#!/usr/bin/env python
##
## @file    flattenArrays.py
## @brief   Flattens the arrays code from the given SBML file.
## @author  Brett G. Olivier
##
##
## <!--------------------------------------------------------------------------
## 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,
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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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## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
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import sys
import os.path
import libsbml

def main (args):
    """usage: flattenArrays.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] {} : No such file.".format(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("flatten arrays", True, "flatten arrays")
    # Optional: validate flattened file ... may take some time
    # props.addOption("performValidation", True, "perform validation before and after trying to flatten")

    result = sbmldoc.convert(props)
    if (result != libsbml.LIBSBML_OPERATION_SUCCESS):
        print("[Error] Array flattening failed... ({})".format(result))
        sys.exit(1)

    writer.writeSBML(sbmldoc, outfile)
    print("[OK] Flattened arrays file {} to {}".format(infile, outfile))

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