SELECT-based implementation of getIndividualsByVClassURI for SDB

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/IndividualsListingController.java

@@ -25,7 +25,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
 public class IndividualsListingController extends BaseEditController {
 
-    private static final int MAX_INDIVIDUALS = 50;
+    //private static final int MAX_INDIVIDUALS = 50;
 
     public void doGet(HttpServletRequest request, HttpServletResponse response) {
         VitroRequest vrequest = new VitroRequest(request);
@@ -59,7 +59,8 @@ public class IndividualsListingController extends BaseEditController {
         String vclassURI = request.getParameter("VClassURI");
         VClass vc = vcDao.getVClassByURI(vclassURI);
         
-        List inds = dao.getIndividualsByVClassURI(vclassURI,1,MAX_INDIVIDUALS);
+        List inds = dao.getIndividualsByVClassURI(vclassURI);
+        //List inds = dao.getIndividualsByVClassURI(vclassURI,1,MAX_INDIVIDUALS);
 
         ArrayList results = new ArrayList();
         results.add("XX");

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoSDB.java

@@ -71,6 +71,8 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     	return getOntModelSelector().getABoxModel();
     }
     
+    private static final boolean SKIP_INITIALIZATION = true;
+    
     @Override
     public List getIndividualsByVClassURI(String vclassURI, int offset, int quantity ) {
 
@@ -78,7 +80,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
             return null;
         }
         
-        List ents = new ArrayList();
+        List<Individual> ents = new ArrayList<Individual>();
         
         Resource theClass = (vclassURI.indexOf(PSEUDO_BNODE_NS) == 0) 
             ? getOntModel().createResource(new AnonId(vclassURI.split("#")[1]))
@@ -91,54 +93,59 @@ public class IndividualDaoSDB extends IndividualDaoJena {
         		ents.addAll(getIndividualsByVClass(vc));
         	}
         } else {
-        	Model model = null;
-        	try {
     	    DatasetWrapper w = getDatasetWrapper();
     	    Dataset dataset = w.getDataset();
         	dataset.getLock().enterCriticalSection(Lock.READ);
         	try {
         		String query = 
-        	    		"CONSTRUCT " +
+    	    		"SELECT DISTINCT ?ind ?label ?moniker " +
-        	    		"{ ?ind  <" + RDFS.label.getURI() + "> ?ooo. \n" +
+    	    		"WHERE " +
-        	    		   "?ind  a <" + theClass.getURI() + "> . \n" +
-        	    		   "?ind  <" + VitroVocabulary.MONIKER + "> ?moniker \n" +
-        	    		 "} WHERE " +
     	    		 "{ GRAPH ?g { \n" +
     	    		    " ?ind a <" + theClass.getURI() + ">  \n" +
     	    		    "} \n" +
-        	    		 	"OPTIONAL { GRAPH ?h { ?ind  <" + RDFS.label.getURI() + "> ?ooo } }\n" +
+    	    		 	"OPTIONAL { GRAPH ?h { ?ind  <" + RDFS.label.getURI() + "> ?label } }\n" +
     	    		 	"OPTIONAL { GRAPH ?i { ?ind  <" + VitroVocabulary.MONIKER + "> ?moniker } } \n" +
-        	    		 "}";
+    	    		 "} ORDER BY ?label";
-            		model = QueryExecutionFactory.create(QueryFactory.create(query), dataset).execConstruct();
+        		ResultSet rs =QueryExecutionFactory.create(
+        		        QueryFactory.create(query), dataset)
+        		        .execSelect();
+        		Resource res = null;
+        		while (rs.hasNext()) {
+        		    QuerySolution sol = rs.nextSolution();
+        		    Resource currRes = sol.getResource("ind");
+        		    if ((res == null || !res.equals(currRes)) 
+        		            && !currRes.isAnon()) {    		        
+        		        res = currRes;
+        		        Individual ent = new IndividualSDB(currRes.getURI(), 
+                                this.dwf, getWebappDaoFactory(), 
+                                SKIP_INITIALIZATION);
+        		        Literal label = sol.getLiteral("label");
+        		        if (label != null) {
+        		            ent.setName(label.getLexicalForm());
+        		        }
+        		        Literal moniker = sol.getLiteral("moniker");
+        		        if (moniker != null) {
+        		            ent.setMoniker(moniker.getLexicalForm());
+        		        }
+                        ents.add(ent);
+        		    }
+        		}
         	} finally {
         		dataset.getLock().leaveCriticalSection();
         		w.close();
         	} 
-                ResIterator resIt = model.listSubjects();
-                try {
-                    while (resIt.hasNext()) {
-                        Resource ind = resIt.nextResource();
-                        if (!ind.isAnon()) {
-                            //Individual indd = new IndividualImpl(ind.getURI());
-                            //indd.setLocalName(ind.getLocalName());
-                            //indd.setName(ind.getLocalName());
-                            //ents.add(indd);
-                        	ents.add(new IndividualSDB(ind.getURI(), this.dwf, getWebappDaoFactory(), model));
         }
-                    }
-                } finally {
-                    resIt.close();
-                }
-        	} finally {
-        	    if (model != null && !model.isClosed()) {
-        	        model.close();
-        	    }
-        	}
-        }
-     
         
         java.util.Collections.sort(ents);
         
+        if (quantity > 0 && offset > 0) {
+            List<Individual> sublist = new ArrayList<Individual>();
+            for (int i = offset - 1; i < ((offset - 1) + quantity); i++) {
+                sublist.add(ents.get(i));
+            }
+            return sublist;
+        }
+        
         return ents;
 
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualSDB.java

@@ -97,26 +97,22 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	
     	OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, model);
     	this.ind = ontModel.createOntResource(individualURI);  
-    	
+    	setUpURIParts(ind);
-    	if (ind != null) {
-	        if (ind.isAnon()) {
-	        	this.setNamespace(VitroVocabulary.PSEUDO_BNODE_NS);
-	        	this.setLocalName(ind.getId().toString());
-	        } else {
-	        	this.URI = ind.getURI();
-	        	this.namespace = ind.getNameSpace();
-	        	this.localName = ind.getLocalName();
-	        }
-    	} else if (individualURI != null) {
-    		log.warn("Null individual returned for URI " + individualURI);
-    	}
         this.webappDaoFactory = wadf;
     }
     
-    public IndividualSDB(String individualURI, DatasetWrapperFactory datasetWrapperFactory, WebappDaoFactoryJena wadf) {
+    public IndividualSDB(String individualURI, 
+            DatasetWrapperFactory datasetWrapperFactory, 
+            WebappDaoFactoryJena wadf,
+            boolean skipInitialization) {
     	this.individualURI = individualURI;
     	this.dwf = datasetWrapperFactory;
     	
+    	if (skipInitialization) {
+            OntModel ontModel = ModelFactory.createOntologyModel(
+                    OntModelSpec.OWL_MEM);
+            this.ind = ontModel.createOntResource(individualURI);  
+    	} else {
         	DatasetWrapper w = getDatasetWrapper();
         	Dataset dataset = w.getDataset();
         	try {
@@ -142,7 +138,20 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         	OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, model);
         	
         	this.ind = ontModel.createOntResource(individualURI);  
+    	}
+    	setUpURIParts(ind);
+        this.webappDaoFactory = wadf;
+    }
     
+    private static final boolean SKIP_INITIALIZATION = true;
+    
+    public IndividualSDB(String individualURI, 
+            DatasetWrapperFactory datasetWrapperFactory, 
+            WebappDaoFactoryJena wadf) {
+        this(individualURI, datasetWrapperFactory, wadf, !SKIP_INITIALIZATION);
+    }
+    
+    private void setUpURIParts(OntResource ind) {
         if (ind != null) {
             if (ind.isAnon()) {
                 this.setNamespace(VitroVocabulary.PSEUDO_BNODE_NS);
@@ -155,7 +164,6 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         } else if (individualURI != null) {
             log.warn("Null individual returned for URI " + individualURI);
         }
-        this.webappDaoFactory = wadf;
     }
 
     private DatasetWrapper getDatasetWrapper() {
@@ -1016,21 +1024,30 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     }
     
     private List<VClass> getMyVClasses(boolean direct) {
-        long mstart = System.currentTimeMillis();
 		List<VClass> vClassList = new ArrayList<VClass>(); 
-		//this.dataset.getLock().enterCriticalSection(Lock.READ);
+		Model tempModel = null;
-		//Model tempModel = ModelFactory.createDefaultModel();
+		if (ind.getModel().size() > 0) {
-		Model tempModel = ind.getModel();
+		    tempModel = ind.getModel();
-		//try {
+		}
-			//String getTypes = 
+		else {		
-        	//	"CONSTRUCT{ <" + this.individualURI + "> <" + RDF.type + "> ?types }\n" +
+			String getTypes = 
-        	//	"WHERE{ GRAPH " + ((true) ? "<http://vitro.mannlib.cornell.edu/default/vitro-kb-2>" : "?g") 
+        		"CONSTRUCT{ <" + this.individualURI + "> <" + RDF.type + "> ?types }\n" +
-        	//	+ " { <" + this.individualURI +"> <" +RDF.type+ "> ?types \n" +
+        		"WHERE{ GRAPH " + ((true) ? "<http://vitro.mannlib.cornell.edu/default/vitro-kb-2>" : "?g") 
-        	//			"} } \n";
+        		+ " { <" + this.individualURI +"> <" +RDF.type+ "> ?types \n" +
-        	//long startTime = System.currentTimeMillis();
+        				"} } \n";        	
-        	//tempModel = QueryExecutionFactory.create(QueryFactory.create(getTypes), dataset).execConstruct();
+        	DatasetWrapper w = getDatasetWrapper();
-        	//System.out.println((System.currentTimeMillis() - startTime));
+        	Dataset dataset = w.getDataset();
-        	StmtIterator stmtItr = tempModel.listStatements((Resource) null, RDF.type, (RDFNode) null);
+        	dataset.getLock().enterCriticalSection(Lock.READ);
+        	try {
+        	    tempModel = QueryExecutionFactory.create(
+        	            QueryFactory.create(getTypes), dataset).execConstruct();
+        	} finally {
+        	    dataset.getLock().leaveCriticalSection();
+        	    w.close();
+        	}        	
+		}
+    	StmtIterator stmtItr = tempModel.listStatements(
+    	        (Resource) null, RDF.type, (RDFNode) null);
     	LinkedList<String> list = new LinkedList<String>();
     	while(stmtItr.hasNext()){
     		Statement stmt = stmtItr.nextStatement();
@@ -1058,14 +1075,15 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         		}while(done.contains(currentType));
         		
         		if(directTypes)
-        			break;                 // check to see if its all over otherwise start comparing
+        			break; 
+        		    // check to see if it's all over otherwise start comparing
         		else
         	    itr = list.listIterator();	
         		
             	while(itr.hasNext()){
             		String nextType = itr.next();
-        	    if(checkSubClass.isSubClassOf(currentType, nextType) && !currentType.equalsIgnoreCase(nextType)){
+            	    if(checkSubClass.isSubClassOf(currentType, nextType) 
-        	    	//System.out.println(currentType + " is subClassOf " + nextType);
+            	            && !currentType.equalsIgnoreCase(nextType)){
             	    	itr.remove();
             	    }
             	}
@@ -1076,30 +1094,31 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	
     	/* Loop for comparing ends here */
 	    Iterator<String> typeIt = list.iterator();
-			try {
+		
 		for (Iterator it = typeIt; it.hasNext();) {
-					Resource type = ResourceFactory.createResource(it.next().toString());
+			Resource type = ResourceFactory
-					String typeURI = (!type.isAnon()) ? type.getURI() : VitroVocabulary.PSEUDO_BNODE_NS + type.getId().toString();
+			        .createResource(it.next().toString());
-					if (type.getNameSpace() == null || (!webappDaoFactory.getNonuserNamespaces().contains(type.getNameSpace())) ) {
+			String typeURI = (!type.isAnon()) 
-						VClass vc = webappDaoFactory.getVClassDao().getVClassByURI(type.getURI());
+			        ? type.getURI() 
+			        : VitroVocabulary.PSEUDO_BNODE_NS 
+			                + type.getId().toString();
+			if (type.getNameSpace() == null || 
+			        (!webappDaoFactory.getNonuserNamespaces()
+			                .contains(type.getNameSpace())) ) {
+				VClass vc = webappDaoFactory.getVClassDao()
+				        .getVClassByURI(type.getURI());
 				if (vc != null) {
 					vClassList.add(vc);
 				}
 			}
+		}
 
-				}
-			} finally {
-				//typeIt.close();
-			}
-		//} finally {
-		//	tempModel.close();
-		//	this.dataset.getLock().leaveCriticalSection();
-		//}
 		try {
 			Collections.sort(vClassList);
-		} catch (Exception e) {}
+		} catch (Exception e) {
+		    log.error("Unable to sort VClass list", e);
+		}
 		
-		//System.out.println("Overall: " + (System.currentTimeMillis() - mstart));
 		return vClassList;
 	}