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/**
* @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.
* ------------------------------------------------------------------------ -->
*/
import java.util.List;
import java.util.Vector;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLExternalValidator;
import org.sbml.libsbml.libsbml;
public class callExternalValidator {
public static void main(String[] args) {
System.loadLibrary("sbmlj");
if (args.length < 3) {
System.out
.println("Usage: callExternalValidator filename externalValidator [ tempSBMLFile outputFile [ ADDITIONAL-ARGS] ]");
System.exit(1);
}
String filename = args[0];
// read additional args
String externalValidator = args[1];
String tempSBMLFileName = filename + "_temp.xml";
if (args.length > 2)
tempSBMLFileName = args[2];
String outputFile = filename + "_out.xml";
if (args.length > 3)
outputFile = args[3];
List<String> additionalArgs = new Vector<String>();
for (int i = 4; i < args.length; i++)
additionalArgs.add(args[i]);
// add the output file as additional arg
additionalArgs.add(outputFile);
// read the file name
SBMLDocument document = libsbml.readSBML(filename);
// 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 = new SBMLExternalValidator();
validator.setProgram(externalValidator);
validator.setSBMLFileName(tempSBMLFileName);
validator.setOutputFileName(outputFile);
for (String item : additionalArgs) {
validator.addArgument(item);
}
// 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((short) 0);
// add a custom validator
document.addValidator(validator);
// check consistency like before
int numErrors = (int) document.checkConsistency();
// print errors and warnings
document.printErrors();
// return number of errors
System.exit(numErrors);
}
}
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