NIHVIVO-3874 reimplemented change namespace function to work around strange lack of deletion with ResourceUtils.renameResource()
This commit is contained in:
brianjlowe
parent
c052a20271
commit
74662f29d0
1 changed files with 77 additions and 43 deletions
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@ -60,7 +60,6 @@ import com.hp.hpl.jena.sdb.sql.JDBC;
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import com.hp.hpl.jena.sdb.store.DatabaseType;
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import com.hp.hpl.jena.sdb.store.LayoutType;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.util.ResourceUtils;
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import com.hp.hpl.jena.util.iterator.ClosableIterator;
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import edu.cornell.mannlib.vedit.controller.BaseEditController;
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@ -69,13 +68,18 @@ import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
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import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
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import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
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import edu.cornell.mannlib.vitro.webapp.servlet.setup.WebappDaoSetup;
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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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@ -1163,42 +1167,39 @@ public class JenaIngestController extends BaseEditController {
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String result = null;
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Integer counter = 0;
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Boolean namespacePresent = false;
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OntModel baseOntModel = (OntModel)
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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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List<String> urisToChange = new LinkedList<String>();
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ontModel.enterCriticalSection(Lock.READ);
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RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(
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getServletContext()).getRDFService();
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try {
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Iterator<Individual> indIter = ontModel.listIndividuals();
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while( indIter.hasNext()){
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Individual ind = indIter.next();
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String namespace = ind.getNameSpace();
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if( namespace != null ){
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if( oldNamespace.equals(namespace) ){
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uri = ind.getURI();
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urisToChange.add(uri);
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namespacePresent = true;
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Model baseOntModel = RDFServiceGraph.createRDFServiceModel
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(new RDFServiceGraph(
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rdfService, JenaDataSourceSetupBase.JENA_DB_MODEL));
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OntModel ontModel = (OntModel)
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getServletContext().getAttribute("jenaOntModel");
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List<String> urisToChange = new LinkedList<String>();
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ontModel.enterCriticalSection(Lock.READ);
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try {
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Iterator<Individual> indIter = ontModel.listIndividuals();
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while( indIter.hasNext()){
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Individual ind = indIter.next();
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String namespace = ind.getNameSpace();
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if( namespace != null ){
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if( oldNamespace.equals(namespace) ){
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uri = ind.getURI();
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urisToChange.add(uri);
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namespacePresent = true;
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}
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}
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}
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} finally {
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ontModel.leaveCriticalSection();
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}
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} finally {
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ontModel.leaveCriticalSection();
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}
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if(!namespacePresent){
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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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baseOntModel.enterCriticalSection(Lock.WRITE);
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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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if(!namespacePresent){
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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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long time1 = System.currentTimeMillis();
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Resource res = baseOntModel.getResource(oldURIStr);
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Resource infRes = infOntModel.getResource(oldURIStr);
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long time2 = System.currentTimeMillis();
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String newURIStr=null;
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Pattern p = Pattern.compile(oldNamespace);
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@ -1209,21 +1210,54 @@ public class JenaIngestController extends BaseEditController {
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log.debug("time to get new uri: " +
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Long.toString(time3 - time2));
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log.debug("Renaming "+ oldURIStr + " to " + newURIStr);
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ResourceUtils.renameResource(res,newURIStr);
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ResourceUtils.renameResource(infRes,newURIStr);
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String whereClause = "} WHERE { \n" +
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" GRAPH <" + JenaDataSourceSetupBase.JENA_DB_MODEL + "> { \n" +
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" { <" + oldURIStr + "> ?p <" + oldURIStr + "> } \n " +
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" UNION \n" +
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" { <" + oldURIStr + "> ?q ?o } \n " +
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" UNION \n" +
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" { ?s ?r <" + oldURIStr + "> } \n" +
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" } \n" +
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"}";
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String removeQuery = "CONSTRUCT { \n" +
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" <" + oldURIStr + "> ?p <" + oldURIStr + "> . \n " +
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" <" + oldURIStr + "> ?q ?o . \n " +
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" ?s ?r <" + oldURIStr + "> \n" + whereClause;
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String addQuery = "CONSTRUCT { \n" +
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" <" + newURIStr + "> ?p <" + newURIStr + "> . \n " +
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" <" + newURIStr + "> ?q ?o . \n " +
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" ?s ?r <" + newURIStr + "> \n" + whereClause;
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try {
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ChangeSet cs = rdfService.manufactureChangeSet();
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cs.addAddition(rdfService.sparqlConstructQuery(
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addQuery, RDFService.ModelSerializationFormat.N3),
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RDFService.ModelSerializationFormat.N3,
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JenaDataSourceSetupBase.JENA_DB_MODEL);
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cs.addRemoval(rdfService.sparqlConstructQuery(
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removeQuery, RDFService.ModelSerializationFormat.N3),
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RDFService.ModelSerializationFormat.N3,
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JenaDataSourceSetupBase.JENA_DB_MODEL);
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rdfService.changeSetUpdate(cs);
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} catch (RDFServiceException e) {
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throw new RuntimeException(e);
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}
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long time4 = System.currentTimeMillis();
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log.debug(" time to rename : " + Long.toString( time4 - time3));
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log.debug(" time for one resource: " +
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Long.toString( time4 -time1));
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} finally {
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infOntModel.leaveCriticalSection();
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ontModel.leaveCriticalSection();
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baseOntModel.leaveCriticalSection();
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Long.toString( time4 -time1));
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counter++;
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}
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result = counter.toString() + " resources renamed";
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return result;
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} finally {
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if (rdfService != null) {
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rdfService.close();
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}
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counter++;
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}
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result = counter.toString() + " resources renamed";
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return result;
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}
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}
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protected void showModelList(VitroRequest vreq, ModelMaker maker, String modelType) {
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