#!/usr/bin/env python

import birchenv
import birchscript
import os
import os.path
import shutil
import subprocess
import sys

# For each name in INFILE, call a SeqHound method, and return
# the result (a single line). Results are concatenated to
# a single output file OUTFILE.

# In a future release of seqhound (after 2.5)
#  SeqHound looks for a .shoundremrc
# file in $HOME, and in the current directory
# Until SeqHound comes up with a better way of finding
# the .shoundremrc file, this script must be run by 
# any program using SeqHound


# Make sure that the user has a ~.shoundremrc file
#if [ ! -e ~/.shoundremrc ] \
#   ln -s $SEQHOUND/shoundremrc ~/.shoundremrc


#------------ SeqHound 2.5 ------------------------
# For now, we use 2.5, but we need to get around the
# requirement that .shoundremrc must be present in every directory
# in which seqhound will be run. The solution is to create a lock file
# for every instance of leash. When a leash job terminates,
# the lock file is removed. If no more lock files remain,
# leash removes .shoundremrc.

LOCK = "leash.lock." + os.getpid()
h_lock = open (LOCK, "w")
print >> h_lock, "This file is created when an instance of leash is running."
print >> h_lock, "It should automatically be removed when leash terminates. "

if not os.path.exists(".shoundremrc"):
    shutil.copyfile(os.path.join(birchenv.BIRCH, "java", "Leash", "shoundremrc"), os.path.join(os.getcwd(), ".shoundremrc"))

h_INFILE  = open(sys.argv[1], "r")
h_OUTFILE = open(sys.argv[2], "w")
TEMPFILE  = "leash." + os.getpid()

for name in h_INFILE:
    print name
    command = ["java", "-jar", os.path.join(birchenv.BIRCH, "java", "Leash", "Leash.jar"), "-mpi", name]
    command[5:] = sys.argv[3:]
    command[-1:] = [command[-1][0], "-of", TEMPFILE]
    subprocess.call(command)
    birchscript.cat_to(TEMPFILE, h_OUTFILE)

h_OUTFILE.close()
h_INFILE.close()
os.remove(LOCK)
os.remove(TEMPFILE)

COUNT = 0
for file in os.listdir(os.getcwd()):
    if file.startswith("leash.lock"):
        COUNT += 1
if COUNT == 0:
    os.remove(".shoundremrc")