void handleXMLError(const xmlErrorPtr e) {
if(!e)
return;
if(e->domain == XML_FROM_IO && e->code == XML_IO_LOAD_ERROR && e->level == XML_ERR_WARNING)
return;
switch(e->level) {
case XML_ERR_WARNING:
fprintf(stderr, "WARNING - ");
break;
case XML_ERR_ERROR:
fprintf(stderr, "ERROR - ");
break;
case XML_ERR_FATAL:
fprintf(stderr, "FATAL - ");
break;
default:
break;
}
if(e->file && e->line) {
fprintf(stderr, "%s:%d: ", e->file, e->line);
}
else {
if(e->file) {
fprintf(stderr, "%s: ", e->file);
}
}
fprintf(stderr, "%s", e->message);
xmlResetError(e);
}
static void dealloc(xmlErrorPtr ptr)
{
NOKOGIRI_DEBUG_START(ptr);
xmlResetError(ptr);
xmlFree(ptr);
NOKOGIRI_DEBUG_END(ptr);
}
void clearErrors() {
for (auto& error : *this) {
xmlResetError(&error);
}
}
bool XMLConversion::ReadXML(XMLBaseFormat* pFormat, OBBase* pOb)
{
if(_requestedpos)
{
//The initial stream position was not at the start, probably because of fastsearch
//Read and discard the first object to synchronize the reader,
//then continue getting the requested object.
//Assumes the objects are all at the same level in the DOM tree.
SetOneObjectOnly(); //probably already set
streampos SavedReqestedPos = _requestedpos;
_requestedpos=0;//don't do this again
ReadXML(pFormat,pOb);
GetInStream()->seekg(SavedReqestedPos);
}
//**Parse
int result=1;
while(GetInStream()->good() && (_SkipNextRead || (result=xmlTextReaderRead(_reader))==1)) //read may not be called
{
_SkipNextRead=false;
if(_LookingForNamespace)
{
const xmlChar* puri = xmlTextReaderConstNamespaceUri(_reader);
if(puri)
{
string uri((const char*)puri);
//Look up appropriate format class from the namespace URI
NsMapType::iterator nsiter;
nsiter = Namespaces().find(uri);
if(nsiter!=Namespaces().end())
{
XMLBaseFormat* pNewFormat = nsiter->second;
//Must have same target, e.g. OBMol, as current format
if(pNewFormat->GetType() == pFormat->GetType())
{
_LookingForNamespace=false;
_SkipNextRead=true;
SetInFormat(pNewFormat);
pNewFormat->ReadMolecule(pOb,this);
return true;
}
}
}
}
const xmlChar* pname = xmlTextReaderConstLocalName(_reader);
int typ = xmlTextReaderNodeType(_reader);
if(typ==XML_READER_TYPE_SIGNIFICANT_WHITESPACE || !pname)
continue; //Text nodes handled in format class
string ElName((const char*)pname);
//Pass the node on to the appropriate format class
bool ret;
if(typ==XML_READER_TYPE_ELEMENT)
ret= pFormat->DoElement(ElName);
else if(typ==XML_READER_TYPE_END_ELEMENT)
ret= pFormat->EndElement(ElName);
else
continue;
_lastpos = GetInStream()->tellg();
if(!ret)
//derived format callback has stopped processing by returning false;
//leave reader intact so it can be continued to be used.
if(!IsOption("n",OBConversion::INOPTIONS))
{
_LookingForNamespace = true;
return true;
}
}
if(result==-1)
{
xmlError* perr = xmlGetLastError();
if(perr && perr->level!=XML_ERR_NONE)
{
obErrorLog.ThrowError("XML Parser " + GetInFilename(),
perr->message, obError);
}
xmlResetError(perr);
GetInStream()->setstate(ios::eofbit);
return false;
}
return GetInStream()->good() && result!=0;
}
