callExternalValidator.cs

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.
 *
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 * 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:
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 * all copies or substantial portions of the Software.
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 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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 * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
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using System;
using System.Collections.Generic;
using libsbmlcs;

internal class CallExternalValidator
{
    public static int Main(string[] args)
    {
        if (args.Length < 3)
        {
            Console.WriteLine("Usage: callExternalValidator filename externalValidator [ tempSBMLFile outputFile [ ADDITIONAL-ARGS] ]");
            return 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 List<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);
        foreach (string item in 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(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
        return numErrors;


    }
}