libSBML C++ API  5.18.0
validateSBML.cpp

Validates one or more SBML files.

/**
* @file validateSBML.cpp
* @brief Validates an SBML file against the appropriate schema
* @author Sarah Keating
* @author Ben Bornstein
* @author Michael Hucka
* @author Akiya Jouraku
*
* <!--------------------------------------------------------------------------
* 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 <sstream>
#include <sbml/SBMLTypes.h>
#include "util.h"
using namespace std;
bool validateSBML(const string& filename, bool enableUnitCheck=true);
const string usage = "Usage: validateSBML [-u] filename [...]\n"
" -u : disable unit consistency check";
#ifdef WIN32
#include <conio.h>
/**
* Basic callback class that interrupts reading the document upon a keypress
*/
class ProcessingCB : public Callback
{
public:
virtual int process(SBMLDocument* doc)
{
if (kbhit())
}
};
#endif // WIN32
int
main (int argc, char* argv[])
{
bool enableUnitCheck = true;
if (argc < 2)
{
cout << usage << endl;
return 1;
}
else if (argc == 2)
{
if ( string("-u") == string(argv[1]) )
{
cout << usage << endl;
return 1;
}
}
# ifdef WIN32
ProcessingCB cb;
CallbackRegistry::addCallback(&cb);
cout << "(Registered callback, press any key to interrupt validation)" << endl;
#endif
int argIndex = 1;
if ( string("-u") == string(argv[1]) )
{
enableUnitCheck = false;
++argIndex;
}
int numInvalidFiles = 0;
for (int i=argIndex; i < argc; i++)
{
if (!validateSBML(argv[i], enableUnitCheck))
++numInvalidFiles;
cout << "---------------------------------------------------------------------------\n";
}
int numFiles = (enableUnitCheck) ? argc - 1 : argc - 2;
cout << "Validated " << numFiles << " files, " << (numFiles - numInvalidFiles) << " valid files, "
<< numInvalidFiles << " invalid files" << endl;
if (!enableUnitCheck)
cout << "(Unit consistency checks skipped)" << endl;
return numInvalidFiles;
}
bool validateSBML(const string& filename, bool enableUnitCheck)
{
SBMLDocument* document;
SBMLReader reader;
#ifdef __BORLANDC__
unsigned long start, stop;
#else
unsigned long long start, stop;
#endif
start = getCurrentMillis();
document = reader.readSBML(filename);
stop = getCurrentMillis();
double timeRead = (double)(stop - start);
unsigned int errors = document->getNumErrors();
bool seriousErrors = false;
unsigned int numReadErrors = 0;
unsigned int numReadWarnings = 0;
string errMsgRead = "";
if (errors > 0)
{
for (unsigned int i = 0; i < errors; i++)
{
if (document->getError(i)->isFatal() || document->getError(i)->isError())
{
seriousErrors = true;
++numReadErrors;
break;
}
else
++numReadWarnings;
}
ostringstream oss;
document->printErrors(oss);
errMsgRead = oss.str();
}
// If serious errors are encountered while reading an SBML document, it
// does not make sense to go on and do full consistency checking because
// the model may be nonsense in the first place.
unsigned int numCCErrors = 0;
unsigned int numCCWarnings = 0;
string errMsgCC = "";
bool skipCC = false;
double timeCC = 0.0;
bool isValid = true;
if (seriousErrors)
{
skipCC = true;
isValid = false;
errMsgRead += "Further consistency checking and validation aborted.";
}
else
{
unsigned int failures = 0;
start = getCurrentMillis();
failures = document->checkConsistency();
stop = getCurrentMillis();
timeCC = (double)(stop - start);
if (failures > 0)
{
for (unsigned int i = 0; i < failures; i++)
{
if (document->getError(i)->isFatal() || document->getError(i)->isError())
{
++numCCErrors;
isValid = false;
}
else
++numCCWarnings;
}
ostringstream oss;
document->printErrors(oss);
errMsgCC = oss.str();
}
}
//
// Print Results
//
cout << " filename : " << filename << endl;
cout << " file size (byte) : " << getFileSize(filename.c_str()) << endl;
cout << " read time (ms) : " << timeRead << endl;
if (!skipCC)
{
cout << " c-check time (ms) : " << timeCC << endl;
}
else
{
cout << " c-check time (ms) : skipped" << endl;
}
cout << " validation error(s) : " << numReadErrors + numCCErrors << endl;
if (!skipCC)
cout << " (consistency error(s)): " << numCCErrors << endl;
else
cout << " (consistency error(s)): skipped" << endl;
cout << " validation warning(s) : " << numReadWarnings + numCCWarnings << endl;
if (!skipCC)
cout << " (consistency warning(s)): " << numCCWarnings << endl;
else
cout << " (consistency warning(s)): skipped" << endl;
if ( !errMsgRead.empty() || !errMsgCC.empty() )
{
cout << "\n===== validation error/warning messages =====\n";
if (!errMsgRead.empty())
cout << errMsgRead << endl;
if (!errMsgCC.empty())
{
cout << "\n*** consistency check ***\n";
cout << errMsgCC << endl;
}
}
delete document;
return (isValid) ? true: false;
}