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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 $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/FORMAT/VALIDATORS/XMLValidator.h>
#include <OpenMS/FORMAT/CompressedInputSource.h>
#include <xercesc/sax2/SAX2XMLReader.hpp>
#include <xercesc/framework/LocalFileInputSource.hpp>
#include <xercesc/sax2/XMLReaderFactory.hpp>
#include <fstream>
#include <iomanip> // setprecision etc.
using namespace std;
namespace OpenMS
{
namespace Internal
{
/// This class ensures that the reset() method of the XMLHandler is called when it goes out of scope.
/// useful when used in exeption handling
class XMLCleaner_
{
public:
explicit XMLCleaner_(XMLHandler * handler) :
p_(handler)
{
}
~XMLCleaner_()
{
p_->reset();
}
private:
XMLHandler * p_;
};
XMLFile::XMLFile()
{
}
XMLFile::XMLFile(const String & schema_location, const String & version) :
schema_location_(schema_location),
schema_version_(version)
{
}
XMLFile::~XMLFile()
{
}
void XMLFile::enforceEncoding_(const String& encoding)
{
enforced_encoding_ = encoding;
}
void XMLFile::parse_(const String & filename, XMLHandler * handler)
{
// ensure handler->reset() is called to save memory (in case the XMLFile reader, e.g. FatureXMLFile, is used again)
XMLCleaner_ clean(handler);
//try to open file
if (!File::exists(filename))
{
throw Exception::FileNotFound(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);
}
// initialize parser
try
{
xercesc::XMLPlatformUtils::Initialize();
}
catch (const xercesc::XMLException & toCatch)
{
throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, "", String("Error during initialization: ") + StringManager().convert(toCatch.getMessage()));
}
xercesc::SAX2XMLReader * parser = xercesc::XMLReaderFactory::createXMLReader();
parser->setFeature(xercesc::XMLUni::fgSAX2CoreNameSpaces, false);
parser->setFeature(xercesc::XMLUni::fgSAX2CoreNameSpacePrefixes, false);
parser->setContentHandler(handler);
parser->setErrorHandler(handler);
//is it bzip2 or gzip compressed?
std::ifstream file(filename.c_str());
char bz[2];
file.read(bz, 2);
xercesc::InputSource * source;
char g1 = 0x1f;
char g2 = 0;
g2 |= 1 << 7;
g2 |= 1 << 3;
g2 |= 1 << 1;
g2 |= 1 << 0;
//g2 = static_cast<char>(0x8b); // can make troubles if it is casted to 0x7F which is the biggest number signed char can save
if ((bz[0] == 'B' && bz[1] == 'Z') || (bz[0] == g1 && bz[1] == g2))
{
source = new CompressedInputSource(StringManager().convert(filename.c_str()), bz);
}
else
{
source = new xercesc::LocalFileInputSource(StringManager().convert(filename.c_str()));
}
// what if no encoding given http://xerces.apache.org/xerces-c/apiDocs-3/classInputSource.html
if (!enforced_encoding_.empty())
{
static const XMLCh* s_enc = xercesc::XMLString::transcode(enforced_encoding_.c_str());
source->setEncoding(s_enc);
}
// try to parse file
try
{
parser->parse(*source);
delete(parser);
delete source;
}
catch (const xercesc::XMLException & toCatch)
{
throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, "", String("XMLException: ") + StringManager().convert(toCatch.getMessage()));
}
catch (const xercesc::SAXException & toCatch)
{
throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, "", String("SAXException: ") + StringManager().convert(toCatch.getMessage()));
}
catch (const XMLHandler::EndParsingSoftly & /*toCatch*/)
{
//nothing to do here, as this exception is used to softly abort the parsing for whatever reason.
}
}
void XMLFile::save_(const String & filename, XMLHandler * handler) const
{
std::ofstream os(filename.c_str());
//set high precision for writing of floating point numbers
os.precision(writtenDigits(DoubleReal()));
if (!os)
{
throw Exception::UnableToCreateFile(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);
}
// write data and close stream
handler->writeTo(os);
os.close();
}
void writeXMLEscape(const String & to_escape, ostream & os)
{
XMLCh * xmlch = xercesc::XMLString::transcode(to_escape.c_str());
std::string out = "";
OpenMSXMLFormatTarget ft(out);
xercesc::XMLFormatter f("UTF-8", /* XMLUni::fgVersion1_1 */ "1.1", &ft);
f << xercesc::XMLFormatter::StdEscapes << xmlch;
os << out;
xercesc::XMLString::release(&xmlch);
return;
}
String writeXMLEscape(const String & to_escape)
{
stringstream ss;
writeXMLEscape(to_escape, ss);
return String(ss.str());
}
String encodeTab(const String & to_encode)
{
String _copy = to_encode;
_copy.substitute("\t", "	");
return _copy;
}
bool XMLFile::isValid(const String & filename, std::ostream & os)
{
if (schema_location_.empty())
{
throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
}
String current_location = File::find(schema_location_);
return XMLValidator().isValid(filename, current_location, os);
}
const String & XMLFile::getVersion() const
{
return schema_version_;
}
} // namespace Internal
} // namespace OpenMS
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