#!/bin/sh

# This is a simple script for running the BioLegato blfiles application
# for testing purposes.

#------------------------ BIRCH and BIRCH_PLATFORM ---------------
#
#  Set these two variables and everything else should work unchanged.
#
# In a full BIRCH system, these variables are set by getbirch as
# part of an install or update.

# Set BIRCH environment variable, on which everything else depends
BIRCH=/home/psgendb/BIRCHDEV/java/bioLegato/test
export BIRCH

# Uncomment one choice for BIRCH_PLATFORM
BIRCH_PLATFORM="linux-x86_64"
#BIRCH_PLATFORM="osx-x86_64"
export BIRCH_PLATFORM
#-----------------------------------------------------------------


#Path should include the script directory
PATH=$BIRCH/script:$BIRCH/bin-$BIRCH_PLATFORM:$PATH
export PATH

# Set environment variables for helper applications
. $BIRCH/admin/setblenv.profile.$BIRCH_PLATFORM.source

# Location of BioLegato .jar files
BIOLEGATO_HOME=$BIRCH/java/bioLegato
export BIOLEGATO_HOME

# The location of anciliary data files used by bioLegato.
BL_TABLES_DIR=$BIRCH/dat/blfiles
export BL_TABLES_DIR

BL_PROPERTIES=$BIRCH/dat/blfiles/blfiles.properties
export BL_PROPERTIES

NOAUTONAMES="0"
# The -dir switch is mainly for launching bioLegato from the birch launcher. By 
# prompting the user for a working folder, we help enforce good file organization
# habits.
if [ $# -gt 0 ]
then
   if [ ${1} = "-dir" ]
   then

      # Get rid of the -dir switch, and send the remaining command line arguments to bioLegato
      shift

      #Prompt the user to choose a working directory
      CHANGEDIR=`java -jar $BIRCH/script/DirChooser2.jar "Where do you want to work? Choose a folder."`

      if [ -d "$CHANGEDIR" ]; then
	  cd "$CHANGEDIR"
      fi
   elif [ ${1} = "-noautonames" ]; then
      NOAUTONAMES="1"
   fi
fi

# blfiles starts with a list of files in the current working directory
# If that list is empty, bldirtab.py will create a list of all files
# in the current working directory.
if [ "$NOAUTONAMES" -eq "0" ]
then
    # $$ in bash is the process id of the current shell
    DIRFILE=$$.filelist
    #echo '#'$PWD > $DIRFILE
    #ls -1 >> $DIRFILE
    bldirtab.py $DIRFILE
else
    DIRFILE=""
fi


# We need to explicitly set the default look and feel. On Mac OSX, the default for the 
# table canvas has no borders around cells, which detracts from readability.
java -Dswing.defaultlaf=javax.swing.plaf.metal.MetalLookAndFeel -jar $BIOLEGATO_HOME/table.jar $* $DIRFILE

if [ ! "$DIRFILE" == "" ]
then
    rm $DIRFILE
fi