Index: src/org/ecoinformatics/seek/datasource/darwincore/DarwinCoreDataSource.java
===================================================================
RCS file: /cvs/kepler/src/org/ecoinformatics/seek/datasource/darwincore/DarwinCoreDataSource.java,v
retrieving revision 1.16
diff -u -r1.16 DarwinCoreDataSource.java
--- src/org/ecoinformatics/seek/datasource/darwincore/DarwinCoreDataSource.java	17 Nov 2004 20:29:21 -0000	1.16
+++ src/org/ecoinformatics/seek/datasource/darwincore/DarwinCoreDataSource.java	9 Dec 2004 21:05:44 -0000
@@ -1191,20 +1191,20 @@
               for (Enumeration e = table.getFields().elements(); e.hasMoreElements();)
               {
                   DSTableFieldIFace field = (DSTableFieldIFace)e.nextElement();
-                  queryBuf.append("  <returnfield>/" + field.getName() + "</returnfield>");
+                  queryBuf.append("  <returnField>/" + field.getName() + "</returnField>");
               }
           } else 
           {
-              queryBuf.append("  <returnfield>/Species</returnfield>");
-              queryBuf.append("  <returnfield>/ScientificName</returnfield>");
-              queryBuf.append("  <returnfield>/Collector</returnfield>");
-              queryBuf.append("  <returnfield>/YearCollected</returnfield>");
-              queryBuf.append("  <returnfield>/InstitutionCode</returnfield>");
-              queryBuf.append("  <returnfield>/CollectionCode</returnfield>");
-              queryBuf.append("  <returnfield>/CatalogNumber</returnfield>");
-              queryBuf.append("  <returnfield>/CatalogNumberText</returnfield>");
-              queryBuf.append("  <returnfield>/DecimalLatitude</returnfield>");
-              queryBuf.append("  <returnfield>/DecimalLongitude</returnfield>");
+              queryBuf.append("  <returnField>/Species</returnField>");
+              queryBuf.append("  <returnField>/ScientificName</returnField>");
+              queryBuf.append("  <returnField>/Collector</returnField>");
+              queryBuf.append("  <returnField>/YearCollected</returnField>");
+              queryBuf.append("  <returnField>/InstitutionCode</returnField>");
+              queryBuf.append("  <returnField>/CollectionCode</returnField>");
+              queryBuf.append("  <returnField>/CatalogNumber</returnField>");
+              queryBuf.append("  <returnField>/CatalogNumberText</returnField>");
+              queryBuf.append("  <returnField>/DecimalLatitude</returnField>");
+              queryBuf.append("  <returnField>/DecimalLongitude</returnField>");
           }
           queryBuf.append("  <condition operator=\"LIKE\" concept=\"ScientificName\">" + searchStr +"</condition>");
           queryBuf.append("</egq:query>");
@@ -1221,6 +1221,7 @@
                   inx = providerStr.lastIndexOf('=');
                   String resource = providerStr.substring(inx+1, providerStr.length()).replaceAll("%20", " ");
                   //System.out.println(queryBuf.toString());
+                  
                   StringReader       strReader = new StringReader(queryBuf.toString());
                   EcogridQueryParser parser    = new EcogridQueryParser(strReader);
                   parser.parseXML();
Index: src/org/ecoinformatics/seek/ecogrid/SearchQueryGenerator.java
===================================================================
RCS file: /cvs/kepler/src/org/ecoinformatics/seek/ecogrid/SearchQueryGenerator.java,v
retrieving revision 1.6
diff -u -r1.6 SearchQueryGenerator.java
--- src/org/ecoinformatics/seek/ecogrid/SearchQueryGenerator.java	11 Oct 2004 23:46:12 -0000	1.6
+++ src/org/ecoinformatics/seek/ecogrid/SearchQueryGenerator.java	9 Dec 2004 21:05:44 -0000
@@ -33,24 +33,15 @@
 package org.ecoinformatics.seek.ecogrid;
 
 import java.util.Hashtable;
-import java.util.Vector;
 
 import javax.xml.transform.TransformerException;
 
 import org.apache.axis.types.URI;
-import org.apache.xpath.XPathAPI;
-import org.ecoinformatics.ecogrid.ANDType;
-import org.ecoinformatics.ecogrid.ConditionType;
-import org.ecoinformatics.ecogrid.LimitedXPathExpression;
-import org.ecoinformatics.ecogrid.ORType;
-import org.ecoinformatics.ecogrid.OperatorType;
+import org.ecoinformatics.ecogrid.EcogridQueryParser;
 import org.ecoinformatics.ecogrid.QueryType;
-import org.ecoinformatics.ecogrid.QueryType_namespace;
 import org.ecoinformatics.seek.ecogrid.exception.InvalidEcogridQueryException;
 import org.ecoinformatics.util.Config;
 import org.ecoinformatics.util.DebugPrinter;
-import org.w3c.dom.Element;
-import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
@@ -63,24 +54,13 @@
 
 public class SearchQueryGenerator 
 {
-  private String queryId           = null;
-  private Hashtable replacementMap = null;
-  private QueryType query          = new QueryType();
-  private DebugPrinter dbg         = DebugPrinter.getInstance();
-  private Vector returnFieldList   = new Vector();
+  private String       _queryId        = null;
+  private Hashtable    _replacementMap = null;
+  private QueryType    _query          = new QueryType();
+  private DebugPrinter _dbg            = DebugPrinter.getInstance();
   
   private final static String QUERYPATH   = "//ecogridService/queryList/query[@queryId='";
-  private final static String NAMESPACE   = "namespace";
-  private final static String RETURNFIELD = "returnField";
-  private final static String TITLE       = "title";
-  private final static String AND         = "AND";
-  private final static String OR          = "OR";
   private final static String CONDITION   = "condition";
-  private final static String SYSTEM      = "system";
-  private final static String OPERATOR    = "operator";
-  private final static String CONCEPT     = "concept";
-  private static final int NAMESPACEARRAYLENGTH = 1;
-  private static final int TITLEEARRAYLENGTH = 1;
   
   /**
    * Constructor of SearchQueryGenerator
@@ -91,12 +71,13 @@
    * For example, if key is "#value#", and value is "soil". This means any
    * element and attribute in xml has value "#value#" will be replaced by soil
    */
-  public SearchQueryGenerator(String queryId, Hashtable replacementMap)
+  public SearchQueryGenerator(String    queryId, 
+                              Hashtable replacementMap)
                                   throws  InvalidEcogridQueryException
 
   {
-    this.queryId        = queryId;
-    this.replacementMap = replacementMap;
+    _queryId        = queryId;
+    _replacementMap = replacementMap;
     try
     {
       generateQuery();
@@ -113,9 +94,48 @@
    */
   public QueryType getQuery()
   {
-    return this.query;
+    return _query;
   }//getQuery
   
+  /**
+   * Recursively walks the tree looking for Condition values inorder to subsitute in the search value
+   * @param aNode the parent node
+   * @param aIsChildCond indicates whether the current parent node is a Condition node
+   */
+  private void mapInValue(Node aNode, boolean aIsChildCond)
+  {
+      NodeList childList = aNode.getChildNodes();
+      if ( childList == null)
+      {
+        return;
+      }
+      
+      // go through every child element
+      int length = childList.getLength();
+      for (int i=0; i<length; i++)
+      {
+        Node kid = childList.item(i);
+        if (kid.getNodeName().equals(CONDITION) || aIsChildCond)
+        {
+          String value = kid.getNodeValue();
+          // replace the value by search value if this value in replacementMap
+          if (value != null && _replacementMap.containsKey(value))
+          {
+            value = (String)_replacementMap.get(value);
+             kid.setNodeValue(value);
+          } 
+          else 
+          {
+            mapInValue(kid, true);
+          }
+        }
+        else
+        {
+          mapInValue(kid, false);
+        }
+      }
+  }
+  
   /*
    * Method to read config file and generate a query(It will chose the first one
    * if it has more than one in configure file)
@@ -124,343 +144,33 @@
                                       TransformerException,
                                       InvalidEcogridQueryException
   {
-    String xpath = QUERYPATH + queryId+ "']";
+    String xpath   = QUERYPATH + _queryId+ "']";
     Node queryNode = null;
-    NodeList list = Config.getNodeListFromPath(xpath);
+    NodeList list   = Config.getNodeListFromPath(xpath);
     if (list == null)
     {
       return;
     }
+    
     // chose first query
     queryNode = list.item(0);
-    //set query attributes
-    setQuerySystem(queryNode);
-    setQueryId();
-    
     NodeList queryChildrenList = queryNode.getChildNodes();
     if ( queryChildrenList == null)
     {
       return;
     }
-    int length = queryChildrenList.getLength();
-    // go through every child element
-    for (int i=0; i<length; i++)
-    {
-      Node kid = queryChildrenList.item(i);
-      if (kid !=null && kid.getNodeType() ==Node.ELEMENT_NODE)
-      {
-        if (kid.getNodeName() != null && kid.getNodeName().equals(NAMESPACE))
-        {
-          setQueryNamespace(kid);
-        }//namespace
-        else if (kid.getNodeName() != null && kid.getNodeName().equals(TITLE))
-        {
-          setQueryTitle(kid);
-        }//title
-        else if (kid.getNodeName() != null && kid.getNodeName().equals(RETURNFIELD))
-        {
-          putReturnFieldIntoVector(kid);
-        }//returnfield
-        else if (kid.getNodeName() != null && kid.getNodeName().equals(AND))
-        {
-          ANDType topAnd = new ANDType();
-          setQueryANDType(kid,topAnd);
-          dbg.print("In top AND", 2);
-          query.setAND(topAnd);
-        }//AND
-        else if (kid.getNodeName() != null && kid.getNodeName().equals(OR))
-        {
-          ORType topOr = new ORType();
-          setQueryORType(kid, topOr);
-          dbg.print("In top OR", 2);
-          query.setOR(topOr);
-        }//OR
-        else if (kid.getNodeName() != null && kid.getNodeName().equals(CONDITION))
-        {
-          ConditionType topCondition = setQueryConditionType(kid);
-          dbg.print("In top condtion", 2);
-          query.setCondition(topCondition);
-        }//condition
-      }//if
-    }//for
-    //put vector of return fields into array and set it to query
-    setQueryReturnField();
-  }//generateQuery
-  
-  /*
-   * Method to set query namesapce
-   */
-  private void setQueryNamespace(Node node) throws URI.MalformedURIException
-  {
-    Node value = node.getFirstChild();
-    if (value.getNodeType() == Node.TEXT_NODE)
-    {
-      String namespaceStr = value.getNodeValue();
-      URI namespaceURI    = new URI(namespaceStr);
-      dbg.print("The ecogrid query search namespace is " + 
-                 namespaceURI.toString(), 2);
-      QueryType_namespace namespaceQuery = new QueryType_namespace(namespaceURI);
-      QueryType_namespace[] namespaceArray = 
-                                  new QueryType_namespace[NAMESPACEARRAYLENGTH];
-      namespaceArray[0]= namespaceQuery;
-      query.setNamespace(namespaceArray);
-    }//if
-  }//setQuerynamespace
-  
-  /*
-   * Method to set query system
-   */
-  private void setQuerySystem(Node node) throws URI.MalformedURIException 
-  {
-    NamedNodeMap attributes = node.getAttributes();
-    Node system = attributes.getNamedItem(SYSTEM);
-    String systemStr = system.getNodeValue();
-    URI systemURI = null;
-    systemURI = new URI(systemStr);
-    dbg.print("The ecogrid query system is " + systemURI.toString(), 2);
-    query.setSystem(systemURI);
-  }//setQuerySystem
-  
-  /* 
-   * Method to set query title
-   */
-  private void setQueryTitle(Node node)
-  {
-    Node value = node.getFirstChild();
-    if (value.getNodeType() == Node.TEXT_NODE)
-    {
-      String queryTitle = value.getNodeValue();
-      dbg.print("The ecogrid query title is "+ queryTitle, 2);
-      String [] queryTitleArray = new String[TITLEEARRAYLENGTH];
-      queryTitleArray[0] = queryTitle;
-      query.setTitle(queryTitleArray);
-    }//if
-  }//setQueryTitle
-  
-  /*
-   * Method to set query id
-   */
-  private void setQueryId()
-  {
-    query.setQueryId(queryId);
-  }//setQueryId
-  
-  
-  /*
-   * Put one return field to a vector
-   */
-  private void putReturnFieldIntoVector(Node node)
-  {
-    Node value = node.getFirstChild();
-    if (value.getNodeType() == Node.TEXT_NODE)
-    {
-      String returnField = value.getNodeValue();
-      dbg.print("The return ecogrid query is "+ returnField, 2);
-      if (returnField != null && !returnField.trim().equals(""))
-      {
-        returnField = returnField.trim();
-        dbg.print("The return ecogrid query is "+ returnField, 2);
-        returnFieldList.addElement(returnField);
-      }
-    }//if
-
-  }//putReturnFieldIntoVector
-  /*
-   * Method to transfer a return field actor a array and set the array to query
-   */
-  private void setQueryReturnField()
-  {
-    if (returnFieldList != null)
-    {
-      int size = returnFieldList.size();
-      String[] returnFieldArray = new String[size];
-      for (int i=0; i<size; i++)
-      {
-        returnFieldArray[i] = (String)returnFieldList.elementAt(i);
-      }
-      query.setReturnfield(returnFieldArray);
-    }
-  }//setQueryReturnField
-  
-  /*
-   * Method to set AND type to query
-   */
-  private void setQueryANDType(Node node, ANDType and) 
-                     throws TransformerException, InvalidEcogridQueryException
-  {
-    dbg.print("In AND", 2);
-    setType(node, and, null);
-  }//setQueryANDType
-  
-  /*
-   * Method to set OR type to query
-   */
-  private void setQueryORType(Node node, ORType or) 
-                     throws TransformerException, InvalidEcogridQueryException
-  {
-    dbg.print("In OR", 2);
-    setType(node, null, or);
-  }//setQueryORType
-  
-  /*
-   * Method can handle both OR and AND
-   */
-  private void setType(Node node, ANDType and, ORType or) 
-                    throws TransformerException, InvalidEcogridQueryException
-  {
-    //make sure parameter works
-     if (node == null)
-     {
-       return;
-     }
-     NodeList andList = XPathAPI.selectNodeList(node, AND);
-     NodeList orList  = XPathAPI.selectNodeList(node, OR);
-     NodeList conList = XPathAPI.selectNodeList(node, CONDITION);
-     int andLength = andList.getLength();
-     int orLength  = orList.getLength();
-     int conLength = conList.getLength();
-     // and type children
-     if (andLength != 0)
-     {
-       ANDType[] andArray = new ANDType[andLength];
-       // get and type children
-       for ( int i=0; i<andLength; i++)
-       {
-         ANDType andChild = new ANDType();
-         andArray[i] = andChild;
-         Node childNode = andList.item(i);
-         // call handleANDype again
-         setType(childNode, andChild, null);//make usre or type is null
-       }
-       //set children to parent
-       if (and != null)
-       {
-         and.setAND(andArray);
-       }
-       else if (or != null)
-       {
-         or.setAND(andArray);
-       }
-     }
-     //or type children
-     if (orLength != 0)
-     {
-       ORType[] orArray = new ORType[orLength];
-       // get or type children
-       for ( int i=0; i< orLength; i++)
-       {
-         ORType orChild = new ORType();
-         orArray[i] = orChild;
-         Node childNode = orList.item(i);
-         setType(childNode, null, orChild);//make sure ANDType is null
-       }
-       if (and !=null)
-       {
-         and.setOR(orArray);
-       }
-       else if (or != null)
-       {
-         or.setOR(orArray);
-       }
-
-     }
-     // conditiontype
-     if ( conLength != 0 )
-     {
-       ConditionType[] conditionArray = new ConditionType[conLength];
-       for ( int i=0; i< conLength; i++)
-       {
-         Node childNode = conList.item(i);
-         ConditionType condition = setQueryConditionType(childNode);
-         conditionArray[i] = condition;
-       }//for
-       if (and !=null)
-       {
-         and.setCondition(conditionArray);
-       }
-       else if (or != null)
-       {
-         or.setCondition(conditionArray);
-      }
-     }//if
-
-  }//setType
-  
-  /*
-   * Method to set Condition type to query
-   */
-  private ConditionType setQueryConditionType(Node node) throws InvalidEcogridQueryException
-  {
-    ConditionType condition = null;
-    dbg.print("In condition type", 2);
-    Element coditionElement = (Element) node;
-    // get attribute operator from node
-    String operatorString = coditionElement.getAttribute(OPERATOR);
-    dbg.print("operator string is "+ operatorString, 2);
-    // get attribute concept
-    String conceptString = coditionElement.getAttribute(CONCEPT);
-    dbg.print("concept string is "+ conceptString, 2);
-    // get element value
-    String value = coditionElement.getFirstChild().getNodeValue();
-    dbg.print("value string is "+ value, 2);
-    condition = generateConditionType(conceptString, operatorString, value);
-    return condition;
-  }//setConditionType
-  
-  /*
-   * Generate a condition type base on concept, operator, value
-   */
-  private ConditionType generateConditionType(String concept,
-                                       String operator, String value)
-                                       throws InvalidEcogridQueryException
-  {
-    // check the parameters
-    if ( concept == null || concept.trim().equals(""))
-    {
-      throw new InvalidEcogridQueryException("Should set up concept value in " +
-                                         "condition type in ecogrid query");
-    }
-    else if (operator == null || operator.trim().equals(""))
-    {
-      throw new InvalidEcogridQueryException("Should set up operator value in "+
-                                         "condition type in ecogrid query");
-    }
-    else if (value == null || value.trim().equals(""))
-    {
-      throw new InvalidEcogridQueryException("Should set up search value in " +
-                                        "condition type in ecogrid query");
-    }
+    mapInValue(queryNode, false);
     
-    // replace the value by search value if this value in replacementMap
-    if(replacementMap.containsKey(value))
-    {
-      dbg.print("replace " + value + " by ", 2 );
-      value = (String)replacementMap.get(value);
-      dbg.print(" new value "+ value, 2);
+    try {
+        EcogridQueryParser queryParser = new EcogridQueryParser(queryNode);
+        queryParser.parseXML();
+        _query = queryParser.getEcogridQuery();
+        //System.out.println(EcogridQueryTransformer.toXMLString(query));
+    } catch (Exception e)
+    {
+        System.err.println(e);
     }
-    
-    // set up the limitedPathExpression (xpath)
-    LimitedXPathExpression path = new LimitedXPathExpression(concept);
 
-    // set up the operator
-    OperatorType operatorType = null;
-    try
-    {
-      operatorType = OperatorType.fromString(operator);
-    }
-    catch(IllegalStateException e)
-    {
-     throw new InvalidEcogridQueryException(e.getMessage());
-    }
-
-    //set up condition type
-    ConditionType condition = new ConditionType();
-    condition.setConcept(path);
-    condition.setOperator(operatorType);
-    condition.setValue(value);
-    return condition;
-
-  }//generateConditionType
-
-  
-}//SearchQueryGenerator
\ No newline at end of file
+  }  // generateQuery
+   
+}  // SearchQueryGenerator
Index: src/org/ecoinformatics/util/DebugPrinter.java
===================================================================
RCS file: /cvs/kepler/src/org/ecoinformatics/util/DebugPrinter.java,v
retrieving revision 1.6
diff -u -r1.6 DebugPrinter.java
--- src/org/ecoinformatics/util/DebugPrinter.java	20 Sep 2004 15:05:50 -0000	1.6
+++ src/org/ecoinformatics/util/DebugPrinter.java	9 Dec 2004 21:05:44 -0000
@@ -78,6 +78,7 @@
         "environment variable DBGPRN was not set to 0, 1 or 2.");
       DEBUG_LEVEL=0;
     }
+    //DEBUG_LEVEL=0;
   }
 
   /**