callExternalValidator.cpp

Example that shows how to call an external program for validation.

Example that shows how to call an external program for validation.

/**
 * @file    callExternalValidator.cpp
 * @brief   Example that shows how to call an external program for 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
 * 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 <string>
#include <vector>
#include <sbml/SBMLTypes.h>
 
#include <sbml/validator/SBMLExternalValidator.h>
 
using namespace std;
LIBSBML_CPP_NAMESPACE_USE
 
int
main (int argc, char *argv[])
{
  if (argc < 3)
  {
    cout << endl << "Usage: callExternalValidator filename externalValidator [ tempSBMLFile outputFile [ ADDITIONAL-ARGS] ]" << endl << endl;
    return 1;
  }
 
  string filename   = argv[1];  
 
  // read additional args
  string externalValidator = argv[2];
 
  string tempSBMLFileName = filename + "_temp.xml";
  if (argc > 3)
    tempSBMLFileName = argv[3];
 
  string outputFile = filename + "_out.xml";
  if (argc > 4)
    outputFile = argv[4];
 
  vector<string> additionalArgs;
  for (int i = 5; i < argc; i++)
    additionalArgs.push_back(argv[i]);
 
  // add the output file as additional arg
  additionalArgs.push_back(outputFile);
 
   // read the file name
  SBMLDocument* document = readSBML(filename.c_str());
 
  // create a new external validator that will write the model to 
  // tempFile, then call teh externalValidator with the given number of arguments
  // to produce the output file. This output file will then be parsed and its
  // errors will be added to the error log.
  SBMLExternalValidator validator;
 
  validator.setProgram(externalValidator);
  validator.setSBMLFileName(tempSBMLFileName);
  validator.setOutputFileName(outputFile);
  validator.setArguments(additionalArgs);
 
  // this means that the external program will be called with the following arguments
  // 
  //    externalValidator tempSBMLFileName additionalArgs
  //
  // (where additionalargs contains the output file as last argument)
  //
  // The output file that is generated should be an XML document following the 
  // Validator XML format as described here: http://sbml.org/validator/api/#xml
  //
 
  // disable all regular checks
  document->setApplicableValidators(0);
 
  // add a custom validator
  document->addValidator(&validator);
 
  // check consistency like before
  int numErrors = document->checkConsistency();
 
  // print errors and warnings
  document->printErrors();
 
  delete document;
 
  // return number of errors
  return  numErrors;
 
 
}