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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm, Andreas Bertsch $
// --------------------------------------------------------------------------
#include <OpenMS/config.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/VALIDATORS/SemanticValidator.h>
#include <OpenMS/FORMAT/CVMappingFile.h>
#include <OpenMS/FORMAT/ControlledVocabulary.h>
#include <OpenMS/DATASTRUCTURES/CVMappings.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_SemanticValidator SemanticValidator
@brief SemanticValidator for analysisXML and mzML files.
This util is able to validate analysisXML and mzML files
using an instance document and a mapping file.
<B>The command line parameters of this tool are:</B>
@verbinclude UTILS_SemanticValidator.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_SemanticValidator.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPSemanticValidator :
public TOPPBase
{
public:
TOPPSemanticValidator() :
TOPPBase("SemanticValidator", "SemanticValidator for analysisXML and mzML files.", false)
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "Input file, either analysisXML or mzML.");
setValidFormats_("in", StringList::create("analysisXML,mzML"));
registerInputFile_("mapping_file", "<file>", "", "Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates).");
setValidFormats_("mapping_file", StringList::create("xml"));
}
ExitCodes main_(int, const char**)
{
String in_file = getStringOption_("in");
String mapping_file = getStringOption_("mapping_file");
CVMappings mappings;
CVMappingFile().load(mapping_file, mappings, false);
ControlledVocabulary cv;
cv.loadFromOBO("PSI-MOD", File::find("/CHEMISTRY/PSI-MOD.obo"));
cv.loadFromOBO("PATO", File::find("/CV/quality.obo"));
cv.loadFromOBO("UO", File::find("/CV/unit.obo"));
cv.loadFromOBO("brenda", File::find("/CV/brenda.obo"));
cv.loadFromOBO("GO", File::find("/CV/goslim_goa.obo"));
cv.loadFromOBO("UNIMOD", File::find("/CV/unimod.obo"));
cv.loadFromOBO("PSI-MS", File::find("/CV/psi-ms.obo"));
// check cv params
Internal::SemanticValidator semantic_validator(mappings, cv);
semantic_validator.setCheckTermValueTypes(true);
semantic_validator.setCheckUnits(true);
StringList errors, warnings;
/*bool valid =*/ semantic_validator.validate(in_file, errors, warnings);
for (Size i = 0; i < warnings.size(); ++i)
{
cout << "Warning: " << warnings[i] << endl;
}
for (Size i = 0; i < errors.size(); ++i)
{
cout << "Error: " << errors[i] << endl;
}
if (warnings.empty() && errors.empty())
{
cout << "Congratulations, the file is valid!" << endl;
}
return EXECUTION_OK;
}
};
int main(int argc, const char** argv)
{
TOPPSemanticValidator tool;
return tool.main(argc, argv);
}
/// @endcond
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