NIHVIVO-1499 Refactor merge and permanent URI utilities
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1 changed files with 207 additions and 0 deletions
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@ -4,6 +4,7 @@ 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.InvocationTargetException;
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import java.lang.reflect.Method;
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import java.lang.reflect.Method;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.Iterator;
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@ -13,16 +14,21 @@ import java.util.Random;
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import java.util.Set;
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import java.util.Set;
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import java.util.regex.Pattern;
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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.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.ontology.OntModel;
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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.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.Literal;
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import com.hp.hpl.jena.rdf.model.Model;
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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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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.ModelMaker;
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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.ResIterator;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.Statement;
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@ -33,6 +39,11 @@ 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.OWL;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDF;
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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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public class JenaIngestUtils {
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private static final Log log = LogFactory.getLog(JenaIngestUtils.class.getName());
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private static final Log log = LogFactory.getLog(JenaIngestUtils.class.getName());
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@ -466,4 +477,200 @@ public class JenaIngestUtils {
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}
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}
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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){
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boolean functionalPresent = false;
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Resource res1 = baseOntModel.getResource(uri1);
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Resource res2 = baseOntModel.getResource(uri2);
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String result = null;
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baseOntModel.enterCriticalSection(Lock.WRITE);
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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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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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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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}
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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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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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if(oprop!=null && oprop.isFunctionalProperty()){
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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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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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}
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}
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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.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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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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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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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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}
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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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WebappDaoFactory wdf = vreq.getFullWebappDaoFactory();
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Model m = maker.getModel(oldModel);
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Model saveModel = maker.getModel(newModel);
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Model tempModel = ModelFactory.createDefaultModel();
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ResIterator rsItr = null;
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ArrayList<String> urlCheck = new ArrayList<String>();
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String changeNamespace = null;
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boolean urlFound = false;
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if(!oldModel.equals(newModel)){
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StmtIterator stmtItr = m.listStatements();
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while(stmtItr.hasNext()){
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Statement stmt = stmtItr.nextStatement();
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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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rsItr = m.listResourcesWithProperty((Property)null);
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}
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String uri = null;
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while(rsItr.hasNext()){
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Resource res = rsItr.next();
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if(oldNamespace.equals(res.getNameSpace())){
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if(!newNamespace.equals("")){
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do{
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uri = getUnusedURI(newNamespace,wdf);
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if(!urlCheck.contains(uri)){
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urlCheck.add(uri);
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urlFound = true;
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}
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}while(!urlFound);
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urlFound = false;
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}
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else if(dNamespace.equals(vreq.getFullWebappDaoFactory().getDefaultNamespace())){
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try{
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do{
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uri = wdf.getIndividualDao().getUnusedURI(null);
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if(!urlCheck.contains(uri)){
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urlCheck.add(uri);
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urlFound = true;
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}
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}while(!urlFound);
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urlFound = false;
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}catch(InsertException ex){
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log.error("could not create uri");
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}
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}
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ResourceUtils.renameResource(res, uri);
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}
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}
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boolean statementDone = false;
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if(!newNamespace.equals("")){
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changeNamespace = newNamespace;
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}
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else if(dNamespace.equals(vreq.getFullWebappDaoFactory().getDefaultNamespace())){
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changeNamespace = dNamespace;
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}
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if(!oldModel.equals(newModel)){
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StmtIterator stmtItr = tempModel.listStatements();
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while(stmtItr.hasNext()){
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statementDone = false;
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Statement stmt = stmtItr.nextStatement();
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Resource sRes = stmt.getSubject();
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Resource oRes = null;
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if(sRes.getNameSpace().equals(changeNamespace)){
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saveModel.add(stmt);
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statementDone = true;
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}
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try{
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oRes = (Resource)stmt.getObject();
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if(oRes.getNameSpace().equals(changeNamespace) && !statementDone){
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saveModel.add(stmt);
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statementDone = true;
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}
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}
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catch(Exception e){
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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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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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Random random = new Random();
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boolean uriIsGood = false;
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int attempts = 0;
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while( uriIsGood == false && attempts < 30 ){
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uri = newNamespace + "n" + random.nextInt( Math.min(Integer.MAX_VALUE,(int)Math.pow(2,attempts + 13)) );
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errMsg = wdf.checkURI(uri);
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if( errMsg != null)
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uri = null;
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else
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uriIsGood = true;
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attempts++;
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}
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return uri;
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}
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}
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}
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