XdmfCoreReader.cpp 11.6 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;
122 123 124 125 126

    while(currNode != NULL) {
      if(currNode->type == XML_ELEMENT_NODE) {
        if(xmlStrcmp(currNode->name, (xmlChar*)"include") == 0) {
          // Deal with proper reading of XIncludes
127 128 129 130

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

131 132 133 134 135
          xmlAttrPtr currAttribute = currNode->properties;
          while(currAttribute != NULL) {
            if(xmlStrcmp(currAttribute->name, (xmlChar*)"xpointer") == 0) {
              xpointer = currAttribute->children->content;
            }
136 137 138 139 140 141 142 143
            if(xmlStrcmp(currAttribute->name, (xmlChar*)"href") == 0) {
              href = currAttribute->children->content;
            }
            currAttribute = currAttribute->next;
          }

          xmlXPathContextPtr context = mXPathContext;
          if(href) {
144
	    xmlDocPtr document;
145
            xmlChar * filePath = xmlBuildURI(href, mDocument->URL);
146 147 148 149 150 151 152 153 154 155
	    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;
	    }

156
            context = xmlXPtrNewContext(document, NULL, NULL);           
157
          }
158

159
          if(xpointer) {
160 161 162 163
            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],
164 165 166
                                     myItems);
              }
            }
167 168 169 170 171
            xmlXPathFreeObject(result);
          }

          if(href) {
            xmlXPathFreeContext(context);
172
          }
173

174 175 176
        }
        else {
          // Normal reading
177
          this->readSingleNode(currNode, myItems);
178 179 180 181 182 183 184 185 186 187 188 189 190 191
        }
      }
      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,
192
                 std::vector<shared_ptr<XdmfItem> > & myItems)
193
  {
194
    // Check to see if the node is already in the XPath Map (seen previously)
195
    std::map<xmlNodePtr, shared_ptr<XdmfItem> >::const_iterator iter =
196
      mXPathMap.find(currNode);
197
    // If it is grab it from the previously stored items
198
    if(iter != mXPathMap.end()) {
199 200
      myItems.push_back(iter->second);
    }
201
    else {
202
      // Otherwise, generate a new Item from the node
203
      std::map<std::string, std::string> itemProperties;
204 205

      xmlNodePtr childNode = currNode->children;
206 207
      if (XdmfArray::ItemTag.compare((char *)currNode->name) == 0 ||
          strcmp("DataStructure", (char *)currNode->name) == 0) {
208 209 210
        while(childNode != NULL) {
          if(childNode->type == XML_TEXT_NODE && childNode->content) {
            
211 212
            std::string content((char *)childNode->content);
            boost::algorithm::trim(content);
213
            
214
            if(content.size() != 0) {
215 216 217
              itemProperties.insert(std::make_pair("Content", content));
              itemProperties.insert(std::make_pair("XMLDir", mXMLDir));
              break;
218 219
            }
          }
220
          childNode = childNode->next;
221
        }
222
      }
223
    
224 225
      xmlAttrPtr currAttribute = currNode->properties;
      while(currAttribute != NULL) {
226 227
        itemProperties.insert(std::make_pair((char *)currAttribute->name,
                                             (char *)currAttribute->children->content));
228 229
        currAttribute = currAttribute->next;
      }
230 231 232 233 234 235 236

      const std::vector<shared_ptr<XdmfItem> > childItems =
        this->read(currNode->children);
      shared_ptr<XdmfItem> newItem = 
        mItemFactory->createItem((const char *)currNode->name,
                                 itemProperties,
                                 childItems);
237
      
238 239 240 241
      if(newItem == NULL) {
        XdmfError::message(XdmfError::FATAL, 
                           "mItemFactory failed to createItem in "
                           "XdmfCoreReader::XdmfCoreReaderImpl::readSingleNode");
242
      }
243 244 245 246 247 248 249 250 251 252

      if (newItem->getItemTag().compare((const char *)currNode->name) != 0) {
        newItem->populateItem(itemProperties,
                              std::vector<shared_ptr<XdmfItem> >(),
                              mCoreReader);
      }
      else {
        newItem->populateItem(itemProperties,
                              childItems,
                              mCoreReader);
253
      }
254 255
      myItems.push_back(newItem);
      mXPathMap.insert(std::make_pair(currNode, newItem));
256 257 258 259 260
    }
  }

  void
  readPathObjects(const std::string & xPath,
261
                  std::vector<shared_ptr<XdmfItem> > & myItems)
262 263 264 265 266
  {
    xmlXPathObjectPtr xPathObject =
      xmlXPathEvalExpression((xmlChar*)xPath.c_str(), mXPathContext);
    if(xPathObject && xPathObject->nodesetval) {
      for(int i=0; i<xPathObject->nodesetval->nodeNr; ++i) {
267
        this->readSingleNode(xPathObject->nodesetval->nodeTab[i], myItems);
268 269 270 271 272 273
      }
    }
    xmlXPathFreeObject(xPathObject);
  }

  xmlDocPtr mDocument;
274
  std::map<std::string, xmlDocPtr> mDocuments;
275
  const XdmfCoreReader * const mCoreReader;
276
  const shared_ptr<const XdmfCoreItemFactory> mItemFactory;
277 278
  std::string mXMLDir;
  xmlXPathContextPtr mXPathContext;
279
  std::map<xmlNodePtr, shared_ptr<XdmfItem> > mXPathMap;
280 281
};

282
XdmfCoreReader::XdmfCoreReader(const shared_ptr<const XdmfCoreItemFactory> itemFactory) :
283
  mImpl(new XdmfCoreReaderImpl(itemFactory, this))
284 285 286 287 288
{
}

XdmfCoreReader::~XdmfCoreReader()
{
289
  delete mImpl;
290 291
}

292 293 294
shared_ptr<XdmfItem >
XdmfCoreReader::parse(const std::string & lightData) const
{
295
  mImpl->parse(lightData);
296
  const xmlNodePtr currNode = xmlDocGetRootElement(mImpl->mDocument);
297
  std::vector<shared_ptr<XdmfItem> > toReturn;
298 299 300 301
  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);
302
  }
303 304
  else {
    toReturn = mImpl->read(currNode);
305
  }
306 307 308 309
  mImpl->closeFile();
  return(toReturn[0]);
}

310
std::vector<shared_ptr<XdmfItem> >
311
XdmfCoreReader::readItems(const std::string & filePath) const
312
{
313 314 315 316 317 318
  mImpl->openFile(filePath);
  const xmlNodePtr currNode = xmlDocGetRootElement(mImpl->mDocument);
  const std::vector<shared_ptr<XdmfItem> > toReturn =
    mImpl->read(currNode->children);
  mImpl->closeFile();
  return toReturn;
319 320
}

321
shared_ptr<XdmfItem>
322
XdmfCoreReader::read(const std::string & filePath) const
323
{
324 325 326
  const std::vector<shared_ptr<XdmfItem> > toReturn = readItems(filePath);
  if (toReturn.size() == 0) {
    return(shared_ptr<XdmfItem>());
327
  }
328
  return(toReturn[0]);
329
}
330

331
std::vector<shared_ptr<XdmfItem> >
332 333
XdmfCoreReader::read(const std::string & filePath,
                     const std::string & xPath) const
334
{
335 336 337 338
  mImpl->openFile(filePath);
  std::vector<shared_ptr<XdmfItem> > toReturn = this->readPathObjects(xPath);
  mImpl->closeFile();
  return toReturn;
339
}
340

341
std::vector<shared_ptr<XdmfItem> >
342
XdmfCoreReader::readPathObjects(const std::string & xPath) const
343
{
344
  std::vector<shared_ptr<XdmfItem> > toReturn;
345
  mImpl->readPathObjects(xPath, toReturn);
346
  return toReturn;
347 348
}