$1" = "notebook" ]; then
    shift 1
    KERNEL_CMD="[\"java\", \"-Xms128M\", \"${MEMSIZE}\", \"-Dfile.encoding=UTF-8\", \"-cp\", \"${ALL_LIBS}\",
                 \"-Dcoursier.mainJar=jupyter.scala.JupyterScala\", \"jupyter.scala.JupyterScala\", 
                 \"--id\", \"bidmat\", \"--name\", \"BIDMat\", \"--connection-file\", \"{connection_file}\"]"
    KERNEL_JSON="{\"language\" : \"bidmat\", \"display_name\" : \"BIDMat\", \"argv\" : ${KERNEL_CMD} }"
    mkdir -p "${JUPYTER_DIR}/kernels/bidmat"
    echo "${KERNEL_JSON}" > ${JUPYTER_DIR}/kernels/bidmat/kernel.json
    cp ${BIDMAT_ROOT}/logo-64x64.png ${JUPYTER_DIR}/kernels/bidmat
    jupyter notebook --KernelManager.kernel_cmd=${KERNEL_CMD} $@
else
    userargs=""
    if [ "$2" != "" ]; then
	userargs="-Duser.arg0=$2"
	j=1;
	for i in ${*:3}; do
	    userargs="$userargs -Duser.arg$j=$i"
	    j=$((j+1))
	done
    fi
    runscript=""
    if [ "$1" != "" ]; then
	runscript="-I ${1}"
    fi
    ${BIDMAT_ROOT0}/command/scala -Dscala.repl.maxprintstring=8000 ${userargs} -nobootcp -toolcp "${TOOL_LIBS}" \
		   -cp "${ALL_LIBS}" -Yrepl-sync -I ${LIBDIR}/bidmat_init.sc $runscript
fi