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// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * 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 Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS 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.
// Author: Derek Barnett
#include "XmlReader.h"
#include "StringUtils.h"
#include "pugixml/pugixml.hpp"
#include <iostream>
#include <fstream>
#include <memory>
#include <vector>
#include <cassert>
using namespace PacBio;
using namespace PacBio::BAM;
using namespace PacBio::BAM::internal;
using namespace std;
namespace PacBio {
namespace BAM {
namespace internal {
static
void UpdateRegistry(const string& attributeName,
const string& attributeValue,
NamespaceRegistry& registry)
{
vector<string> nameParts = Split(attributeName, ':');
assert(!nameParts.empty());
if (nameParts.size() > 2)
throw std::runtime_error("malformed xmlns attribute: " + attributeName);
const bool isDefault = (nameParts.size() == 1);
const XsdType& xsd = registry.XsdForUri(attributeValue);
if (isDefault)
registry.SetDefaultXsd(xsd);
else {
assert(nameParts.size() == 2);
const string& name = nameParts.at(1);
const string& uri = attributeValue;
NamespaceInfo namespaceInfo(name, uri);
registry.Register(xsd, namespaceInfo);
}
}
static
void FromXml(const pugi::xml_node& xmlNode, DataSetElement& parent)
{
// ignore non-named XML nodes
//
// pugi::xml separates XML parts into more node types than we use
//
const string& label = xmlNode.name();
if (label.empty())
return;
// label & text
DataSetElement e(xmlNode.name(), FromInputXml());
e.Text(xmlNode.text().get());
// iterate attributes
auto attrIter = xmlNode.attributes_begin();
auto attrEnd = xmlNode.attributes_end();
for ( ; attrIter != attrEnd; ++attrIter )
e.Attribute(attrIter->name(), attrIter->value());
// iterate children, recursively building up subtree
auto childIter = xmlNode.begin();
auto childEnd = xmlNode.end();
for ( ; childIter != childEnd; ++childIter ) {
pugi::xml_node childNode = *childIter;
FromXml(childNode, e);
}
// add our element to its parent
parent.AddChild(e);
}
} // namespace internal
} // namespace BAM
} // namespace PacBio
std::unique_ptr<DataSetBase> XmlReader::FromStream(istream& in)
{
pugi::xml_document doc;
const pugi::xml_parse_result& loadResult = doc.load(in);
if (loadResult.status != pugi::status_ok)
throw std::runtime_error(string("could not read XML file, error code:") + to_string(loadResult.status) );
// parse top-level attributes
pugi::xml_node rootNode = doc.document_element();
if (rootNode == pugi::xml_node())
throw std::runtime_error("could not fetch XML root node");
// create dataset matching type strings
std::unique_ptr<DataSetBase> dataset(new DataSetBase);
dataset->Label(rootNode.name());
// iterate attributes, capture namespace info
const string xmlnsPrefix("xmlns");
auto attrIter = rootNode.attributes_begin();
auto attrEnd = rootNode.attributes_end();
for ( ; attrIter != attrEnd; ++attrIter ) {
const string& name = attrIter->name();
const string& value = attrIter->value();
dataset->Attribute(name, value);
if (name.find(xmlnsPrefix) == 0)
UpdateRegistry(name, value, dataset->Namespaces());
}
// iterate children, recursively building up subtree
auto childIter = rootNode.begin();
auto childEnd = rootNode.end();
for ( ; childIter != childEnd; ++childIter ) {
pugi::xml_node childNode = *childIter;
internal::FromXml(childNode, *dataset.get());
}
return dataset;
}
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