NIHVIVO-3516 fixed merge tool so it doesn't strand triples in a graph named with SDB's union URI

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java

@@ -80,6 +80,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetup;
 import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestWorkflowProcessor;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.WorkflowOntology;
@@ -621,23 +622,25 @@ public class JenaIngestController extends BaseEditController {
           if(uri1!=null){
               JenaIngestUtils utils = new JenaIngestUtils();
               /*
-               * get baseOnt, Ont and infOnt models
+               * get baseOnt and infOnt models
                */
-              OntModel baseOntModel = (OntModel) getServletContext().getAttribute("baseOntModel");
+              OntModel baseOntModel = ModelContext.getBaseOntModel(
-              OntModel ontModel = (OntModel)
+                      getServletContext());
-              getServletContext().getAttribute("jenaOntModel");
+              OntModel tboxOntModel = ModelContext.getUnionOntModelSelector(
-              OntModel infOntModel = (OntModel)
+                      getServletContext()).getTBoxModel();
-              getServletContext().getAttribute(JenaBaseDao.INFERENCE_ONT_MODEL_ATTRIBUTE_NAME);
+              
               /*
                * calling method that does the merge operation.
                */
-              String result = utils.doMerge(uri1,uri2,baseOntModel,ontModel,infOntModel,usePrimaryLabelOnly);
+              MergeResult result = utils.doMerge(
-              vreq.getSession().setAttribute("leftoverModel", utils.getLeftOverModel());
+                      uri1, uri2, baseOntModel, tboxOntModel, usePrimaryLabelOnly);
-              vreq.setAttribute("result",result);
+              
-              vreq.setAttribute("title","Merge Resources");
+              vreq.getSession().setAttribute(
-              vreq.setAttribute("bodyJsp",MERGE_RESULT);
+                      "leftoverModel", result.getLeftoverModel());
-          }
+              vreq.setAttribute("result", result);
-          else{
+              vreq.setAttribute("title", "Merge Resources");
+              vreq.setAttribute("bodyJsp", MERGE_RESULT);
+          } else{
               vreq.setAttribute("title","Merge Resources");
               vreq.setAttribute("bodyJsp",MERGE_RESOURCES);  
           }
@@ -1192,7 +1195,7 @@ public class JenaIngestController extends BaseEditController {
             ontModel.leaveCriticalSection();
         }
         if(!namespacePresent){
-            result = "0 resource renamed";
+            result = "no resources renamed";
             return result;
         }    
         for( String oldURIStr : urisToChange){

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaIngestUtils.java

@@ -2,7 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.utils.jena;
 
-import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -16,15 +15,12 @@ import java.util.Random;
 import java.util.Set;
 import java.util.regex.Pattern;
 
-import javax.servlet.http.HttpServletRequest;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.openrdf.model.vocabulary.RDFS;
 
+import com.hp.hpl.jena.ontology.FunctionalProperty;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
-import com.hp.hpl.jena.ontology.OntProperty;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -41,11 +37,11 @@ import com.hp.hpl.jena.util.ResourceUtils;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
 
 public class JenaIngestUtils {
 
@@ -591,132 +587,151 @@ public class JenaIngestUtils {
         }
     }
 
-	public String doMerge(String uri1,String uri2,OntModel baseOntModel,OntModel ontModel,OntModel infOntModel,String usePrimaryLabelOnly){
+    public class MergeResult {
+        private String resultText;
+        private Model leftoverModel;
+
+        public MergeResult() {}
+
+        public MergeResult(String resultText, Model leftoverModel) {
+            this.resultText = resultText;
+            this.leftoverModel = leftoverModel;
+        }
+
+        public void setResultText(String resultText) {
+            this.resultText = resultText;
+        }
+
+        public String getResultText() {
+            return this.resultText;
+        }
+
+        public void setLeftoverModel(Model leftoverModel) {
+            this.leftoverModel = leftoverModel;
+        }
+
+        public Model getLeftoverModel() {
+            return this.leftoverModel;
+        }    
+    }
+
+    public MergeResult doMerge(String uri1, String uri2, OntModel baseOntModel, 
+            OntModel tboxOntModel, String usePrimaryLabelOnly){
 
         boolean functionalPresent = false;
+
         Resource res1 = baseOntModel.getResource(uri1); // primary resource
+        Model res1Model = ModelFactory.createDefaultModel();        
         Resource res2 = baseOntModel.getResource(uri2); // secondary resource
-		String result = null;
+        Model res2Model = ModelFactory.createDefaultModel();
-		baseOntModel.enterCriticalSection(Lock.WRITE);
 
-		/*
+        // get statements of both the resources
-		 * get statements of both the resources
+        baseOntModel.enterCriticalSection(Lock.READ);
-		 */
+        try {        
-		StmtIterator stmtItr1 = baseOntModel.listStatements(res1,(Property)null,(RDFNode)null);
+            res1Model.add(
-		StmtIterator stmtItr2 = baseOntModel.listStatements(res2,(Property)null,(RDFNode)null);
+                    baseOntModel.listStatements(res1, (Property)null, (RDFNode)null));
-		StmtIterator stmtItr3 = baseOntModel.listStatements((Resource)null,(Property)null,(RDFNode)res2);
+            res2Model.add(
+                    baseOntModel.listStatements(res2, (Property)null, (RDFNode)null));
+            res2Model.add(
+                    baseOntModel.listStatements(
+                            (Resource)null, (Property)null, (RDFNode)res2));
+        } finally {
+            baseOntModel.leaveCriticalSection();
+        }
 
-		/*
+        // if primary resource has no statements, return
-		 * if primary resource has no statements, return
+        if (res1Model.isEmpty()){
-		 */
+            return new MergeResult("resource 1 not present", null);
-		if(!stmtItr1.hasNext()){
+        } else if(res2Model.isEmpty()){
-			result = "resource 1 not present";
+            return new MergeResult("resource 2 not present", null);
-			res1.removeAll((Property)null);
-			baseOntModel.leaveCriticalSection();
-			return result;
-		}
-		/*
-		 * if secondary resource has no statements, return
-		 */
-		else if(!stmtItr2.hasNext()){
-			result = "resource 2 not present";
-			res2.removeAll((Property)null);
-			baseOntModel.leaveCriticalSection();
-			return result;
         }
+
         int counter = 0;
         Model leftoverModel = ModelFactory.createDefaultModel();
-		ontModel.enterCriticalSection(Lock.WRITE);
-		infOntModel.enterCriticalSection(Lock.WRITE);
-		try{
-		
-			/*
-			 * Iterate through statements of secondary resource
-			 */
 
+        // Iterate through statements of secondary resource
+        StmtIterator stmtItr2 = res2Model.listStatements(
+                res2, (Property) null, (RDFNode) null);            
         while(stmtItr2.hasNext()){
-		
+            Statement stmt = stmtItr2.nextStatement();            
-			Statement stmt = stmtItr2.next();
+            if(isFunctional(stmt.getPredicate(), tboxOntModel)) {
-			Property prop = stmt.getPredicate();
+                // if the property is null or functional then dump the statement into 
-			OntProperty oprop = baseOntModel.getOntProperty(prop.getURI());
+                // the leftover model, else add it to base, ont and inf models as a 
-			
+                // part of the primary resource.
-			/*
+                leftoverModel.add(res2, stmt.getPredicate(), stmt.getObject());
-			 * if the property is null or functional then dump the statement into leftover model
-			 * else add it to base, ont and inf models as a part of primary resource.
-			 */
-		    if(oprop!=null && oprop.isFunctionalProperty()){
-		    	leftoverModel.add(res2,stmt.getPredicate(),stmt.getObject());
                 functionalPresent = true;
-		    }
+            } else if (stmt.getPredicate().equals(RDFS.label) &&
-		    /*
+                    usePrimaryLabelOnly!=null && !usePrimaryLabelOnly.isEmpty()) {
-		     * if the checkbox is checked, use primary resource rdfs:labels only and dump secondary resource rdfs:labels
+                // if the checkbox is checked, use primary resource rdfs:labels only  
-		     * into leftoverModel
+                // and dump secondary resource rdfs:labels into leftoverModel
-		     */
+                leftoverModel.add(res2, stmt.getPredicate(), stmt.getObject());
-		    else if(prop.getURI().equals("http://www.w3.org/2000/01/rdf-schema#label") && 
-		    		usePrimaryLabelOnly!=null && !usePrimaryLabelOnly.isEmpty()){
-		    		leftoverModel.add(res2,stmt.getPredicate(),stmt.getObject());
                 functionalPresent = true;        
-		    }
+            } else {
-		    else{
+                baseOntModel.enterCriticalSection(Lock.WRITE);
-		    	baseOntModel.add(res1,stmt.getPredicate(),stmt.getObject()); 
+                try {
-		    	ontModel.add(res1,stmt.getPredicate(),stmt.getObject());
+                    baseOntModel.add(res1, stmt.getPredicate(), stmt.getObject());
-		    	infOntModel.add(res1,stmt.getPredicate(),stmt.getObject());
                     counter++;
+                } finally {
+                    baseOntModel.leaveCriticalSection();
                 }
             }
-		  /*
+        }
-		   * replace secondary resource with primary resource in all the statements where
+
-		   * secondary resource is present as an object.
+        // replace secondary resource with primary resource in all the statements 
-		   */
+        // where secondary resource is present as an object.
-		while(stmtItr3.hasNext()){
+        StmtIterator stmtItr3 = res2Model.listStatements(
+                (Resource) null, (Property) null, res2);
+        while (stmtItr3.hasNext()){
             Statement stmt = stmtItr3.nextStatement();
             Resource sRes = stmt.getSubject();
             Property sProp = stmt.getPredicate();
-			baseOntModel.add(sRes,sProp,res1);
+            baseOntModel.enterCriticalSection(Lock.WRITE);
-			ontModel.add(sRes,sProp,res1);
+            try {
-			infOntModel.add(sRes,sProp,res1);
+                baseOntModel.add(sRes, sProp, res1);
-		}
+                counter++;
-		Resource ontRes = ontModel.getResource(res2.getURI());
+            } finally {
-		Resource infRes = infOntModel.getResource(res2.getURI());
-		
-		/*
-		 * Remove all the statements of secondary resource from all the models.
-		 */
-		
-		baseOntModel.removeAll((Resource)null,(Property)null,(RDFNode)res2);
-		ontModel.removeAll((Resource)null,(Property)null,(RDFNode)res2);
-		infOntModel.removeAll((Resource)null,(Property)null,(RDFNode)res2);
-		res2.removeAll((Property)null);
-		ontRes.removeAll((Property)null);
-		infRes.removeAll((Property)null);
-		}
-		finally{
                 baseOntModel.leaveCriticalSection();
-	    infOntModel.leaveCriticalSection();
-		ontModel.leaveCriticalSection();
             }
-		setLeftOverModel(leftoverModel);
+        }
-		if(counter>0 && functionalPresent)
+
-		result = "merged " + counter + " statements. Some statements could not be merged.";
+        // Remove all the statements of secondary resource 
-		else if(counter>0 && !functionalPresent)
+        baseOntModel.enterCriticalSection(Lock.WRITE);
-		result = "merged " + counter + " statements.";	
+        try {
-		else if(counter==0)
+            baseOntModel.remove(res2Model);
-		result = "No statements merged";
+        } finally {
+            baseOntModel.leaveCriticalSection();
+        }
+
+        MergeResult result = new MergeResult();
+        if (!leftoverModel.isEmpty()) {
+            result.setLeftoverModel(leftoverModel);   
+        }
+
+        if (counter > 0 && functionalPresent) {
+            result.setResultText("merged " + counter + 
+                    " statements. Some statements could not be merged.");
+        } else if(counter>0 && !functionalPresent) {
+            result.setResultText("merged " + counter + " statements.");    
+        } else if (counter==0) {
+            result.setResultText("No statements merged");
+        }
         return result;
 
     }
-	private Model leftoverModel = ModelFactory.createDefaultModel();
     
-	public void setLeftOverModel(Model leftoverModel){
+    private boolean isFunctional(Property property, OntModel tboxOntModel) {
-		this.leftoverModel = leftoverModel;
+        tboxOntModel.enterCriticalSection(Lock.READ);
+        try {
+            return (tboxOntModel.contains(
+                    property, RDF.type, OWL.FunctionalProperty));
+        } finally {
+            tboxOntModel.leaveCriticalSection();
         }
-	public Model getLeftOverModel(){
-		return this.leftoverModel;
     }
 
-	public void doPermanentURI(String oldModel,String newModel,String oldNamespace,
+    public void doPermanentURI(String oldModel, String newModel, String oldNamespace,
-			String newNamespace,String dNamespace,ModelMaker maker,VitroRequest vreq){
+            String newNamespace, String dNamespace, ModelMaker maker, 
-			
+            VitroRequest vreq) {
 
         WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
         Model m = maker.getModel(oldModel);
@@ -733,8 +748,7 @@ public class JenaIngestUtils {
                 tempModel.add(stmt);
             }
             rsItr = tempModel.listResourcesWithProperty((Property)null);
-			}
+        } else{
-			else{
             rsItr = m.listResourcesWithProperty((Property)null); 
         }
 
@@ -799,9 +813,9 @@ public class JenaIngestUtils {
                     continue;
                 }
             }
+        }
+    }    
 
-			}
-			}	
     public String getUnusedURI(String newNamespace,WebappDaoFactory wdf){
         String uri = null;
         String errMsg = null;

webapp/web/jenaIngest/merge_result.jsp

@@ -1,5 +1,6 @@
 <%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
 
+<%@page import="edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult"%>
 <%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%>
 
 <%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
@@ -11,8 +12,13 @@
 
 <h2><a class="ingestMenu" href="ingest">Ingest Menu</a> > Merge Individuals</h2>
 
-<%String result = (String) request.getAttribute("result");%>
+<%
+    MergeResult resultObj = (MergeResult) request.getAttribute("result");
+    String result = resultObj.getResultText();
+%>
+
 <p><b><%=result%></b></p>
+
 <%if(!result.equals("resource 1 not present") && !result.equals("resource 2 not present")){ 
 if(!result.equals("No statements merged") && !result.endsWith("statements.")){%>
 <p>Download non-mergeable statements.</p>