Kepler

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;

   }

   /**