/**
 * @file    flattenModelAdvanced.cpp
 * @brief   advanced SBML hierarchical composition flattening example
 *          if an SBase element has a name, this name will also hint 
 *          where the element came from. 
 *           
 * @author  Sarah Keating
 * @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) 2013-2018 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.
 *
 * Permission is hereby granted, free of charge, to any person obtaining a
 * 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
 * Software is furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
 * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 * DEALINGS IN THE SOFTWARE.
 *
 * 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
 * or promote products derived from this software without specific prior
 * written permission.
 * ------------------------------------------------------------------------ -->
 */

#include <iostream>
#include <sstream>

#include <sbml/SBMLTypes.h>
#include <sbml/extension/SBMLExtensionRegister.h>
#include <sbml/conversion/SBMLConverterRegistry.h>
#include <sbml/util/PrefixTransformer.h>

#ifdef  LIBSBML_HAS_PACKAGE_COMP
#include <sbml/packages/comp/common/CompExtensionTypes.h>
#else
#error This example requires libSBML to be compiled with support for COMP.
#endif


LIBSBML_CPP_NAMESPACE_USE
using namespace std;

const string usage = "Usage: flattenModelAdvanced [-p] inputFile outputFile\n"
" -p : list unused ports";


class CPrefixNameTransformer : public PrefixTransformer
{
public:
  CPrefixNameTransformer() {}

  static void replaceStringInPlace(std::string& subject, const std::string& search,
  const std::string& replace)
  {
    size_t pos = 0;

    while ((pos = subject.find(search, pos)) != std::string::npos)
    {
      subject.replace(pos, search.length(), replace);
      pos += replace.length();
    }
  }

  static inline std::string &rtrim(std::string &str)
  {
    size_t endpos = str.find_last_not_of(" \t");

    if (string::npos != endpos)
    {
      str = str.substr(0, endpos + 1);
    }

    return str;
  }

  const std::string& cleanName(std::string& prefix)
  {
    std::replace(prefix.begin(), prefix.end(), '_', ' ');
    replaceStringInPlace(prefix, "  ", " ");
    rtrim(prefix);
    return prefix;
  }

  virtual int transform(SBase* element)
  {
    if (element == NULL || getPrefix().empty())
    return LIBSBML_OPERATION_SUCCESS;

    // set up ids
    // this will rename the SIds and SIdRefs as
    // the comp flattening routine does by default
    PrefixTransformer::transform(element);

    // skip local parameters, as they are not renamed
    if (element->getTypeCode() == SBML_LOCAL_PARAMETER)
    return LIBSBML_OPERATION_SUCCESS;

    // setup names
    // here we want to rename the name attribute to also indicate if
    // the element came from a subModel
    if (element->isSetName())
    {
      std::stringstream newName;
      std::string prefix = getPrefix();
      newName << element->getName() << " (" << cleanName(prefix) << ")";
      element->setName(newName.str());
    }

    return LIBSBML_OPERATION_SUCCESS;
  }
};


int main(int argc,char** argv)
{
  bool leavePorts = false;
  if (argc < 3)
  {
    cout << usage << endl;
    return 1;
  }
  else if (argc == 3)
  {
    if ( string("-p") == string(argv[1]) )
    {
      cout << usage << endl;
      return 1;
    }       
  }

  int  argIndex = 1;

  if ( string("-p") == string(argv[1]) )
  {
    leavePorts = true;
    ++argIndex;
  }     

  if (SBMLExtensionRegistry::isPackageEnabled("comp") == false)
  {
    cerr << "The version of libsbml being used does not have the comp"
         << " package code enabled" << endl;
    return 1;
  }

  const char* inputFile   = argv[argIndex];
  const char* outputFile  = argv[argIndex+1];

  SBMLDocument* document = readSBML(inputFile);

  if (document->getNumErrors(LIBSBML_SEV_ERROR) > 0)
  {
    cerr << "Encountered the following SBML errors:" << endl;
    document->printErrors(cerr);
    return 1;
  }

  // add the advanced prefix transformer to the comp plugin
  // this transformer will be used during the flattening process
  // to rename SIds and SIdRefs (as would happen by default)
  // but allows the user to specify other changes that they
  // may wish to be made (e.g. rename the name attribute)
  CompModelPlugin* mPlug = dynamic_cast<CompModelPlugin*>(document->getModel()->getPlugin("comp"));
  CPrefixNameTransformer trans;

  if (mPlug != NULL)
  {
    mPlug->setTransformer(&trans);
  }

  ConversionProperties* props = new ConversionProperties();

  props->addOption("flatten comp");
  props->addOption("leavePorts", leavePorts);

  SBMLConverter* converter = 
  SBMLConverterRegistry::getInstance().getConverterFor(*props);


  converter->setDocument(document);

  // NOTE: after a call to convert, the comp model plugin pointer 
  // is no longer valid and has to be retrieved again. 
  int result = converter->convert();

  if (result != LIBSBML_OPERATION_SUCCESS)
  {
    cerr << "Conversion failed\n";
    document->printErrors();
  }
  
  writeSBML(document, outputFile);

  delete converter;
  delete document;

}