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//
// $Id$
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2007 Spielberg Family Center for Applied Proteomics
// Cedars-Sinai Medical Center, Los Angeles, California 90048
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#define PWIZ_SOURCE
#include "XMLWriter.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "boost/iostreams/filtering_stream.hpp"
#include "boost/iostreams/filter/counter.hpp"
#include <boost/spirit/include/karma.hpp>
namespace pwiz {
namespace minimxml {
template <typename T>
struct double12_policy : boost::spirit::karma::real_policies<T>
{
// we want to generate up to 12 fractional digits
static unsigned int precision(T) { return 12; }
};
PWIZ_API_DECL void XMLWriter::Attributes::add(const string& name, const double& valueRef)
{
double value = valueRef;
// HACK: karma has a stack overflow on subnormal values, so we clamp to normalized values
if (value > 0)
value = max(numeric_limits<double>::min(), value);
else if (value < 0)
value = min(-numeric_limits<double>::min(), value);
using namespace boost::spirit::karma;
typedef real_generator<double, double12_policy<double> > double12_type;
static const double12_type double12 = double12_type();
char buffer[256];
char* p = buffer;
generate(p, double12, value);
*p = '\0';
push_back(make_pair(name, std::string(&buffer[0], p)));
}
PWIZ_API_DECL void XMLWriter::Attributes::add(const string& name, const int& value)
{
using namespace boost::spirit::karma;
static const int_generator<int> intgen = int_generator<int>();
char buffer[256];
char* p = buffer;
generate(p, intgen, value);
*p = '\0';
push_back(make_pair(name, std::string(&buffer[0], p)));
}
class XMLWriter::Impl
{
public:
Impl(ostream& os, const Config& config);
void pushStyle(unsigned int flags);
void popStyle();
void processingInstruction(const string& name, const string& data);
void startElement(const string& name,
const Attributes& attributes,
EmptyElementTag emptyElementTag);
void endElement();
void characters(const string& text, bool autoEscape);
bio::stream_offset position() const;
bio::stream_offset positionNext() const;
private:
ostream& os_;
Config config_;
stack<string> elementStack_;
stack<unsigned int> styleStack_;
string indentation() const {return string(elementStack_.size()*config_.indentationStep, ' ');}
string indentation(size_t depth) const {return string(depth*config_.indentationStep, ' ');}
bool style(StyleFlag styleFlag) const {return styleStack_.top() & styleFlag ? true : false;}
};
XMLWriter::Impl::Impl(ostream& os, const Config& config)
: os_(os), config_(config)
{
styleStack_.push(config.initialStyle);
}
void XMLWriter::Impl::pushStyle(unsigned int flags)
{
styleStack_.push(flags);
}
void XMLWriter::Impl::popStyle()
{
styleStack_.pop();
if (styleStack_.empty())
throw runtime_error("[XMLWriter] Style stack underflow.");
}
void XMLWriter::Impl::processingInstruction(const string& name, const string& data)
{
ostream* os = &os_;
if (config_.outputObserver) os = new ostringstream;
*os << indentation() << "<?" << name << " " << data << "?>\n";
if (config_.outputObserver)
{
config_.outputObserver->update(static_cast<ostringstream*>(os)->str());
os_ << static_cast<ostringstream*>(os)->str();
delete os;
}
}
void writeEscapedAttributeXML(ostream& os, const string& str)
{
for (size_t i=0, end=str.size(); i < end; ++i)
{
const char& c = str[i];
switch (c)
{
case '&': os << "&"; break;
case '"': os << """; break;
case '\'': os << "'"; break;
case '<': os << "<"; break;
case '>': os << ">"; break;
default: os << c; break;
}
}
}
void writeEscapedTextXML(ostream& os, const string& str)
{
for (size_t i=0, end=str.size(); i < end; ++i)
{
const char& c = str[i];
switch (c)
{
case '&': os << "&"; break;
case '<': os << "<"; break;
case '>': os << ">"; break;
default: os << c; break;
}
}
}
void XMLWriter::Impl::startElement(const string& name,
const Attributes& attributes,
EmptyElementTag emptyElementTag)
{
ostream* os = &os_;
if (config_.outputObserver) os = new ostringstream;
if (!style(StyleFlag_InlineOuter))
*os << indentation();
*os << "<" << name;
string attributeIndentation(name.size()+1, ' ');
for (Attributes::const_iterator it=attributes.begin(); it!=attributes.end(); ++it)
{
*os << " " << it->first << "=\"";
writeEscapedAttributeXML(*os, it->second);
*os << "\"";
if (style(StyleFlag_AttributesOnMultipleLines) && (it+1)!=attributes.end())
*os << "\n" << indentation() << attributeIndentation;
}
*os << (emptyElementTag==EmptyElement ? "/>" : ">");
if (!style(StyleFlag_InlineInner) ||
(!style(StyleFlag_InlineOuter) && emptyElementTag==EmptyElement))
*os << "\n";
if (emptyElementTag == NotEmptyElement)
elementStack_.push(name);
if (config_.outputObserver)
{
config_.outputObserver->update(static_cast<ostringstream*>(os)->str());
os_ << static_cast<ostringstream*>(os)->str();
delete os;
}
}
void XMLWriter::Impl::endElement()
{
ostream* os = &os_;
if (config_.outputObserver) os = new ostringstream;
if (elementStack_.empty())
throw runtime_error("[XMLWriter] Element stack underflow.");
if (!style(StyleFlag_InlineInner))
*os << indentation(elementStack_.size()-1);
*os << "</" << elementStack_.top() << ">";
elementStack_.pop();
if (!style(StyleFlag_InlineOuter))
*os << "\n";
if (config_.outputObserver)
{
config_.outputObserver->update(static_cast<ostringstream*>(os)->str());
os_ << static_cast<ostringstream*>(os)->str();
delete os;
}
}
void XMLWriter::Impl::characters(const string& text, bool autoEscape)
{
ostream* os = &os_;
if (config_.outputObserver) os = new ostringstream;
if (!style(StyleFlag_InlineInner))
*os << indentation();
if (autoEscape)
writeEscapedTextXML(*os, text);
else
*os << text;
if (!style(StyleFlag_InlineInner))
*os << "\n";
if (config_.outputObserver)
{
config_.outputObserver->update(static_cast<ostringstream*>(os)->str());
os_ << static_cast<ostringstream*>(os)->str();
delete os;
}
}
XMLWriter::stream_offset XMLWriter::Impl::position() const
{
os_ << flush;
// check to see if we're actually writing to a gzip file
boost::iostreams::filtering_ostream *zipper = dynamic_cast<boost::iostreams::filtering_ostream *>(&os_);
if (zipper)
{ // os_ is actually a boost::iostreams::filtering_ostream with gzip and a counter
return zipper->component<0, pwiz::minimxml::charcounter>()->characters();
}
else
{ // OK to do a simple ftellp because seek is implemented, unlike with gzip
return boost::iostreams::position_to_offset(os_.tellp());
}
}
XMLWriter::stream_offset XMLWriter::Impl::positionNext() const
{
stream_offset offset = position();
if (!style(StyleFlag_InlineOuter))
offset += indentation().size();
return offset;
}
//
// XMLWriter forwarding functions
//
PWIZ_API_DECL XMLWriter::XMLWriter(ostream& os, const Config& config)
: impl_(new Impl(os, config))
{}
PWIZ_API_DECL void XMLWriter::pushStyle(unsigned int flags) {impl_->pushStyle(flags);}
PWIZ_API_DECL void XMLWriter::popStyle() {impl_->popStyle();}
PWIZ_API_DECL void XMLWriter::processingInstruction(const string& name, const string& data)
{
impl_->processingInstruction(name, data);
}
PWIZ_API_DECL void XMLWriter::startElement(const string& name,
const Attributes& attributes,
EmptyElementTag emptyElementTag)
{
impl_->startElement(name, attributes, emptyElementTag);
}
PWIZ_API_DECL void XMLWriter::endElement() {impl_->endElement();}
PWIZ_API_DECL void XMLWriter::characters(const string& text, bool autoEscape) {impl_->characters(text, autoEscape);}
PWIZ_API_DECL XMLWriter::stream_offset XMLWriter::position() const {return impl_->position();}
PWIZ_API_DECL XMLWriter::stream_offset XMLWriter::positionNext() const {return impl_->positionNext();}
namespace {
// NCName ::= NCNameStartChar (NCNameChar)*
// NCNameStartChar ::= [A-Z] | '_' | [a-z]
// NCNameChar ::= NCNameStartChar | [0-9] | '.' | '-'
//
// Note: If we were working in Unicode, there's a lot of other valid characters,
// but here we'll just encode any non-ASCII value.
bool isNCNameStartChar(char& c)
{
return std::isalpha(c, std::locale::classic()) || c == '_';
}
bool isNCNameChar(char& c)
{
return isNCNameStartChar(c) ||
std::isdigit(c, std::locale::classic()) ||
c == '.' ||
c == '-';
}
const char hex[] = "0123456789abcdef";
void insertEncodedChar(string& str, string::iterator& itr)
{
char c = *itr;
*itr = '_';
str.insert(size_t(itr-str.begin()), "_x0000");
itr += 4;
*itr = hex[(c & 0xF0) >> 4];
*(++itr) = hex[c & 0x0F];
++itr;
}
} // namespace
PWIZ_API_DECL string& encode_xml_id(string& str)
{
if (str.empty())
throw std::invalid_argument("[encode_xml_id] xml:IDs and xml:IDREFs cannot be empty strings");
// reserve size for the worst case scenario (all characters need replacing),
// this should be a reasonable guarantee that the iterator won't be invalidated
str.reserve(str.length()*7);
string::iterator itr = str.begin();
if (!isNCNameStartChar(*itr))
insertEncodedChar(str, itr);
for (; itr != str.end(); ++itr)
if (!isNCNameChar(*itr))
insertEncodedChar(str, itr);
return str;
}
PWIZ_API_DECL string encode_xml_id_copy(const string& str)
{
string copy(str);
return encode_xml_id(copy);
}
} // namespace minimxml
} // namespace pwiz
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