/**
 *#########################################################################
 *
 * A component of the Gatherer application, part of the Greenstone digital
 * library suite from the New Zealand Digital Library Project at the
 * University of Waikato, New Zealand.
 *
 * Methods to read collectionConfig.xml files into internal XML form, and write 
 * them back out again.
 *
 * Copyright (C) 1999 New Zealand Digital Library Project
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 *########################################################################
 */
package org.greenstone.gatherer.cdm;

import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.StringTokenizer;

import org.greenstone.gatherer.DebugStream;
import org.greenstone.gatherer.metadata.MetadataElement;
import org.greenstone.gatherer.metadata.MetadataTools;
import org.greenstone.gatherer.util.XMLTools;
import org.greenstone.gatherer.util.StaticStrings;
import org.greenstone.gatherer.util.Utility;

import org.w3c.dom.*;

public class CollectionConfigXMLReadWrite {

  static final private String PLUGOUT_ELEMENT = "plugout";//used by building flax collections

  /** ********************************************************************************************************
      The code from this point below are used for greenstone 3 collection configuration, i.e., read ColletionConfig.xml
      * into the internal DOM tree, and convert the internal DOM tree back to CollectionConfig.xml.
      *
      Methods named 'doXXXX' are for convert collectionConfig.xml into the internal configuration xml structure;
      Methods named 'convertXXXX' are for convert the internal configuration xml structure back to collectionConfig.xml.
      ************************************************************************************************************ */
    
  /**Arguments:  metadataListNode->the 'displayItemList' element in collectionConfig.xml
     name_value->the value of the 'name' attribute of 'index' element;
     att_value->the value of the 'name' attribute of 'displayItem' element
     return:     an ArrayList of the contructed 'CollectionMetadata' elements
  */
  static private ArrayList doDisplayItemList (Document to, Node displayListNode, String att_value, String name_value) {
    Element toElement = to.getDocumentElement ();
    ArrayList display_item_list = new ArrayList ();
    ArrayList item_list = XMLTools.getNamedElementList ((Element)displayListNode,
							StaticStrings.DISPLAYITEM_STR, StaticStrings.NAME_ATTRIBUTE, att_value);
    if (item_list == null) {
      return null;
    }
        
    for (int i=0; i<item_list.size (); i++) {
      Element item = (Element)item_list.get (i);
      String text = XMLTools.getNodeText (item);
            
      //If there is nothing to display, don't bother creating the element
      if (text == "") {
	continue;
      }
      //get the value in 'lang=value'
      String lang = item.getAttribute (StaticStrings.LANG_STR);
            
      Element e = to.createElement (StaticStrings.COLLECTIONMETADATA_ELEMENT);
      e.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
      e.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_value);
      e.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, lang);
      XMLTools.setNodeText (e, text);
      display_item_list.add (e);
    }
    return display_item_list;
  }
    
  static private ArrayList doMetadataList (Document to, Node metadataListNode, String ele_name, String att_value) {
    Element toElement = to.getDocumentElement ();
    ArrayList metadata_list = new ArrayList ();
        
    ArrayList item_list = XMLTools.getNamedElementList ((Element)metadataListNode,
							StaticStrings.METADATA_STR, StaticStrings.NAME_ATTRIBUTE, att_value);
    if (item_list == null) {
      return null;
    }
        
    for (int i=0; i<item_list.size (); i++) {
      Element item = (Element)item_list.get (i);
      String text = XMLTools.getNodeText (item);
            
      //If there is nothing to display, don't bother creating the element
      if (text == "") {
	continue;
      }
      //get the value in 'lang=value'
      String lang = item.getAttribute (StaticStrings.LANG_STR);
            
      Element element = to.createElement (ele_name);
      element.setAttribute (StaticStrings.NAME_ATTRIBUTE, att_value);
      element.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, lang);
      element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
      element.setAttribute (StaticStrings.SPECIAL_ATTRIBUTE, StaticStrings.TRUE_STR);
      XMLTools.setNodeText (element, text);
            
      metadata_list.add (element);
    }
    return metadata_list;
  }
  // 'to' is the internal structure
  static private void doMGIndexes (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    Element indexes_element = to.createElement (StaticStrings.INDEXES_ELEMENT);//<Indexes>
    indexes_element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
    indexes_element.setAttribute (StaticStrings.MGPP_ATTRIBUTE, StaticStrings.FALSE_STR);
        
    NodeList index_children = ((Element)searchNode).getElementsByTagName (StaticStrings.INDEX_LOW_STR);//index
    int num_nodes = index_children.getLength ();
        
    for (int i=0; i<num_nodes; i++) {
      Element e = (Element)index_children.item (i);
      String index_str = e.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      String index_str_display = index_str;//used for creating collectionmetadata for this index
      Element index_element = to.createElement (StaticStrings.INDEX_ELEMENT);//<Index>
            
      // For mg, it's the 'Old G2.38 and earlier' that use level:source tuplets, but we double check it anyway
      boolean old_index = true;
      if(index_str.indexOf (StaticStrings.COLON_CHARACTER) == -1) {
	// It doesn't contain ':' character
	System.err.println ("Something is wrong! the index should be level:source tuplets.");
	old_index = false;
      }
      else {
	// Handling 'index' element
	index_element.setAttribute (StaticStrings.LEVEL_ATTRIBUTE,
				    index_str.substring (0, index_str.indexOf (StaticStrings.COLON_CHARACTER)));
	index_str = index_str.substring (index_str.indexOf (StaticStrings.COLON_CHARACTER) + 1);
                
	//Each index may have a list of comma-separated strings.
	//split them into 'content' elements in the internal structure
	StringTokenizer content_tokenizer = new StringTokenizer (index_str, StaticStrings.COMMA_CHARACTER);
	//index_str = "";
	while(content_tokenizer.hasMoreTokens ()) {
	  // Replace index_str to be qualified name, eg. dc.Subject and keywords insread of dc.Subject.
                    
                    
	  Element content_element = to.createElement (StaticStrings.CONTENT_ELEMENT);
	  String content_str = content_tokenizer.nextToken ();
	  // Since the contents of indexes have to be certain keywords, or metadata elements,
	  //if the content isn't a keyword and doesn't yet have a namespace, append the extracted metadata namespace.
	  if(content_str.indexOf (StaticStrings.NS_SEP) == -1) {
	    if(content_str.equals (StaticStrings.TEXT_STR) ||
	       (!old_index && content_str.equals (StaticStrings.ALLFIELDS_STR))) {
	      // in this case, do nothing
	    }
	    else {
	      content_str = StaticStrings.EXTRACTED_NAMESPACE + content_str;
	    }
	  }
                    
	  content_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, content_str);
	  index_element.appendChild (content_element);
	  content_element = null;
	} 	// while ends
                
	indexes_element.appendChild (index_element);
                
	// Handling 'displayItem' elements and Constructing 'collectionmetadata' elements
	// Use the fully qualified index names
	ArrayList collectionmetadata_list = doDisplayItemList (to, e, StaticStrings.NAME_ATTRIBUTE, index_str_display);
	appendArrayList (toElement, collectionmetadata_list);
      } //else ends
    } //for loop ends
    appendProperly (toElement, indexes_element);
        
    //***//
    // create another set of <indexes> which will be used when user switches to MGPP/LUCENE
    // i.e. we build a default index set for a start
        
    String []index_strs =
      {StaticStrings.TEXT_STR,
       StaticStrings.EXTRACTED_NAMESPACE + StaticStrings.TITLE_ELEMENT,
       StaticStrings.EXTRACTED_NAMESPACE + StaticStrings.SOURCE_ELEMENT};
         
    Element mgpp_indexes = to.createElement (StaticStrings.INDEXES_ELEMENT);//<Indexes>
    mgpp_indexes.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.FALSE_STR);
    mgpp_indexes.setAttribute (StaticStrings.MGPP_ATTRIBUTE, StaticStrings.TRUE_STR);
    for (int i=0; i<index_strs.length; i++) {
      Element index_element = to.createElement (StaticStrings.INDEX_ELEMENT);//<Index>
      Element content_element = to.createElement (StaticStrings.CONTENT_ELEMENT);
      content_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, index_strs[i]);
      index_element.appendChild (content_element);
      mgpp_indexes.appendChild (index_element);
             
      // Contructing 'collectionmetadata' elements for 'mgpp' indexes
      Element collectionmetadata = to.createElement (StaticStrings.COLLECTIONMETADATA_ELEMENT);
      collectionmetadata.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
      collectionmetadata.setAttribute (StaticStrings.NAME_ATTRIBUTE, index_strs[i]);
      collectionmetadata.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, StaticStrings.ENGLISH_LANGUAGE_STR);
      if (index_strs[i].indexOf (StaticStrings.NS_SEP) != -1) {
	index_strs[i] = index_strs[i].substring (index_strs[i].indexOf (StaticStrings.NS_SEP) + 1);
      }
      XMLTools.setNodeText (collectionmetadata, index_strs[i]);
             
      appendProperly (toElement, collectionmetadata);
             
    }
    appendProperly (toElement, mgpp_indexes);
  }
    
  //This is actually doing indexes for both mgpp and lucene
  static private void doMGPPIndexes (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    Element indexes_element = to.createElement (StaticStrings.INDEXES_ELEMENT);//<Indexes>
    indexes_element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
    indexes_element.setAttribute (StaticStrings.MGPP_ATTRIBUTE, StaticStrings.TRUE_STR);
        
    NodeList index_children = ((Element)searchNode).getElementsByTagName (StaticStrings.INDEX_LOW_STR);//index
    int num_nodes = index_children.getLength ();
        
    for (int i=0; i<num_nodes; i++) {
            
      Element index_element = to.createElement (StaticStrings.INDEX_ELEMENT);//<Index>
      Element e = (Element)index_children.item (i);
      String index_str = e.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      String index_str_display = index_str;//for creating collectionmetadata for this index 
            
      // Handling 'index' element
      // Double check to make sure it's not colon separated style index.
      boolean old_index = false;
      if(index_str.indexOf (StaticStrings.COLON_CHARACTER) != -1) {
	System.err.println ("Something is wrong! the index should NOT be level:source tuplets style.");
	old_index = true;
      }
      //Each index may have a list of comma-separated strings.
      //split them into 'content' elements in the internal structure
      StringTokenizer content_tokenizer = new StringTokenizer (index_str, StaticStrings.COMMA_CHARACTER);
      //index_str = "";
      while(content_tokenizer.hasMoreTokens ()) {
	// Replace index_str to be qualified name, eg. dc.Subject and keywords insread of dc.Subject.             
                
	Element content_element = to.createElement (StaticStrings.CONTENT_ELEMENT);
	String content_str = content_tokenizer.nextToken ();
	// Since the contents of indexes have to be certain keywords, or metadata elements, if the content isn't a keyword and doesn't yet have a namespace, append the extracted metadata namespace.
	if(content_str.indexOf (StaticStrings.NS_SEP) == -1) {
	  if(content_str.equals (StaticStrings.TEXT_STR)) {
	    // in this case, do nothing
	  }
	  else {
	    content_str = StaticStrings.EXTRACTED_NAMESPACE + content_str;
	  }
	}
	content_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, content_str);
	index_element.appendChild (content_element);
	content_element = null;
      } //while ends
            
      indexes_element.appendChild (index_element);
            
            
      index_element = null;
            
      // Handling 'displayItem' element of this 'index' element
      // 'e' is the parent element 'index' of 'displayItem' element
      ArrayList collectionmetadata_list = doDisplayItemList (to, e, StaticStrings.NAME_ATTRIBUTE, index_str_display);
      appendArrayList (toElement, collectionmetadata_list);
            
            
    } // for loop ends
    toElement.appendChild (indexes_element);
        
    // create another set of <indexes> which will be used when user switches to MG
    // i.e. we build a default index set for a start
    Element mg_indexes = to.createElement (StaticStrings.INDEXES_ELEMENT);//<Indexes>
    mg_indexes.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.FALSE_STR);
    mg_indexes.setAttribute (StaticStrings.MGPP_ATTRIBUTE, StaticStrings.FALSE_STR);
        
    //put the namespace '.ex' as prefix to the indexes
    String []index_strs =
      {StaticStrings.TEXT_STR,
       StaticStrings.EXTRACTED_NAMESPACE + StaticStrings.TITLE_ELEMENT,
       StaticStrings.EXTRACTED_NAMESPACE + StaticStrings.SOURCE_ELEMENT};
    for (int i=0; i<index_strs.length; i++) {
      Element index_element = to.createElement (StaticStrings.INDEX_ELEMENT);//<Index>
      index_element.setAttribute (StaticStrings.LEVEL_ATTRIBUTE, StaticStrings.DOCUMENT_STR);
      Element content_element = to.createElement (StaticStrings.CONTENT_ELEMENT);
      content_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, index_strs[i]);
      index_element.appendChild (content_element);
             
      mg_indexes.appendChild (index_element);
             
      // Contructing 'collectionmetadata' elements for 'mg' indexes
      Element collectionmetadata = to.createElement (StaticStrings.COLLECTIONMETADATA_ELEMENT);
      collectionmetadata.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
      String temp = StaticStrings.DOCUMENT_STR.concat (StaticStrings.COLON_CHARACTER).concat (index_strs[i]);
      collectionmetadata.setAttribute (StaticStrings.NAME_ATTRIBUTE, temp);
      collectionmetadata.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, StaticStrings.ENGLISH_LANGUAGE_STR);
      if (index_strs[i].indexOf (StaticStrings.NS_SEP) != -1) {
	index_strs[i] = index_strs[i].substring (index_strs[i].indexOf (StaticStrings.NS_SEP) + 1);
      }
      XMLTools.setNodeText (collectionmetadata, index_strs[i]);
             
      appendProperly (toElement, collectionmetadata);
             
    }
    toElement.appendChild (mg_indexes);
         
  }
    
  static private void doDisplayFormat (Document to, Element from) {
    //display element in the xml file
    Element de = (Element)XMLTools.getChildByTagName (from, StaticStrings.DISPLAY_STR);
    if (de == null) {
      return;
    }
    //format element in the display element
    Element fe = (Element)XMLTools.getChildByTagName (de, StaticStrings.FORMAT_STR);

    to.getDocumentElement ().appendChild (doFormat(to, fe, StaticStrings.DISPLAY_STR));
  }

  //construct 'DefaultIndex' element in the internal structure from collectionConfig.xml
  static private void doDefaultIndex (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    Element default_index_element = to.createElement (StaticStrings.INDEX_DEFAULT_ELEMENT);
    default_index_element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
        
    Element e = (Element)XMLTools.getChildByTagName (searchNode, StaticStrings.INDEX_DEFAULT_ELEMENT_LOWERCASE);//defaultIndex
    if (e == null) {
      return;
    }
    String index_str = e.getAttribute (StaticStrings.NAME_ATTRIBUTE);
        
    boolean old_index = false;
    if(index_str.indexOf (StaticStrings.COLON_CHARACTER) != -1) {
      //The index is 'level:source tuplets' which is for mg. Take out 'level'
      old_index = true;
      default_index_element.setAttribute (StaticStrings.LEVEL_ATTRIBUTE,
					  index_str.substring (0, index_str.indexOf (StaticStrings.COLON_CHARACTER)));
      index_str = index_str.substring (index_str.indexOf (StaticStrings.COLON_CHARACTER) + 1);
    } else {
      default_index_element.setAttribute (StaticStrings.LEVEL_ATTRIBUTE, "");
    }
        
    //Each index may have a list of comma-separated strings.
    //split them into 'content' elements in the internal structure
    StringTokenizer content_tokenizer = new StringTokenizer (index_str, StaticStrings.COMMA_CHARACTER);
    while(content_tokenizer.hasMoreTokens ()) {
      Element content_element = to.createElement (StaticStrings.CONTENT_ELEMENT);
      String content_str = content_tokenizer.nextToken ();
      // Since the contents of indexes have to be certain keywords, or metadata elements, if the content isn't a keyword and doesn't yet have a namespace, append the extracted metadata namespace.
      if(content_str.indexOf (StaticStrings.NS_SEP) == -1) {
	if(content_str.equals (StaticStrings.TEXT_STR) ||
	   (!old_index && content_str.equals (StaticStrings.ALLFIELDS_STR))) {
	  // in this case, do nothing
	}
	else {
	  content_str = StaticStrings.EXTRACTED_NAMESPACE + content_str;
	}
      }

      content_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, content_str);
      default_index_element.appendChild (content_element);
      content_element = null;
    }
    appendProperly (toElement, default_index_element);
  }
  // For mg, this method is still called, but make it 'assigned=false'
  static private void doDefaultLevel (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    Element default_index_option = to.createElement (StaticStrings.INDEXOPTION_DEFAULT_ELEMENT);
    default_index_option.setAttribute (StaticStrings.NAME_STR, StaticStrings.LEVEL_DEFAULT_STR);
        
    Element e = (Element)XMLTools.getChildByTagName (searchNode, StaticStrings.LEVEL_DEFAULT_ELEMENT);
    if (e != null) {
      default_index_option.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
      String level = e.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      default_index_option.setAttribute (StaticStrings.VALUE_ATTRIBUTE, level);
    } else {
      //In the case of mg, there's no level! build a default one using 'assigned=false value=document'
      default_index_option.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.FALSE_STR);
      default_index_option.setAttribute (StaticStrings.VALUE_ATTRIBUTE, StaticStrings.DOCUMENT_STR);
    }
    appendProperly (toElement, default_index_option);
  }
    
  // Transform plugins (pluginListNode) of collectionConfig.xml into the internal structure (i.e. Document to)
  static private void doPlugin (Document to, Node pluginListNode) {
    Element toElement = to.getDocumentElement ();
    NodeList plugin_children = ((Element)pluginListNode).getElementsByTagName (StaticStrings.PLUGIN_STR);
    int plugin_nodes = plugin_children.getLength ();
        
    if (plugin_nodes < 1) {
      return;
    }
        
    for (int i=0; i<plugin_nodes; i++) {
      Element e = (Element)plugin_children.item (i);
      String str = e.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      str = Utility.ensureNewPluginName(str);
      Element plugin_element = to.createElement (StaticStrings.PLUGIN_ELEMENT);
      plugin_element.setAttribute (StaticStrings.TYPE_ATTRIBUTE, str);
            
            
      NodeList option_children = e.getElementsByTagName (StaticStrings.OPTION_STR);
            
      for (int j=0; j<option_children.getLength (); j++) {
	Element el = (Element)option_children.item (j);
	String name_str = el.getAttribute (StaticStrings.NAME_ATTRIBUTE);
	if (name_str.startsWith (StaticStrings.MINUS_CHARACTER)) {
	  name_str = name_str.substring (1);
	}
	String value_str = el.getAttribute (StaticStrings.VALUE_ATTRIBUTE);
	Element option_element = null;
                
	if (name_str.equals ("") && !value_str.equals ("")) {
	  continue;
	}
                
                
	option_element = to.createElement (StaticStrings.OPTION_ELEMENT);
	option_element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
	if(name_str.equals (StaticStrings.RECPLUG_STR) && value_str.equals (StaticStrings.USE_METADATA_FILES_ARGUMENT)) {
	  continue; // ignore this option
	}
                
	if(value_str != null) {
	  // Remove any speech marks appended in strings containing whitespace
	  if(value_str.startsWith (StaticStrings.SPEECH_CHARACTER) && value_str.endsWith (StaticStrings.SPEECH_CHARACTER)) {
	    value_str = value_str.substring (1, value_str.length () - 1);
	  }
	  if(name_str.equals (StaticStrings.METADATA_STR)) {
	    // The metadata argument must be the fully qualified name of a metadata element, so if it doesn't yet have a namespace, append the extracted metadata namespace.
	    String[] values = value_str.split (StaticStrings.COMMA_CHARACTER);
	    value_str = "";
	    for (int k=0; k<=values.length-1; k++) {
	      if (values[k].indexOf (StaticStrings.NS_SEP) == -1) {
		values[k] = StaticStrings.EXTRACTED_NAMESPACE + values[k];
	      }

	      if (k < values.length-1) {
		value_str = value_str + values[k] + StaticStrings.COMMA_CHARACTER;
                                
	      } else {
		value_str = value_str + values[k];
	      }
	    }
	  }
	}
	if (!name_str.equals ("")) {
	  option_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
	}
	if (!value_str.equals ("")) {
	  XMLTools.setNodeText (option_element, value_str);
	}
	plugin_element.appendChild (option_element);
                
      }
            
      appendProperly (toElement, plugin_element);
    }
        
  }
    
  //Handle classifiers
  static private void doClassifier (Document to, Node browseNode) {
    Element toElement = to.getDocumentElement ();
    NodeList classifier_children = ((Element)browseNode).getElementsByTagName (StaticStrings.CLASSIFIER_STR);
    int num_nodes = classifier_children.getLength ();
        
    if (num_nodes < 1) {
      return;
    }
        
    for (int i=0; i<num_nodes; i++) {
      Element e = (Element)classifier_children.item (i);
      String str = e.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      Element classify_element = to.createElement (StaticStrings.CLASSIFY_ELEMENT);
      classify_element.setAttribute (StaticStrings.TYPE_ATTRIBUTE, str);
            
      String options_str = "";
      NodeList option_children = e.getElementsByTagName (StaticStrings.OPTION_STR);
      for (int j=0; j<option_children.getLength (); j++) {
	Element el = (Element)option_children.item (j);
	String name_str = el.getAttribute (StaticStrings.NAME_ATTRIBUTE);
	options_str = options_str + ((name_str.equals(""))? "" : (" " + name_str));
	if (name_str.startsWith (StaticStrings.MINUS_CHARACTER)) {
	  name_str = name_str.substring (1);
	}
	String value_str = el.getAttribute (StaticStrings.VALUE_ATTRIBUTE);
	options_str = options_str + ((name_str.equals(""))? "" : (" " + value_str));
	Element option_element = null;
                
	if (name_str.equals ("") && !value_str.equals ("")) {
	  continue; //invalid condition
	}
                
	option_element = to.createElement (StaticStrings.OPTION_ELEMENT);
	option_element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
                
	if (!name_str.equals ("")) {
	  option_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
	}
                
	if (!value_str.equals ("") && name_str.equals (StaticStrings.METADATA_STR)) {
	  // The metadata argument must be the fully qualified name of a metadata element, so if it doesn't yet have a namespace, append the extracted metadata namespace.
	  String[] values = value_str.split (StaticStrings.COMMA_CHARACTER);
	  value_str = "";
	  for (int k=0; k<=values.length-1; k++) {
	    if (values[k].indexOf (StaticStrings.NS_SEP) == -1) {
	      values[k] = StaticStrings.EXTRACTED_NAMESPACE + values[k];
	    }
	    else {
	      MetadataElement metadata_element = MetadataTools.getMetadataElementWithName (values[k]);
	      if (metadata_element != null) {
		values[k] = metadata_element.getDisplayName ();
	      }
	    }
	    if (k < values.length-1) {
	      value_str = value_str + values[k] + StaticStrings.COMMA_CHARACTER;
	    } else {
	      value_str = value_str + values[k];
	    }
	  }
	}
                
	if (value_str != null && !value_str.equals ("")) {
	  XMLTools.setNodeText (option_element, value_str);
	}
	classify_element.appendChild (option_element);
      }
      //format element for this classifier
      Element format = (Element)XMLTools.getChildByTagName (e, StaticStrings.FORMAT_STR);
      if(format != null) {
	classify_element.appendChild (doFormat(to, format, null));
      }
      appendProperly (toElement, classify_element);
    }
        
    // default format statement for all classifiers
    Element default_classifier_format = (Element)XMLTools.getChildByTagName (browseNode, StaticStrings.FORMAT_STR);

    to.getDocumentElement ().appendChild (doFormat(to, default_classifier_format, StaticStrings.BROWSE_STR));
  }
  static private Element doFormat(Document to, Element format, String name_str) {
    Element format_element = to.createElement (StaticStrings.FORMAT_STR);
    if (name_str != null) {
      format_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
    }
    
    // Don't write out an empty format statement of <format/> (i.e. format has no child nodes)
    // as this will end up embedded in another format statement as <format><format/><format />
    // This doubling up of format stmts will then prevent GLI from opening the collection again.
    if (format != null && format.hasChildNodes()) { // not an empty format statement
      String gsf_text = XMLTools.xmlNodeToStringWithoutIndenting(format);

      if (gsf_text.startsWith("<") && (gsf_text.indexOf("<") != gsf_text.lastIndexOf("<"))) {
	gsf_text = gsf_text.substring(gsf_text.indexOf("<gsf"),
				      gsf_text.indexOf(StaticStrings.FORMAT_END_TAG));
      }
      
      XMLTools.setNodeText(format_element, gsf_text);
    }
    return format_element;
  }
  // Handling 'subcollection' elements in 'search' element of 'collectionConfig.xml'
  static private void doSubcollection (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    NodeList sub_children = ((Element)searchNode).getElementsByTagName (StaticStrings.SUBCOLLECTION_STR);
    int sub_nodes = sub_children.getLength ();
        
    // There is no subcollection
    if (sub_nodes < 1) {
      return;
    }
        
    for (int i=0; i<sub_nodes; i++) {
      Element sub_child = (Element)sub_children.item (i);
      String name_str = sub_child.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      String filter_str = sub_child.getAttribute (StaticStrings.FILTER_ATTRIBUTE);
            
      // filter_str is in the form '<! (if set)><metadata>/<metadata value>/<flag (if any)>'
            
      int pos = filter_str.indexOf (StaticStrings.SEPARATOR_CHARACTER);
      String meta_str = "";
      String meta_value_str = "";
      String clude_str = "";
      String flag_str = "";
      if (pos == -1) {
                
	meta_str = meta_value_str = filter_str;
	clude_str = StaticStrings.INCLUDE_STR;
      } else {
	clude_str = StaticStrings.INCLUDE_STR;
	if (filter_str.startsWith (StaticStrings.EXCLAMATION_CHARACTER)) {
	  clude_str = StaticStrings.EXCLUDE_STR;
	  // Peel off "!"
	  filter_str = filter_str.substring (StaticStrings.EXCLAMATION_CHARACTER.length ());
	}
                
	String[] strs = filter_str.split (StaticStrings.SEPARATOR_CHARACTER);
	if (strs[0] != null && strs[0] != "") {
	  meta_str = strs[0];
	}
	if(!meta_str.equals (StaticStrings.FILENAME_STR) && meta_str.indexOf (StaticStrings.NS_SEP) == -1) {
	  meta_str = StaticStrings.EXTRACTED_NAMESPACE + meta_str;
	}
                
	if (strs[1] != null && strs[1] != "") {
	  meta_value_str = strs[1];
	}
	if (strs.length > 2) {
	  //This means there has been set a flag
	  if (strs[2] != null && strs[2] != "") {
	    flag_str = strs[2];
	  }
	}
      }
      Element subcollection_element = to.createElement (StaticStrings.SUBCOLLECTION_ELEMENT);
      subcollection_element.setAttribute (StaticStrings.NAME_STR, name_str);
      subcollection_element.setAttribute (StaticStrings.CONTENT_ATTRIBUTE, meta_str);
      subcollection_element.setAttribute (StaticStrings.TYPE_ATTRIBUTE, clude_str);
      if (flag_str != "") {
	subcollection_element.setAttribute (StaticStrings.OPTIONS_ATTRIBUTE, flag_str);
      }
      XMLTools.setNodeText (subcollection_element, meta_value_str);
            
      toElement.appendChild (subcollection_element);
    }
  }
  //Handle levels (document, section). In the internal structure, the element is called 'IndexOption'
  static private void doLevel (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    NodeList level_children = ((Element)searchNode).getElementsByTagName (StaticStrings.LEVEL_ATTRIBUTE);
    int level_nodes = level_children.getLength ();
        
    // it's mg, there's no level. So we construct a default 'indexOption' in the internal structure
    if (level_nodes < 1) {
      Element index_option = to.createElement (StaticStrings.INDEXOPTIONS_ELEMENT);
      index_option.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.FALSE_STR);
      index_option.setAttribute (StaticStrings.NAME_STR, StaticStrings.LEVELS_STR);
            
      Element option_element = to.createElement (StaticStrings.OPTION_ELEMENT);
      option_element.setAttribute (StaticStrings.NAME_STR, StaticStrings.DOCUMENT_STR);
      index_option.appendChild (option_element);
            
      appendProperly (toElement, index_option);
            
      return;
    }
        
    Element index_option = to.createElement (StaticStrings.INDEXOPTIONS_ELEMENT);
    index_option.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
    index_option.setAttribute (StaticStrings.NAME_STR, StaticStrings.LEVELS_STR);
        
    for (int i=0; i<level_nodes; i++) {
      Element level_element = (Element)level_children.item (i);
      String level_str = level_element.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      Element option_element = to.createElement (StaticStrings.OPTION_ELEMENT);
      option_element.setAttribute (StaticStrings.NAME_STR, level_str);
      index_option.appendChild (option_element);
            
            
      // Contructing 'collectionmetadata' elements from the 'displayItem' of this 'level' element
      ArrayList displayItem_list = XMLTools.getNamedElementList (level_element,
								 StaticStrings.DISPLAYITEM_STR, StaticStrings.NAME_ATTRIBUTE, StaticStrings.NAME_STR);
      if (displayItem_list == null) {
	return ;
      }
      for (int j=0; j<displayItem_list.size (); j++) {
	Element item = (Element)displayItem_list.get (j);
	String text = XMLTools.getNodeText (item);
	String lang = item.getAttribute (StaticStrings.LANG_ATTRIBUTE);
                
	//If there is nothing to display, don't bother creating the element
	if (text == "") {
	  continue;
	}
	Element collectionmetadata = to.createElement (StaticStrings.COLLECTIONMETADATA_ELEMENT);
	collectionmetadata.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
	collectionmetadata.setAttribute (StaticStrings.NAME_ATTRIBUTE, level_str);
	collectionmetadata.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, lang);
	XMLTools.setNodeText (collectionmetadata, text);
                
	appendProperly (toElement, collectionmetadata);
      }
    }
    appendProperly (toElement, index_option);
  }
  //Handle 'indexSubcollection' element of collectionConfig.xml,  which is called 'SubcollectionIndexes' in the internal structure. These contain the subcollection indexes (i.e. the filter or filter combinations), and displayed words for the filter names.
  static private void doIndexSubcollection (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    NodeList index_sub_children = ((Element)searchNode).getElementsByTagName (StaticStrings.SUBCOLLECTION_INDEX_ELEMENT);
    int num_nodes = index_sub_children.getLength ();
        
    // there is no subcollection index
    if (num_nodes < 1) {
      return;
    }
        
    Element subcollection_indexes = to.createElement (StaticStrings.SUBCOLLECTION_INDEXES_ELEMENT);
        
    for (int i=0; i<num_nodes; i++) {
      Element index_element = to.createElement (StaticStrings.INDEX_ELEMENT);
      Element index_sub_child = (Element)index_sub_children.item (i);
      String name_str = index_sub_child.getAttribute (StaticStrings.NAME_ATTRIBUTE);
            
      // name_str is in the form of comma separated strings, each of which is a subcollection filter name
      String[] filters = name_str.split (StaticStrings.COMMA_CHARACTER);
      for (int j=0; j<filters.length; j++) {
                
	Element content_element = to.createElement (StaticStrings.CONTENT_ELEMENT);
	content_element.setAttribute (StaticStrings.NAME_STR, filters[j]);
	index_element.appendChild (content_element);
      }
      subcollection_indexes.appendChild (index_element);
            
      // Contructing 'collectionmetadata' elements from the 'displayItem' of this 'indexSubcollection' element
      ArrayList displayItem_list = XMLTools.getNamedElementList (index_sub_child,
								 StaticStrings.DISPLAYITEM_STR, StaticStrings.NAME_ATTRIBUTE, StaticStrings.NAME_STR);
      if (displayItem_list == null) {
	// there is no display item for this element
	continue;
      }
      for (int j=0; j<displayItem_list.size (); j++) {
	Element item = (Element)displayItem_list.get (j);
	String text = XMLTools.getNodeText (item);
	String lang = item.getAttribute (StaticStrings.LANG_ATTRIBUTE);
                
	//If there is nothing to display, don't bother creating the element
	if (text == "") {
	  continue;
	}
	Element collectionmetadata = to.createElement (StaticStrings.COLLECTIONMETADATA_ELEMENT);
	collectionmetadata.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
	collectionmetadata.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
	collectionmetadata.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, lang);
	XMLTools.setNodeText (collectionmetadata, text);
                
	appendProperly (toElement, collectionmetadata);
      }
    }
    appendProperly (toElement, subcollection_indexes);
  }
  //Handle 'indexLanguage' element of collectionConfig.xml,  which is called 'Languages' in the internal structure. These contain the language indexes, and displayed words for those language index names.
  static private void doIndexLanguage (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    NodeList index_sub_children = ((Element)searchNode).getElementsByTagName (StaticStrings.LANGUAGE_INDEX_ELEMENT);
    int num_nodes = index_sub_children.getLength ();
        
    // there is no subcollection index
    if (num_nodes < 1) {
      return;
    }
        
    Element language_indexes = to.createElement (StaticStrings.LANGUAGES_ELEMENT);
        
    for (int i=0; i<num_nodes; i++) {
      Element language_element = to.createElement (StaticStrings.LANGUAGE_ELEMENT);
      Element index_sub_child = (Element)index_sub_children.item (i);
      String name_str = index_sub_child.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      language_element.setAttribute (StaticStrings.NAME_STR, name_str);
      language_indexes.appendChild (language_element);
            
      // Contructing 'collectionmetadata' elements from the 'displayItem' of this 'indexLanguage' element
      ArrayList displayItem_list = XMLTools.getNamedElementList (index_sub_child,
								 StaticStrings.DISPLAYITEM_STR, StaticStrings.NAME_ATTRIBUTE, StaticStrings.NAME_STR);
      if (displayItem_list == null) {
	// there is no display item for this element
	continue;
      }
      for (int j=0; j<displayItem_list.size (); j++) {
	Element item = (Element)displayItem_list.get (j);
	String text = XMLTools.getNodeText (item);
	String lang = item.getAttribute (StaticStrings.LANG_ATTRIBUTE);
                
	//If there is nothing to display, don't bother creating the element
	if (text == "") {
	  continue;
	}
	Element collectionmetadata = to.createElement (StaticStrings.COLLECTIONMETADATA_ELEMENT);
	collectionmetadata.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
	collectionmetadata.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
	collectionmetadata.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, lang);
	XMLTools.setNodeText (collectionmetadata, text);
                
	appendProperly (toElement, collectionmetadata);
      }
    }
    toElement.appendChild (language_indexes);
  }

  // Handling search types
  static private void doSearchType (Document to, Node searchNode) {
    NodeList type_children = ((Element)searchNode).getElementsByTagName (StaticStrings.SEARCHTYPE_ELEMENT);
    int num_types = type_children.getLength();
    String searchtype_str = "";
    if (num_types < 1) {
      // not defined yet, add in default
      searchtype_str = "plain,simpleform,advancedform";
    }
    else {
      for(int i=0; i<num_types; i++) {
	Node e = type_children.item (i);
	String t = ((Element)e).getAttribute (StaticStrings.NAME_ATTRIBUTE);
	if (i>0) {
	  searchtype_str += ",";
	}
	searchtype_str += t;
      }
    }
    
    // pretend its a format statement
    Element search_type_element = to.createElement (StaticStrings.FORMAT_STR);
    search_type_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, StaticStrings.SEARCHTYPE_ELEMENT);
    XMLTools.setNodeText(search_type_element, searchtype_str);
    appendProperly (to.getDocumentElement (), search_type_element);
    
  }

  // Handling search format statement
  static private void doSearchFormat (Document to, Node searchNode) {
    // THere is currently just one format element for search. HOwever, need to check for old config files which used to have <format name="searchTypes">
    NodeList format_children = ((Element)searchNode).getElementsByTagName (StaticStrings.FORMAT_STR);
    int format_nodes = format_children.getLength ();
    if (format_nodes < 1) {
      return;
    }
    Element format = null;
    for(int i=0; i<format_nodes; i++) {
      Node e = format_children.item (i);
      if (e.hasAttributes () == false) {
	//The format element for format statement has no attribute
	format = (Element)e;
      }
    }
    //format statement for search
    if (format != null) {            
      (to.getDocumentElement ()).appendChild (doFormat(to, format, StaticStrings.SEARCH_STR));
    }
  }
  // Handling defaultIndexLanguage and languageMetadata in collectionConfig.xml ('elementNameFrom'); in the internal structure, they are called 'DefaultLanguage' and 'LanguageMetadata' ('elementNameTo') respectively.
  // Converting from collectionConfig.xml to the internal xml structure.
  static private void doLanguageMetadata (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    String elementNameFrom = StaticStrings.LANGUAGE_METADATA_ELEMENT_STR;
    String elementNameTo = StaticStrings.LANGUAGE_METADATA_ELEMENT;
    Node from_element = XMLTools.getChildByTagName (searchNode, elementNameFrom);
    if (from_element == null) {
      return; // such an element not found
    }
        
    Element to_element = to.createElement (elementNameTo);
        
    String name_str = ((Element)from_element).getAttribute (StaticStrings.NAME_ATTRIBUTE);
    if (name_str.indexOf (StaticStrings.NS_SEP) == -1) {
      name_str = StaticStrings.EXTRACTED_NAMESPACE + name_str;
    }
    to_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
    to_element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
        
    toElement.appendChild (to_element);
  }
  static private void doReplaceListRef (Document to, Element from) {
    Element toElement = to.getDocumentElement ();
        
    NodeList replace_elements = from.getElementsByTagName(StaticStrings.REPLACELISTREF_STR);
    int num_elems = replace_elements.getLength();
    if (num_elems < 1) {
      return;
    }
    for (int i=0; i<num_elems; i++) {
      Element to_element = XMLTools.duplicateElement (to, (Element)replace_elements.item(i), true);
      toElement.appendChild (to_element);
    }
  }
  static private void convertReplaceListRef (Document from, Document to) {
    Element toElement = to.getDocumentElement ();
        
    NodeList replace_elements = from.getDocumentElement().getElementsByTagName(StaticStrings.REPLACELISTREF_STR);
    int num_elems = replace_elements.getLength();
    if (num_elems < 1) {
      return;
    }
    for (int i=0; i<num_elems; i++) {
      Element to_element = XMLTools.duplicateElement (to, (Element)replace_elements.item(i), true);
      toElement.appendChild (to_element);
    }
  }

  /** serviceRackList is currently not editable in GLI - just copy it in from config file and write it out again. */
  static private void doServiceRackList (Document to, Element from) {
    Element toElement = to.getDocumentElement ();
        
    Node srl_element = XMLTools.getChildByTagName (from, StaticStrings.SERVICE_RACK_LIST_ELEMENT);
    if (srl_element == null) {
      return; // such an element not found
    }
        
    Element to_element = XMLTools.duplicateElement (to, (Element)srl_element, true);
    toElement.appendChild (to_element);
  }
  static private void convertServiceRackList (Document from, Document to) {
    Element toElement = to.getDocumentElement ();
        
    Node srl_element = XMLTools.getChildByTagName (from.getDocumentElement (), StaticStrings.SERVICE_RACK_LIST_ELEMENT);
    if (srl_element == null) {
      return; // such an element not found
    }
        
    Element to_element = XMLTools.duplicateElement (to, (Element)srl_element, true);
    toElement.appendChild (to_element);
  }
  static private void doDefaultIndexLanguage (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    String elementNameFrom = StaticStrings.LANGUAGE_DEFAULT_INDEX_ELEMENT;
    String elementNameTo = StaticStrings.LANGUAGE_DEFAULT_ELEMENT;
    Node from_element = XMLTools.getChildByTagName (searchNode, elementNameFrom);
    if (from_element == null) {
      return; // such an element not found
    }
        
    Element to_element = to.createElement (elementNameTo);
        
    String name_str = ((Element)from_element).getAttribute (StaticStrings.NAME_ATTRIBUTE);
    to_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
    to_element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
        
    toElement.appendChild (to_element);
  }
    
  //Handle 'indexOption' (i.e. casefold, stem etc). In the internal structure, the element is called 'IndexOption'
  static private void doIndexOption (Document to, Node searchNode) {
    Element toElement = to.getDocumentElement ();
    Node index_option_node = XMLTools.getChildByTagName (searchNode, StaticStrings.INDEXOPTION_STR);
    if (index_option_node == null) {
      return;
    }
    NodeList option_children = ((Element)index_option_node).getElementsByTagName (StaticStrings.OPTION_STR);
    int option_nodes = option_children.getLength ();
        
    // for lucene, there is no 'indexOption'. We build a default 'indexOption' and 'assigned=false' in case the user switches to mg or mgpp
    if (option_nodes < 1) {
      Element index_option = to.createElement (StaticStrings.INDEXOPTIONS_ELEMENT);
      index_option.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.FALSE_STR);
      index_option.setAttribute (StaticStrings.NAME_STR, StaticStrings.INDEXOPTIONS_STR);
      String[] option_str =
	{ StaticStrings.CASEFOLD_OPTION_STR, StaticStrings.STEM_OPTION_STR };
      for (int i=0; i<option_str.length; i++) {
	Element option_element = to.createElement (StaticStrings.OPTION_ELEMENT);
	option_element.setAttribute (StaticStrings.NAME_STR, option_str[i]);
	index_option.appendChild (option_element);
      }
      appendProperly (toElement, index_option);
      return;
    }
        
    Element index_option = to.createElement (StaticStrings.INDEXOPTIONS_ELEMENT);
    index_option.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
    index_option.setAttribute (StaticStrings.NAME_STR, StaticStrings.INDEXOPTIONS_STR);
        
    for (int i=0; i<option_nodes; i++) {
      String option_str = ((Element)option_children.item (i)).getAttribute (StaticStrings.NAME_ATTRIBUTE);
      Element option_element = to.createElement (StaticStrings.OPTION_ELEMENT);
      option_element.setAttribute (StaticStrings.NAME_STR, option_str);
      index_option.appendChild (option_element);
    }
    appendProperly (toElement, index_option);
  }
    
  static private Element doBuildType (Document to, String att_value) {
        
    //construct 'BuildType' element
    Element element = to.createElement (StaticStrings.BUILDTYPE_ELEMENT);
    element.setAttribute (StaticStrings.NAME_ATTRIBUTE, StaticStrings.BUILDTYPE_STR);
    element.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, StaticStrings.ENGLISH_LANGUAGE_STR);
    element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
    element.setAttribute (StaticStrings.SPECIAL_ATTRIBUTE, StaticStrings.TRUE_STR);

    XMLTools.setNodeText (element, att_value);
        
    return element;
  }
 
  static private Element doDatabaseType (Document to, String att_value) {
        
    //construct 'DatabaseType' element
    Element element = to.createElement (StaticStrings.DATABASETYPE_ELEMENT);
    element.setAttribute (StaticStrings.NAME_ATTRIBUTE, StaticStrings.DATABASETYPE_STR);
    element.setAttribute (StaticStrings.LANGUAGE_ATTRIBUTE, StaticStrings.ENGLISH_LANGUAGE_STR);
    element.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
    element.setAttribute (StaticStrings.SPECIAL_ATTRIBUTE, StaticStrings.TRUE_STR);

    XMLTools.setNodeText (element, att_value);
        
    return element;
  }
    
  // Convert 'description', 'smallicon' etc.
  static private void convertDisplayItemList (Document from, Document to) {
    Element displayItemList = to.createElement (StaticStrings.DISPLAYITEMLIST_STR);
    Element destination = to.getDocumentElement ();
        
    String []att_values =
      {StaticStrings.COLLECTIONMETADATA_COLLECTIONEXTRA_STR,
       StaticStrings.COLLECTIONMETADATA_ICONCOLLECTIONSMALL_STR,
       StaticStrings.COLLECTIONMETADATA_ICONCOLLECTION_STR,
       StaticStrings.COLLECTIONMETADATA_COLLECTIONNAME_STR};
         
    String []map_attrs =
      {StaticStrings.DESCRIPTION_STR,
       StaticStrings.SMALLICON_STR,
       StaticStrings.ICON_STR,
       StaticStrings.NAME_STR};
          
    for (int i=0; i<att_values.length; i++) {
              
      //dOc
      ArrayList e_list = XMLTools.getNamedElementList (from.getDocumentElement (),
						       StaticStrings.COLLECTIONMETADATA_ELEMENT,
						       StaticStrings.NAME_ATTRIBUTE, att_values[i]);
      // if such elements don't exist, don't bother
      if (e_list == null) {
	continue;
      }
      for (int j=0; j<e_list.size (); j++) {
	Element e = (Element)e_list.get (j);
	if (e.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	  continue;
	}
	String text = XMLTools.getNodeText (e);
	String lang = e.getAttribute (StaticStrings.LANGUAGE_ATTRIBUTE);
                  
	Element displayItem = constructElement (StaticStrings.DISPLAYITEM_STR, map_attrs[i],
						StaticStrings.LANG_STR, lang, text, to);
	displayItemList.appendChild (displayItem);
      }
              
    }
    destination.appendChild (displayItemList);
  }
  // This method creates a DisplayItem element of the type of 'to' by using the ingredients from the element 'e'
  static private Element constructDisplayItem (Element e, Document to) {
    String lang_string = e.getAttribute (StaticStrings.LANGUAGE_ATTRIBUTE);
    String text = XMLTools.getNodeText (e);
    Element displayItem = to.createElement (StaticStrings.DISPLAYITEM_STR);
    displayItem.setAttribute (StaticStrings.NAME_ATTRIBUTE, StaticStrings.NAME_ATTRIBUTE);
    displayItem.setAttribute (StaticStrings.LANG_STR, lang_string);
    XMLTools.setNodeText (displayItem, text);
    return displayItem;
  }
  static private void convertMetadataList (Document from, Document to) {
    Element metadataList = to.createElement (StaticStrings.METADATALIST_STR);
    Element destination = to.getDocumentElement ();
        
    String []ele_names =
      {StaticStrings.COLLECTIONMETADATA_CREATOR_ELEMENT,
       StaticStrings.COLLECTIONMETADATA_MAINTAINER_ELEMENT,
       StaticStrings.COLLECTIONMETADATA_PUBLIC_ELEMENT};
    String []att_names =
      {StaticStrings.COLLECTIONMETADATA_CREATOR_STR,
       StaticStrings.COLLECTIONMETADATA_MAINTAINER_STR,
       StaticStrings.COLLECTIONMETADATA_PUBLIC_STR};
    for (int i=0; i<ele_names.length; i++) {
      Element e = XMLTools.getNamedElement (from.getDocumentElement (),
					    ele_names[i], StaticStrings.NAME_ATTRIBUTE, att_names[i]);
      if (e == null) {
	continue;
      }
      String text = XMLTools.getNodeText (e);
      Element metadata = to.createElement (StaticStrings.METADATA_STR);
      metadata.setAttribute (StaticStrings.NAME_ATTRIBUTE, att_names[i]);
      metadata.setAttribute (StaticStrings.LANG_STR, StaticStrings.ENGLISH_LANGUAGE_STR);
      XMLTools.setNodeText (metadata, text);
      metadataList.appendChild (metadata);
    }

    destination.appendChild (metadataList);
  }
  // This method creates an element with the name 'element_name' of the type of 'to' by using the other three strings
  static private Element constructElement (String element_name, String name_value, String lang_att, String lang_value, String text, Document to) {
    Element e = to.createElement (element_name);
    e.setAttribute (StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
    e.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_value);
    e.setAttribute (lang_att, lang_value);
    XMLTools.setNodeText (e, text);
        
    return e;
  }
  // Convert classify in the internal(i.e. Document from) to collectionconfig.xml (i.e. Document to)
  static private void convertClassifier (Document from, Document to) {
    Element browse_element = to.createElement (StaticStrings.BROWSE_STR);
    NodeList children = from.getDocumentElement ().getElementsByTagName (StaticStrings.CLASSIFY_ELEMENT);
        
    int num_children = (children == null)? 0 : children.getLength ();
        
    if (num_children == 0) {
      return ;
    }
        
    for (int i=0; i<num_children; i++) {
            
      Element child =  (Element)children.item (i);
      if (child.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	continue;
      }
      String str = child.getAttribute (StaticStrings.TYPE_ATTRIBUTE);
      Element classifier_element = to.createElement (StaticStrings.CLASSIFIER_STR);
      classifier_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, str);
            
      NodeList option_children = child.getElementsByTagName (StaticStrings.OPTION_ELEMENT);
      for (int j=0; j<option_children.getLength (); j++) {
	Element el = (Element)option_children.item (j);
	if (el.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	  continue;
	}
	String name_str = el.getAttribute (StaticStrings.NAME_ATTRIBUTE);
	String value_str = XMLTools.getNodeText (el);
                
                
	if (name_str == null && value_str == null) {
	  continue;
	}
	Element option_element = to.createElement (StaticStrings.OPTION_STR);
	if (name_str != null && name_str.equals (StaticStrings.METADATA_STR)) {
                    
	  // The metadata argument is the fully qualified name of a metadata element, so if it contains a namespace, remove the extracted metadata namespace as the build process doesn't know about it.
	  String[] values = value_str.split (StaticStrings.COMMA_CHARACTER);
	  value_str = "";
	  for (int k=0; k<=values.length-1; k++) {
	    if(values[k].startsWith (StaticStrings.EXTRACTED_NAMESPACE) && values[k].indexOf(StaticStrings.NS_SEP, StaticStrings.EXTRACTED_NAMESPACE.length()) == -1) {
	      values[k] = values[k].substring (StaticStrings.EXTRACTED_NAMESPACE.length ());
	    }
	    else {
	      MetadataElement metadata_element = MetadataTools.getMetadataElementWithDisplayName (values[k]);
	      if (metadata_element != null) {
		values[k] = metadata_element.getFullName ();
	      }
	    }
	    if (k < values.length-1) {
	      value_str = value_str + values[k] + StaticStrings.COMMA_CHARACTER;
	    } else {
	      value_str = value_str + values[k];
	    }
	  }
	}
                
	if (!name_str.equals ("")) {
	  if (!name_str.startsWith (StaticStrings.MINUS_CHARACTER)) {
	    name_str = StaticStrings.MINUS_CHARACTER + name_str;
	  }
	  option_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
	}
                
	if (!value_str.equals ("")) {
	  option_element.setAttribute (StaticStrings.VALUE_ATTRIBUTE, value_str);
	}
                
	classifier_element.appendChild (option_element);
      }
            
      //format element for this classifier
      Element e = (Element)XMLTools.getChildByTagName (child, StaticStrings.FORMAT_STR);
            
      if (e != null) {
	classifier_element.appendChild (convertFormat(to, e));
      }
      browse_element.appendChild (classifier_element);
    }
        
    //convert default classifier format
    Element e = XMLTools.getNamedElement (from.getDocumentElement (), StaticStrings.FORMAT_STR,
					  StaticStrings.NAME_ATTRIBUTE,  StaticStrings.BROWSE_STR);
    browse_element.appendChild (convertFormat(to, e));
        
    to.getDocumentElement ().appendChild (browse_element);
  }
  static private Element convertFormat(Document to, Element e) {
    String format_str = XMLTools.getNodeText(e);
    Element format = to.createElement (StaticStrings.FORMAT_STR);
    //XMLTools.copyAllChildren (format, e);
    XMLTools.setNodeText(format, format_str); 
    return format;
  }
  //convert format statement for search
  static private void convertSearchFormat (Document from, Document to) {
    Element search = (Element)XMLTools.getChildByTagName (to.getDocumentElement (), StaticStrings.SEARCH_STR);
    Element e = XMLTools.getNamedElement (from.getDocumentElement (), StaticStrings.FORMAT_STR,
					  StaticStrings.NAME_ATTRIBUTE,  StaticStrings.SEARCH_STR);
                                                
    search.appendChild (convertFormat(to, e));
        
  }
  //convert format statement for display of the documents
  static private void convertDisplayFormat (Document from, Document to) {
    Element e = XMLTools.getNamedElement (from.getDocumentElement (), StaticStrings.FORMAT_STR,
					  StaticStrings.NAME_ATTRIBUTE,  StaticStrings.DISPLAY_STR);
    if (e == null) {
      return;
    }
    Element display = to.createElement (StaticStrings.DISPLAY_STR);
    display.appendChild (convertFormat(to, e));
    to.getDocumentElement ().appendChild (display);
  }
  // Convert plugins in the internal(i.e. Document from) to collectionconfig.xml (i.e. Document to)
  static private void convertPlugin (Document from, Document to) {
    Element import_element = to.createElement (StaticStrings.IMPORT_STR);
    Element plugin_list_element = to.createElement (StaticStrings.PLUGINLIST_STR);
        
    NodeList children = from.getDocumentElement ().getElementsByTagName (StaticStrings.PLUGIN_ELEMENT);
    int num_children = (children == null)? 0 : children.getLength ();
    if (num_children == 0) {
      return ;
    }
        
    for (int i=0; i<num_children; i++) {
            
      Element child =  (Element)children.item (i);
      if (child.getAttribute (StaticStrings.SEPARATOR_ATTRIBUTE).equals (StaticStrings.TRUE_STR)) {
	continue;
      }
      if (child.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	continue;
      }
            
      String str = child.getAttribute (StaticStrings.TYPE_ATTRIBUTE);
      Element plugin_element = to.createElement (StaticStrings.PLUGIN_STR);
      plugin_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, str);
            
      NodeList option_children = child.getElementsByTagName (StaticStrings.OPTION_ELEMENT);
      for (int j=0; j<option_children.getLength (); j++) {
	Element el = (Element)option_children.item (j);
	if(!el.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.TRUE_STR)) {
	  continue;
	}
	String name_str = el.getAttribute (StaticStrings.NAME_ATTRIBUTE);
	String value_str = XMLTools.getNodeText (el);
                
                
	if (name_str == null && value_str == null) {
	  continue;
	}
	Element option_element = to.createElement (StaticStrings.OPTION_STR);
	if (name_str != null && name_str.equals (StaticStrings.METADATA_STR)) {
                    
	  // The metadata argument is the fully qualified name of a metadata element, so if it contains a namespace, remove the extracted metadata namespace as the build process doesn't know about it, but ONLY if it is not embedded metadata (e.g. ex.dc.*)
	  String[] values = value_str.split (StaticStrings.COMMA_CHARACTER);
	  value_str = "";
	  for (int k=0; k<=values.length-1; k++) {
	    if(values[k].startsWith (StaticStrings.EXTRACTED_NAMESPACE) && values[k].indexOf(StaticStrings.NS_SEP, StaticStrings.EXTRACTED_NAMESPACE.length()) == -1) {
	      values[k] = values[k].substring (StaticStrings.EXTRACTED_NAMESPACE.length ());
	    }

	    if (k < values.length-1) {
	      value_str = value_str + values[k] + StaticStrings.COMMA_CHARACTER;
	    } else {
	      value_str = value_str + values[k];
	    }
	  }
	}
                
	if (!name_str.equals ("")) {
	  if (!name_str.startsWith (StaticStrings.MINUS_CHARACTER)) {
	    name_str = StaticStrings.MINUS_CHARACTER + name_str;
	  }
	  option_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
	}
                
	if (!value_str.equals ("")) {
	  option_element.setAttribute (StaticStrings.VALUE_ATTRIBUTE, value_str);
	}
                
	plugin_element.appendChild (option_element);
      }//for loop ends
            
      plugin_list_element.appendChild (plugin_element);
    }//for loop ends
        
    import_element.appendChild (plugin_list_element);
        
    //do the plugout element (used by building flax collections)
    Node plugout = XMLTools.getChildByTagNameIndexed (from.getDocumentElement (), PLUGOUT_ELEMENT, 0);
    if (plugout != null) {
      Element to_element = XMLTools.duplicateElement (to, (Element)plugout, true);
      import_element.appendChild (to_element);
    }
        
    to.getDocumentElement ().appendChild (import_element);
  }

  //Handle 'searchType' of collectionConfig.xml. In the internal structure, its also called 'searchType', eg. plain, form
  static private void convertSearchType (Document from, Document to) {
    Element e = XMLTools.getNamedElement (from.getDocumentElement (), StaticStrings.FORMAT_STR,
					  StaticStrings.NAME_ATTRIBUTE,  StaticStrings.SEARCHTYPE_ELEMENT);//searchType
        
    if (e == null) {
      return;
    }
    String searchtype_str = XMLTools.getNodeText(e); 
    //Get the 'search' element from 'to'
    Element search = (Element)XMLTools.getChildByTagName (to.getDocumentElement (), StaticStrings.SEARCH_STR);

    String[] types = searchtype_str.split(",");
    for (int i=0; i<types.length; i++) {
      Element search_type_element = to.createElement (StaticStrings.SEARCHTYPE_ELEMENT);
      search_type_element.setAttribute(StaticStrings.NAME_ATTRIBUTE, types[i]);
      search.appendChild (search_type_element);
    }
  }
    
  static private void convertBuildType (Document from, Document to) {
    Element e = XMLTools.getNamedElement (from.getDocumentElement (),
					  StaticStrings.BUILDTYPE_ELEMENT,
					  StaticStrings.NAME_ATTRIBUTE, StaticStrings.BUILDTYPE_STR);
    if (e == null) {
      return;
    }
    String indexer = XMLTools.getNodeText (e);
    Element search = to.createElement (StaticStrings.SEARCH_STR);
    search.setAttribute (StaticStrings.TYPE_ATTRIBUTE, indexer);
    to.getDocumentElement ().appendChild (search);
  }
  static private void convertDatabaseType (Document from, Document to) {
    Element e = XMLTools.getNamedElement (from.getDocumentElement (),
					  StaticStrings.DATABASETYPE_ELEMENT,
					  StaticStrings.NAME_ATTRIBUTE, 
					  StaticStrings.DATABASETYPE_STR);
    if (e == null) {
      return;
    }
    String db = XMLTools.getNodeText (e);
    Element dbtype = to.createElement (StaticStrings.INFODB_STR);
    dbtype.setAttribute (StaticStrings.TYPE_ATTRIBUTE, db);
    to.getDocumentElement ().appendChild (dbtype);
  }
  static private void convertDefaultIndex (Document from, Document to, Element search) {
    Element source = from.getDocumentElement ();
        
    Element default_index_element = (Element)XMLTools.getChildByTagName (source, StaticStrings.INDEX_DEFAULT_ELEMENT);
    if (default_index_element == null) {
      return;
    }
        
    String indexer = search.getAttribute (StaticStrings.TYPE_ATTRIBUTE);
    String level_str = default_index_element.getAttribute (StaticStrings.LEVEL_ATTRIBUTE);
    // Debugging purposes
    if (level_str.equals ("") && indexer.equals (StaticStrings.MG_STR) ) {
      System.out.println ("Bug: DefaultIndex should have its level attribute not empty.");
    }
        
    NodeList content_elements = default_index_element.getElementsByTagName (StaticStrings.CONTENT_ELEMENT);
    int content_elements_length = content_elements.getLength ();
        
    // Don't output anything if no indexes are set
    if(content_elements_length == 0) {
      return ;//
    }
        
    String index_str = "";
        
    if (indexer.equals (StaticStrings.MG_STR)) {
      //combine level with indexes
      index_str = level_str + StaticStrings.COLON_CHARACTER;
    }
    else { //for mgpp/lucene, just take index
      //do nothing
    }
        
    for(int k = 0; k < content_elements_length; k++) {
      Element content_element = (Element) content_elements.item (k);
      if (content_element.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	continue;
      }
      String name_str = content_element.getAttribute (StaticStrings.NAME_ATTRIBUTE);
            
      if(name_str.startsWith (StaticStrings.EXTRACTED_NAMESPACE) && name_str.indexOf(StaticStrings.NS_SEP, StaticStrings.EXTRACTED_NAMESPACE.length()) == -1) {
	name_str = name_str.substring (StaticStrings.EXTRACTED_NAMESPACE.length ());
      }

      index_str = index_str + name_str;
            
      // Make it comma separated string
      if(k < content_elements_length - 1) {
	index_str = index_str + StaticStrings.COMMA_CHARACTER;
      }
      content_element = null;
    }//for loop ends
        
        
    Element default_index = to.createElement (StaticStrings.INDEX_DEFAULT_ELEMENT_LOWERCASE);
    default_index.setAttribute (StaticStrings.NAME_ATTRIBUTE, index_str);
    search.appendChild (default_index);
        
  }
  static private void convertSubcollection (Document from, Document to) {
    Element source = from.getDocumentElement ();
    //Get the 'search' element from 'to' which has already been created in 'convertBuildType'
    Element search = (Element)XMLTools.getChildByTagName (to.getDocumentElement (), StaticStrings.SEARCH_STR);
        
    // Get the Subcollection element from the internal structure
    NodeList subcollection_elements = source.getElementsByTagName (StaticStrings.SUBCOLLECTION_ELEMENT);
    if (subcollection_elements == null) {
      return;
    }
    int subcollection_elements_length = subcollection_elements.getLength ();
        
    if (subcollection_elements_length == 0) { // no
      return ;
    }
        
    for(int j = 0; j < subcollection_elements_length; j++) {
            
      Element e = (Element) subcollection_elements.item (j);
      if (e.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	continue;
      }
      String content = e.getAttribute (StaticStrings.CONTENT_ATTRIBUTE);
      String name = e.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      String options = e.getAttribute (StaticStrings.OPTIONS_ATTRIBUTE);
      String type = e.getAttribute (StaticStrings.TYPE_ATTRIBUTE);
      String text = XMLTools.getNodeText (e);
            
      String filter = "";
      if (type.equals (StaticStrings.EXCLUDE_STR)) {
	filter = StaticStrings.EXCLAMATION_CHARACTER;
      }
            
      if(content.startsWith (StaticStrings.EXTRACTED_NAMESPACE) && content.indexOf(StaticStrings.NS_SEP, StaticStrings.EXTRACTED_NAMESPACE.length()) == -1) {
	content = content.substring (StaticStrings.EXTRACTED_NAMESPACE.length ());
      }
      filter = filter + content + StaticStrings.SEPARATOR_CHARACTER + text;
      if (options != null && options != "") {
	filter = filter + StaticStrings.SEPARATOR_CHARACTER + options;
      }
      Element subcollection = to.createElement (StaticStrings.SUBCOLLECTION_STR);
      subcollection.setAttribute (StaticStrings.FILTER_ATTRIBUTE, filter);
      subcollection.setAttribute (StaticStrings.NAME_ATTRIBUTE, name);
            
      search.appendChild (subcollection);
    }
  }
  static private void convertSubcollectionIndexes (Document from, Document to) {
    Element source = from.getDocumentElement ();
    //Get the 'search' element from 'to' which has already been created in 'convertBuildType'
    Element search = (Element)XMLTools.getChildByTagName (to.getDocumentElement (), StaticStrings.SEARCH_STR);
        
    // Get the SubcollectionIndexes element from the internal structure
    Element subcollection_indexes = (Element)XMLTools.getChildByTagName (source, StaticStrings.SUBCOLLECTION_INDEXES_ELEMENT);
    if (subcollection_indexes == null) {
      return;
    }
    NodeList index_elements = subcollection_indexes.getElementsByTagName (StaticStrings.INDEX_ELEMENT);
    int index_elements_length = index_elements.getLength ();
        
    if (index_elements_length == 0) { // no indexes
      return ;
    }
        
    for(int j = 0; j < index_elements_length; j++) {
      Element index_element = (Element) index_elements.item (j);
      if (index_element.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	continue;
      }
            
      Element index = to.createElement (StaticStrings.SUBCOLLECTION_INDEX_ELEMENT);
            
      String index_value = "";
            
      NodeList content_elements = index_element.getElementsByTagName (StaticStrings.CONTENT_ELEMENT);
      int content_elements_length = content_elements.getLength ();
            
      for(int k = 0; k < content_elements_length; k++) {
	Element content_element = (Element) content_elements.item (k);
	if (content_element.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	  continue;
	}
	String name_str = content_element.getAttribute (StaticStrings.NAME_ATTRIBUTE);
	index_value += name_str;
	// Make it comma separated string
	if(k < content_elements_length - 1) {
	  index_value += StaticStrings.COMMA_CHARACTER;
	}
	content_element = null;
      }//for loop ends
            
      index.setAttribute (StaticStrings.NAME_ATTRIBUTE, index_value);
            
      // Now constructing 'displayItem' element for this 'indexSubcollection' element
      // from the collectionmetadata element
      ArrayList collectionmetadata_list = XMLTools.getNamedElementList (source,
									StaticStrings.COLLECTIONMETADATA_ELEMENT,
									StaticStrings.NAME_ATTRIBUTE, index_value);
            
      if (collectionmetadata_list != null) {
                
	for(int k = 0; k < collectionmetadata_list.size (); k++) {
	  Element collectionmetadata = (Element)collectionmetadata_list.get (k);
	  if (collectionmetadata.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	    continue;
	  }
	  Element displayItem = constructDisplayItem (collectionmetadata, to);
	  index.appendChild (displayItem);
	}
      }
            
      search.appendChild (index);
            
    } //for loop ends
  }
    
  static private void convertLanguages (Document from, Document to) {
    Element source = from.getDocumentElement ();
    //Get the 'search' element from 'to' which has already been created in 'convertBuildType'
    Element search = (Element)XMLTools.getChildByTagName (to.getDocumentElement (), StaticStrings.SEARCH_STR);
        
    // Get the Languages element from the internal structure
    Element languages = (Element)XMLTools.getChildByTagName (source, StaticStrings.LANGUAGES_ELEMENT);
    if (languages == null) {
      return;
    }
    NodeList language_elements = languages.getElementsByTagName (StaticStrings.LANGUAGE_ELEMENT);
    int language_elements_length = language_elements.getLength ();
        
    if (language_elements_length == 0) {
      return ;
    }
        
    for(int j = 0; j < language_elements_length; j++) {
      Element element = (Element) language_elements.item (j);
      if (element.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	continue;
      }
            
      // Create indexLanguage element
      Element index_language = to.createElement (StaticStrings.LANGUAGE_INDEX_ELEMENT);
            
      String name_str = element.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      index_language.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
            
      // Now constructing 'displayItem' element for this 'indexLanguage' element
      // from the collectionmetadata element
      ArrayList collectionmetadata_list = XMLTools.getNamedElementList (source,
									StaticStrings.COLLECTIONMETADATA_ELEMENT,
									StaticStrings.NAME_ATTRIBUTE, name_str);
            
      if (collectionmetadata_list != null) {
                
	for(int k = 0; k < collectionmetadata_list.size (); k++) {
	  Element collectionmetadata = (Element)collectionmetadata_list.get (k);
	  if (collectionmetadata.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	    continue;
	  }
	  Element displayItem = constructDisplayItem (collectionmetadata, to);
	  index_language.appendChild (displayItem);
	}
      }
            
      search.appendChild (index_language);
            
    } //for loop ends
        
    // Convert DefaultLanguage
    // Get the DefaultLanguage element from the internal structure
    Element default_language = (Element)XMLTools.getChildByTagName (source, StaticStrings.LANGUAGE_DEFAULT_ELEMENT);
    if(default_language != null) {
      String lang_name = default_language.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      Element default_index_language = to.createElement (StaticStrings.LANGUAGE_DEFAULT_INDEX_ELEMENT);
      default_index_language.setAttribute (StaticStrings.NAME_ATTRIBUTE, lang_name);
      search.appendChild (default_index_language);
    }
    // Convert LanguageMetadata
    // Get the LanguageMetadata element from the internal structure
    Element language_metadata = (Element)XMLTools.getChildByTagName (source, StaticStrings.LANGUAGE_METADATA_ELEMENT);
    if(language_metadata != null) {
      String meta_name = language_metadata.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      Element language_meta = to.createElement (StaticStrings.LANGUAGE_METADATA_ELEMENT_STR);
      if(meta_name.startsWith (StaticStrings.EXTRACTED_NAMESPACE) && meta_name.indexOf(StaticStrings.NS_SEP, StaticStrings.EXTRACTED_NAMESPACE.length()) == -1) {
	meta_name = meta_name.substring (StaticStrings.EXTRACTED_NAMESPACE.length ());
      }
      language_meta.setAttribute (StaticStrings.NAME_ATTRIBUTE, meta_name);
      search.appendChild (language_meta);
    }
  }
    
  //convert indexes and their displayItems, which go in 'search' element in collectionConfig.xml
  //parameter 'to' is the document to be saved as collectionConfig.xml
  //parameter 'from' is the internal xml structure
  static private void convertIndex (Document from, Document to) {
    Element source = from.getDocumentElement ();
    //Get the 'search' element from 'to' which has already been created in 'convertBuildType'
    Element search = (Element)XMLTools.getChildByTagName (to.getDocumentElement (), StaticStrings.SEARCH_STR);
        
    //THere are two sets of indexes elements, find the one which is assigned 'true'
    Element indexes = XMLTools.getNamedElement (source,
						StaticStrings.INDEXES_ELEMENT,
						StaticStrings.ASSIGNED_ATTRIBUTE, StaticStrings.TRUE_STR);
    if (indexes == null) {
      return;
    }
    NodeList index_elements = indexes.getElementsByTagName (StaticStrings.INDEX_ELEMENT);
    int index_elements_length = index_elements.getLength ();
        
    if (index_elements_length == 0) { // no indexes
      return ;
    }
        
    //find out it's mg or mgpp/lucene
    String mg = search.getAttribute (StaticStrings.TYPE_ATTRIBUTE);
    boolean mg_indexer = false;
    if (mg.equals (StaticStrings.MG_STR)) {
      mg_indexer = true;//it's mg, then the level is set as attribute of
    }
    if (mg_indexer == false) {
      // It's mgpp. Construct 'level' and 'defaultLevel' elements separately.
      convertLevels (from, to, search);
    }
        
    for(int j = 0; j < index_elements_length; j++) {
      Element index_element = (Element) index_elements.item (j);
      if (index_element.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	continue;
      }
            
      Element index_ele = to.createElement (StaticStrings.INDEX_LOW_STR);//index
            
      // Used for creating displayItem for this element 'index_ele' further below
      // full_index_names contain 'ex.'
      String full_index_name = "";
      String level_str = "";
            
      StringBuffer index_value = new StringBuffer ();
      if (mg_indexer == true) {
	// For mg indexer, there is a 'level' attribute in the index element of the internal structure
	// But mgpp/lucene don't
	level_str = index_element.getAttribute (StaticStrings.LEVEL_ATTRIBUTE);
	if(level_str.length () > 0) {
	  index_value.append (level_str).append (StaticStrings.COLON_CHARACTER);
	  //index_value = index_value.StaticStrings.COLON_CHARACTER;
	}
      }
            
      NodeList content_elements = index_element.getElementsByTagName (StaticStrings.CONTENT_ELEMENT);
      int content_elements_length = content_elements.getLength ();
            
      for(int k = 0; k < content_elements_length; k++) {
	Element content_element = (Element) content_elements.item (k);
	if (content_element.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	  continue;
	}
	String name_str = content_element.getAttribute (StaticStrings.NAME_ATTRIBUTE);
                
	full_index_name = full_index_name + name_str;
	if (k < content_elements_length - 1) {
	  full_index_name = full_index_name + StaticStrings.COMMA_CHARACTER;
	}
                
	if(name_str.startsWith (StaticStrings.EXTRACTED_NAMESPACE) && name_str.indexOf(StaticStrings.NS_SEP, StaticStrings.EXTRACTED_NAMESPACE.length()) == -1) {
	  name_str = name_str.substring (StaticStrings.EXTRACTED_NAMESPACE.length ());
	}

	index_value.append (name_str);
	name_str = null;
	// Make it comma separated string
	if(k < content_elements_length - 1) {
	  index_value.append (StaticStrings.COMMA_CHARACTER);
	}
	content_element = null;
      }//for loop ends
            
      String temp_str = index_value.toString ();
      index_ele.setAttribute (StaticStrings.NAME_ATTRIBUTE, temp_str);
            
      // Now constructing 'displayItem' element for this 'index_ele' element
      // The index names in the collectionmetadata elements in the internal structure are not the names that
      // are used in the content elements (i.e. ex.Source or dc.Subject and keywords), but the names that are
      // in the configuration files (i.e. Source or dc.Subject)
      ArrayList collectionmetadata_list = XMLTools.getNamedElementList (source,
									StaticStrings.COLLECTIONMETADATA_ELEMENT,
									StaticStrings.NAME_ATTRIBUTE, temp_str);
            
      if (collectionmetadata_list == null) {
	//try the full name, i.e. with 'ex.'
	if (mg_indexer == true) {
	  // but first append level info if we are mg
	  full_index_name = level_str+StaticStrings.COLON_CHARACTER+full_index_name;
	}
	collectionmetadata_list = XMLTools.getNamedElementList (source,
								StaticStrings.COLLECTIONMETADATA_ELEMENT,
								StaticStrings.NAME_ATTRIBUTE, full_index_name);
      }
	
      if (collectionmetadata_list != null) {
                
	for(int k = 0; k < collectionmetadata_list.size (); k++) {
	  Element collectionmetadata = (Element)collectionmetadata_list.get (k);
	  if (collectionmetadata.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
	    continue;
	  }
	  Element displayItem = constructDisplayItem (collectionmetadata, to);
                    
	  index_ele.appendChild (displayItem);
	}
      }
            
      search.appendChild (index_ele);
            
    } //for loop ends
        
    //Convert default index
    convertDefaultIndex (from, to, search);
    convertIndexOptions(from, to, search);
  }
  // Convert levels for mgpp/lucene. This method is called by converIndex() when mgpp indexer is detected.
  static private void convertLevels (Document from, Document to, Element search) {
    Element source = from.getDocumentElement ();
    Element index_option = XMLTools.getNamedElement (source,
						     StaticStrings.INDEXOPTIONS_ELEMENT,
						     StaticStrings.NAME_ATTRIBUTE, StaticStrings.LEVELS_STR);
    if (index_option == null) {
      return;
    }
    //Debugging purposes
    if (index_option.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
      DebugStream.println ("For mgpp, there should be an IndexOption element for levels which is assigned 'true': possible bug.");
    }
        
    NodeList option_elements = index_option.getElementsByTagName (StaticStrings.OPTION_ELEMENT);
    int num_elements = option_elements.getLength ();
        
    // Don't output anything if no indexes are set
    if(num_elements == 0) {
      return ;//
    }
        
    for(int k = 0; k < num_elements; k++) {
      Element e = (Element) option_elements.item (k);
      String name_str = e.getAttribute (StaticStrings.NAME_ATTRIBUTE);
      Element level_element = to.createElement (StaticStrings.LEVEL_ELEMENT);
      level_element.setAttribute (StaticStrings.NAME_ATTRIBUTE, name_str);
            
      //Now construct displayItem for this level element from collectionmetadata
      ArrayList collectionmetadata_list = XMLTools.getNamedElementList (source,
									StaticStrings.COLLECTIONMETADATA_ELEMENT,
									StaticStrings.NAME_ATTRIBUTE, name_str);
            
      if (collectionmetadata_list != null) {
                
	for(int j = 0; j < collectionmetadata_list.size (); j++) {
	  Element collectionmetadata = (Element)collectionmetadata_list.get (j);
                    
	  Element displayItem = constructDisplayItem (collectionmetadata, to);
	  level_element.appendChild (displayItem);
	}
      }
      search.appendChild (level_element);
    }
        
    //Convert default level
    Element default_index_option = XMLTools.getNamedElement (source,
							     StaticStrings.INDEXOPTION_DEFAULT_ELEMENT,
							     StaticStrings.NAME_ATTRIBUTE, StaticStrings.LEVEL_DEFAULT_STR);
    if (default_index_option == null) {
      return;
    }
    Element default_level = to.createElement (StaticStrings.LEVEL_DEFAULT_ELEMENT);
    String default_level_str = default_index_option.getAttribute (StaticStrings.VALUE_ATTRIBUTE);
    default_level.setAttribute (StaticStrings.NAME_ATTRIBUTE, default_level_str);
    search.appendChild (default_level);
        
  }
  // Convert indexoptions for mg/mgpp/lucene. This method is called by convertIndex().
  static private void convertIndexOptions (Document from, Document to, Element search) {
    Element source = from.getDocumentElement ();
    Element index_option = XMLTools.getNamedElement (source,
						     StaticStrings.INDEXOPTIONS_ELEMENT,
						     StaticStrings.NAME_ATTRIBUTE, StaticStrings.INDEXOPTIONS_STR);
    if (index_option == null) {
      return;
    }
    //Debugging purposes
    if (index_option.getAttribute (StaticStrings.ASSIGNED_ATTRIBUTE).equals (StaticStrings.FALSE_STR)) {
      DebugStream.println ("There should be an IndexOption element which is assigned 'true': possible bug.");
    }
    Element indexOptionEl = to.createElement(StaticStrings.INDEXOPTION_STR);
    NodeList option_elements = index_option.getElementsByTagName (StaticStrings.OPTION_ELEMENT);
    int num_elements = option_elements.getLength ();        
    // Don't output anything if no index
    if(num_elements == 0) {
      return ;//
    }
    search.appendChild (indexOptionEl);
        
    for(int k = 0; k < num_elements; k++) {
      Element e = (Element) option_elements.item (k);
      String name_att = e.getAttribute(StaticStrings.NAME_ATTRIBUTE);
      Element optionEl = to.createElement(StaticStrings.OPTION_STR);
      optionEl.setAttribute(StaticStrings.NAME_ATTRIBUTE, name_att);
      indexOptionEl.appendChild(optionEl);
    }
           
  }
  // Append the element son to the element mother in the appropriate position.
  static public void appendProperly (Element mother, Element son) {
    if (son == null)
      return;
        
    Node reference_node = findInsertionPoint (mother, son);
    if(reference_node != null) {
      mother.insertBefore (son, reference_node);
    }
    else {
      mother.appendChild (son);
    }
  }
  /** Find the best insertion position for the given DOM Element 'target_element' in the DOM Element 'document_element'. This should try to match command tag, and if found should then try to group by name or type (eg CollectionMeta), or append to end is no such grouping exists (eg Plugins). Failing a command match it will check against the command order for the best insertion location.
   * @param target_element the command Element to be inserted
   * @return the Element which the given command should be inserted before, or null to append to end of list
   */
  static public Node findInsertionPoint (Element document_element, Element target_element) {
    ///ystem.err.println("Find insertion point: " + target_element.getNodeName());
    String target_element_name = target_element.getNodeName ();
        
    // Try to find commands with the same tag.
    NodeList matching_elements = document_element.getElementsByTagName (target_element_name);
    // If we found matching elements, then we have our most likely insertion location, so check within for groupings
    if(matching_elements.getLength () != 0) {
      ///ystem.err.println("Found matching elements.");
      // Only CollectionMeta are grouped.
      if(target_element_name.equals (StaticStrings.COLLECTIONMETADATA_ELEMENT)) {
	///ystem.err.println("Dealing with collection metadata");
	// Special case: CollectionMeta can be added at either the start or end of a collection configuration file. However the start position is reserved for special metadata, so if no non-special metadata can be found we must append to the end.
	// So if the command to be added is special add it immediately after any other special command
	if(target_element.getAttribute (StaticStrings.SPECIAL_ATTRIBUTE).equals (StaticStrings.TRUE_STR)) {
	  int index = 0;
	  Element matched_element = (Element) matching_elements.item (index);
	  Element sibling_element = (Element) matched_element.getNextSibling ();
	  while(sibling_element.getAttribute (StaticStrings.SPECIAL_ATTRIBUTE).equals (StaticStrings.TRUE_STR)) {
	    index++;
	    matched_element = (Element) matching_elements.item (index);
	    sibling_element = (Element) matched_element.getNextSibling ();
	  }
	  if(sibling_element.getNodeName ().equals (CollectionConfiguration.NEWLINE_ELEMENT)) {
	    Element newline_element = document_element.getOwnerDocument().createElement (CollectionConfiguration.NEWLINE_ELEMENT);
	    document_element.insertBefore (newline_element, sibling_element);
	  }
	  return sibling_element;
	}
	// Otherwise try to find a matching 'name' and add after the last one in that group.
	else {
	  int index = 0;
	  target_element_name = target_element.getAttribute (StaticStrings.NAME_ATTRIBUTE);
	  boolean found = false;
	  // Skip all of the special metadata
	  Element matched_element = (Element) matching_elements.item (index);
	  while(matched_element.getAttribute (StaticStrings.SPECIAL_ATTRIBUTE).equals (StaticStrings.TRUE_STR)) {
	    index++;
	    matched_element = (Element) matching_elements.item (index);
	  }
	  // Begin search
	  while(!found && matched_element != null) {
	    if(matched_element.getAttribute (StaticStrings.NAME_ATTRIBUTE).equals (target_element_name)) {
	      found = true;
	    }
	    else {
	      index++;
	      matched_element = (Element) matching_elements.item (index);
	    }
	  }
	  // If we found a match, we need to continue checking until we find the last name match.
	  if(found) {
	    index++;
	    Element previous_sibling = matched_element;
	    Element sibling_element = (Element) matching_elements.item (index);
	    while(sibling_element != null && sibling_element.getAttribute (StaticStrings.NAME_ATTRIBUTE).equals (target_element_name)) {
	      previous_sibling = sibling_element;
	      index++;
	      sibling_element = (Element) matching_elements.item (index);
	    }
	    // Previous sibling now holds the command immediately before where we want to add, so find its next sibling and add to that. In this one case we can ignore new lines!
	    return previous_sibling.getNextSibling ();
	  }
	  // If not found we just add after last metadata element
	  else {
	    Element last_element = (Element) matching_elements.item (matching_elements.getLength () - 1);
	    return last_element.getNextSibling ();
	  }
	}
                
      }
      else {
	///ystem.err.println("Not dealing with collection meta.");
	Element matched_element = (Element) matching_elements.item (matching_elements.getLength () - 1);
	// One final quick test. If the matched element is immediately followed by a NewLine command, then we insert another NewLine after the matched command, then return the NewLine instead (thus the about to be inserted command will be placed between the two NewLines)
	Node sibling_element = matched_element.getNextSibling ();
	if(sibling_element != null && sibling_element.getNodeName ().equals (CollectionConfiguration.NEWLINE_ELEMENT)) {
	  Element newline_element = document_element.getOwnerDocument().createElement (CollectionConfiguration.NEWLINE_ELEMENT);
	  document_element.insertBefore (newline_element, sibling_element);
	}
	return sibling_element; // Note that this may be null
      }
    }
    ///ystem.err.println("No matching elements found.");
    // Locate where this command is in the ordering
    int command_index = -1;
    for(int i = 0; command_index == -1 && i < CollectionConfiguration.COMMAND_ORDER.length; i++) {
      if(CollectionConfiguration.COMMAND_ORDER[i].equals (target_element_name)) {
	command_index = i;
      }
    }
    ///ystem.err.println("Command index is: " + command_index);
    // Now move forward, checking for existing elements in each of the preceeding command orders.
    int preceeding_index = command_index - 1;
    ///ystem.err.println("Searching before the target command.");
    while(preceeding_index >= 0) {
      matching_elements = document_element.getElementsByTagName (CollectionConfiguration.COMMAND_ORDER[preceeding_index]);
      // If we've found a match
      if(matching_elements.getLength () > 0) {
	// We add after the last element
	Element matched_element = (Element) matching_elements.item (matching_elements.getLength () - 1);
	// One final quick test. If the matched element is immediately followed by a NewLine command, then we insert another NewLine after the matched command, then return the NewLine instead (thus the about to be inserted command will be placed between the two NewLines)
	Node sibling_element = matched_element.getNextSibling ();
	if(sibling_element != null && sibling_element.getNodeName ().equals (CollectionConfiguration.NEWLINE_ELEMENT)) {
	  Element newline_element = document_element.getOwnerDocument().createElement (CollectionConfiguration.NEWLINE_ELEMENT);
	  document_element.insertBefore (newline_element, sibling_element);
	}
	return sibling_element; // Note that this may be null
      }
      preceeding_index--;
    }
    // If all that fails, we now move backwards through the commands
    int susceeding_index = command_index + 1;
    ///ystem.err.println("Searching after the target command.");
    while(susceeding_index < CollectionConfiguration.COMMAND_ORDER.length) {
      matching_elements = document_element.getElementsByTagName (CollectionConfiguration.COMMAND_ORDER[susceeding_index]);
      // If we've found a match
      if(matching_elements.getLength () > 0) {
	// We add before the first element
	Element matched_element = (Element) matching_elements.item (0);
	// One final quick test. If the matched element is immediately preceeded by a NewLine command, then we insert another NewLine before the matched command, then return this new NewLine instead (thus the about to be inserted command will be placed between the two NewLines)
	Node sibling_element = matched_element.getPreviousSibling ();
	if(sibling_element != null && sibling_element.getNodeName ().equals (CollectionConfiguration.NEWLINE_ELEMENT)) {
	  Element newline_element = document_element.getOwnerDocument().createElement (CollectionConfiguration.NEWLINE_ELEMENT);
	  document_element.insertBefore (newline_element, sibling_element);
	}
	return sibling_element; // Note that this may be null
      }
      susceeding_index++;
    }
    // Well. Apparently there are no other commands in this collection configuration. So append away...
    return null;
  }
  // From collectionConfig.xml to internal structure:add 'ex.' namespace (if none).
  // From internal structure to collectionConfig.xml:always peel off 'ex.' namespace (if any), except for format statement
  //This method parses 'xml_file_doc' into 'dOc'
  static public void parse(File xml_file, Document dOc) {
        
    Document xml_file_doc = XMLTools.parseXMLFile (xml_file);
    Element fromElement = xml_file_doc.getDocumentElement ();
    Element toElement = dOc.getDocumentElement ();
        
    // It's deliberately set that 'creator', 'maintainer', and 'public' are only in English (as they are just names).
    // So the following ArrayList have only one element.
    Node metadataListNode = XMLTools.getChildByTagNameIndexed (fromElement, StaticStrings.METADATALIST_STR, 0);
    if (metadataListNode != null) {
      ArrayList creator = doMetadataList (dOc, metadataListNode, StaticStrings.COLLECTIONMETADATA_CREATOR_ELEMENT,
					  StaticStrings.COLLECTIONMETADATA_CREATOR_STR);
      ArrayList maintainer = doMetadataList (dOc, metadataListNode,
					     StaticStrings.COLLECTIONMETADATA_MAINTAINER_ELEMENT,
					     StaticStrings.COLLECTIONMETADATA_MAINTAINER_STR);
      ArrayList is_public = doMetadataList (dOc, metadataListNode, StaticStrings.COLLECTIONMETADATA_PUBLIC_ELEMENT,
					    StaticStrings.COLLECTIONMETADATA_PUBLIC_STR);
            
      appendArrayList (toElement, creator);
      appendArrayList (toElement, maintainer);
      appendArrayList (toElement, is_public);
    }

    Node databaseNode = XMLTools.getChildByTagNameIndexed (fromElement, StaticStrings.INFODB_STR, 0);
    String databasetype_value = "gdbm";
    if(databaseNode != null) {
	databasetype_value = ((Element)databaseNode).getAttribute (StaticStrings.TYPE_ATTRIBUTE);//might be gdbm|jdbm|sqlite OR not yet set (in which case it should default to gdbm)
    }
    
    Element databasetype = doDatabaseType(dOc, databasetype_value);
    appendProperly (toElement, databasetype);
        
    Node searchNode = XMLTools.getChildByTagNameIndexed (fromElement, StaticStrings.SEARCH_STR, 0);
    String buildtype_value = ((Element)searchNode).getAttribute (StaticStrings.TYPE_ATTRIBUTE);//might be mg|mgpp|lucene
    Element buildtype = doBuildType (dOc, buildtype_value);
    appendProperly (toElement, buildtype);
        
        
    Node importNode = XMLTools.getChildByTagNameIndexed (fromElement, StaticStrings.IMPORT_STR, 0);
    if (importNode == null) {
      System.out.println ("There is no content in the 'import' block.");
    }
    if (importNode != null) {
      //do plugin list nodes
      Node pluginListNode = XMLTools.getChildByTagNameIndexed ((Element)importNode, StaticStrings.PLUGINLIST_STR, 0);           
      if (pluginListNode == null) {
	System.out.println ("There is no pluginlist set.");
      }
      if (pluginListNode != null) {
                
	doPlugin (dOc, pluginListNode);
      }
            
      //do the plugout element (used by building flax collections)
      Node plugout = XMLTools.getChildByTagNameIndexed ((Element)importNode, PLUGOUT_ELEMENT, 0);
      if (plugout != null) {
	Element to_element = XMLTools.duplicateElement (dOc, (Element)plugout, true);
	toElement.appendChild (to_element);
      }
    }
        
    Node browseNode = XMLTools.getChildByTagNameIndexed (fromElement, StaticStrings.BROWSE_STR, 0);
    if (browseNode != null) {
      if (browseNode == null) {
	System.out.println ("There is no classifier.");
      }
      doClassifier (dOc, browseNode);
    }
        
    Node displayItemListNode = XMLTools.getChildByTagNameIndexed (fromElement, StaticStrings.DISPLAYITEMLIST_STR, 0);
    if (displayItemListNode != null) {
      ArrayList description = doDisplayItemList (dOc, displayItemListNode, StaticStrings.DESCRIPTION_STR,
						 StaticStrings.COLLECTIONMETADATA_COLLECTIONEXTRA_STR);
      ArrayList smallicon = doDisplayItemList (dOc, displayItemListNode, StaticStrings.SMALLICON_STR,
					       StaticStrings.COLLECTIONMETADATA_ICONCOLLECTIONSMALL_STR);
      ArrayList icon = doDisplayItemList (dOc, displayItemListNode, StaticStrings.ICON_STR,
					  StaticStrings.COLLECTIONMETADATA_ICONCOLLECTION_STR);
      ArrayList name = doDisplayItemList (dOc, displayItemListNode, StaticStrings.NAME_STR,
					  StaticStrings.COLLECTIONMETADATA_COLLECTIONNAME_STR);
            
      appendArrayList (toElement, description);
      appendArrayList (toElement, smallicon);
      appendArrayList (toElement, icon);
      appendArrayList (toElement, name);
    }
        
    if (buildtype_value.equalsIgnoreCase ("mg")) {
      doMGIndexes (dOc, searchNode);
    }
    else {
      doMGPPIndexes (dOc, searchNode);
    }
        
    doDefaultIndex (dOc, searchNode);
    doDefaultLevel (dOc, searchNode);
    doLevel (dOc, searchNode);
    doIndexOption (dOc, searchNode);
    doSubcollection (dOc, searchNode);
    doIndexSubcollection (dOc, searchNode);
    doIndexLanguage (dOc, searchNode);
    doDefaultIndexLanguage (dOc, searchNode);
    doLanguageMetadata (dOc, searchNode);
    doSearchType (dOc, searchNode);
    doSearchFormat (dOc, searchNode);
    doDisplayFormat (dOc, fromElement);
    doReplaceListRef (dOc, fromElement);
    doServiceRackList (dOc, fromElement);
        
  }
    
    
  static public String generateStringVersion(Document doc) {
    return XMLTools.xmlNodeToString(doc);
  }
  
  static public void save (File collect_config_xml_file, Document doc) {
        
    Document collection_config_xml_document = convertInternalToCollectionConfig (doc);
    String[] nonEscapingTagNames = {StaticStrings.FORMAT_STR};
    XMLTools.writeXMLFile (collect_config_xml_file, collection_config_xml_document, nonEscapingTagNames);
       
  }

  //Convert the internal XML DOM tree (dOc) into that of collectionConfig.xml (skeleton)
  static private Document convertInternalToCollectionConfig (Document dOc) {
    //first parse an empty skeleton of xml config file
    //The aim is to convert the internal structure into this skeleton
    Document skeleton = XMLTools.parseXMLFile ("xml/CollectionConfig.xml", true);
    //Element internal = dOc.getDocumentElement();
    convertMetadataList (dOc, skeleton);
    convertDisplayItemList (dOc, skeleton);
    convertBuildType (dOc, skeleton);
    convertDatabaseType (dOc, skeleton);
    convertIndex (dOc, skeleton);
    convertPlugin (dOc, skeleton);//also do the plugout element
    convertClassifier (dOc, skeleton);
    convertSubcollectionIndexes (dOc, skeleton);
    convertLanguages (dOc, skeleton);
    convertSubcollection (dOc, skeleton);
    convertSearchType (dOc, skeleton);
    convertSearchFormat (dOc, skeleton);
    convertDisplayFormat (dOc, skeleton);
    convertReplaceListRef (dOc, skeleton);
    convertServiceRackList(dOc, skeleton);

    return skeleton;
  }

  // Append the elements, which are of Element type, in 'list' to Element 'to'
  static private void appendArrayList (Element to, ArrayList list) {
    if (list == null) return;
        
    for (int i=0; i<list.size (); i++) {
      appendProperly (to, (Element)list.get (i));
    }
  }


  
}