#!/usr/bin/env python
##
## @file    convertCobraToFbc.py
## @brief   Convert COBRA L2 to L3 with FBC
## @author  Frank T. Bergmann
##
##
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
## of libSBML.  This program uses the open-source MIT license, as follows:
##
## Copyright (c) 2013-2017 by the California Institute of Technology
## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
## and the University of Heidelberg (Germany), with support from the National
## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
##
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## copy of this software and associated documentation files (the "Software"),
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## the rights to use, copy, modify, merge, publish, distribute, sublicense,
## and/or sell copies of the Software, and to permit persons to whom the
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##
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## all copies or substantial portions of the Software.
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## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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## Neither the name of the California Institute of Technology (Caltech), nor
## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
## of Heidelberg, nor the names of any contributors, may be used to endorse
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import sys
import os.path
import libsbml

def main (args):
  """usage: convertCobraToFbc.py input-filename output-filename
  """
  if len(args) != 3:
    print(main.__doc__)
    sys.exit(1)

  infile  = args[1]
  outfile = args[2]

  if not os.path.exists(infile):
    print("[Error] %s : No such file." % (infile))
    sys.exit(1)

  reader  = libsbml.SBMLReader()
  writer  = libsbml.SBMLWriter()
  sbmldoc = reader.readSBML(infile)

  if sbmldoc.getNumErrors() > 0:
    if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
      # Handle case of unreadable file here.
      sbmldoc.printErrors()
    elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
      # Handle case of other file error here.
      sbmldoc.printErrors()
    else:
      # Handle other error cases here.
      sbmldoc.printErrors()

    sys.exit(1)

  props = libsbml.ConversionProperties()
  props.addOption("convert cobra", True, "Convert Cobra model")
  result = sbmldoc.convert(props)
  if (result != libsbml.LIBSBML_OPERATION_SUCCESS):
	print("[Error] Conversion failed... (%d)" %(result))
	sys.exit(1)

  writer.writeSBML(sbmldoc, outfile)
  print("[OK] converted file %s to %s" % (infile, outfile))

if __name__ == '__main__':
  main(sys.argv)
