NIHVIVO-3516 fixed merge tool so it doesn't strand triples in a graph named with SDB's union URI
This commit is contained in:
brianjlowe
parent
f3d6e33a01
commit
2bdb44685f
3 changed files with 814 additions and 791 deletions
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@ -80,6 +80,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
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import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetup;
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import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestWorkflowProcessor;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.WorkflowOntology;
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@ -621,23 +622,25 @@ public class JenaIngestController extends BaseEditController {
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if(uri1!=null){
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JenaIngestUtils utils = new JenaIngestUtils();
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/*
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* get baseOnt, Ont and infOnt models
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* get baseOnt and infOnt models
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*/
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OntModel baseOntModel = (OntModel) getServletContext().getAttribute("baseOntModel");
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OntModel ontModel = (OntModel)
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getServletContext().getAttribute("jenaOntModel");
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OntModel infOntModel = (OntModel)
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getServletContext().getAttribute(JenaBaseDao.INFERENCE_ONT_MODEL_ATTRIBUTE_NAME);
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OntModel baseOntModel = ModelContext.getBaseOntModel(
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getServletContext());
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OntModel tboxOntModel = ModelContext.getUnionOntModelSelector(
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getServletContext()).getTBoxModel();
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/*
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* calling method that does the merge operation.
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*/
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String result = utils.doMerge(uri1,uri2,baseOntModel,ontModel,infOntModel,usePrimaryLabelOnly);
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vreq.getSession().setAttribute("leftoverModel", utils.getLeftOverModel());
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MergeResult result = utils.doMerge(
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uri1, uri2, baseOntModel, tboxOntModel, usePrimaryLabelOnly);
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vreq.getSession().setAttribute(
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"leftoverModel", result.getLeftoverModel());
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vreq.setAttribute("result", result);
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vreq.setAttribute("title", "Merge Resources");
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vreq.setAttribute("bodyJsp", MERGE_RESULT);
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}
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else{
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} else{
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vreq.setAttribute("title","Merge Resources");
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vreq.setAttribute("bodyJsp",MERGE_RESOURCES);
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}
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@ -1192,7 +1195,7 @@ public class JenaIngestController extends BaseEditController {
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ontModel.leaveCriticalSection();
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}
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if(!namespacePresent){
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result = "0 resource renamed";
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result = "no resources renamed";
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return result;
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}
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for( String oldURIStr : urisToChange){
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@ -2,7 +2,6 @@
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package edu.cornell.mannlib.vitro.webapp.utils.jena;
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import java.lang.reflect.InvocationTargetException;
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import java.lang.reflect.Method;
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import java.util.ArrayList;
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import java.util.Collections;
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@ -16,15 +15,12 @@ import java.util.Random;
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import java.util.Set;
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import java.util.regex.Pattern;
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import javax.servlet.http.HttpServletRequest;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.openrdf.model.vocabulary.RDFS;
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import com.hp.hpl.jena.ontology.FunctionalProperty;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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import com.hp.hpl.jena.ontology.OntProperty;
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import com.hp.hpl.jena.rdf.model.Literal;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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@ -41,11 +37,11 @@ import com.hp.hpl.jena.util.ResourceUtils;
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import com.hp.hpl.jena.util.iterator.ClosableIterator;
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import com.hp.hpl.jena.vocabulary.OWL;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDFS;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
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public class JenaIngestUtils {
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@ -591,132 +587,151 @@ public class JenaIngestUtils {
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}
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}
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public String doMerge(String uri1,String uri2,OntModel baseOntModel,OntModel ontModel,OntModel infOntModel,String usePrimaryLabelOnly){
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public class MergeResult {
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private String resultText;
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private Model leftoverModel;
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public MergeResult() {}
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public MergeResult(String resultText, Model leftoverModel) {
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this.resultText = resultText;
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this.leftoverModel = leftoverModel;
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}
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public void setResultText(String resultText) {
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this.resultText = resultText;
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}
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public String getResultText() {
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return this.resultText;
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}
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public void setLeftoverModel(Model leftoverModel) {
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this.leftoverModel = leftoverModel;
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}
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public Model getLeftoverModel() {
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return this.leftoverModel;
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}
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}
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public MergeResult doMerge(String uri1, String uri2, OntModel baseOntModel,
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OntModel tboxOntModel, String usePrimaryLabelOnly){
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boolean functionalPresent = false;
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Resource res1 = baseOntModel.getResource(uri1); // primary resource
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Model res1Model = ModelFactory.createDefaultModel();
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Resource res2 = baseOntModel.getResource(uri2); // secondary resource
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String result = null;
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baseOntModel.enterCriticalSection(Lock.WRITE);
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Model res2Model = ModelFactory.createDefaultModel();
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/*
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* get statements of both the resources
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*/
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StmtIterator stmtItr1 = baseOntModel.listStatements(res1,(Property)null,(RDFNode)null);
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StmtIterator stmtItr2 = baseOntModel.listStatements(res2,(Property)null,(RDFNode)null);
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StmtIterator stmtItr3 = baseOntModel.listStatements((Resource)null,(Property)null,(RDFNode)res2);
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// get statements of both the resources
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baseOntModel.enterCriticalSection(Lock.READ);
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try {
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res1Model.add(
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baseOntModel.listStatements(res1, (Property)null, (RDFNode)null));
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res2Model.add(
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baseOntModel.listStatements(res2, (Property)null, (RDFNode)null));
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res2Model.add(
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baseOntModel.listStatements(
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(Resource)null, (Property)null, (RDFNode)res2));
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} finally {
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baseOntModel.leaveCriticalSection();
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}
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/*
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* if primary resource has no statements, return
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*/
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if(!stmtItr1.hasNext()){
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result = "resource 1 not present";
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res1.removeAll((Property)null);
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baseOntModel.leaveCriticalSection();
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return result;
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}
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/*
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* if secondary resource has no statements, return
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*/
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else if(!stmtItr2.hasNext()){
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result = "resource 2 not present";
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res2.removeAll((Property)null);
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baseOntModel.leaveCriticalSection();
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return result;
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// if primary resource has no statements, return
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if (res1Model.isEmpty()){
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return new MergeResult("resource 1 not present", null);
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} else if(res2Model.isEmpty()){
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return new MergeResult("resource 2 not present", null);
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}
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int counter = 0;
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Model leftoverModel = ModelFactory.createDefaultModel();
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ontModel.enterCriticalSection(Lock.WRITE);
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infOntModel.enterCriticalSection(Lock.WRITE);
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try{
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/*
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* Iterate through statements of secondary resource
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*/
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// Iterate through statements of secondary resource
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StmtIterator stmtItr2 = res2Model.listStatements(
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res2, (Property) null, (RDFNode) null);
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while(stmtItr2.hasNext()){
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Statement stmt = stmtItr2.next();
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Property prop = stmt.getPredicate();
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OntProperty oprop = baseOntModel.getOntProperty(prop.getURI());
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/*
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* if the property is null or functional then dump the statement into leftover model
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* else add it to base, ont and inf models as a part of primary resource.
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*/
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if(oprop!=null && oprop.isFunctionalProperty()){
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Statement stmt = stmtItr2.nextStatement();
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if(isFunctional(stmt.getPredicate(), tboxOntModel)) {
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// if the property is null or functional then dump the statement into
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// the leftover model, else add it to base, ont and inf models as a
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// part of the primary resource.
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leftoverModel.add(res2, stmt.getPredicate(), stmt.getObject());
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functionalPresent = true;
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}
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/*
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* if the checkbox is checked, use primary resource rdfs:labels only and dump secondary resource rdfs:labels
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* into leftoverModel
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*/
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else if(prop.getURI().equals("http://www.w3.org/2000/01/rdf-schema#label") &&
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} else if (stmt.getPredicate().equals(RDFS.label) &&
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usePrimaryLabelOnly!=null && !usePrimaryLabelOnly.isEmpty()) {
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// if the checkbox is checked, use primary resource rdfs:labels only
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// and dump secondary resource rdfs:labels into leftoverModel
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leftoverModel.add(res2, stmt.getPredicate(), stmt.getObject());
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functionalPresent = true;
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}
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else{
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} else {
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baseOntModel.enterCriticalSection(Lock.WRITE);
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try {
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baseOntModel.add(res1, stmt.getPredicate(), stmt.getObject());
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ontModel.add(res1,stmt.getPredicate(),stmt.getObject());
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infOntModel.add(res1,stmt.getPredicate(),stmt.getObject());
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counter++;
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} finally {
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baseOntModel.leaveCriticalSection();
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}
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}
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/*
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* replace secondary resource with primary resource in all the statements where
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* secondary resource is present as an object.
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*/
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}
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// replace secondary resource with primary resource in all the statements
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// where secondary resource is present as an object.
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StmtIterator stmtItr3 = res2Model.listStatements(
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(Resource) null, (Property) null, res2);
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while (stmtItr3.hasNext()){
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Statement stmt = stmtItr3.nextStatement();
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Resource sRes = stmt.getSubject();
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Property sProp = stmt.getPredicate();
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baseOntModel.enterCriticalSection(Lock.WRITE);
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try {
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baseOntModel.add(sRes, sProp, res1);
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ontModel.add(sRes,sProp,res1);
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infOntModel.add(sRes,sProp,res1);
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}
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Resource ontRes = ontModel.getResource(res2.getURI());
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Resource infRes = infOntModel.getResource(res2.getURI());
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/*
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* Remove all the statements of secondary resource from all the models.
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*/
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baseOntModel.removeAll((Resource)null,(Property)null,(RDFNode)res2);
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ontModel.removeAll((Resource)null,(Property)null,(RDFNode)res2);
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infOntModel.removeAll((Resource)null,(Property)null,(RDFNode)res2);
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res2.removeAll((Property)null);
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ontRes.removeAll((Property)null);
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infRes.removeAll((Property)null);
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}
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finally{
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counter++;
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} finally {
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baseOntModel.leaveCriticalSection();
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infOntModel.leaveCriticalSection();
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ontModel.leaveCriticalSection();
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}
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setLeftOverModel(leftoverModel);
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if(counter>0 && functionalPresent)
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result = "merged " + counter + " statements. Some statements could not be merged.";
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else if(counter>0 && !functionalPresent)
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result = "merged " + counter + " statements.";
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else if(counter==0)
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result = "No statements merged";
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}
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// Remove all the statements of secondary resource
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baseOntModel.enterCriticalSection(Lock.WRITE);
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try {
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baseOntModel.remove(res2Model);
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} finally {
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baseOntModel.leaveCriticalSection();
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}
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MergeResult result = new MergeResult();
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if (!leftoverModel.isEmpty()) {
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result.setLeftoverModel(leftoverModel);
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}
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if (counter > 0 && functionalPresent) {
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result.setResultText("merged " + counter +
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" statements. Some statements could not be merged.");
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} else if(counter>0 && !functionalPresent) {
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result.setResultText("merged " + counter + " statements.");
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} else if (counter==0) {
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result.setResultText("No statements merged");
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}
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return result;
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}
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private Model leftoverModel = ModelFactory.createDefaultModel();
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public void setLeftOverModel(Model leftoverModel){
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this.leftoverModel = leftoverModel;
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private boolean isFunctional(Property property, OntModel tboxOntModel) {
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tboxOntModel.enterCriticalSection(Lock.READ);
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try {
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return (tboxOntModel.contains(
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property, RDF.type, OWL.FunctionalProperty));
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} finally {
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tboxOntModel.leaveCriticalSection();
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}
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public Model getLeftOverModel(){
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return this.leftoverModel;
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}
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public void doPermanentURI(String oldModel, String newModel, String oldNamespace,
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String newNamespace,String dNamespace,ModelMaker maker,VitroRequest vreq){
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String newNamespace, String dNamespace, ModelMaker maker,
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VitroRequest vreq) {
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WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
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Model m = maker.getModel(oldModel);
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@ -733,8 +748,7 @@ public class JenaIngestUtils {
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tempModel.add(stmt);
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}
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rsItr = tempModel.listResourcesWithProperty((Property)null);
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}
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else{
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} else{
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rsItr = m.listResourcesWithProperty((Property)null);
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}
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@ -799,9 +813,9 @@ public class JenaIngestUtils {
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continue;
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}
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}
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}
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}
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}
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}
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public String getUnusedURI(String newNamespace,WebappDaoFactory wdf){
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String uri = null;
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String errMsg = null;
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@ -1,5 +1,6 @@
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<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
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<%@page import="edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult"%>
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<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%>
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<%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
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@ -11,8 +12,13 @@
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<h2><a class="ingestMenu" href="ingest">Ingest Menu</a> > Merge Individuals</h2>
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<%String result = (String) request.getAttribute("result");%>
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<%
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MergeResult resultObj = (MergeResult) request.getAttribute("result");
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String result = resultObj.getResultText();
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%>
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<p><b><%=result%></b></p>
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<%if(!result.equals("resource 1 not present") && !result.equals("resource 2 not present")){
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if(!result.equals("No statements merged") && !result.endsWith("statements.")){%>
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<p>Download non-mergeable statements.</p>
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