Index: DarwinCoreMetaDataSpecification.java
===================================================================
RCS file: /cvs/kepler/src/org/ecoinformatics/seek/datasource/darwincore/DarwinCoreMetaDataSpecification.java,v
retrieving revision 1.14
diff -c -r1.14 DarwinCoreMetaDataSpecification.java
*** DarwinCoreMetaDataSpecification.java	19 Jul 2005 17:16:06 -0000	1.14
--- DarwinCoreMetaDataSpecification.java	8 Sep 2005 16:34:15 -0000
***************
*** 32,41 ****
  
  package org.ecoinformatics.seek.datasource.darwincore;
  
- import java.io.File;
  import java.io.IOException;
  import java.util.Enumeration;
  import java.util.Hashtable;
  import java.util.Vector;
  
  import org.apache.axis.types.URI;
--- 32,42 ----
  
  package org.ecoinformatics.seek.datasource.darwincore;
  
  import java.io.IOException;
+ import java.util.Collections;
  import java.util.Enumeration;
  import java.util.Hashtable;
+ import java.util.Iterator;
  import java.util.Vector;
  
  import org.apache.axis.types.URI;
***************
*** 47,53 ****
  import org.ecoinformatics.ecogrid.ResultsetType_record_returnField;
  import org.ecoinformatics.ecogrid.ResultsetType_resultsetMetadata;
  import org.ecoinformatics.ecogrid.ResultsetType_resultsetMetadata_system;
- import org.ecoinformatics.ecogrid.digir.impl.DigirProxyImpl;
  
  import org.kepler.objectmanager.cache.DataCacheManager;
  import org.ecoinformatics.seek.datasource.EcogridDataCacheItem;
--- 48,53 ----
***************
*** 75,124 ****
  
  public class DarwinCoreMetaDataSpecification extends MetadataSpecificationInterface
  {
!   private DebugPrinter dbg = DebugPrinter.getInstance();
!   private static final String REPLACE      = "#value#";
!   private static final String QUERYID      = "darwincore-quick-search-query";
! 
!   private String  _searchString           = "";
!   private boolean _returnResultsBySpecies = true;
!   private int     _numResults             = 0;
!   
!   /**
!    * Default constructor
!    */
!   public DarwinCoreMetaDataSpecification()
!   {
! 
!   } // DarwinCoreMetaDataSpecification
! 
!   /**
!    * Method to create a quick query search
!    * @param value String
!    * @return QueryType
!    */
!   public QueryType getQuickSearchEcoGridQuery(String aValue)
!                                          throws InvalidEcogridQueryException
!   {
!       _searchString = aValue;
!       
!       Hashtable replaceMapping = new Hashtable();
!       replaceMapping.put(REPLACE, aValue);
!       SearchQueryGenerator darwinCoreQueryGenerator = new SearchQueryGenerator(QUERYID, replaceMapping);
!       QueryType ecogridQuery = darwinCoreQueryGenerator.getQuery();
!       return ecogridQuery;
! 
!   } // getQuickSearchEcoGridQuery
!   
!   /**
!    * Method to create a ecogrid query
!    * @return QueryType
!    */
!   public QueryType getEcoGridQuery()
!   {
!     QueryType ecogridQuery = null;
!     return ecogridQuery;
!   }  // getEcoGridQuery
! 
      /**
       * Returns the human readable Provider and Resource name for a given provider URL and Reource Code
       * @param aURI the provider URL
--- 75,124 ----
  
  public class DarwinCoreMetaDataSpecification extends MetadataSpecificationInterface
  {
!     private DebugPrinter dbg = DebugPrinter.getInstance();
!     private static final String REPLACE      = "#value#";
!     private static final String QUERYID      = "darwincore-quick-search-query";
!     
!     private String  _searchString           = "";
!     private boolean _returnResultsBySpecies = true;
!     private int     _numResults             = 0;
!     
!     /**
!      * Default constructor
!      */
!     public DarwinCoreMetaDataSpecification()
!     {
!         
!     } // DarwinCoreMetaDataSpecification
!     
!     /**
!      * Method to create a quick query search
!      * @param value String
!      * @return QueryType
!      */
!     public QueryType getQuickSearchEcoGridQuery(String aValue)
!     throws InvalidEcogridQueryException
!     {
!         _searchString = aValue;
!         
!         Hashtable replaceMapping = new Hashtable();
!         replaceMapping.put(REPLACE, aValue);
!         SearchQueryGenerator darwinCoreQueryGenerator = new SearchQueryGenerator(QUERYID, replaceMapping);
!         QueryType ecogridQuery = darwinCoreQueryGenerator.getQuery();
!         return ecogridQuery;
!         
!     } // getQuickSearchEcoGridQuery
!     
!     /**
!      * Method to create a ecogrid query
!      * @return QueryType
!      */
!     public QueryType getEcoGridQuery()
!     {
!         QueryType ecogridQuery = null;
!         return ecogridQuery;
!     }  // getEcoGridQuery
!     
      /**
       * Returns the human readable Provider and Resource name for a given provider URL and Reource Code
       * @param aURI the provider URL
***************
*** 146,213 ****
              
              
              String resourceCode = str.substring(inx+1, str.length()).replaceAll("%20", " ");
-         
-             DigirProxyImpl digir = new DigirProxyImpl();
              
!             boolean useCache = true;
!             if (!useCache) 
!             {
!                 int status = digir.doHTTPRequest(urlStr);
!                 File dataCacheFile = digir.getCacheFile();
!                 if (dataCacheFile != null)
!                 {
!                     dataCacheName = dataCacheFile.getAbsolutePath();
!                     dataWasOK = true;
!                 }
!                 
!             } else 
              {
!                 dataCacheName = "ResourceInfo " + resourceCode;
!                 EcogridDataCacheItem dataCacheItem = (EcogridDataCacheItem)DataCacheManager.getCacheItem(null, dataCacheName, urlStr, EcogridDataCacheItem.class.getName());
!                 if (dataCacheItem != null)
                  {
!                   dataCacheItem.doWork();
!                   dataWasOK = dataCacheItem.isReady();
!                   if (dataWasOK)
!                   {
!                       dataCacheName = dataCacheItem.getLocalFileName();
!                   }
                  }
-                 
              }
              
              if (dataWasOK)
              {
!               Document dom = EcogridUtils.readXMLFile2DOM(dataCacheName);
!               if (dom != null) 
!               {
!                   Node name = EcogridUtils.findNodeWithXPath(dom, "/response/content/metadata/provider/name");
!                   if (name != null)
!                   {
!                       String providerName = EcogridUtils.getNodeValue(name);
!                       Node provider = EcogridUtils.findNodeWithXPath(dom, "/response/content/metadata/provider");
!                       if (provider != null)
!                       {
!                           EcogridUtilsNamedNodeIterator nodeIter = new EcogridUtilsNamedNodeIterator(provider, "resource"); 
!                           while (nodeIter.hasMoreNodes())
!                           {
!                               Node resNode = nodeIter.nextNode();
!                               String resCode = EcogridUtils.findNodeValue(resNode, "code");
!                               if (resCode != null && resCode.equals(resourceCode)) 
!                               {   
!                                   String fullName = providerName + " - " + EcogridUtils.findNodeValue(resNode, "name");
!                                   resourceName = fullName.replace('.', ' ');
!                                   dataWasOK = true;
!                               }
!                           }
!                       }
!                       
!                   }
!               }
!           } else
!           {
!               System.err.println("Could not contact URL for provide/resource name: " + aURI);
!           }
          } catch (Exception e)
          {
              System.err.println(e);
--- 146,197 ----
              
              
              String resourceCode = str.substring(inx+1, str.length()).replaceAll("%20", " ");
              
!             dataCacheName = "ResourceInfo " + resourceCode;
!             EcogridDataCacheItem dataCacheItem = (EcogridDataCacheItem)DataCacheManager.getCacheItem(null, dataCacheName, urlStr, EcogridDataCacheItem.class.getName());
!             if (dataCacheItem != null)
              {
!                 dataCacheItem.doWork();
!                 dataWasOK = dataCacheItem.isReady();
!                 if (dataWasOK)
                  {
!                     dataCacheName = dataCacheItem.getLocalFileName();
                  }
              }
              
+             
              if (dataWasOK)
              {
!                 Document dom = EcogridUtils.readXMLFile2DOM(dataCacheName);
!                 if (dom != null) 
!                 {
!                     Node name = EcogridUtils.findNodeWithXPath(dom, "/response/content/metadata/provider/name");
!                     if (name != null)
!                     {
!                         String providerName = EcogridUtils.getNodeValue(name);
!                         Node provider = EcogridUtils.findNodeWithXPath(dom, "/response/content/metadata/provider");
!                         if (provider != null)
!                         {
!                             EcogridUtilsNamedNodeIterator nodeIter = new EcogridUtilsNamedNodeIterator(provider, "resource"); 
!                             while (nodeIter.hasMoreNodes())
!                             {
!                                 Node resNode = nodeIter.nextNode();
!                                 String resCode = EcogridUtils.findNodeValue(resNode, "code");
!                                 if (resCode != null && resCode.equals(resourceCode)) 
!                                 {   
!                                     String fullName = providerName + " - " + EcogridUtils.findNodeValue(resNode, "name");
!                                     resourceName = fullName.replace('.', ' ');
!                                     dataWasOK = true;
!                                 }
!                             }
!                         }
!                         
!                     }
!                 }
!             } else
!             {
!                 System.err.println("Could not contact URL for provide/resource name: " + aURI);
!             }
          } catch (Exception e)
          {
              System.err.println(e);
***************
*** 218,224 ****
              System.err.println(e);
              e.printStackTrace();
          }
!                                                                                                      
          
          if (dataWasOK) 
          {
--- 202,208 ----
              System.err.println(e);
              e.printStackTrace();
          }
!         
          
          if (dataWasOK) 
          {
***************
*** 243,272 ****
       * @throws IllegalActionException
       */
      public boolean addResultsetByProvider(ResultsetType   aResults,
!                                           String          aEndPointURLStr,
!                                           CompositeEntity aContainer, 
!                                           Vector          aResultList) 
!         throws NameDuplicationException, IllegalActionException
!       {
!           if (aResults == null)
!           {
!               return false;
!           }
!           
!           int numAdded = 0;
!           ResultsetType_resultsetMetadata metaData = aResults.getResultsetMetadata();
!           if (metaData != null)
!           {
!               ResultsetType_resultsetMetadata_system[] system = metaData.getSystem();
!               if (system != null)
!               {
!                   String providerURI = ""; 
!                   for (int i=0;i<system.length;i++) 
!                   {
!                       String fullName = getDigirResourceName(system[i].getValue());
!                       fullName = MetadataSpecificationInterface.replaceDotByDash(fullName);
!                       if (fullName != null)
!                       {
                          DarwinCoreDataSource darwinDS = new DarwinCoreDataSource(aContainer, fullName);
                          darwinDS.setInitFromData("yes");
                          darwinDS.setSearchData(_searchString);
--- 227,256 ----
       * @throws IllegalActionException
       */
      public boolean addResultsetByProvider(ResultsetType   aResults,
!             String          aEndPointURLStr,
!             CompositeEntity aContainer, 
!             Vector          aResultList) 
!     throws NameDuplicationException, IllegalActionException
!     {
!         if (aResults == null)
!         {
!             return false;
!         }
!         
!         int numAdded = 0;
!         ResultsetType_resultsetMetadata metaData = aResults.getResultsetMetadata();
!         if (metaData != null)
!         {
!             ResultsetType_resultsetMetadata_system[] system = metaData.getSystem();
!             if (system != null)
!             {
!                 String providerURI = ""; 
!                 for (int i=0;i<system.length;i++) 
!                 {
!                     String fullName = getDigirResourceName(system[i].getValue());
!                     fullName = MetadataSpecificationInterface.replaceDotByDash(fullName);
!                     if (fullName != null)
!                     {
                          DarwinCoreDataSource darwinDS = new DarwinCoreDataSource(aContainer, fullName);
                          darwinDS.setInitFromData("yes");
                          darwinDS.setSearchData(_searchString);
***************
*** 274,289 ****
                          darwinDS.setProvider(system[i].getValue().toString());
                          aResultList.addElement(darwinDS);
                          numAdded++;
!                       } else
!                       {
!                           System.err.println("Couldn't get full name for provider and resource - Id:[" + system[i].getId() + "] value: [" + system[i].getValue().toString()+"]");
!                       }
!                   }
!               }
!           }
!           _numResults = numAdded;
!           return numAdded > 0;
!       }
      
      /**
       * Helper class to return a named field's value (content)
--- 258,273 ----
                          darwinDS.setProvider(system[i].getValue().toString());
                          aResultList.addElement(darwinDS);
                          numAdded++;
!                     } else
!                     {
!                         System.err.println("Couldn't get full name for provider and resource - Id:[" + system[i].getId() + "] value: [" + system[i].getValue().toString()+"]");
!                     }
!                 }
!             }
!         }
!         _numResults = numAdded;
!         return numAdded > 0;
!     }
      
      /**
       * Helper class to return a named field's value (content)
***************
*** 320,408 ****
       * @throws IllegalActionException
       */
      public boolean addResultsetByScientificName(ResultsetType   aResults,
!                                                 String          aEndPointURLStr,
!                                                 CompositeEntity aContainer, 
!                                                 Vector          aResultList) 
!         throws NameDuplicationException, IllegalActionException
!       {
!           if (aResults == null)
!           {
!               return false;
!           }
!           
!           Hashtable speciesHash        = new Hashtable();
!           Hashtable systemProviderHash = new Hashtable();
!           
!           // collect all the providers into a hash table
!           int numAdded = 0;
!           ResultsetType_resultsetMetadata metaData = aResults.getResultsetMetadata();
!           if (metaData != null)
!           {
!               ResultsetType_resultsetMetadata_system[] system = metaData.getSystem();
!               if (system != null)
!               {
!                   String providerURI = ""; 
!                   for (int i=0;i<system.length;i++) 
!                   {
!                       systemProviderHash.put(system[i].getId(), system[i].getValue().toString());
!                   }
!               }
!           }
!           
!           numAdded = 0;
!           ResultsetType_record[] records = aResults.getRecord();
!           if (records != null)
!           {
!               numAdded = records.length;
!               for (int i=0;i<records.length;i++) 
!               {
!                   ResultsetType_record rec = records[i];
!                   String               scientificName = getReturnFieldValue(rec, "ScientificName");
!                   scientificName = MetadataSpecificationInterface.replaceDotByDash(scientificName);
!                   if (scientificName != null && scientificName.trim().length() > 0)
!                   {
!                       Hashtable providers = (Hashtable)speciesHash.get(scientificName);
!                       if (providers == null)
!                       {
!                           providers = new Hashtable();
!                           speciesHash.put(scientificName, providers);
!                           //System.out.println("*** Putting ScientificName["+scientificName+"]");
!                       }
!                       providers.put(rec.getSystem(), rec.getSystem());
!                       //System.out.println("  System["+rec.getSystem()+"]");
!                   }
!               }
!           }
!           
!           for (Enumeration e = speciesHash.keys();e.hasMoreElements();)
!           {
!               String       scientificName = (String)e.nextElement();
!               Hashtable    providers      = (Hashtable)speciesHash.get(scientificName);
!               StringBuffer providerList   = new StringBuffer();
!               for (Enumeration ep = providers.keys();ep.hasMoreElements();)
!               {
!                   String providerId = (String)ep.nextElement();
!                   String provider   = (String)systemProviderHash.get(providerId);
!                   if (providerList.length() > 0)
!                   {
!                       providerList.append(",");
!                   }
!                   providerList.append(provider);
!               }
!               
!               //System.out.println("*** ProviderList["+scientificName+"]["+providerList+"]");
!               DarwinCoreDataSource darwinDS = new DarwinCoreDataSource(aContainer, scientificName); 
!               darwinDS.setInitFromData("yes");
!               darwinDS.setSearchData(_searchString);
!               darwinDS.setEndpoint(aEndPointURLStr);
!               darwinDS.setProvider(providerList.toString());
!               aResultList.addElement(darwinDS);
!               _numResults++;
!               
!           }
!           
!           return numAdded > 0;
!       }
      
      /**
       * Creates a DarwinCore DataSource which extends Source
--- 304,399 ----
       * @throws IllegalActionException
       */
      public boolean addResultsetByScientificName(ResultsetType   aResults,
!             String          aEndPointURLStr,
!             CompositeEntity aContainer, 
!             Vector          aResultList) 
!     throws NameDuplicationException, IllegalActionException
!     {
!         if (aResults == null)
!         {
!             return false;
!         }
!         
!         Hashtable speciesHash        = new Hashtable();
!         Hashtable systemProviderHash = new Hashtable();
!         
!         // collect all the providers into a hash table
!         int numAdded = 0;
!         ResultsetType_resultsetMetadata metaData = aResults.getResultsetMetadata();
!         if (metaData != null)
!         {
!             ResultsetType_resultsetMetadata_system[] system = metaData.getSystem();
!             if (system != null)
!             {
!                 String providerURI = ""; 
!                 for (int i=0;i<system.length;i++) 
!                 {
!                     systemProviderHash.put(system[i].getId(), system[i].getValue().toString());
!                 }
!             }
!         }
!         
!         ResultsetType_record[] records = aResults.getRecord();
!         if (records == null)
!         {
!             return false;
!         }
! 
!         numAdded = records.length;
!         for (int i=0;i<records.length;i++) 
!         {
!             ResultsetType_record rec = records[i];
!             // convert the scientific name to lowercase -- effictively making the hash table case insensitive.
!             String               scientificName = getReturnFieldValue(rec, "ScientificName").toLowerCase();
!             scientificName = MetadataSpecificationInterface.replaceDotByDash(scientificName);
!             if (scientificName == null && scientificName.trim().length() == 0)
!             {
!                 continue;
!             }
!             Hashtable providers = (Hashtable)speciesHash.get(scientificName);
!             if (providers == null)
!             {
!                 providers = new Hashtable();
!                 speciesHash.put(scientificName, providers);
!                 //System.out.println("*** Putting ScientificName["+scientificName+"]");
!             }   
!             providers.put(rec.getSystem(), rec.getSystem());
!             //System    .out.println("  System["+rec.getSystem()+"]");
!         }
!     
!         // Sort the keys alphabetically for presentation.
!         Vector sortedKeys = new Vector( speciesHash.keySet());
!         Collections.sort(sortedKeys);
!         Iterator it = sortedKeys.iterator();
!         while ( it.hasNext() )
!         {
!             String       scientificName = (String)it.next();
!             Hashtable    providers      = (Hashtable)speciesHash.get(scientificName);
!             StringBuffer providerList   = new StringBuffer();
!             for (Enumeration ep = providers.keys();ep.hasMoreElements();)
!             {
!                 String providerId = (String)ep.nextElement();
!                 String provider   = (String)systemProviderHash.get(providerId);
!                 if (providerList.length() > 0)
!                 {
!                     providerList.append(",");
!                 }
!                 providerList.append(provider);
!             }
!             
!             //System.out.println("*** ProviderList["+scientificName+"]["+providerList+"]");
!             DarwinCoreDataSource darwinDS = new DarwinCoreDataSource(aContainer, scientificName); 
!             darwinDS.setInitFromData("yes");
!             darwinDS.setSearchData(_searchString);
!             darwinDS.setEndpoint(aEndPointURLStr);
!             darwinDS.setProvider(providerList.toString());
!             aResultList.addElement(darwinDS);
!             _numResults++;
!             
!         }
!         
!         return numAdded > 0;
!     }
      
      /**
       * Creates a DarwinCore DataSource which extends Source
***************
*** 417,426 ****
       * @throws IllegalActionException
       */
      public boolean addResultsetRecordsToContainer(ResultsetType   aResults,
!                                                   String          aEndPointURLStr,
!                                                   CompositeEntity aContainer, 
!                                                   Vector          aResultList) 
!         throws NameDuplicationException, IllegalActionException
      {
          if (_returnResultsBySpecies) 
          {
--- 408,417 ----
       * @throws IllegalActionException
       */
      public boolean addResultsetRecordsToContainer(ResultsetType   aResults,
!             String          aEndPointURLStr,
!             CompositeEntity aContainer, 
!             Vector          aResultList) 
!     throws NameDuplicationException, IllegalActionException
      {
          if (_returnResultsBySpecies) 
          {
***************
*** 440,446 ****
      {
          return getClass().getName();
      }
! 
      /**
       * 
       */
--- 431,437 ----
      {
          return getClass().getName();
      }
!     
      /**
       * 
       */
***************
*** 464,470 ****
      class SpeciesCollector
      {
          public Hashtable _providers = new Hashtable();     
!    
      }
      
!   } // DarwinCoreMetaDataSpecification
--- 455,461 ----
      class SpeciesCollector
      {
          public Hashtable _providers = new Hashtable();     
!         
      }
      
! } // DarwinCoreMetaDataSpecification