[MOBY-guts] biomoby commit

Gary Schiltz gss at pub.open-bio.org
Tue Nov 1 16:28:12 UTC 2005


gss
Tue Nov  1 11:28:11 EST 2005
Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv9543/src/org/semanticmoby/ref/tools

Modified Files:
	InvocationBroker.java KeywordFinder.java KeywordList.java 
	URIInvestigator.java KeywordQuery.java DiscoveryQuery.java 
Log Message:
Changes to reflect change of name from Service to Resource

s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools InvocationBroker.java,1.5,1.6 KeywordFinder.java,1.6,1.7 KeywordList.java,1.3,1.4 URIInvestigator.java,1.6,1.7 KeywordQuery.java,1.6,1.7 DiscoveryQuery.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.java	2005/10/09 01:11:21	1.5
+++ /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.java	2005/11/01 16:28:11	1.6
@@ -9,8 +9,6 @@
 
 import org.semanticmoby.http.*;
 
-import org.semanticmoby.parser.*;
-
 import org.semanticmoby.vocabulary.MOBY;
 
 import java.io.*;
@@ -23,7 +21,7 @@
 
 /**
  * This class is used to invoke and display the results of Semantic
- * MOBY services.
+ * MOBY resources.
  */
 public class InvocationBroker {
 
@@ -54,49 +52,49 @@
         this.response     = response;
     }
 
-    private String rdfxmlString(MOBYService service) {
+    private String rdfxmlString(MOBYResource resource) {
 
         StringWriter writer = new StringWriter();
-        service.getJenaModel().write(writer);
+        resource.getJenaModel().write(writer);
 
         return writer.toString();
     }
 
 
-    private String n3String(MOBYService service) {
+    private String n3String(MOBYResource resource) {
 
         StringWriter writer = new StringWriter();
-        service.getJenaModel().write(writer, "N3");
+        resource.getJenaModel().write(writer, "N3");
 
         return writer.toString();
     }
 
 
     /**
-     * Handle a request to invoke a service at a given URI.
-     * If the service requires inputs, and the service has
+     * Handle a request to invoke a resource at a given URI.
+     * If the resource requires inputs, and the resource has
      * a valid inputURI property, redirect to the URI that is
-     * the value of the property. If the service requires input
+     * the value of the property. If the resource requires input
      * and has no inputURI property, then build a simple input
      * GUI from scratch.
      * <br><br>
-     * If the service doesn't require any inputs, then do an HTTP
-     * POST to the service URI, passing the graph as a parameter.
+     * If the resource doesn't require any inputs, then do an HTTP
+     * POST to the resource URI, passing the graph as a parameter.
      */
-    public void invokeURI(String serviceURI) {
+    public void invokeURI(String resourceURI) {
 
-        // Try to retrieve and parse a service graph from the URI;
+        // Try to retrieve and parse a resource graph from the URI;
         // on failure, print a message and return.
         //
-        MOBYService service = null;
+        MOBYResource resource = null;
 
         try {
 
             Model model = ModelFactory.createDefaultModel();
-            model.read(serviceURI);
+            model.read(resourceURI);
 
             Parser parser = new Parser(model);
-            service = parser.parseService();
+            resource = parser.parseResource();
         } catch (Throwable t) {
 
             t.printStackTrace();
@@ -104,18 +102,18 @@
             return;
         }
 
-        if (requiresInputs(service)) {
+        if (requiresInputs(resource)) {
 
-            // Since the service requires input, either redirect to its
+            // Since the resource requires input, either redirect to its
             // inputURI (if it has one) or build a simple GUI for it.
             //
             try {
 
-                String inputURI = getInputURI(service);
+                String inputURI = getInputURI(resource);
 
                 if (inputURI == null) {
 
-                    buildInputGUI(service);
+                    buildInputGUI(resource);
                 } else {
 
                     // Do an HTTP HEAD request to find out if the
@@ -131,24 +129,24 @@
                         response.sendRedirect(inputURI);
                     } else {
 
-                        buildInputGUI(service);
+                        buildInputGUI(resource);
                     }
                 }
             } catch (Throwable t) {
 
                 t.printStackTrace();
-                buildInputGUI(service);
+                buildInputGUI(resource);
             }
         } else  // No input required
          {
 
             try {
 
-                // Invoke the service
+                // Invoke the resource
                 //
-                HTTPRequest rqst = HTTPRequest.newPostRequest(service.getURI());
+                HTTPRequest rqst = HTTPRequest.newPostRequest(resource.getURI());
                 rqst.addParameter(MOBY.GRAPH_PARAMETER_NAME,
-                                  rdfxmlString(service));
+                                  rdfxmlString(resource));
 
                 HTTPResponse resp = rqst.send();
 
@@ -165,16 +163,16 @@
                     model.read(resp.getBodyAsStream(), "");
 
                     Parser      parser         = new Parser(model);
-                    MOBYService resultsService = parser.parseService();
+                    MOBYResource resultsResource = parser.parseResource();
 
-                    String      outputURI = getOutputURI(resultsService);
+                    String      outputURI = getOutputURI(resultsResource);
 
                     if (outputURI == null) {
 
                         // No output URI was specified, so build a generic
                         // display of the results
                         //
-                        buildOutputGUI(resultsService);
+                        buildOutputGUI(resultsResource);
                     } else {
 
                         // There is an output URI. Conceptually, what we want
@@ -193,7 +191,7 @@
                             //
                             rqst = HTTPRequest.newPostRequest(outputURI);
 
-                            String graphString = rdfxmlString(resultsService);
+                            String graphString = rdfxmlString(resultsResource);
                             rqst.addParameter(MOBY.GRAPH_PARAMETER_NAME,
                                               graphString);
                             resp = rqst.send();
@@ -210,12 +208,12 @@
                                 // The output URI returned a status other than
                                 // 200 OK, so fall back to a default output GUI
                                 //
-                                buildOutputGUI(resultsService);
+                                buildOutputGUI(resultsResource);
                             }
                         } catch (Throwable t) {
 
                             t.printStackTrace();
-                            buildOutputGUI(resultsService);
+                            buildOutputGUI(resultsResource);
                         }
                     }
                 } else {
@@ -252,13 +250,13 @@
     }
 
 
-    private String getInputURI(MOBYService service) {
+    private String getInputURI(MOBYResource resource) {
 
         try {
 
-            Model     model = service.getJenaModel();
+            Model     model = resource.getJenaModel();
             Statement stmt =
-                model.getProperty(service.getResource(), MOBY.inputURI);
+                model.getProperty(resource.getResource(), MOBY.inputURI);
 
             if (stmt != null) {
 
@@ -276,13 +274,13 @@
     }
 
 
-    private String getOutputURI(MOBYService service) {
+    private String getOutputURI(MOBYResource resource) {
 
         try {
 
-            Model     model = service.getJenaModel();
+            Model     model = resource.getJenaModel();
             Statement stmt =
-                model.getProperty(service.getResource(), MOBY.outputURI);
+                model.getProperty(resource.getResource(), MOBY.outputURI);
 
             return stmt.getString();
         } catch (Throwable t) {
@@ -294,30 +292,30 @@
     }
 
 
-    public void buildInputGUI(MOBYService service) {
+    public void buildInputGUI(MOBYResource resource) {
 
         // error message
     }
 
 
-    public void buildOutputGUI(MOBYService service)
+    public void buildOutputGUI(MOBYResource resource)
                         throws IOException, ServletException {
 
         HttpSession session = request.getSession(true);
         session.setAttribute("n3Graph",
-                             n3String(service).replaceAll("<", "&lt;")
+                             n3String(resource).replaceAll("<", "&lt;")
                                  .replaceAll(">", "&gt;").replaceAll("\"",
                                                                      "&quot;"));
         session.setAttribute("rdfxmlGraph",
-                             rdfxmlString(service).replaceAll("<", "&lt;")
+                             rdfxmlString(resource).replaceAll("<", "&lt;")
                                  .replaceAll(">", "&gt;").replaceAll("\"",
                                                                      "&quot;"));
         redirectToPage("/jsp/display.jsp");
     }
 
 
-    private boolean requiresInputs(MOBYService service) {
+    private boolean requiresInputs(MOBYResource resource) {
 
-        return getInputURI(service) != null;
+        return getInputURI(resource) != null;
     }
 }

===================================================================
RCS file: /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.java	2005/10/28 04:12:27	1.6
+++ /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.java	2005/11/01 16:28:11	1.7
@@ -6,8 +6,6 @@
 
 import org.semanticmoby.graph.*;
 
-import org.semanticmoby.parser.*;
-
 import org.semanticmoby.vocabulary.MOBY;
 
 import java.util.*;
@@ -16,15 +14,15 @@
 public class KeywordFinder {
 
     /**
-     * The MOBY service for which to find keywords
+     * The MOBY resource for which to find keywords
      */
-    private MOBYService service;
+    private MOBYResource resource;
 
     /**
-     * The underlying Jena model on which the MOBY service
+     * The underlying Jena model on which the MOBY resource
      * is based
      */
-    private Model serviceModel;
+    private Model resourceModel;
 
     /**
      * A keyword list object to hold the keywords that are
@@ -33,17 +31,17 @@
     private KeywordList keywords = null;
 
     /**
-     * Construct an instance for the given service and model
+     * Construct an instance for the given resource and model
      */
-    public KeywordFinder(MOBYService service) {
+    public KeywordFinder(MOBYResource resource) {
 
-        this.service          = service;
-        this.serviceModel     = service.getJenaModel();
+        this.resource          = resource;
+        this.resourceModel     = resource.getJenaModel();
     }
 
     /**
      * Retrieve, if necessary, and return the keywords associated
-     * with the service.
+     * with the resource.
      */
     public KeywordList getKeywords() throws Exception {
 
@@ -58,20 +56,20 @@
 
 
     /**
-     * Collect keywords for the service
+     * Collect keywords for the resource
      */
-    private void collectKeywords() {  // Add keywords from classes that the service is asserted to
+    private void collectKeywords() {  // Add keywords from classes that the resource is asserted to
 
-        // be an instance of (i.e. service rdf:type <some type>)
+        // be an instance of (i.e. resource rdf:type <some type>)
         //
-        Resource res = service.getResource();
+        Resource res = resource.getResource();
 
-        keywords.addServiceKeywords(getKeywordsFor(res));
+        keywords.addResourceKeywords(getKeywordsFor(res));
 
         // Add keywords from subjects and objects of each
         // operatesOn subgraph
         //
-        for (Iterator it = service.getOperatesOn(); it.hasNext();) {
+        for (Iterator it = resource.getOperatesOn(); it.hasNext();) {
 
             MOBYGraphNode node = (MOBYGraphNode) it.next();
 
@@ -176,7 +174,7 @@
         // Iterate over the resource's rdf:type properties
         //
         StmtIterator it =
-            serviceModel.listStatements(res, RDF.type, (RDFNode) null);
+            resourceModel.listStatements(res, RDF.type, (RDFNode) null);
 
         while (it.hasNext()) {
 

===================================================================
RCS file: /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordList.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordList.java	2005/10/09 01:11:21	1.3
+++ /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordList.java	2005/11/01 16:28:11	1.4
@@ -7,25 +7,25 @@
 
 public class KeywordList {
 
-    private Set serviceKeywords = new HashSet();
+    private Set resourceKeywords = new HashSet();
     private Set subjectKeywords = new HashSet();
     private Set objectKeywords  = new HashSet();
 
-    public void addServiceKeyword(String keyword) {
+    public void addResourceKeyword(String keyword) {
 
-        serviceKeywords.add(keyword);
+        resourceKeywords.add(keyword);
     }
 
 
-    public void addServiceKeywords(List keywords) {
+    public void addResourceKeywords(List keywords) {
 
-        serviceKeywords.addAll(keywords);
+        resourceKeywords.addAll(keywords);
     }
 
 
-    public Iterator getServiceKeywords() {
+    public Iterator getResourceKeywords() {
 
-        return serviceKeywords.iterator();
+        return resourceKeywords.iterator();
     }
 
 

===================================================================
RCS file: /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.java	2005/10/28 04:12:27	1.6
+++ /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.java	2005/11/01 16:28:11	1.7
@@ -9,8 +9,6 @@
 
 import org.semanticmoby.http.*;
 
-import org.semanticmoby.parser.*;
-
 import org.semanticmoby.ref.tools.db.*;
 
 import org.semanticmoby.tools.*;
@@ -46,15 +44,15 @@
      * The URL that is to be investigated for possible inclusion in the
      * metadata repository.
      */
-    private String serviceURL;
+    private String resourceURL;
 
     /**
      * Create an instance for investingating the given resource URL
      * @param resourceURL the URL to investigate
      */
-    private URIInvestigator(String serviceURL) {
+    private URIInvestigator(String resourceURL) {
 
-        this.serviceURL = serviceURL;
+        this.resourceURL = resourceURL;
     }
 
     /**
@@ -64,19 +62,19 @@
      * investigated, then this call is a NO-OP.
      * @param resourceURL the URL to investigate
      */
-    public synchronized static void investigate(String serviceURL) {
+    public synchronized static void investigate(String resourceURL) {
 
         synchronized (instances) {
 
-            if (instances.get(serviceURL) != null) {
+            if (instances.get(resourceURL) != null) {
 
-                syncLog.warn("Already investigating " + serviceURL);
+                syncLog.warn("Already investigating " + resourceURL);
 
                 return;
             }
 
-            URIInvestigator investigator = new URIInvestigator(serviceURL);
-            instances.put(serviceURL, investigator);
+            URIInvestigator investigator = new URIInvestigator(resourceURL);
+            instances.put(resourceURL, investigator);
             investigator.start();
         }
     }
@@ -121,7 +119,7 @@
             //
             synchronized (instances) {
 
-                instances.remove(serviceURL);
+                instances.remove(resourceURL);
             }
         }
     }
@@ -152,13 +150,13 @@
 
         try {
 
-            lastModifiedDate      = manager.getLastModifiedDate(serviceURL);
+            lastModifiedDate      = manager.getLastModifiedDate(resourceURL);
             alreadyRegistered     = (lastModifiedDate != null);
         } catch (StorageException e) {
 
             e.printStackTrace();
             syncLog.error("Couldn't check for last modified date of resource URL " +
-                          serviceURL, e);
+                          resourceURL, e);
             e.printStackTrace();
 
             return;
@@ -166,7 +164,7 @@
 
         // Helper class for making the HTTP GET call
         //
-        HTTPRequest request = HTTPRequest.newGetRequest(serviceURL);
+        HTTPRequest request = HTTPRequest.newGetRequest(resourceURL);
 
         // If there was a last modified date, then request that the graph only
         // be sent if it has been modified since that date
@@ -190,7 +188,7 @@
         } catch (HTTPException e) {
 
             e.printStackTrace();
-            syncLog.warn("Couldn't reach suggested resource " + serviceURL);
+            syncLog.warn("Couldn't reach suggested resource " + resourceURL);
 
             return;
         }
@@ -202,7 +200,7 @@
                 // The resource has not been modified since it was
                 // registered, so there is nothing to do but log a message.
                 //
-                syncLog.info("IN-SYNC : " + serviceURL);
+                syncLog.info("IN-SYNC : " + resourceURL);
 
                 break;
 
@@ -214,10 +212,10 @@
                 if (alreadyRegistered) {
 
                     deregisterResource(manager, true);
-                    syncLog.info("ALREADY REGISTERED : " + serviceURL);
+                    syncLog.info("ALREADY REGISTERED : " + resourceURL);
                 } else {
 
-                    syncLog.info("IGNORED : " + serviceURL + " doesn't exist");
+                    syncLog.info("IGNORED : " + resourceURL + " doesn't exist");
                 }
 
                 break;
@@ -245,7 +243,7 @@
                     //
                     e.printStackTrace();
                     syncLog.warn("Unable to get Last-Modified date for " +
-                                 serviceURL + "; using current date");
+                                 resourceURL + "; using current date");
                     lastModifiedDate = new Date();
                 } catch (Throwable t) {
 
@@ -254,7 +252,7 @@
                     //
                     t.printStackTrace();
                     syncLog.warn("Unparsable Last-Modified date " + "(\"" +
-                                 dateString + "\") for " + serviceURL +
+                                 dateString + "\") for " + resourceURL +
                                  "; ignoring");
                 }
 
@@ -270,48 +268,48 @@
                 } catch (HTTPException e) {
 
                     e.printStackTrace();
-                    syncLog.error("Couldn't retrieve graph from " + serviceURL);
+                    syncLog.error("Couldn't retrieve graph from " + resourceURL);
 
                     return;
                 }
 
-                MOBYService service = null;
+                MOBYResource resource = null;
 
                 try {
 
                     Parser parser =
                         Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
-                    service = parser.parseService();
+                    resource = parser.parseResource();
                 } catch (Throwable t) {
 
                     t.printStackTrace();
                     System.err.println("Parse error: " + t);
                 }
 
-                if (service == null) {
+                if (resource == null) {
 
                     // De-register the resource, printing a removal message if
-                    // a service couldn't be parsed
-                    deregisterResource(manager, service == null);
-                    syncLog.error("Couldn't parse a resource from graph at " + serviceURL);
+                    // a resource couldn't be parsed
+                    deregisterResource(manager, resource == null);
+                    syncLog.error("Couldn't parse a resource from graph at " + resourceURL);
 
-                // If a service was parsed, then register it
+                // If a resource was parsed, then register it
                 } else {
 
                     try {
 
-                        manager.registerResource(service, lastModifiedDate);
+                        manager.registerResource(resource, lastModifiedDate);
 
                         // Log a message about successfully registering the graph:
                         //
                         syncLog.info((
                                          alreadyRegistered ? "UPDATED : "
                                                            : "ADDED   : "
-                                     ) + serviceURL);
+                                     ) + resourceURL);
                     } catch (Exception e) {
 
                         e.printStackTrace();
-                        syncLog.error("Error storing graph for " + serviceURL, e);
+                        syncLog.error("Error storing graph for " + resourceURL, e);
                     }
                 }
 
@@ -322,7 +320,7 @@
                 // Log a message about the failed attempt to contact the URL
                 //
                 syncLog.error("Status " + status + " received while trying " +
-                              "to contact resource " + serviceURL);
+                              "to contact resource " + resourceURL);
 
                 break;
         }
@@ -333,16 +331,16 @@
 
         try {
 
-            manager.deregisterResource(serviceURL);
+            manager.deregisterResource(resourceURL);
 
             if (removing) {
 
-                syncLog.info("REMOVED : " + serviceURL);
+                syncLog.info("REMOVED : " + resourceURL);
             }
         } catch (StorageException e) {
 
             e.printStackTrace();
-            syncLog.error("Unable to de-register resource " + serviceURL, e);
+            syncLog.error("Unable to de-register resource " + resourceURL, e);
         }
     }
 }

===================================================================
RCS file: /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.java	2005/10/28 04:12:27	1.6
+++ /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.java	2005/11/01 16:28:11	1.7
@@ -5,8 +5,6 @@
 
 import org.semanticmoby.graph.*;
 
-import org.semanticmoby.parser.Parser;
-
 import org.semanticmoby.ref.tools.db.*;
 
 import org.semanticmoby.tools.Util;
@@ -50,7 +48,7 @@
             while (rs.next()) {
 
                 String      uri      = rs.getString("resource_uri");
-                MOBYService resource = serviceAt(uri, model);
+                MOBYResource resource = resourceAt(uri, model);
 
                 if (resource != null) {
 
@@ -75,7 +73,7 @@
     }
 
 
-    private MOBYService serviceAt(String uri, Model model) {
+    private MOBYResource resourceAt(String uri, Model model) {
 
         Model    resourceModel = ModelFactory.createDefaultModel();
         Resource resource = resourceModel.createResource(uri);
@@ -86,7 +84,7 @@
 
             Parser parser = new Parser(resourceModel);
 
-            return parser.parseService();
+            return parser.parseResource();
         } catch (Throwable t) {
 
             t.printStackTrace();

===================================================================
RCS file: /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.java	2005/10/28 04:12:27	1.6
+++ /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.java	2005/11/01 16:28:11	1.7
@@ -10,8 +10,6 @@
 
 import org.semanticmoby.graph.*;
 
-import org.semanticmoby.parser.*;
-
 import org.semanticmoby.ref.tools.db.*;
 
 import org.semanticmoby.tools.Util;
@@ -53,7 +51,7 @@
     /**
      * The graph that serves as a template for resources that match.
      */
-    private MOBYService queryResource;
+    private MOBYResource queryResource;
 
     /**
      * Flag indicating which statements should be returned: URI_ONLY,
@@ -79,25 +77,25 @@
      * @param statementsToReturn which statements should be returned: URI_ONLY,
      * QUERY_STMTS_ONLY, or ALL_STMTS (use the static constants on this class).
      */
-    private DiscoveryQuery(MOBYService queryResource, int statementsToReturn) {
+    private DiscoveryQuery(MOBYResource queryResource, int statementsToReturn) {
 
         this.queryResource          = queryResource;
         this.statementsToReturn     = statementsToReturn;
     }
 
-    public static DiscoveryQuery newMinimalStmtsQuery(MOBYService resource) {
+    public static DiscoveryQuery newMinimalStmtsQuery(MOBYResource resource) {
 
         return new DiscoveryQuery(resource, MINIMAL_STMTS);
     }
 
 
-    public static DiscoveryQuery newQueryStmtsQuery(MOBYService resource) {
+    public static DiscoveryQuery newQueryStmtsQuery(MOBYResource resource) {
 
         return new DiscoveryQuery(resource, QUERY_STMTS);
     }
 
 
-    public static DiscoveryQuery newReachableStmtsQuery(MOBYService resource) {
+    public static DiscoveryQuery newReachableStmtsQuery(MOBYResource resource) {
 
         return new DiscoveryQuery(resource, REACHABLE_STMTS);
     }
@@ -114,7 +112,7 @@
     }
 
 
-    public MOBYServiceSet findMatchingGraphs() {
+    public MOBYResourceSet findMatchingGraphs() {
 
         init();
 
@@ -123,7 +121,7 @@
         try {
 
             Model          queryModel =
-                ((MOBYService) queryResource).getJenaModel();
+                ((MOBYResource) queryResource).getJenaModel();
             String         queryString = buildQueryString(queryModel);
             StorageManager manager     = new StorageManager();
             dbModel = manager.openDBModel();
@@ -142,14 +140,14 @@
 
             results.close();
 
-            MOBYServiceSet returnSet = new MOBYServiceSet();
+            MOBYResourceSet returnSet = new MOBYResourceSet();
 
             for (Iterator it = matching.iterator(); it.hasNext();) {
 
                 Object      next = it.next();
-                MOBYService mp =
+                MOBYResource mp =
                     buildGraphModel(dbModel, queryModel, (ResultBinding) next);
-                returnSet.addService(mp);
+                returnSet.addResource(mp);
             }
 
             return returnSet;
@@ -273,7 +271,7 @@
      * @param binding bindings for variables
      * @return
      */
-    private MOBYService buildGraphModel(Model dbModel, Model queryModel,
+    private MOBYResource buildGraphModel(Model dbModel, Model queryModel,
                                         ResultBinding binding)
                                  throws NonCanonicalException {
 
@@ -313,7 +311,7 @@
         //
         Parser parser = new Parser(adjusted);
 
-        return parser.parseService();
+        return parser.parseResource();
     }
 
 
@@ -361,7 +359,7 @@
         try {
 
             Statement resourceTypeStmt =
-                original.listStatements(null, RDF.type, MOBY.Service)
+                original.listStatements(null, RDF.type, MOBY.Resource)
                         .nextStatement();
             minimal.add(resourceTypeStmt);
 
@@ -433,7 +431,7 @@
         try {
 
             Statement resourceTypeStmt =
-                original.listStatements(null, RDF.type, MOBY.Service)
+                original.listStatements(null, RDF.type, MOBY.Resource)
                         .nextStatement();
             Resource  subject = resourceTypeStmt.getSubject();
             Util.addReachableStmts(dbModel, reachable, subject, subject.getURI());




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