XdmfCoreReader.cpp 12 KB
Newer Older
Kenneth Leiter's avatar
Kenneth Leiter committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
/*****************************************************************************/
/*                                    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.                                                 */
/*                                                                           */
/*****************************************************************************/
23

24
#include <libxml/uri.h>
25
#include <libxml/xpointer.h>
26
#include <libxml/xmlreader.h>
27 28 29
#include <boost/algorithm/string/trim.hpp>
#include <boost/tokenizer.hpp>
#include <cstring>
30
#include <map>
31
#include <sstream>
32 33
#include <utility>
#include "XdmfArray.hpp"
34 35
#include "XdmfArrayType.hpp"
#include "XdmfHDF5Controller.hpp"
36 37
#include "XdmfCoreItemFactory.hpp"
#include "XdmfCoreReader.hpp"
38
#include "XdmfError.hpp"
39
#include "XdmfItem.hpp"
40
#include "XdmfSystemUtils.hpp"
41

42 43 44 45 46 47 48
/**
 * PIMPL
 */
class XdmfCoreReader::XdmfCoreReaderImpl {

public:

49
  XdmfCoreReaderImpl(const shared_ptr<const XdmfCoreItemFactory> itemFactory,
50 51 52 53 54 55 56 57 58 59 60 61 62 63 64
                     const XdmfCoreReader * const coreReader) :
    mCoreReader(coreReader),
    mItemFactory(itemFactory)
  {
  };

  ~XdmfCoreReaderImpl()
  {
  };

  void
  closeFile()
  {
    mXPathMap.clear();
    xmlXPathFreeContext(mXPathContext);
65 66 67 68 69 70
    for(std::map<std::string, xmlDocPtr>::const_iterator iter = 
	  mDocuments.begin(); iter != mDocuments.end(); ++iter) {
      xmlFreeDoc(iter->second);
    }
    mDocuments.clear();
    
71 72 73 74 75 76 77 78 79 80 81 82
    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);
    }

83
    mDocument = xmlReadFile(filePath.c_str(), NULL, XML_PARSE_NOENT);
84 85

    if(mDocument == NULL) {
86 87 88
      XdmfError::message(XdmfError::FATAL,
                         "xmlReadFile could not read " + filePath +
                         " in XdmfCoreReader::XdmfCoreReaderImpl::openFile");
89 90
    }

91 92
    mDocuments.insert(std::make_pair((char*)mDocument->URL, mDocument));

93 94 95 96
    mXPathContext = xmlXPtrNewContext(mDocument, NULL, NULL);
    mXPathMap.clear();
  }

97 98 99 100 101 102
  void
  parse(const std::string & lightData) 
  {
    mDocument = xmlParseDoc((const xmlChar*)lightData.c_str());
                               
    if(mDocument == NULL) {
103 104 105
      XdmfError::message(XdmfError::FATAL,
                         "xmlReadFile could not parse passed light data string"
                         " in XdmfCoreReader::XdmfCoreReaderImpl::parse");
106
    }
107 108
    
    //mDocuments.insert(std::make_pair((char*)mDocument->URL, mDocument));
109 110 111 112
    mXPathContext = xmlXPtrNewContext(mDocument, NULL, NULL);
    mXPathMap.clear();
  }

113 114 115 116 117
  /**
   * Constructs XdmfItems for all nodes in currNode's tree.
   * XdmfItems are constructed by recursively calling this function for all
   * children of currNode.
   */
118
  std::vector<shared_ptr<XdmfItem> >
119 120
  read(xmlNodePtr currNode)
  {
121
    std::vector<shared_ptr<XdmfItem> > myItems;
122 123 124

    while(currNode != NULL) {
      if(currNode->type == XML_ELEMENT_NODE) {
125 126
        // Normal reading
        this->readSingleNode(currNode, myItems);
127 128 129 130 131 132 133 134 135 136 137 138 139
      }
      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,
140
                 std::vector<shared_ptr<XdmfItem> > & myItems)
141
  {
142
    
143 144 145 146 147 148
    // Deal with proper resolution of XIncludes
    if(xmlStrcmp(currNode->name, (xmlChar*)"include") == 0) {
      
      xmlChar * xpointer = NULL;
      xmlChar * href = NULL;
      
149 150
      xmlAttrPtr currAttribute = currNode->properties;
      while(currAttribute != NULL) {
151 152 153 154 155 156
        if(xmlStrcmp(currAttribute->name, (xmlChar*)"xpointer") == 0) {
          xpointer = currAttribute->children->content;
        }
        if(xmlStrcmp(currAttribute->name, (xmlChar*)"href") == 0) {
          href = currAttribute->children->content;
        }
157 158
        currAttribute = currAttribute->next;
      }
159
      
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190
      xmlXPathContextPtr oldContext = 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;
        }
        
        mXPathContext = xmlXPtrNewContext(document, NULL, NULL);           
      }
      
      if(xpointer) {
        xmlXPathObjectPtr result = xmlXPtrEval(xpointer, mXPathContext);
        if(result && !xmlXPathNodeSetIsEmpty(result->nodesetval)) {
          for(int i=0; i<result->nodesetval->nodeNr; ++i) {
            this->readSingleNode(result->nodesetval->nodeTab[i],
                                 myItems);
          }
        }
        else {
          XdmfError::message(XdmfError::FATAL,
                             "Invalid xpointer encountered.");
        }
        xmlXPathFreeObject(result);
191
      }
192 193 194 195 196 197 198 199 200
      
      if(href) {
        xmlXPathFreeContext(mXPathContext);
      }
      
      mXPathContext = oldContext;
      
    }
    else {
201

202 203 204 205 206 207
      // Check to see if the node is already in the XPath Map (seen previously)
      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);
208 209
      }
      else {
210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268
        // Otherwise, generate a new XdmfItem from the node
        std::map<std::string, std::string> itemProperties;
        
        xmlNodePtr childNode = currNode->children;
        if (XdmfArray::ItemTag.compare((char *)currNode->name) == 0 ||
            strcmp("DataStructure", (char *)currNode->name) == 0) {
          while(childNode != NULL) {
            if(childNode->type == XML_TEXT_NODE && childNode->content) {
              
              std::string content((char *)childNode->content);
              boost::algorithm::trim(content);
              
              if(content.size() != 0) {
                itemProperties.insert(std::make_pair("Content", content));
                itemProperties.insert(std::make_pair("XMLDir", mXMLDir));
                break;
              }
            }
            childNode = childNode->next;
          }
        }
        
        // Pull attributes from node
        xmlAttrPtr currAttribute = currNode->properties;
        while(currAttribute != NULL) {
          itemProperties.insert(std::make_pair((char *)currAttribute->name,
                                               (char *)currAttribute->children->content));
          currAttribute = currAttribute->next;
        }
        
        // Build XdmfItem
        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) {
          XdmfError::message(XdmfError::FATAL, 
                             "mItemFactory failed to createItem in "
                             "XdmfCoreReader::XdmfCoreReaderImpl::readSingleNode");
        }
        

        // Populate built XdmfItem
        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));
269 270 271 272 273 274
      }
    }
  }

  void
  readPathObjects(const std::string & xPath,
275
                  std::vector<shared_ptr<XdmfItem> > & myItems)
276 277 278 279 280
  {
    xmlXPathObjectPtr xPathObject =
      xmlXPathEvalExpression((xmlChar*)xPath.c_str(), mXPathContext);
    if(xPathObject && xPathObject->nodesetval) {
      for(int i=0; i<xPathObject->nodesetval->nodeNr; ++i) {
281
        this->readSingleNode(xPathObject->nodesetval->nodeTab[i], myItems);
282 283 284 285 286 287
      }
    }
    xmlXPathFreeObject(xPathObject);
  }

  xmlDocPtr mDocument;
288
  std::map<std::string, xmlDocPtr> mDocuments;
289
  const XdmfCoreReader * const mCoreReader;
290
  const shared_ptr<const XdmfCoreItemFactory> mItemFactory;
291 292
  std::string mXMLDir;
  xmlXPathContextPtr mXPathContext;
293
  std::map<xmlNodePtr, shared_ptr<XdmfItem> > mXPathMap;
294 295
};

296
XdmfCoreReader::XdmfCoreReader(const shared_ptr<const XdmfCoreItemFactory> itemFactory) :
297
  mImpl(new XdmfCoreReaderImpl(itemFactory, this))
298 299 300 301 302
{
}

XdmfCoreReader::~XdmfCoreReader()
{
303
  delete mImpl;
304 305
}

306 307 308
shared_ptr<XdmfItem >
XdmfCoreReader::parse(const std::string & lightData) const
{
309
  mImpl->parse(lightData);
310
  const xmlNodePtr currNode = xmlDocGetRootElement(mImpl->mDocument);
311
  std::vector<shared_ptr<XdmfItem> > toReturn;
312 313 314 315
  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);
316
  }
317 318
  else {
    toReturn = mImpl->read(currNode);
319
  }
320 321 322 323
  mImpl->closeFile();
  return(toReturn[0]);
}

324
std::vector<shared_ptr<XdmfItem> >
325
XdmfCoreReader::readItems(const std::string & filePath) const
326
{
327 328 329 330 331 332
  mImpl->openFile(filePath);
  const xmlNodePtr currNode = xmlDocGetRootElement(mImpl->mDocument);
  const std::vector<shared_ptr<XdmfItem> > toReturn =
    mImpl->read(currNode->children);
  mImpl->closeFile();
  return toReturn;
333 334
}

335
shared_ptr<XdmfItem>
336
XdmfCoreReader::read(const std::string & filePath) const
337
{
338 339 340
  const std::vector<shared_ptr<XdmfItem> > toReturn = readItems(filePath);
  if (toReturn.size() == 0) {
    return(shared_ptr<XdmfItem>());
341
  }
342
  return(toReturn[0]);
343
}
344

345
std::vector<shared_ptr<XdmfItem> >
346 347
XdmfCoreReader::read(const std::string & filePath,
                     const std::string & xPath) const
348
{
349 350 351 352
  mImpl->openFile(filePath);
  std::vector<shared_ptr<XdmfItem> > toReturn = this->readPathObjects(xPath);
  mImpl->closeFile();
  return toReturn;
353
}
354

355
std::vector<shared_ptr<XdmfItem> >
356
XdmfCoreReader::readPathObjects(const std::string & xPath) const
357
{
358
  std::vector<shared_ptr<XdmfItem> > toReturn;
359
  mImpl->readPathObjects(xPath, toReturn);
360
  return toReturn;
361 362
}