/**
 * \file    addingEvidenceCodes_1.cpp
 * \brief   adds controlled vocabulary terms to a reaction in a model
 * \author  Sarah Keating
 *
 * <!--------------------------------------------------------------------------
 * 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
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 */

#include <iostream>
#include <sbml/SBMLTypes.h>

#include <sbml/annotation/CVTerm.h>
using namespace std;
LIBSBML_CPP_NAMESPACE_USE

int
main (int argc, char *argv[])
{

  SBMLDocument* d;
  unsigned int  errors, n;
  Reaction *r;

  if (argc != 3)
  {
    cout << endl
         << "  usage: addingEvidenceCodes_1 <input-filename> <output-filename>" << endl
         << "  Adds controlled vocabulary term to a reaction"        << endl
         << endl;
    return 2;
  }


  d      = readSBML(argv[1]);
  errors = d->getNumErrors();

  if (errors > 0)
  {
    cout << "Read Error(s):" << endl;
	  d->printErrors(cout);

    cout << "Correct the above and re-run." << endl;
  }
  else
  {
  
    n = d->getModel()->getNumReactions();
    
    if (n <= 0)
    {
      cout << "Model has no reactions.\n Cannot add CV terms\n";
    }
    else
    {
      r = d->getModel()->getReaction(0);

      /* check that the reaction has a metaid
       * no CVTerms will be added if there is no metaid to reference
       */
      if (!r->isSetMetaId())
        r->setMetaId("metaid_0000052");

      CVTerm * cv1 = new CVTerm(BIOLOGICAL_QUALIFIER);
      cv1->setBiologicalQualifierType(BQB_IS_DESCRIBED_BY);
      cv1->addResource("urn:miriam:obo.eco:ECO%3A0000183");

      r->addCVTerm(cv1);
      delete cv1;

      CVTerm * cv2 = new CVTerm(BIOLOGICAL_QUALIFIER);
      cv2->setBiologicalQualifierType(BQB_IS);
      cv2->addResource("urn:miriam:kegg.reaction:R00756");
      cv2->addResource("urn:miriam:reactome:REACT_736");

      r->addCVTerm(cv2);
      delete cv2;

      writeSBML(d, argv[2]);
    }
  }

  delete d;
  return errors;
}
