#
# @file    flattenModel.R
# @brief   Flattens the comp code from the given SBML file.
# @author  Frank 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) 2013-2018 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"),
# to deal in the Software without restriction, including without limitation
# 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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# of Heidelberg, nor the names of any contributors, may be used to endorse
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#
#
# Usage: R --slave -f flattenModel.R --args <full path to input file> <full path to output file>
#
#
library(libSBML)

args <- commandArgs(trailingOnly = TRUE)

if (length(args) != 2)
{
  stop("Usage: flattenModel input-filename output-filename\n");
}

doc = readSBML(args[1]);

if (SBMLDocument_getNumErrors(doc) > 0) {
  SBMLDocument_printErrors(doc);
} else {
  props = ConversionProperties();
  ConversionProperties_addOption(props, "flatten comp", TRUE, "flatten comp");
  ConversionProperties_addOption(props, "leavePorts", FALSE, "Leave unused ports");
  if (SBMLDocument_convert(doc, props) != 0) {
	  SBMLDocument_printErrors(doc);
  	stop("Error: conversion failed...\n");
  }
  writeSBML(doc, args[2]);
}

