addCustomValidator.cpp

Example of creating a custom validator to be called during validation.

Example of creating a custom validator to be called during validation.

/**
 * @file    addCustomValidator.cpp
 * @brief   Example creating a custom validator to be called during validation
 * @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
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 * 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
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 */
 
#include <iostream>
#include <sbml/SBMLTypes.h>
 
#include <sbml/validator/SBMLValidator.h>
 
 
 
using namespace std;
LIBSBML_CPP_NAMESPACE_USE
 
/** 
 * Declares a custom validator to be called. This allows you to validate 
 * any aspect of an SBML Model that you want to be notified about. You could 
 * use this to notify your application that a model contains an unsupported 
 * feature of SBML (either as warning). 
 * 
 * In this example the validator will go through the model and test for the 
 * presence of 'fast' reactions and algebraic rules. If either is used a 
 * warning will be added to the error log. 
 */
class MyCustomValidator : public SBMLValidator
{
public:
  // Implicitly defined constructors are adequate here
 
  virtual SBMLValidator* clone() const { return new MyCustomValidator(*this); }
 
  virtual unsigned int validate() {
    // if we don't have a model we don't apply this validator.
    if (getDocument() == NULL || getModel() == NULL)
      return 0;
 
    // if we have no rules and reactions we don't apply this validator either
    if (getModel()->getNumReactions() == 0 && getModel()->getNumRules() == 0)
      return 0;
 
    unsigned int numErrors = 0;
    // test for algebraic rules
    for (unsigned int i = 0; i < getModel()->getNumRules(); i++)
    {
      if (getModel()->getRule(i)->getTypeCode() == SBML_ALGEBRAIC_RULE) {
        
        getErrorLog()->add(SBMLError(99999, 3, 1, 
          "This model uses algebraic rules, however this application does not support them.",
          0, 0, 
          LIBSBML_SEV_WARNING, // or LIBSBML_SEV_ERROR if you want to stop
          LIBSBML_CAT_SBML // or whatever category you prefer
          ));
        
        numErrors++;
      }
    }
 
    // test for fast reactions
    for (unsigned int i = 0; i < getModel()->getNumReactions(); i++)
    {
      // test whether value is set, and true
      if (getModel()->getReaction(i)->isSetFast() && 
          getModel()->getReaction(i)->getFast()) {
 
        getErrorLog()->add(SBMLError(99999, 3, 1, 
          "This model uses fast reactions, however this application does not support them.",
          0, 0, 
          LIBSBML_SEV_WARNING, // or LIBSBML_SEV_ERROR if you want to stop
          LIBSBML_CAT_SBML // or whatever category you prefer
          ));
 
        numErrors++;
 
      }
    }
 
    return numErrors;
  }
 
};
 
 
int
main (int argc, char *argv[])
{
  if (argc != 2)
  {
    cout << endl << "Usage: addCustomValidator filename" << endl << endl;
    return 1;
  }
  
  const char* filename   = argv[1];
 
  // read the file name
  SBMLDocument* document = readSBML(filename);
 
  // add a custom validator
  MyCustomValidator* myCustomValidator = new MyCustomValidator();
  document->addValidator(myCustomValidator);
  delete myCustomValidator;
 
  // check consistency like before
  int numErrors = document->checkConsistency();
 
  // print errors and warnings
  document->printErrors();
  delete document;
 
  // return number of errors
  return  numErrors;
}