#!/usr/bin/env python3

#import birchenv
import copy
import os
import os.path
import subprocess
import sys

# Wrapper for tbl2asn March 3, 2020
"""
We need to run tbl2asn through a wrapper because the NCBI tbl2asn
binary needs one or more libraries, including libidn.so.11.
The solution is to run tbl2asn from a script that puts the libraries
into LD_LIBRARY_PATH or DYLD_LIBRARY_PATH. 
Using a bash script,I have been unable to get tbl2asn from a  to run
using the -j option, escaping in all possible ways single and double quotes.
For some reason, running tbl2asn works from a Python script.  
"""

if 'BIRCH' in os.environ:
    BIRCH = os.environ.get('BIRCH')
    print('BIRCH=' + BIRCH)
else :
    print('tbl2asn.py: BIRCH environment variable not set')
    exit(1)

if 'BIRCH_PLATFORM' in os.environ:
    BIRCH_PLATFORM = os.environ.get('BIRCH_PLATFORM')
    print('BIRCH_PLATFORM=' + BIRCH_PLATFORM)

#if 'LD_LIBRARY_PATH' in os.environ:
#    LD_LIBRARY_PATH = os.environ.get('LD_LIBRARY_PATH')
#else:
#    LD_LIBRARY_PATH = ""
#print('LD_LIBRARY_PATH=' + LD_LIBRARY_PATH)

if BIRCH_PLATFORM == 'osx-x86_64':
    DYLD_LIBRARY_PATH = os.path.join(BIRCH, 'lib-' + BIRCH_PLATFORM, 'tbl2asn')
    print('DYLD_LIBRARY_PATH=' + DYLD_LIBRARY_PATH)  
    os.environ["DYLD_LIBRARY_PATH"] = DYLD_LIBRARY_PATH
elif BIRCH_PLATFORM == 'macos-arm64':
    DYLD_LIBRARY_PATH = os.path.join(BIRCH, 'lib-' + BIRCH_PLATFORM, 'tbl2asn')
    print('DYLD_LIBRARY_PATH=' + DYLD_LIBRARY_PATH)  
    os.environ["DYLD_LIBRARY_PATH"] = DYLD_LIBRARY_PATH
elif BIRCH_PLATFORM == "linux-x86_64":
    LD_LIBRARY_PATH = os.path.join(BIRCH, 'lib-' + BIRCH_PLATFORM, 'tbl2asn')
    print('LD_LIBRARY_PATH=' + LD_LIBRARY_PATH)  
    os.environ["LD_LIBRARY_PATH"] = LD_LIBRARY_PATH
else :
    print("Platform " + BIRCH_PLATFORM + "not supported.")
    exit 
    
cmd_run = copy.copy(sys.argv)
cmd_run[0] = 'tbl2asn.bin'
print(cmd_run)
subprocess.call(cmd_run, env=os.environ)