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- issue #3227: reimplement parsing using DOM
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@fbergmann
fbergmann committed May 27, 2024
1 parent 650aeec commit 07246a9
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Showing 3 changed files with 189 additions and 192 deletions.
260 changes: 68 additions & 192 deletions copasi/MIRIAM/CRDFGraph.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -724,197 +724,82 @@ bool CRDFNode::removeTripletFromGraph(const CRDFTriplet & triplet) const
}


#include <sbml/xml/XMLInputStream.h>
#include <sbml/xml/XMLNode.h>
#include <sbml/xml/XMLToken.h>
#include <sbml/xml/XMLErrorLog.h>

std::string trim(const std::string & str)
{
std::string s = str;

// Trim leading whitespace, newline, and carriage return characters
s.erase(s.begin(), std::find_if(s.begin(), s.end(), [](unsigned char ch) {
return !std::isspace(ch) && ch != '\n' && ch != '\r';
}));

// Trim trailing whitespace, newline, and carriage return characters
s.erase(std::find_if(s.rbegin(), s.rend(), [](unsigned char ch) {
return !std::isspace(ch) && ch != '\n' && ch != '\r';
}).base(),
s.end());

return s;
}

void addNewTokenToGraph(CRDFGraph & graph, XMLToken & next, XMLInputStream & stream, CRDFSubject & subject, const std::string & rdfUrl, const std::string & unusedPredicate = "")
void addXmlNodeToGraph(CRDFGraph & graph, XMLNode & current, CRDFSubject & subject, const std::string & rdfUri, const std::string & unusedPredicate = "")
{
CRDFObject object;
CRDFLiteral literal;
XMLToken current = stream.next();
XMLToken nextOne = stream.peek();

std::string elementName = current.getName();
std::string predicate = current.getURI() + elementName;
bool haveResource = current.hasAttr("resource", rdfUrl);
bool isBlank = !current.hasAttr("about", rdfUrl) && !haveResource;

if (elementName == "Description" && current.isStart())
{
object.setType(CRDFObject::BLANK_NODE);
object.setBlankNodeId(graph.generatedNodeId());
graph.addTriplet(subject, unusedPredicate.empty() ? predicate : unusedPredicate, object);

CRDFSubject newSubject;
newSubject.setType(CRDFSubject::BLANK_NODE);
newSubject.setBlankNodeId(object.getBlankNodeID());

while (stream.isGood())
{
stream.skipText();
auto token = stream.peek();
if (token.isEndFor(current))
{
stream.next();
break;
}
addNewTokenToGraph(graph, token, stream, newSubject, rdfUrl);
}
return;
}
else if (elementName == "Bag" && current.isStart())
bool isDescription = elementName == "Description";
bool isBag = elementName == "Bag";
if (isDescription && !unusedPredicate.empty())
predicate = unusedPredicate;
bool haveResource = current.hasAttr("resource", rdfUri);
bool haveText = current.getNumChildren() == 1 && current.getChild(0).isText();
bool isBlank = !current.hasAttr("about", rdfUri) && !haveResource && !haveText;

if (haveResource)
{
object.setType(CRDFObject::RESOURCE);
object.setResource(predicate, false);
predicate = current.getURI() + "type";

object.setResource(current.getAttrValue("resource", rdfUri), false);
graph.addTriplet(subject, predicate, object);
}
else if (haveText)
{
std::string dataType = current.getAttrValue("datatype", rdfUri);
std::string language = current.getAttrValue("lang", rdfUri);

std::string dataType = current.getAttrValue("datatype", rdfUrl);
std::string language = current.getAttrValue("lang", rdfUrl);
while (stream.isGood())
object.setType(CRDFObject::LITERAL);
if (!dataType.empty())
{
// grab literals first
std::string text;
while (stream.isGood() && stream.peek().isText())
{
text += stream.next().getCharacters();
}

text = trim(text);

if (!text.empty())
{
object.setType(CRDFObject::LITERAL);
if (!dataType.empty())
{
literal.setType(CRDFLiteral::TYPED);
literal.setDataType(dataType);
}
else
{
literal.setType(CRDFLiteral::PLAIN);
literal.setLanguage(language);
}
literal.setLexicalData(text);
object.setLiteral(literal);
graph.addTriplet(subject, predicate, object);
}

//grab the next element
XMLToken child = stream.peek();

// break when done
if (child.isEndFor(current))
break;

isBlank = !child.hasAttr("resource", rdfUrl);
addNewTokenToGraph(graph, child, stream, subject, rdfUrl);
literal.setType(CRDFLiteral::TYPED);
literal.setDataType(dataType);
}
stream.skipText();
XMLToken pos = stream.peek();
if (pos.isEndFor(current))
stream.next();
return;
}
else if (haveResource && current.isStart())
{
object.setType(CRDFObject::RESOURCE);
object.setResource(current.getAttrValue("resource", rdfUrl), false);
else
{
literal.setType(CRDFLiteral::PLAIN);
literal.setLanguage(language);
}
literal.setLexicalData(current.getChild(0).getCharacters());
object.setLiteral(literal);
graph.addTriplet(subject, predicate, object);
return;
}
else
{
std::string dataType = current.getAttrValue("datatype", rdfUrl);
std::string language = current.getAttrValue("lang", rdfUrl);

while (stream.isGood())
if (isBag)
{
// grab literals first
std::string text;
while (stream.isGood() && stream.peek().isText())
{
text += stream.next().getCharacters();
}
object.setType(CRDFObject::RESOURCE);
object.setResource(predicate, false);
predicate = current.getURI() + "type";

text = trim(text);
graph.addTriplet(subject, predicate, object);
}

if (!text.empty())
{
object.setType(CRDFObject::LITERAL);
if (!dataType.empty())
{
literal.setType(CRDFLiteral::TYPED);
literal.setDataType(dataType);
}
else
{
literal.setType(CRDFLiteral::PLAIN);
literal.setLanguage(language);
}
literal.setLexicalData(text);
object.setLiteral(literal);
graph.addTriplet(subject, predicate, object);
}
if (isBlank && !isDescription && !isBag)
{
object.setType(CRDFObject::BLANK_NODE);
object.setBlankNodeId(graph.generatedNodeId());
graph.addTriplet(subject, predicate, object);

//grab the next element
XMLToken child1 = stream.peek();
CRDFSubject newSubject;
newSubject.setType(CRDFSubject::BLANK_NODE);
newSubject.setBlankNodeId(object.getBlankNodeID());

// break when done
if (child1.isEndFor(current))
for (int i = 0; i < current.getNumChildren(); ++i)
{
stream.next();
break;
addXmlNodeToGraph(graph, current.getChild(i), newSubject, rdfUri, predicate);
}

if (child1.isStart())
}
else
{
for (int i = 0; i < current.getNumChildren(); ++i)
{
if (child1.getName() == "Bag")
{
object.setType(CRDFObject::BLANK_NODE);
object.setBlankNodeId(graph.generatedNodeId());
graph.addTriplet(subject, predicate, object);

CRDFSubject newSubject;
newSubject.setType(CRDFSubject::BLANK_NODE);
newSubject.setBlankNodeId(object.getBlankNodeID());
addNewTokenToGraph(graph, child1, stream, newSubject, rdfUrl);

stream.skipText();
XMLToken pos = stream.peek();
if (pos.isEndFor(child1))
stream.next();
}
else
{
addNewTokenToGraph(graph, child1, stream, subject, rdfUrl, predicate);

stream.skipText();
XMLToken pos = stream.peek();
if (pos.isEndFor(child1))
stream.next();
}
addXmlNodeToGraph(graph, current.getChild(i), subject, rdfUri, predicate);
}
}
}
Expand All @@ -924,47 +809,38 @@ CRDFGraph * CRDFGraph::fromString(const std::string & miriam)
{
CRDFGraph * graph = new CRDFGraph();

XMLErrorLog log1;
XMLInputStream stream(miriam.c_str(), false, "", &log1);
XMLNode * content = XMLNode::convertStringToXMLNode(miriam);

std::string rdfUri;

if ((stream.peek().isStart()) && (stream.peek().getName() == "RDF"))
for (int i = 0; i < content->getNamespaces().getLength(); ++i)
{
XMLToken rdfToken = stream.next();
std::string rdfUrl = rdfToken.getURI();
std::string prefix = content->getNamespaces().getPrefix(i);
std::string uri = content->getNamespaces().getURI(i);
graph->addNameSpace(prefix, uri);

for (int i = 0; i < rdfToken.getNamespaces().getLength(); ++i)
{
std::string prefix = rdfToken.getNamespaces().getPrefix(i);
std::string uri = rdfToken.getNamespaces().getURI(i);
graph->addNameSpace(prefix, uri);
}
if (prefix == "rdf")
rdfUri = uri;
}

stream.skipText();
rdfToken = stream.next();
// ensure that this is the description token
if (rdfToken.getName() == "Description" && rdfToken.hasAttr("about", rdfUrl))
if (content->getNumChildren() > 0)
{
XMLNode & desc = content->getChild("Description");
std::string about = desc.getAttrValue("about", rdfUri);

for (int i = 0; i < desc.getNumChildren(); ++i)
{
std::string about = rdfToken.getAttrValue("about", rdfUrl);

CRDFSubject subject;
subject.setType(CRDFSubject::RESOURCE);
subject.setResource(about, true);

while (stream.isGood())
{
stream.skipText();
//grab the next element
XMLToken next = stream.peek();

// break when done
if (next.isEndFor(rdfToken))
break;

// otherwise add new triple
addNewTokenToGraph(*graph, next, stream, subject, rdfUrl);
}
addXmlNodeToGraph(*graph, desc.getChild(i), subject, rdfUri);
}
}

pdelete(content);

graph->guessGraphRoot();
return graph;
}
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