XdmfCoreReader.cpp

/*****************************************************************************/
/*                                    XDMF                                   */
/*                       eXtensible Data Model and Format                    */
/*                                                                           */
/*  Id : XdmfCoreReader.cpp                                                  */
/*                                                                           */
/*  Author:                                                                  */
/*     Kenneth Leiter                                                        */
/*     kenneth.leiter@arl.army.mil                                           */
/*     US Army Research Laboratory                                           */
/*     Aberdeen Proving Ground, MD                                           */
/*                                                                           */
/*     Copyright @ 2011 US Army Research Laboratory                          */
/*     All Rights Reserved                                                   */
/*     See Copyright.txt for details                                         */
/*                                                                           */
/*     This software is distributed WITHOUT ANY WARRANTY; without            */
/*     even the implied warranty of MERCHANTABILITY or FITNESS               */
/*     FOR A PARTICULAR PURPOSE.  See the above copyright notice             */
/*     for more information.                                                 */
/*                                                                           */
/*****************************************************************************/

#include <libxml/uri.h>
#include <libxml/xpointer.h>
#include <libxml/xmlreader.h>
#include "boost/tokenizer.hpp"
#include <map>
#include <sstream>
#include <cstring>
#include <utility>
#include "XdmfArray.hpp"
#include "XdmfArrayType.hpp"
#include "XdmfHDF5Controller.hpp"
#include "XdmfCoreItemFactory.hpp"
#include "XdmfCoreReader.hpp"
#include "XdmfError.hpp"
#include "XdmfItem.hpp"
#include "XdmfSystemUtils.hpp"

/**
 * PIMPL
 */
class XdmfCoreReader::XdmfCoreReaderImpl {

public:

  XdmfCoreReaderImpl(const shared_ptr<const XdmfCoreItemFactory> itemFactory,
                     const XdmfCoreReader * const coreReader) :
    mCoreReader(coreReader),
    mItemFactory(itemFactory)
  {
  };

  ~XdmfCoreReaderImpl()
  {
  };

  void
  closeFile()
  {
    mXPathMap.clear();
    xmlXPathFreeContext(mXPathContext);
    for(std::map<std::string, xmlDocPtr>::const_iterator iter = 
	  mDocuments.begin(); iter != mDocuments.end(); ++iter) {
      xmlFreeDoc(iter->second);
    }
    mDocuments.clear();
    
    xmlCleanupParser();
  }

  void
  openFile(const std::string & filePath)
  {
    mXMLDir = XdmfSystemUtils::getRealPath(filePath);
    size_t index = mXMLDir.find_last_of("/\\");
    if(index != std::string::npos) {
      mXMLDir = mXMLDir.substr(0, index + 1);
    }

    mDocument = xmlReadFile(filePath.c_str(), NULL, 0);

    if(mDocument == NULL) {
      try {
        XdmfError::message(XdmfError::FATAL,
                           "xmlReadFile could not read " + filePath +
                           " in XdmfCoreReader::XdmfCoreReaderImpl::openFile");
      }
      catch (XdmfError e) {
        throw e;
      }
    }

    mDocuments.insert(std::make_pair((char*)mDocument->URL, mDocument));

    mXPathContext = xmlXPtrNewContext(mDocument, NULL, NULL);
    mXPathMap.clear();
  }

  void
  parse(const std::string & lightData) 
  {
    mDocument = xmlParseDoc((const xmlChar*)lightData.c_str());
                               
    if(mDocument == NULL) {
      try {
        XdmfError::message(XdmfError::FATAL,
                           "xmlReadFile could not parse passed light data string"
                           " in XdmfCoreReader::XdmfCoreReaderImpl::parse");
      }
      catch (XdmfError e) {
        throw e;
      }
    }

    //    mDocuments.insert(std::make_pair((char*)mDocument->URL, mDocument));
    mXPathContext = xmlXPtrNewContext(mDocument, NULL, NULL);
    mXPathMap.clear();
  }

  /**
   * Constructs XdmfItems for all nodes in currNode's tree.
   * XdmfItems are constructed by recursively calling this function for all
   * children of currNode.
   */
  std::vector<shared_ptr<XdmfItem> >
  read(xmlNodePtr currNode)
  {
    std::vector<shared_ptr<XdmfItem> > myItems;

    while(currNode != NULL) {
      if(currNode->type == XML_ELEMENT_NODE) {
        if(xmlStrcmp(currNode->name, (xmlChar*)"include") == 0) {
          // Deal with proper reading of XIncludes

          xmlChar * xpointer = NULL;
          xmlChar * href = NULL;

          xmlAttrPtr currAttribute = currNode->properties;
          while(currAttribute != NULL) {
            if(xmlStrcmp(currAttribute->name, (xmlChar*)"xpointer") == 0) {
              xpointer = currAttribute->children->content;
            }
            if(xmlStrcmp(currAttribute->name, (xmlChar*)"href") == 0) {
              href = currAttribute->children->content;
            }
            currAttribute = currAttribute->next;
          }

          xmlXPathContextPtr context = mXPathContext;
          if(href) {
	    xmlDocPtr document;
            xmlChar * filePath = xmlBuildURI(href, mDocument->URL);
	    std::map<std::string, xmlDocPtr>::const_iterator iter = 
	      mDocuments.find((char*)filePath);
	    if(iter == mDocuments.end()) {
	      document = xmlReadFile((char*)filePath, NULL, 0);
	      mDocuments.insert(std::make_pair((char*)document->URL, document));
	    }
	    else {
	      document = iter->second;
	    }

            context = xmlXPtrNewContext(document, NULL, NULL);           
          }

          if(xpointer) {
            xmlXPathObjectPtr result = xmlXPtrEval(xpointer, context);
            if(result && !xmlXPathNodeSetIsEmpty(result->nodesetval)) {
              for(int i=0; i<result->nodesetval->nodeNr; ++i) {
                this->readSingleNode(result->nodesetval->nodeTab[i],
                                     myItems);
              }
            }
            xmlXPathFreeObject(result);
          }

          if(href) {
            xmlXPathFreeContext(context);
          }

        }
        else {
          // Normal reading
          try {
            this->readSingleNode(currNode, myItems);
          }
          catch (XdmfError e) {
            throw e;
          }
        }
      }
      currNode = currNode->next;
    }
    return myItems;
  }

  /**
   * Reads a single xmlNode into an XdmfItem object in memory. The constructed
   * XdmfItem is added to myItems and an entry is added mapping the xmlNodePtr
   * to the new XdmfItem in the mXPathMap.
   */
  void
  readSingleNode(const xmlNodePtr currNode,
                 std::vector<shared_ptr<XdmfItem> > & myItems)
  {
    // Check to see if the node is already in the Xpath
    std::map<xmlNodePtr, shared_ptr<XdmfItem> >::const_iterator iter =
      mXPathMap.find(currNode);
    // If it is grab it from the previously stored items
    if(iter != mXPathMap.end()) {
      myItems.push_back(iter->second);
    }
    else {
      // Otherwise, generate it from the node
      std::map<std::string, std::string> itemProperties;

      xmlNodePtr childNode = currNode->children;
      if (XdmfArray::ItemTag.compare((char *)currNode->name) == 0) {
        while(childNode != NULL) {
          if(childNode->type == XML_TEXT_NODE && childNode->content) {
            const char * content = (char*)childNode->content;
            
            // Determine if content is whitespace
            bool whitespace = true;
            
            const char * contentPtr = content;
            // Step through to end of pointer
            while(contentPtr != NULL) {
              // If not a whitespace character, break
              if(!isspace(*contentPtr++)) {
                whitespace = false;
                break;
              }
            }
            
            if(!whitespace) {
              itemProperties.insert(std::make_pair("Content", content));
              itemProperties.insert(std::make_pair("XMLDir", mXMLDir));
              break;
            }
          }
          childNode = childNode->next;
        }
      }
    
      xmlAttrPtr currAttribute = currNode->properties;
      while(currAttribute != NULL) {
        itemProperties.insert(std::make_pair((char *)currAttribute->name,
                                             (char *)currAttribute->children->content));
        currAttribute = currAttribute->next;
      }
      try {
        const std::vector<shared_ptr<XdmfItem> > childItems =
          this->read(currNode->children);
        shared_ptr<XdmfItem> newItem = 
          mItemFactory->createItem((const char *)currNode->name,
                                   itemProperties,
                                   childItems);
      
        if(newItem == NULL) {
          try {
            XdmfError::message(XdmfError::FATAL, 
                               "mItemFactory failed to createItem in "
                               "XdmfCoreReader::XdmfCoreReaderImpl::readSingleNode");
          }
          catch (XdmfError e) {
            throw e;
          }
        }
        if (newItem->getItemTag().compare((const char *)currNode->name) != 0) {
          newItem->populateItem(itemProperties,
                                std::vector<shared_ptr<XdmfItem> >(),
                                mCoreReader);
        }
        else {
          newItem->populateItem(itemProperties,
          childItems,
          mCoreReader);
        }
        myItems.push_back(newItem);
        mXPathMap.insert(std::make_pair(currNode, newItem));
      }
      catch (XdmfError e) {
        throw e;
      }
    }
  }

  void
  readPathObjects(const std::string & xPath,
                  std::vector<shared_ptr<XdmfItem> > & myItems)
  {
    xmlXPathObjectPtr xPathObject =
      xmlXPathEvalExpression((xmlChar*)xPath.c_str(), mXPathContext);
    if(xPathObject && xPathObject->nodesetval) {
      for(int i=0; i<xPathObject->nodesetval->nodeNr; ++i) {
        try {
          this->readSingleNode(xPathObject->nodesetval->nodeTab[i], myItems);
        }
        catch (XdmfError e) {
          throw e;
        }
      }
    }
    xmlXPathFreeObject(xPathObject);
  }

  xmlDocPtr mDocument;
  std::map<std::string, xmlDocPtr> mDocuments;
  const XdmfCoreReader * const mCoreReader;
  const shared_ptr<const XdmfCoreItemFactory> mItemFactory;
  std::string mXMLDir;
  xmlXPathContextPtr mXPathContext;
  std::map<xmlNodePtr, shared_ptr<XdmfItem> > mXPathMap;
};

XdmfCoreReader::XdmfCoreReader(const shared_ptr<const XdmfCoreItemFactory> itemFactory) :
  mImpl(new XdmfCoreReaderImpl(itemFactory, this))
{
}

XdmfCoreReader::~XdmfCoreReader()
{
  delete mImpl;
}

shared_ptr<XdmfItem >
XdmfCoreReader::parse(const std::string & lightData) const
{
  try {
    mImpl->parse(lightData);
  }
  catch (XdmfError e) {
    throw e;
  }
  const xmlNodePtr currNode = xmlDocGetRootElement(mImpl->mDocument);
  std::vector<shared_ptr<XdmfItem> > toReturn;
  try {
    if(mImpl->mItemFactory->createItem((const char*)currNode->name,
                                       std::map<std::string, std::string>(),
                                       std::vector<shared_ptr<XdmfItem> >()) == NULL) {
      toReturn = mImpl->read(currNode->children);
    }
    else {
      toReturn = mImpl->read(currNode);
    }
  }
  catch (XdmfError e) {
    throw e;
  }
  mImpl->closeFile();
  return(toReturn[0]);
}

std::vector<shared_ptr<XdmfItem> >
XdmfCoreReader::readItems(const std::string & filePath) const
{
  try {
    mImpl->openFile(filePath);
    const xmlNodePtr currNode = xmlDocGetRootElement(mImpl->mDocument);
    const std::vector<shared_ptr<XdmfItem> > toReturn =
      mImpl->read(currNode->children);
    mImpl->closeFile();
    return toReturn;
  }
  catch (XdmfError e) {
    throw e;
  }

}

shared_ptr<XdmfItem>
XdmfCoreReader::read(const std::string & filePath) const
{
  try {
    const std::vector<shared_ptr<XdmfItem> > toReturn = readItems(filePath);
    if (toReturn.size() == 0) {
      return(shared_ptr<XdmfItem>());
    }
    return(toReturn[0]);
  }
  catch (XdmfError e) {
    throw e;
  }
}

std::vector<shared_ptr<XdmfItem> >
XdmfCoreReader::read(const std::string & filePath,
                     const std::string & xPath) const
{
  try {
    mImpl->openFile(filePath);
    std::vector<shared_ptr<XdmfItem> > toReturn = this->readPathObjects(xPath);
    mImpl->closeFile();
    return toReturn;
  }
  catch (XdmfError e) {
    throw e;
  }
}

std::vector<shared_ptr<XdmfItem> >
XdmfCoreReader::readPathObjects(const std::string & xPath) const
{
  std::vector<shared_ptr<XdmfItem> > toReturn;
  try {
    mImpl->readPathObjects(xPath, toReturn);
  }
  catch (XdmfError e) {
    throw e;
  }
  return toReturn;
}