[MOBY-guts] biomoby commit

Gary Schiltz gss at pub.open-bio.org
Wed Sep 14 22:06:55 UTC 2005


gss
Wed Sep 14 18:06:55 EDT 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv17172/src/org/semanticmoby/ref/tools

Modified Files:
	InvocationBroker.java KeywordFinder.java KeywordList.java 
	URIInvestigator.java KeywordQuery.java DiscoveryQuery.java 
Log Message:
Changed to work after major API overhaul

moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools InvocationBroker.java,1.2,1.3 KeywordFinder.java,1.2,1.3 KeywordList.java,1.1,1.2 URIInvestigator.java,1.2,1.3 KeywordQuery.java,1.2,1.3 DiscoveryQuery.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.java	2005/03/21 21:42:01	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.java	2005/09/14 22:06:55	1.3
@@ -16,7 +16,7 @@
 
 /**
  * This class is used to invoke and display the results of Semantic
- * MOBY providers.
+ * MOBY services.
  */
 public class InvocationBroker
 {
@@ -55,64 +55,64 @@
 		this.out      = out;
 	}
 	
-	private String rdfxmlString(MOBYProvider provider)
+	private String rdfxmlString(MOBYService service)
 	{
 		StringWriter writer = new StringWriter();
-		provider.getModel().write(writer);
+        service.getJenaModel().write(writer);
 		return writer.toString();
 	}
 	
-	private String n3String(MOBYProvider provider)
+	private String n3String(MOBYService service)
 	{
 		StringWriter writer = new StringWriter();
-		provider.getModel().write(writer, "N3");
+        service.getJenaModel().write(writer, "N3");
 		return writer.toString();
 	}
 	
 	/**
-	 * Handle a request to invoke a provider at a given URI.
-	 * If the provider requires inputs, and the provider has
+	 * Handle a request to invoke a service at a given URI.
+	 * If the service requires inputs, and the service has
 	 * a valid inputURI property, redirect to the URI that is
-	 * the value of the property. If the provider requires input
+	 * the value of the property. If the service requires input
 	 * and has no inputURI property, then build a simple input
 	 * GUI from scratch.
 	 * <br><br>
-	 * If the provider doesn't require any inputs, then do an HTTP
-	 * POST to the provider URI, passing the graph as a parameter.
+	 * If the service doesn't require any inputs, then do an HTTP
+	 * POST to the service URI, passing the graph as a parameter.
 	 */
-	public void invokeURI(String providerURI)
+	public void invokeURI(String serviceURI)
 	{
-		// Try to retrieve and parse a provider graph from the URI;
+		// Try to retrieve and parse a service graph from the URI;
 		// on failure, print a message and return.
 		//
-		MOBYProvider canonicalProvider = null;
+		MOBYService service = null;
 		
 		try
 		{
 			Model model = ModelFactory.createDefaultModel();
-			model.read(providerURI);
+			model.read(serviceURI);
 			Parser parser = new Parser(model);
-			canonicalProvider = parser.parseProvider();
+            service = parser.parseService();
 		}
 		catch (Throwable t)
 		{
-			out.println("No valid provider could be found at");
-			out.print("<a href=\"" + providerURI + "\">");
-			out.print("  "); out.println(providerURI); out.println("</a>");
+			out.println("No valid service could be found at");
+			out.print("<a href=\"" + serviceURI + "\">");
+			out.print("  "); out.println(serviceURI); out.println("</a>");
 			return;
 		}
 		
-		if (requiresInputs(canonicalProvider))
+		if (requiresInputs(service))
 		{
-			// Since the provider requires input, either redirect to its
+			// Since the service requires input, either redirect to its
 			// inputURI (if it has one) or build a simple GUI for it.
 			//
 			try
 			{
-				String inputURI = getInputURI(canonicalProvider);
+				String inputURI = getInputURI(service);
 				
 				if (inputURI == null) {
-					buildInputGUI(canonicalProvider);
+					buildInputGUI(service);
 				}
 				else
 				{
@@ -128,23 +128,23 @@
 					if (status == HttpStatus.SC_OK) {
 						response.sendRedirect(inputURI);
 					} else {
-						buildInputGUI(canonicalProvider);
+						buildInputGUI(service);
 					}
 				}
 			} catch (Throwable t) {
-				buildInputGUI(canonicalProvider);
+				buildInputGUI(service);
 			}
 		}
 		else // No input required
 		{
 			try
 			{
-				// Invoke the provider
+				// Invoke the service
 				//
 				HTTPRequest rqst =
-					HTTPRequest.newPostRequest(canonicalProvider.getURI());
+					HTTPRequest.newPostRequest(service.getURI());
 				rqst.addParameter(MOBY.GRAPH_PARAMETER_NAME,
-				    rdfxmlString(canonicalProvider));
+				    rdfxmlString(service));
 				HTTPResponse resp = rqst.send();
 				
 				// Check the status
@@ -158,16 +158,16 @@
 					Model model = ModelFactory.createDefaultModel();
 					model.read(resp.getBodyAsStream(), "");
 					Parser parser = new Parser(model);
-					MOBYProvider resultsProvider = parser.parseProvider();
+					MOBYService resultsService = parser.parseService();
 					
-					String outputURI = getOutputURI(resultsProvider);
+					String outputURI = getOutputURI(resultsService);
 					
 					if (outputURI == null)
 					{
 						// No output URI was specified, so build a generic
 						// display of the results
 						//
-						buildOutputGUI(resultsProvider);
+						buildOutputGUI(resultsService);
 					}
 					else
 					{
@@ -186,7 +186,7 @@
 							// by trying to invoke it.
 							//
 							rqst = HTTPRequest.newPostRequest(outputURI);
-							String graphString = rdfxmlString(resultsProvider);
+							String graphString = rdfxmlString(resultsService);
 							rqst.addParameter(
 								MOBY.GRAPH_PARAMETER_NAME, graphString);
 							resp = rqst.send();
@@ -204,22 +204,22 @@
 								// The output URI returned a status other than
 								// 200 OK, so fall back to a default output GUI
 								//
-								buildOutputGUI(resultsProvider);
+								buildOutputGUI(resultsService);
 							}
 						}
 						catch (Throwable t)
 						{
-							buildOutputGUI(resultsProvider);
+							buildOutputGUI(resultsService);
 						}
 					}
 				} else {
-					out.println("Sorry - an error occurred invoking the provider");
+					out.println("Sorry - an error occurred invoking the service");
 				}
 				
 			}
 			catch (Throwable t)
 			{
-				out.println("Sorry - an error occurred invoking the provider");
+				out.println("Sorry - an error occurred invoking the service");
 				return;
 			}
 		}
@@ -243,57 +243,55 @@
 		dispatcher.forward(request, response);
 	}
 	
-	private String getInputURI(MOBYProvider provider)
+	private String getInputURI(MOBYService service)
 	{
 		try {
-			Model model = provider.getModel();
-			Statement stmt = model.listStatements(
-				provider.getResource(), MOBY.inputURI,
-				(String) null).nextStatement();
+			Model model = service.getJenaModel();
+			Statement stmt =
+                model.getProperty(service.getResource(), MOBY.inputURI);
 			return stmt.getString();
 		} catch (Throwable t) {
 			return null;
 		}
 	}
 	
-	private String getOutputURI(MOBYProvider provider)
+	private String getOutputURI(MOBYService service)
 	{
 		try {
-			Model model = provider.getModel();
-			Statement stmt = model.listStatements(
-				provider.getResource(), MOBY.outputURI,
-				(String) null).nextStatement();
+			Model model = service.getJenaModel();
+            Statement stmt =
+                model.getProperty(service.getResource(), MOBY.outputURI);
 			return stmt.getString();
 		} catch (Throwable t) {
 			return null;
 		}
 	}
 	
-	public void buildInputGUI(MOBYProvider provider)
+	public void buildInputGUI(MOBYService service)
 	{
-		out.println("This provider has not provided a valid URL for");
+		out.println("This service has not provided a valid URL for");
 		out.println("gathering its required inputs.");
 	}
 	
-	public void buildOutputGUI(MOBYProvider provider)
+	public void buildOutputGUI(MOBYService service)
 		throws IOException, ServletException
 	{
 		HttpSession session = request.getSession(true);
 		session.setAttribute("n3Graph",
-			    n3String(provider)
+			    n3String(service)
 			        .replaceAll("<", "&lt;")
 			        .replaceAll(">", "&gt;")
 			    	.replaceAll("\"", "&quot;"));
 		session.setAttribute("rdfxmlGraph",
-		    rdfxmlString(provider)
+		    rdfxmlString(service)
 		        .replaceAll("<", "&lt;")
 		        .replaceAll(">", "&gt;")
 		    	.replaceAll("\"", "&quot;"));
 	    redirectToPage("/jsp/display.jsp");
 	}
 	
-	private boolean requiresInputs(MOBYProvider provider)
+	private boolean requiresInputs(MOBYService service)
 	{
-        return getInputURI(provider) != null;
+        return getInputURI(service) != null;
 	}
 }
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.java	2005/03/21 21:42:01	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.java	2005/09/14 22:06:55	1.3
@@ -12,15 +12,15 @@
 public class KeywordFinder
 {
 	/**
-	 * The MOBY provider for which to find keywords
+	 * The MOBY service for which to find keywords
 	 */
-	private MOBYProvider provider;
+	private MOBYService service;
 	
 	/**
-	 * The underlying Jena model on which the MOBY provider
+	 * The underlying Jena model on which the MOBY service
 	 * is based
 	 */
-	private Model providerModel;
+	private Model serviceModel;
 	
 	/**
 	 * A keyword list object to hold the keywords that are
@@ -29,17 +29,17 @@
 	private KeywordList keywords = null;
 	
 	/**
-	 * Construct an instance for the given provider and model
+	 * Construct an instance for the given service and model
 	 */
-	public KeywordFinder(MOBYProvider provider, Model providerModel)
+	public KeywordFinder(MOBYService service)
 	{
-		this.provider = provider;
-		this.providerModel = providerModel;
+		this.service = service;
+		this.serviceModel = service.getJenaModel();
 	}
 	
 	/**
 	 * Retrieve, if necessary, and return the keywords associated
-	 * with the provider.
+	 * with the service.
 	 */
 	public KeywordList getKeywords()
 		throws Exception
@@ -53,21 +53,20 @@
 	}
 	
 	/**
-	 * Collect keywords for the provider
+	 * Collect keywords for the service
 	 */
 	private void collectKeywords()
 	{
-		// Add keywords from classes that the provider is asserted to
-		// be an instance of (i.e. provider rdf:type <some type>)
+		// Add keywords from classes that the service is asserted to
+		// be an instance of (i.e. service rdf:type <some type>)
 		//
-		Resource res = provider.getResource();
-		keywords.addProviderKeywords(getKeywordsFor(res));
+		Resource res = service.getResource();
+		keywords.addServiceKeywords(getKeywordsFor(res));
 		
 		// Add keywords from subjects and objects of each
 		// operatesOn subgraph
 		//
-		MOBYCollection coll = provider.getOperatesOn();
-		for (Iterator it = coll.iterator(); it.hasNext();)
+		for (Iterator it = service.getOperatesOn(); it.hasNext();)
 		{
 			MOBYGraphNode node = (MOBYGraphNode) it.next();
 			addGraphKeywordsFor(node);
@@ -104,10 +103,11 @@
 			MOBYSubject subject = (MOBYSubject) node;
 			keywords.addSubjectKeywords(
 				getKeywordsFor(subject.getResource()));
-			Iterator it = subject.getDirectMappings().iterator();
+			Iterator it = subject.getDirectMappings();
 			while (it.hasNext())
 			{
-				MOBYGraphNode node2 = (MOBYGraphNode) it.next();
+                Object obj = it.next();
+				MOBYGraphNode node2 = (MOBYGraphNode) obj;
 				addObjectKeywordsFor(node2);
 			}
 		}
@@ -123,6 +123,11 @@
 		}
 	}
 	
+    // TODO: Note that in some cases, this doesn't work,
+    // when node is a MOBYObject that has no defining
+    // statement (see the discussion in the class doc for
+    // its parent class MappingObject). So, this as well
+    // as addSubjectKeywordsFor() needs to be fixed
 	private void addObjectKeywordsFor(MOBYGraphNode node)
 	{
 		if (node instanceof MOBYObject)
@@ -153,9 +158,9 @@
 		
 		// Iterate over the resource's rdf:type properties
 		//
-		StmtIterator it = providerModel.listStatements(
-			res, RDF.type, (RDFNode) null);
-		
+		StmtIterator it =
+            serviceModel.listStatements(res, RDF.type, (RDFNode) null);
+        
 		while (it.hasNext())
 		{
 			Statement s1 = it.nextStatement();
@@ -163,7 +168,7 @@
 			
 			// If the value of the rdf:type property is a resource
 			//
-			if (node.canAs(Resource.class))
+			if ((res != null) && (node.canAs(Resource.class)))
 			{
 				Resource classNode = (Resource) node.as(Resource.class);
 				
@@ -188,7 +193,7 @@
 				}
 			}
 			
-			if (res.canAs(Bag.class))
+			if ((res != null) && (res.canAs(Bag.class)))
 			{
 				Bag bag = (Bag) res.as(Bag.class);
 				for (Iterator it2 = bag.iterator(); it2.hasNext();)
@@ -236,40 +241,4 @@
 		
 		return list;
 	}
-	
-	public static void main(String[] args)
-		throws Exception
-	{
-		Model model = ModelFactory.createDefaultModel();
-//		model.read("http://brebiou.cshl.org:8080/get-individuals");
-		model.read("http://www.semanticmoby.org/examples/hello-world");
-		Parser parser = new Parser(model);
-		MOBYProvider provider = parser.parseProvider();
-		KeywordFinder kf = new KeywordFinder(provider, model);
-		KeywordList list = kf.getKeywords();
-		
-		System.out.print("Provider keywords: ");
-		for (Iterator it = list.getProviderKeywords(); it.hasNext();) {
-			System.out.print("\"");
-			System.out.print(it.next().toString());
-			System.out.print("\" ");
-		}
-		System.out.println();
-		
-		System.out.print("Subject keywords: ");
-		for (Iterator it = list.getSubjectKeywords(); it.hasNext();) {
-			System.out.print("\"");
-			System.out.print(it.next().toString());
-			System.out.print("\" ");
-		}
-		System.out.println();
-
-		System.out.print("Object keywords: ");
-		for (Iterator it = list.getObjectKeywords(); it.hasNext();) {
-			System.out.print("\"");
-			System.out.print(it.next().toString());
-			System.out.print("\" ");
-		}
-		System.out.println();
-	}
 }
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordList.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordList.java	2004/11/22 22:58:40	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordList.java	2005/09/14 22:06:55	1.2
@@ -6,20 +6,20 @@
 
 public class KeywordList
 {
-	private Set providerKeywords = new HashSet();
+	private Set serviceKeywords = new HashSet();
 	private Set subjectKeywords = new HashSet();
 	private Set objectKeywords = new HashSet();
 	
-	public void addProviderKeyword(String keyword) {
-		providerKeywords.add(keyword);
+	public void addServiceKeyword(String keyword) {
+        serviceKeywords.add(keyword);
 	}
 	
-	public void addProviderKeywords(List keywords) {
-		providerKeywords.addAll(keywords);
+	public void addServiceKeywords(List keywords) {
+        serviceKeywords.addAll(keywords);
 	}
 	
-	public Iterator getProviderKeywords() {
-		return providerKeywords.iterator();
+	public Iterator getServiceKeywords() {
+		return serviceKeywords.iterator();
 	}
 
 	public void addSubjectKeyword(String keyword) {

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.java	2005/03/21 21:42:01	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.java	2005/09/14 22:06:55	1.3
@@ -16,7 +16,7 @@
 import com.hp.hpl.jena.rdf.model.Model;
 
 /**
- * This class is used to investigate URIs that potentially contain MOBY graphs.
+ * This class is used to investigate URLs that potentially contain MOBY graphs.
  * Multiple instances can exist, each investigating a different URL. Keeping a
  * map of URL->instance mappings in the instances class variable is a simple
  * way to prevent multiple instances from investigating the same URL at any one
@@ -36,7 +36,7 @@
      * The URL that is to be investigated for possible inclusion in the
      * metadata repository.
      */
-    private String providerURI;
+    private String serviceURL;
 
     private final static Log syncLog = LogFactory.getLog("SYNC");
     
@@ -47,17 +47,17 @@
      * investigated, then this call is a NO-OP.
      * @param providerURL the URL to investigate
      */
-    public synchronized static void investigate(String providerURL)
+    public synchronized static void investigate(String serviceURL)
     {
         synchronized (instances)
         {
-        	if (instances.get(providerURL) != null) {
-        		syncLog.warn("Already investigating " + providerURL);
+        	if (instances.get(serviceURL) != null) {
+        		syncLog.warn("Already investigating " + serviceURL);
                 return;
             }
             
-            URIInvestigator investigator = new URIInvestigator(providerURL);
-            instances.put(providerURL, investigator);
+            URIInvestigator investigator = new URIInvestigator(serviceURL);
+            instances.put(serviceURL, investigator);
             investigator.start();
         }
     }
@@ -66,9 +66,9 @@
      * Create an instance for investingating the given provider URL
      * @param providerURL the URL to investigate
      */
-	private URIInvestigator(String providerURL)
+	private URIInvestigator(String serviceURL)
     {
-		this.providerURI = providerURL;
+		this.serviceURL = serviceURL;
     }
     
     /**
@@ -108,7 +108,7 @@
             //
             synchronized (instances)
             {
-                instances.remove(providerURI);
+                instances.remove(serviceURL);
             }
         }
     }
@@ -137,18 +137,20 @@
         boolean alreadyRegistered = false;
         
         try {
-        	lastModifiedDate = manager.getLastModifiedDate(providerURI);
+        	lastModifiedDate = manager.getLastModifiedDate(serviceURL);
             alreadyRegistered = (lastModifiedDate != null);
         }
         catch (StorageException e)
         {
-        	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
+        	syncLog.error(
+                "Couldn't check for last modified date of provider URL " +
+                serviceURL, e);
             return;
         }
         
         // Helper class for making the HTTP GET call
         //
-        HTTPRequest request = HTTPRequest.newGetRequest(providerURI);
+        HTTPRequest request = HTTPRequest.newGetRequest(serviceURL);
         
         // If there was a last modified date, then request that the graph only
         // be sent if it has been modified since that date
@@ -170,7 +172,7 @@
         }
         catch (HTTPException e)
         {
-        	syncLog.warn("Couldn't reach suggested provider " + providerURI);
+        	syncLog.warn("Couldn't reach suggested provider " + serviceURL);
             return;
         }
         
@@ -181,7 +183,7 @@
                 // The resource has not been modified since it was
                 // registered, so there is nothing to do but log a message.
                 //
-            	syncLog.info("IN-SYNC : " + providerURI);
+            	syncLog.info("IN-SYNC : " + serviceURL);
                 break;
             
             case HttpServletResponse.SC_NOT_FOUND:
@@ -190,9 +192,9 @@
                 // from the database.
                 //
                 if (alreadyRegistered) {
-                	deregisterProvider(manager, true);
+                	deregisterService(manager, true);
                 } else {
-                	syncLog.info("IGNORED : " + providerURI + " doesn't exist");
+                	syncLog.info("IGNORED : " + serviceURL + " doesn't exist");
                 }
                 break;
                 
@@ -203,11 +205,12 @@
                 //
                 lastModifiedDate = null;
                 
-                // Try to parse the Last-Modified header to store in the database
+                // Try to parse the Last-Modified header to store in the DB
                 //
                 String dateString = "";
                 try {
-                    dateString = response.getHeaderValue(MOBY.LAST_MODIFIED_HEADER);
+                    dateString =
+                        response.getHeaderValue(MOBY.LAST_MODIFIED_HEADER);
                     lastModifiedDate = DateParser.parseDate(dateString);
                 }
                 catch (HTTPException e)
@@ -216,7 +219,7 @@
                     // retrievable, but register the graph anyway
                     //
                 	syncLog.warn("Unable to get Last-Modified date for "
-                                 + providerURI + "; using current date");
+                                 + serviceURL + "; using current date");
                 	lastModifiedDate = new Date();
                 }
                 catch (Throwable t)
@@ -224,8 +227,9 @@
                     // Log a message about the last modified date not being
                     // parsable, but register the graph anyway
                     //
-                	syncLog.warn("Unparsable Last-Modified date " + "(\"" + dateString +
-                                "\") for " + providerURI + "; ignoring");
+                	syncLog.warn(
+                        "Unparsable Last-Modified date " + "(\"" + dateString +
+                        "\") for " + serviceURL + "; ignoring");
                 }
 
                 // The client sent back a graph; so try to parse it. If the
@@ -238,38 +242,41 @@
                 }
                 catch (HTTPException e)
                 {
-                	syncLog.error("Couldn't retrieve graph from " + providerURI);
+                	syncLog.error("Couldn't retrieve graph from " + serviceURL);
                     return;
                 }
                 
-                MOBYProvider provider = null;
+                MOBYService service = null;
                 try {
                     Parser parser = Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
-                    provider = parser.parseProvider();
+                    service = parser.parseService();
                 }
                 catch (Throwable t) {
                     System.err.println("Parse error: " + t);
                 }
                 
                 // De-register the provider, printing a removal message if
-                // a provider couldn't be parsed
+                // a service couldn't be parsed
                 //
-                deregisterProvider(manager, provider==null);
+                deregisterService(manager, service==null);
                 
-                // If a provider was parsed, then register it
+                // If a service was parsed, then register it
                 //
-                if (provider != null)
+                if (service != null)
                 {
 	                try
 	                {
-	                    manager.registerProvider(provider, lastModifiedDate);
+	                    manager.registerProvider(service, lastModifiedDate);
 	                    
 	                    // Log a message about successfully registering the graph:
 	                    //
-	                    syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
+	                    syncLog.info(
+                            (alreadyRegistered ? "UPDATED : " : "ADDED   : ") +
+                            serviceURL);
 	                }
 	                catch (StorageException e) {
-	                	syncLog.error("Error storing graph for " + providerURI, e);
+	                	syncLog.error(
+                            "Error storing graph for " + serviceURL, e);
 	                }
                 }
                 
@@ -280,21 +287,21 @@
                 // Log a message about the failed attempt to contact the URL
                 //
             	syncLog.error("Status " + status + " received while trying " +
-                             "to contact provider " + providerURI);
+                             "to contact provider " + serviceURL);
                 break;
         }
     }
     
-    private void deregisterProvider(StorageManager manager, boolean removing)
+    private void deregisterService(StorageManager manager, boolean removing)
     {
         try {
-        	manager.deregisterProvider(providerURI);
+        	manager.deregisterProvider(serviceURL);
         	if (removing) {
-            	syncLog.info("REMOVED : " + providerURI);
+            	syncLog.info("REMOVED : " + serviceURL);
         	}
         }
         catch (StorageException e) {
-        	syncLog.error("Unable to de-register provider " + providerURI, e);
+        	syncLog.error("Unable to de-register provider " + serviceURL, e);
         }
     }
 }

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.java	2005/03/21 21:42:01	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.java	2005/09/14 22:06:55	1.3
@@ -44,7 +44,7 @@
 			
 			while (rs.next()) {
 				String uri = rs.getString("provider_uri");
-				MOBYProvider provider = providerAt(uri, model);
+				MOBYService provider = serviceAt(uri, model);
 				if (provider != null) {
 					matching.add(provider);
 				}
@@ -65,7 +65,7 @@
 		return matching;
 	}
 	
-	private MOBYProvider providerAt(String uri, Model model)
+	private MOBYService serviceAt(String uri, Model model)
 	{
 		Model providerModel = ModelFactory.createDefaultModel();
 		Resource provider = providerModel.createResource(uri);
@@ -74,7 +74,7 @@
 		
 		try {
 			Parser parser = new Parser(providerModel);
-			return parser.parseProvider();
+			return parser.parseService();
 		} catch (Throwable t) {
 			return null;
 		}

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.java	2005/03/21 21:42:01	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.java	2005/09/14 22:06:55	1.3
@@ -46,7 +46,7 @@
     /**
      * The graph that serves as a template for providers that match.
      */
-    private MOBYProvider queryProvider;
+    private MOBYService queryProvider;
     
     /**
      * Flag indicating which statements should be returned: URI_ONLY,
@@ -65,17 +65,17 @@
      */
     private int lastBnodeNumber;
     
-    public static DiscoveryQuery newMinimalStmtsQuery(MOBYProvider provider)
+    public static DiscoveryQuery newMinimalStmtsQuery(MOBYService provider)
     {
     	return new DiscoveryQuery(provider, MINIMAL_STMTS);
     }
     
-    public static DiscoveryQuery newQueryStmtsQuery(MOBYProvider provider)
+    public static DiscoveryQuery newQueryStmtsQuery(MOBYService provider)
     {
     	return new DiscoveryQuery(provider, QUERY_STMTS);
     }
     
-    public static DiscoveryQuery newReachableStmtsQuery(MOBYProvider provider)
+    public static DiscoveryQuery newReachableStmtsQuery(MOBYService provider)
     {
     	return new DiscoveryQuery(provider, REACHABLE_STMTS);
     }
@@ -87,7 +87,7 @@
      * @param statementsToReturn which statements should be returned: URI_ONLY,
      * QUERY_STMTS_ONLY, or ALL_STMTS (use the static constants on this class).
      */
-    private DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
+    private DiscoveryQuery(MOBYService queryProvider, int statementsToReturn)
     {
     	this.queryProvider = queryProvider;
         this.statementsToReturn = statementsToReturn;
@@ -103,14 +103,14 @@
         lastBnodeNumber = 0;
     }
     
-    public MOBYProviderSet findMatchingGraphs()
+    public MOBYServiceSet findMatchingGraphs()
 	{
         init();
         
         Model dbModel = null;
 		try
 		{
-		    Model queryModel = ((MOBYProvider) queryProvider).getModel();
+		    Model queryModel = ((MOBYService) queryProvider).getJenaModel();
             String queryString = buildQueryString(queryModel);
             StorageManager manager = new StorageManager();
             dbModel = manager.openDBModel();
@@ -128,14 +128,14 @@
 			}
 			results.close();
 			
-			MOBYProviderSet returnSet = new MOBYProviderSet();
+			MOBYServiceSet returnSet = new MOBYServiceSet();
 			
 			for (Iterator it = matching.iterator(); it.hasNext();)
 			{
 				Object next = it.next();
-				MOBYProvider mp = buildGraphModel(dbModel,
+				MOBYService mp = buildGraphModel(dbModel,
 					queryModel, (ResultBinding) next);
-				returnSet.addProvider(mp);
+				returnSet.addService(mp);
 			}
 			
 			return returnSet;
@@ -244,8 +244,9 @@
 	 * @param binding bindings for variables
 	 * @return
 	 */
-	private MOBYProvider buildGraphModel(
+	private MOBYService buildGraphModel(
 		Model dbModel, Model queryModel, ResultBinding binding)
+        throws NonCanonicalException
 	{
 		// Create a default model to return
 		//
@@ -279,7 +280,7 @@
 		// Parse and return a MOBY provider using the adjusted model
 		//
 		Parser parser = new Parser(adjusted);
-		return parser.parseProvider();
+		return parser.parseService();
 	}
 	
 	/**
@@ -319,7 +320,7 @@
 		//
 		try {
 			Statement providerTypeStmt = original.listStatements(
-				null, RDF.type, MOBY.Provider).nextStatement();
+				null, RDF.type, MOBY.Service).nextStatement();
 			minimal.add(providerTypeStmt);
 			
 			Resource subject = providerTypeStmt.getSubject();
@@ -370,7 +371,7 @@
 		//
 		try {
 			Statement providerTypeStmt = original.listStatements(
-				null, RDF.type, MOBY.Provider).nextStatement();
+				null, RDF.type, MOBY.Service).nextStatement();
 			Resource subject = providerTypeStmt.getSubject();
 			Util.addReachableStmts(dbModel, reachable, subject, subject.getURI());
 		}




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