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fix: concurrent modification of rdfServiceJena getGraphURIs #423

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Oct 30, 2023
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Original file line number Diff line number Diff line change
Expand Up @@ -7,56 +7,51 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;

import java.util.Set;
import java.util.concurrent.CopyOnWriteArrayList;

import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceImpl;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
import edu.cornell.mannlib.vitro.webapp.utils.sparql.ResultSetIterators.ResultSetQuadsIterator;
import edu.cornell.mannlib.vitro.webapp.utils.sparql.ResultSetIterators.ResultSetTriplesIterator;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import org.apache.jena.query.QuerySolutionMap;
import org.apache.jena.query.ReadWrite;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.riot.RDFDataMgr;
import org.apache.log4j.lf5.util.StreamUtils;

import org.apache.jena.graph.Triple;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.QuerySolution;
import org.apache.jena.query.QuerySolutionMap;
import org.apache.jena.query.ReadWrite;
import org.apache.jena.query.ResultSet;
import org.apache.jena.query.ResultSetFormatter;
import org.apache.jena.query.Syntax;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.riot.RDFDataMgr;
import org.apache.jena.sdb.SDB;
import org.apache.jena.shared.Lock;
import org.apache.jena.sparql.core.Quad;

import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceImpl;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
import edu.cornell.mannlib.vitro.webapp.utils.sparql.ResultSetIterators.ResultSetQuadsIterator;
import edu.cornell.mannlib.vitro.webapp.utils.sparql.ResultSetIterators.ResultSetTriplesIterator;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
import org.apache.log4j.lf5.util.StreamUtils;

public abstract class RDFServiceJena extends RDFServiceImpl implements RDFService {

Expand All @@ -66,7 +61,7 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic

protected volatile boolean rebuildGraphURICache = true;
protected volatile boolean isRebuildGraphURICacheRunning = false;
protected final List<String> graphURIs = Collections.synchronizedList(new ArrayList<>());
protected final List<String> graphURIs = new CopyOnWriteArrayList<String>();

@Override
public abstract boolean changeSetUpdate(ChangeSet changeSet) throws RDFServiceException;
Expand Down
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena;

import java.util.Iterator;
import java.util.List;

import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.VitroModelFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.DatasetFactory;
import org.apache.jena.rdf.model.Model;
import org.junit.Test;

public class RDFServiceJenaTest {

@Test
public void getConcurrentGraphUrisTest() throws RDFServiceException, InterruptedException {
Dataset testDataSet = DatasetFactory.createGeneral();
Model m1 = VitroModelFactory.createModel();
testDataSet.addNamedModel("test:init1", m1);
Model m2 = VitroModelFactory.createModel();
testDataSet.addNamedModel("test:init2", m2);
RDFServiceJena rdfService = new RDFServiceModel(testDataSet);
rdfService.getGraphURIs();
long i = 0;
while (rdfService.rebuildGraphURICache) {
Thread.sleep(10);
i += 10;
if (i > 10000) {
throw new RuntimeException();
}
}
List<String> uris = rdfService.getGraphURIs();
for (Iterator<String> iterator = uris.iterator(); iterator.hasNext();) {
Model m = VitroModelFactory.createModel();
testDataSet.addNamedModel("test" + i, m);
rdfService.rebuildGraphURICache = true;
rdfService.getGraphURIs();
while (rdfService.rebuildGraphURICache) {
Thread.sleep(10);
i += 10;
if (i > 20000) {
throw new RuntimeException();
}
}
iterator.next();
i++;
}
}

}
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