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[VIVO-1242] Merge branch 'brianjlowe-writePerformance' into develop

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This commit is contained in:
Graham Triggs 2016-05-03 11:18:39 +01:00
commit a484532b01
32 changed files with 1108 additions and 1415 deletions
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18
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/api/SparqlUpdateApiController.java
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@ -19,6 +19,7 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.ReadWrite;
import com.hp.hpl.jena.update.GraphStore;
import com.hp.hpl.jena.update.GraphStoreFactory;
import com.hp.hpl.jena.update.UpdateAction;
@ -96,19 +97,28 @@ public class SparqlUpdateApiController extends VitroApiServlet {
}
private void executeUpdate(HttpServletRequest req, UpdateRequest parsed) {
ServletContext ctx = req.getSession().getServletContext();
VitroRequest vreq = new VitroRequest(req);
SearchIndexer indexer = ApplicationUtils.instance().getSearchIndexer();
indexer.pause();
try {
Dataset ds = new RDFServiceDataset(vreq.getUnfilteredRDFService());
GraphStore graphStore = GraphStoreFactory.create(ds);
try {
if(indexer != null) {
indexer.pause();
}
if(ds.supportsTransactions()) {
ds.begin(ReadWrite.WRITE);
}
UpdateAction.execute(parsed, graphStore);
} finally {
if(ds.supportsTransactions()) {
ds.commit();
ds.end();
}
if(indexer != null) {
indexer.unpause();
}
}
}
private void do200response(HttpServletResponse resp) throws IOException {
sendShortResponse(SC_OK, "SPARQL update accepted.", resp);

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
View file

@ -73,6 +73,7 @@ import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.VitroModelFactory;
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;
@ -706,14 +707,13 @@ public class JenaIngestController extends BaseEditController {
private void doClearModel(String modelName, ModelMaker modelMaker) {
Model m = modelMaker.getModel(modelName);
OntModel o = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,m);
OntModel o = VitroModelFactory.createOntologyModel(m);
o.enterCriticalSection(Lock.WRITE);
try {
o.removeAll(null,null,null);
o.removeAll();
} finally {
o.leaveCriticalSection();
}
// removeAll() doesn't work with the listeners!
}
private void doLoadRDFData(String modelName, String docLoc, String filePath, String language, ModelMaker modelMaker) {

46
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java
View file

@ -44,6 +44,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
@ -202,9 +203,20 @@ public class RDFUploadController extends JenaIngestController {
}
if (aboxModel != null) {
aboxChangeModel = uploadModel.remove(tboxChangeModel);
aboxstmtCount = operateOnModel(request.getUnfilteredWebappDaoFactory(),
aboxModel, aboxChangeModel, ontModelSelector,
remove, makeClassgroups, loginBean.getUserURI());
aboxstmtCount = aboxChangeModel.size();
ByteArrayOutputStream os = new ByteArrayOutputStream();
aboxChangeModel.write(os, "N3");
ByteArrayInputStream in = new ByteArrayInputStream(os.toByteArray());
if(!remove) {
readIntoModel(in, "N3", request.getRDFService(),
ModelNames.ABOX_ASSERTIONS);
} else {
removeFromModel(in, "N3", request.getRDFService(),
ModelNames.ABOX_ASSERTIONS);
}
// operateOnModel(request.getUnfilteredWebappDaoFactory(),
// aboxModel, aboxChangeModel, ontModelSelector,
// remove, makeClassgroups, loginBean.getUserURI());
}
request.setAttribute("uploadDesc", uploadDesc + ". " + verb + " " +
(tboxstmtCount + aboxstmtCount) + " statements.");
@ -225,9 +237,19 @@ public class RDFUploadController extends JenaIngestController {
}
}
private static final boolean BEGIN = true;
private static final boolean END = !BEGIN;
private ChangeSet makeChangeSet(RDFService rdfService) {
ChangeSet cs = rdfService.manufactureChangeSet();
cs.addPreChangeEvent(new BulkUpdateEvent(null, BEGIN));
cs.addPostChangeEvent(new BulkUpdateEvent(null, END));
return cs;
}
private void addUsingRDFService(InputStream in, String languageStr,
RDFService rdfService) {
ChangeSet changeSet = rdfService.manufactureChangeSet();
ChangeSet changeSet = makeChangeSet(rdfService);
RDFService.ModelSerializationFormat format =
("RDF/XML".equals(languageStr)
|| "RDF/XML-ABBREV".equals(languageStr))
@ -333,7 +355,7 @@ public class RDFUploadController extends JenaIngestController {
RDFService rdfService = new RDFServiceModel(mainModel);
ByteArrayOutputStream out = new ByteArrayOutputStream();
changesModel.write(out, "N-TRIPLE");
ChangeSet cs = rdfService.manufactureChangeSet();
ChangeSet cs = makeChangeSet(rdfService);
ByteArrayInputStream in = new ByteArrayInputStream(out.toByteArray());
cs.addRemoval(in, RDFService.ModelSerializationFormat.NTRIPLE, null);
try {
@ -398,7 +420,7 @@ public class RDFUploadController extends JenaIngestController {
private void readIntoModel(InputStream in, String language,
RDFService rdfService, String modelName) {
ChangeSet cs = rdfService.manufactureChangeSet();
ChangeSet cs = makeChangeSet(rdfService);
cs.addAddition(in, RDFServiceUtils.getSerializationFormatFromJenaString(
language), modelName);
try {
@ -408,6 +430,18 @@ public class RDFUploadController extends JenaIngestController {
}
}
private void removeFromModel(InputStream in, String language,
RDFService rdfService, String modelName) {
ChangeSet cs = makeChangeSet(rdfService);
cs.addRemoval(in, RDFServiceUtils.getSerializationFormatFromJenaString(
language), modelName);
try {
rdfService.changeSetUpdate(cs);
} catch (RDFServiceException e) {
throw new RuntimeException(e);
}
}
private void forwardToFileUploadError( String errrorMsg ,
HttpServletRequest req,
HttpServletResponse response)

40
api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/ABoxJenaChangeListener.java
View file

@ -1,40 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.dao.jena;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames;
public class ABoxJenaChangeListener extends JenaChangeListener {
public ABoxJenaChangeListener(ModelChangedListener listener) {
super(listener);
ignoredGraphs.add(ModelNames.ABOX_INFERENCES);
ignoredGraphs.add(ModelNames.TBOX_ASSERTIONS);
ignoredGraphs.add(ModelNames.TBOX_INFERENCES);
}
@Override
public void addedStatement(String serializedTriple, String graphURI) {
if (isABoxGraph(graphURI)) {
super.addedStatement(serializedTriple, graphURI);
}
}
@Override
public void removedStatement(String serializedTriple, String graphURI) {
if (isABoxGraph(graphURI)) {
super.removedStatement(serializedTriple, graphURI);
}
}
private boolean isABoxGraph(String graphURI) {
return (graphURI == null ||
ModelNames.ABOX_ASSERTIONS.equals(graphURI)
|| (!ignoredGraphs.contains(graphURI)
&& !graphURI.contains("filegraph")
&& !graphURI.contains("tbox")));
}
}

89
api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaChangeListener.java
View file

@ -1,89 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.io.ByteArrayInputStream;
import java.io.UnsupportedEncodingException;
import java.util.HashSet;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.SimpleReasonerSetup;
/**
* A ChangeListener that forwards events to a Jena ModelChangedListener
* @author bjl23
*
*/
public class JenaChangeListener implements ChangeListener {
private static final Log log = LogFactory.getLog(JenaChangeListener.class);
protected HashSet<String> ignoredGraphs = new HashSet<String>();
private ModelChangedListener listener;
private Model m = ModelFactory.createDefaultModel();
public JenaChangeListener(ModelChangedListener listener) {
this.listener = listener;
ignoredGraphs.add(SimpleReasonerSetup.JENA_INF_MODEL_REBUILD);
ignoredGraphs.add(SimpleReasonerSetup.JENA_INF_MODEL_SCRATCHPAD);
}
@Override
public void addedStatement(String serializedTriple, String graphURI) {
if (isRelevantGraph(graphURI)) {
listener.addedStatement(parseTriple(serializedTriple));
}
}
@Override
public void removedStatement(String serializedTriple, String graphURI) {
if (isRelevantGraph(graphURI)) {
listener.removedStatement(parseTriple(serializedTriple));
}
}
private boolean isRelevantGraph(String graphURI) {
return (graphURI == null || !ignoredGraphs.contains(graphURI));
}
@Override
public void notifyEvent(String graphURI, Object event) {
log.debug("event: " + event.getClass());
listener.notifyEvent(m, event);
}
// TODO avoid overhead of Model
private Statement parseTriple(String serializedTriple) {
try {
Model m = ModelFactory.createDefaultModel();
m.read(new ByteArrayInputStream(
serializedTriple.getBytes("UTF-8")), null, "N3");
StmtIterator sit = m.listStatements();
if (!sit.hasNext()) {
throw new RuntimeException("no triple parsed from change event");
} else {
Statement s = sit.nextStatement();
if (sit.hasNext()) {
log.warn("More than one triple parsed from change event");
}
return s;
}
} catch (RuntimeException riot) {
log.error("Unable to parse triple " + serializedTriple, riot);
throw riot;
} catch (UnsupportedEncodingException uee) {
throw new RuntimeException(uee);
}
}
}

3
api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/ModelContext.java
View file

@ -35,8 +35,7 @@ public class ModelContext {
public static void registerListenerForChanges(ServletContext ctx, ModelChangedListener ml){
try {
RDFServiceUtils.getRDFServiceFactory(ctx).registerListener(
new JenaChangeListener(ml));
RDFServiceUtils.getRDFServiceFactory(ctx).registerJenaModelChangedListener(ml);
} catch (RDFServiceException e) {
log.error(e,e);
}

54
api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceDataset.java
View file

@ -5,8 +5,13 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.util.ArrayList;
import java.util.Iterator;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.graph.Graph;
import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.graph.NodeFactory;
import com.hp.hpl.jena.graph.TransactionHandler;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.LabelExistsException;
import com.hp.hpl.jena.query.ReadWrite;
@ -21,6 +26,7 @@ import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
public class RDFServiceDataset implements Dataset {
private RDFServiceDatasetGraph g;
private ReadWrite transactionMode;
public RDFServiceDataset(RDFServiceDatasetGraph g) {
this.g = g;
@ -55,9 +61,13 @@ public class RDFServiceDataset implements Dataset {
return g.getLock();
}
private final static Log log = LogFactory.getLog(RDFServiceDataset.class);
@Override
public Model getNamedModel(String arg0) {
return RDFServiceGraph.createRDFServiceModel(g.getGraph(NodeFactory.createURI(arg0)));
Model model = RDFServiceGraph.createRDFServiceModel(
g.getGraph(NodeFactory.createURI(arg0)));
return model;
}
@Override
@ -108,36 +118,60 @@ public class RDFServiceDataset implements Dataset {
@Override
public boolean supportsTransactions() {
if (g.getDefaultGraph().getTransactionHandler() == null) {
return false;
} else {
return g.getDefaultGraph().getTransactionHandler().transactionsSupported();
}
}
@Override
public boolean isInTransaction() {
return false;
return (transactionMode != null);
}
private boolean supportsTransactions(Graph graph) {
return (graph.getTransactionHandler() != null
&& graph.getTransactionHandler().transactionsSupported());
}
@Override
public void begin(ReadWrite arg0) {
throw new UnsupportedOperationException(this.getClass().getSimpleName()
+ " does not support transactions.");
this.transactionMode = arg0;
g.begin(arg0);
for(String graphURI : g.getGraphCache().keySet()) {
Graph graph = g.getGraphCache().get(graphURI);
if (supportsTransactions(graph)) {
graph.getTransactionHandler().begin();
}
}
}
@Override
public void commit() {
throw new UnsupportedOperationException(this.getClass().getSimpleName()
+ " does not support transactions.");
for(String graphURI : g.getGraphCache().keySet()) {
Graph graph = g.getGraphCache().get(graphURI);
if(supportsTransactions(graph)) {
graph.getTransactionHandler().commit();
}
}
}
@Override
public void abort() {
throw new UnsupportedOperationException(this.getClass().getSimpleName()
+ " does not support transactions.");
for(String graphURI : g.getGraphCache().keySet()) {
Graph graph = g.getGraphCache().get(graphURI);
if(supportsTransactions(graph)) {
graph.getTransactionHandler().abort();
}
}
}
@Override
public void end() {
throw new UnsupportedOperationException(this.getClass().getSimpleName()
+ " does not support transactions.");
// the Graph tranaction handlers don't seem to support .end()
this.transactionMode = null;
g.end();
}
@Override

41
api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceDatasetGraph.java
View file

@ -6,18 +6,19 @@ import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
import com.hp.hpl.jena.graph.Graph;
import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.graph.NodeFactory;
import com.hp.hpl.jena.graph.Triple;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ReadWrite;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.shared.LockMRSW;
import com.hp.hpl.jena.sparql.core.DatasetGraph;
import com.hp.hpl.jena.sparql.core.Quad;
import com.hp.hpl.jena.sparql.resultset.JSONInput;
import com.hp.hpl.jena.sparql.util.Context;
import com.hp.hpl.jena.util.iterator.SingletonIterator;
import com.hp.hpl.jena.util.iterator.WrappedIterator;
@ -32,11 +33,25 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
private RDFService rdfService;
private Lock lock = new LockMRSW();
private Context context = new Context() ;
private Map<String, RDFServiceGraph> graphCache = new ConcurrentHashMap<String, RDFServiceGraph>();
private ReadWrite transactionMode;
public RDFServiceDatasetGraph(RDFService rdfService) {
this.rdfService = rdfService;
}
public Map<String, RDFServiceGraph> getGraphCache() {
return graphCache;
}
public void begin(ReadWrite mode) {
this.transactionMode = mode;
}
public void end() {
this.transactionMode = null;
}
private Graph getGraphFor(Quad q) {
return getGraphFor(q.getGraph());
}
@ -44,7 +59,7 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
private Graph getGraphFor(Node g) {
return (g == Node.ANY)
? new RDFServiceGraph(rdfService)
: new RDFServiceGraph(rdfService, g.getURI());
: getGraph(g);
}
@Override
@ -175,7 +190,22 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
@Override
public RDFServiceGraph getGraph(Node arg0) {
return new RDFServiceGraph(rdfService, arg0.getURI());
String graphURI = arg0.getURI();
if(graphCache.containsKey(graphURI)) {
return graphCache.get(graphURI);
} else {
RDFServiceGraph graph = new RDFServiceGraph(rdfService, arg0.getURI());
graphCache.put(graphURI, graph);
if(transactionMode != null && supportsTransactions(graph)) {
graph.getTransactionHandler().begin();
}
return graph;
}
}
private boolean supportsTransactions(Graph graph) {
return (graph.getTransactionHandler() != null
&& graph.getTransactionHandler().transactionsSupported());
}
@Override
@ -205,13 +235,11 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
@Override
public void removeGraph(Node arg0) {
// TODO Auto-generated method stub
}
@Override
public void setDefaultGraph(Graph arg0) {
// TODO Auto-generated method stub
}
@Override
@ -229,4 +257,5 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
return "RDFServiceDatasetGraph[" + ToString.hashHex(this)
+ ", " + rdfService + "]";
}
}

153
api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceGraph.java
View file

@ -5,9 +5,9 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -23,14 +23,15 @@ import com.hp.hpl.jena.graph.TripleMatch;
import com.hp.hpl.jena.graph.impl.GraphWithPerform;
import com.hp.hpl.jena.graph.impl.SimpleEventManager;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.listeners.StatementListener;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.AddDeniedException;
import com.hp.hpl.jena.shared.Command;
import com.hp.hpl.jena.shared.DeleteDeniedException;
import com.hp.hpl.jena.shared.PrefixMapping;
import com.hp.hpl.jena.shared.impl.PrefixMappingImpl;
import com.hp.hpl.jena.sparql.resultset.JSONInput;
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.util.iterator.SingletonIterator;
import com.hp.hpl.jena.util.iterator.WrappedIterator;
@ -38,6 +39,7 @@ import com.hp.hpl.jena.util.iterator.WrappedIterator;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
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.adapters.VitroModelFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
@ -52,6 +54,10 @@ public class RDFServiceGraph implements GraphWithPerform {
private PrefixMapping prefixMapping = new PrefixMappingImpl();
private GraphEventManager eventManager;
private boolean inTransaction = false;
private Graph additionsGraph = ModelFactory.createDefaultModel().getGraph();
private Graph removalsGraph = ModelFactory.createDefaultModel().getGraph();
/**
* Returns a SparqlGraph for the union of named graphs in a remote repository
* @param endpointURI
@ -91,9 +97,41 @@ public class RDFServiceGraph implements GraphWithPerform {
return sb.toString();
}
private synchronized void flush() {
ChangeSet changeSet = rdfService.manufactureChangeSet();
try {
if(!removalsGraph.isEmpty()) {
String removals = serializeGraph(removalsGraph);
changeSet.addRemoval(RDFServiceUtils.toInputStream(removals),
RDFService.ModelSerializationFormat.N3, graphURI);
removalsGraph.clear();
}
if(!additionsGraph.isEmpty()) {
String additions = serializeGraph(additionsGraph);
changeSet.addAddition(RDFServiceUtils.toInputStream(additions),
RDFService.ModelSerializationFormat.N3, graphURI);
additionsGraph.clear();
}
rdfService.changeSetUpdate(changeSet);
} catch (RDFServiceException rdfse) {
throw new RuntimeException(rdfse);
}
}
private synchronized String serializeGraph(Graph graph) {
String triples = "";
Iterator<Triple> tripIt = graph.find(null, null, null);
while(tripIt.hasNext()) {
triples += " \n" + serialize(tripIt.next());
}
return triples;
}
@Override
public void performAdd(Triple t) {
if(inTransaction) {
stageAddition(t);
} else {
ChangeSet changeSet = rdfService.manufactureChangeSet();
try {
changeSet.addAddition(RDFServiceUtils.toInputStream(serialize(t)),
@ -102,11 +140,22 @@ public class RDFServiceGraph implements GraphWithPerform {
} catch (RDFServiceException rdfse) {
throw new RuntimeException(rdfse);
}
}
}
private void stageAddition(Triple t) {
if(removalsGraph.contains(t)) {
removalsGraph.remove(t.getSubject(), t.getPredicate(), t.getObject());
} else {
additionsGraph.add(t);
}
}
@Override
public void performDelete(Triple t) {
if(inTransaction) {
stageDeletion(t);
} else {
ChangeSet changeSet = rdfService.manufactureChangeSet();
try {
changeSet.addRemoval(RDFServiceUtils.toInputStream(serialize(t)),
@ -116,6 +165,15 @@ public class RDFServiceGraph implements GraphWithPerform {
throw new RuntimeException(rdfse);
}
}
}
private synchronized void stageDeletion(Triple t) {
if(additionsGraph.contains(t)) {
additionsGraph.remove(t.getSubject(), t.getPredicate(), t.getObject());
} else {
removalsGraph.add(t);
}
}
public void removeAll() {
// only to be used with a single graph
@ -124,16 +182,30 @@ public class RDFServiceGraph implements GraphWithPerform {
}
String constructStr = "CONSTRUCT { ?s ?p ?o } WHERE { GRAPH <" + graphURI + "> { ?s ?p ?o } }";
try {
if(inTransaction) {
Model model = ModelFactory.createDefaultModel();
rdfService.sparqlConstructQuery(constructStr, model);
stageRemoveAll(model);
} else {
InputStream model = rdfService.sparqlConstructQuery(
constructStr, RDFService.ModelSerializationFormat.N3);
ChangeSet changeSet = rdfService.manufactureChangeSet();
changeSet.addRemoval(model, RDFService.ModelSerializationFormat.N3, graphURI);
rdfService.changeSetUpdate(changeSet);
}
} catch (RDFServiceException rdfse) {
throw new RuntimeException(rdfse);
}
}
private void stageRemoveAll(Model removals) {
StmtIterator sit = removals.listStatements();
while (sit.hasNext()) {
Triple t = sit.nextStatement().asTriple();
stageDeletion(t);
}
}
@Override
public void close() {
// can't close a remote endpoint
@ -167,7 +239,22 @@ public class RDFServiceGraph implements GraphWithPerform {
ResultSetConsumer.HasResult consumer = new ResultSetConsumer.HasResult();
execSelect(containsQuery.toString(), consumer);
return consumer.hasResult();
boolean initialResult = consumer.hasResult();
if(!inTransaction) {
return initialResult;
} else {
Triple t = Triple.create(subject, predicate, object);
return (initialResult || additionsGraphContains(t))
&& !removalsGraphContains(t);
}
}
private synchronized boolean additionsGraphContains(Triple t) {
return additionsGraph.contains(t);
}
private synchronized boolean removalsGraphContains(Triple t) {
return removalsGraph.contains(t);
}
@Override
@ -260,6 +347,10 @@ public class RDFServiceGraph implements GraphWithPerform {
String queryString = findQuery.toString();
final List<Triple> triplist = new ArrayList<Triple>();
if(inTransaction) {
addAdditions(triplist, additionsGraph.find(subject, predicate, object));
subtractRemovals(triplist, removalsGraph.find(subject, predicate, object));
}
execSelect(queryString, new ResultSetConsumer() {
@Override
@ -287,6 +378,24 @@ public class RDFServiceGraph implements GraphWithPerform {
return WrappedIterator.create(triplist.iterator());
}
private void addAdditions(List<Triple> tripList, ExtendedIterator<Triple> tripIt) {
while(tripIt.hasNext()) {
Triple t = tripIt.next();
if(!tripList.contains(t)) {
tripList.add(t);
}
}
}
private void subtractRemovals(List<Triple> tripList, ExtendedIterator<Triple> tripIt) {
while(tripIt.hasNext()) {
Triple t = tripIt.next();
if(tripList.contains(t)) {
tripList.remove(t);
}
}
}
private boolean isVar(Node node) {
return (node == null || node.isVariable() || node == Node.ANY);
}
@ -325,8 +434,7 @@ public class RDFServiceGraph implements GraphWithPerform {
@Override
public TransactionHandler getTransactionHandler() {
// TODO Auto-generated method stub
return null;
return transactionHandler;
}
@Override
@ -405,6 +513,37 @@ public class RDFServiceGraph implements GraphWithPerform {
}
};
private final TransactionHandler transactionHandler = new TransactionHandler() {
@Override
public synchronized void abort() {
inTransaction = false;
removalsGraph.clear();
additionsGraph.clear();
}
@Override
public synchronized void begin() {
inTransaction = true;
}
@Override
public synchronized void commit() {
flush();
inTransaction = false;
}
@Override
public Object executeInTransaction(Command arg0) {
// TODO Auto-generated method stub
return null;
}
@Override
public boolean transactionsSupported() {
return true;
}
};
private void execSelect(String queryStr, ResultSetConsumer consumer) {
try {
rdfService.sparqlSelectQuery(queryStr, consumer);

36
api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassGroupCache.java
View file

@ -16,6 +16,7 @@ import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.listeners.StatementListener;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.shared.Lock;
@ -33,6 +34,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.WebappDaoFactoryFiltering;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilterUtils;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine;
import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngineException;
@ -161,10 +163,29 @@ public class VClassGroupCache implements SearchIndexer.Listener {
VclassMap = classMap;
}
private boolean paused = false;
private boolean updateRequested = false;
public void pause() {
this.paused = true;
}
public void unpause() {
this.paused = false;
if(updateRequested) {
updateRequested = false;
requestCacheUpdate();
}
}
public void requestCacheUpdate() {
log.debug("requesting update");
if(paused) {
updateRequested = true;
} else {
_cacheRebuildThread.informOfQueueChange();
}
}
protected void requestStop() {
if (_cacheRebuildThread != null) {
@ -460,20 +481,29 @@ public class VClassGroupCache implements SearchIndexer.Listener {
log.debug("subject: " + stmt.getSubject().getURI());
log.debug("predicate: " + stmt.getPredicate().getURI());
}
if (RDF.type.getURI().equals(stmt.getPredicate().getURI())) {
if (RDF.type.equals(stmt.getPredicate())) {
requestCacheUpdate();
} else if (VitroVocabulary.IN_CLASSGROUP.equals(stmt.getPredicate().getURI())) {
requestCacheUpdate();
} else if(VitroVocabulary.DISPLAY_RANK.equals(stmt.getPredicate().getURI())){
requestCacheUpdate();
} else {
OntModel jenaOntModel = ModelAccess.on(context).getOntModel();
} else if (RDFS.label.equals(stmt.getPredicate())){
OntModel jenaOntModel = ModelAccess.on(context).getOntModelSelector().getTBoxModel();
if( isClassNameChange(stmt, jenaOntModel) ) {
requestCacheUpdate();
}
}
}
public void notifyEvent(Model model, Object event) {
if (event instanceof BulkUpdateEvent) {
if(((BulkUpdateEvent) event).getBegin()) {
pause();
} else {
unpause();
}
}
}
}

15
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/ChangeListener.java
View file

@ -9,20 +9,11 @@ package edu.cornell.mannlib.vitro.webapp.rdfservice;
public interface ChangeListener {
/**
* Override this to listen to all statements added to the RDF store.
* Override this to listen to each model change
*
* @param serializedTriple - the added statement in n3 format
* @param graphURI - the graph to which the statement was added
* @param modelChange - the object representing the model change
*/
public void addedStatement(String serializedTriple, String graphURI);
/**
* Override this to listen to all statements removed from the RDF store.
*
* @param serializedTriple - the removed statement in n3 format
* @param graphURI - the graph from which the statement was removed
*/
public void removedStatement(String serializedTriple, String graphURI);
public void notifyModelChange(ModelChange modelChange);
/**
* Override this to listen to events pertaining to the given graphURI.

23
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/RDFService.java
View file

@ -2,12 +2,13 @@
package edu.cornell.mannlib.vitro.webapp.rdfservice;
import com.hp.hpl.jena.rdf.model.Model;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.List;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
/**
* Interface for API to write, read, and update Vitro's RDF store, with support
* to allow listening, logging and auditing.
@ -207,6 +208,24 @@ public interface RDFService {
*/
public boolean isEquivalentGraph(String graphURI, Model graph) throws RDFServiceException;
/**
* Registers a Jena listener to listen to changes in any graph in
* the RDF store.
*
* @param changeListener - the change listener
*/
public void registerJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException;
/**
* Unregisters a Jena listener from listening to changes in
* any graph in the RDF store
*
* @param changeListener - the change listener
*/
public void unregisterJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException;
/**
* Registers a listener to listen to changes in any graph in
* the RDF store.

22
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/RDFServiceFactory.java
View file

@ -2,6 +2,8 @@
package edu.cornell.mannlib.vitro.webapp.rdfservice;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
public interface RDFServiceFactory {
/**
@ -37,11 +39,29 @@ public interface RDFServiceFactory {
/**
* Unregisters a listener from listening to changes in the RDF store.
* Any RDFService objects returned by this factory should notify
* Any RDFService objects returned by this factory should no longer notify
* this listener of changes.
*
* @param changeListener - the change listener
*/
public void unregisterListener(ChangeListener changeListener) throws RDFServiceException;
/**
* Registers a Jena ModelChangedListener to listen to changes in any graph in
* the RDF store. Any RDFService objects returned by this factory
* should notify this listener of changes.
*
* @param changeListener - the change listener
*/
public void registerJenaModelChangedListener(ModelChangedListener changeListener) throws RDFServiceException;
/**
* Unregisters a Jena ModelChangedListener from listening to changes in the RDF store.
* Any RDFService objects returned by this factory should no longer notify
* this listener of changes.
*
* @param changeListener - the change listener
*/
public void unregisterJenaModelChangedListener(ModelChangedListener changeListener) throws RDFServiceException;
}

17
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/filter/LanguageFilteringRDFService.java
View file

@ -12,7 +12,6 @@ import java.util.Comparator;
import java.util.Iterator;
import java.util.List;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -22,6 +21,7 @@ import com.hp.hpl.jena.query.ResultSetFactory;
import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
@ -30,6 +30,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
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.RDFServiceUtils;
public class LanguageFilteringRDFService implements RDFService {
@ -440,7 +441,6 @@ public class LanguageFilteringRDFService implements RDFService {
@Override
public void registerListener(ChangeListener changeListener)
throws RDFServiceException {
// TODO Auto-generated method stub
s.registerListener(changeListener);
}
@ -450,6 +450,19 @@ public class LanguageFilteringRDFService implements RDFService {
s.unregisterListener(changeListener);
}
@Override
public void registerJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
s.registerJenaModelChangedListener(changeListener);
}
@Override
public void unregisterJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
s.unregisterJenaModelChangedListener(changeListener);
}
@Override
public ChangeSet manufactureChangeSet() {
return s.manufactureChangeSet();

13
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/filter/SameAsFilteringRDFServiceFactory.java
View file

@ -10,7 +10,6 @@ import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -23,6 +22,7 @@ import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFactory;
import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
@ -36,6 +36,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
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;
@ -76,6 +77,16 @@ public class SameAsFilteringRDFServiceFactory implements RDFServiceFactory {
f.registerListener(changeListener);
}
@Override
public void registerJenaModelChangedListener(ModelChangedListener changeListener) throws RDFServiceException {
f.registerJenaModelChangedListener(changeListener);
}
@Override
public void unregisterJenaModelChangedListener(ModelChangedListener changeListener) throws RDFServiceException {
f.registerJenaModelChangedListener(changeListener);
}
public class SameAsFilteringRDFService extends RDFServiceImpl implements RDFService {
private final Log log = LogFactory.getLog(SameAsFilteringRDFService.class);

24
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceFactorySingle.java
View file

@ -7,6 +7,8 @@ import java.io.OutputStream;
import java.util.List;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
@ -48,6 +50,16 @@ public class RDFServiceFactorySingle implements RDFServiceFactory {
this.rdfService.unregisterListener(listener);
}
@Override
public void registerJenaModelChangedListener(ModelChangedListener listener) throws RDFServiceException {
this.rdfService.registerJenaModelChangedListener(listener);
}
@Override
public void unregisterJenaModelChangedListener(ModelChangedListener listener) throws RDFServiceException {
this.rdfService.unregisterJenaModelChangedListener(listener);
}
public class UnclosableRDFService implements RDFService {
private RDFService s;
@ -163,6 +175,18 @@ public class RDFServiceFactorySingle implements RDFServiceFactory {
s.unregisterListener(changeListener);
}
@Override
public void registerJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
s.registerJenaModelChangedListener(changeListener);
}
@Override
public void unregisterJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
s.unregisterJenaModelChangedListener(changeListener);
}
@Override
public ChangeSet manufactureChangeSet() {
return s.manufactureChangeSet();

75
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceImpl.java
View file

@ -3,12 +3,12 @@
package edu.cornell.mannlib.vitro.webapp.rdfservice.impl;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.CopyOnWriteArrayList;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -18,20 +18,21 @@ import com.hp.hpl.jena.graph.Triple;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QueryParseException;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.sparql.resultset.XMLInput;
import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange.Operation;
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.utils.logging.ToString;
public abstract class RDFServiceImpl implements RDFService {
@ -42,6 +43,7 @@ public abstract class RDFServiceImpl implements RDFService {
protected String defaultWriteGraphURI;
protected List<ChangeListener> registeredListeners = new CopyOnWriteArrayList<ChangeListener>();
protected List<ModelChangedListener> registeredJenaListeners = new CopyOnWriteArrayList<ModelChangedListener>();
@Override
public void newIndividual(String individualURI,
@ -87,7 +89,6 @@ public abstract class RDFServiceImpl implements RDFService {
@Override
public synchronized void registerListener(ChangeListener changeListener) throws RDFServiceException {
if (!registeredListeners.contains(changeListener)) {
registeredListeners.add(changeListener);
}
@ -98,40 +99,86 @@ public abstract class RDFServiceImpl implements RDFService {
registeredListeners.remove(changeListener);
}
@Override
public synchronized void registerJenaModelChangedListener(ModelChangedListener changeListener) throws RDFServiceException {
if (!registeredJenaListeners.contains(changeListener)) {
registeredJenaListeners.add(changeListener);
}
}
@Override
public synchronized void unregisterJenaModelChangedListener(ModelChangedListener changeListener) throws RDFServiceException {
registeredJenaListeners.remove(changeListener);
}
public synchronized List<ChangeListener> getRegisteredListeners() {
return this.registeredListeners;
}
public synchronized List<ModelChangedListener> getRegisteredJenaModelChangedListeners() {
return this.registeredJenaListeners;
}
@Override
public ChangeSet manufactureChangeSet() {
return new ChangeSetImpl();
}
// I switched the following two methods back to public so they could be
// used by the ListeningGraph, which is common to both implementations.
// This could probably be improved later. BJL
protected void notifyListenersOfChanges(ChangeSet changeSet)
throws IOException {
if (registeredListeners.isEmpty() && registeredJenaListeners.isEmpty()) {
return;
}
for (ModelChange modelChange: changeSet.getModelChanges()) {
notifyListeners(modelChange);
}
}
public void notifyListeners(Triple triple, ModelChange.Operation operation, String graphURI) {
protected void notifyListeners(ModelChange modelChange) throws IOException {
modelChange.getSerializedModel().reset();
Iterator<ChangeListener> iter = registeredListeners.iterator();
while (iter.hasNext()) {
ChangeListener listener = iter.next();
if (operation == ModelChange.Operation.ADD) {
listener.addedStatement(sparqlTriple(triple), graphURI);
} else {
listener.removedStatement(sparqlTriple(triple).toString(), graphURI);
listener.notifyModelChange(modelChange);
}
log.debug(registeredJenaListeners.size() + " registered Jena listeners");
if (registeredJenaListeners.isEmpty()) {
return;
}
modelChange.getSerializedModel().reset();
Model tempModel = ModelFactory.createDefaultModel();
Iterator<ModelChangedListener> jenaIter = registeredJenaListeners.iterator();
while (jenaIter.hasNext()) {
ModelChangedListener listener = jenaIter.next();
log.debug("\t" + listener.getClass().getSimpleName());
tempModel.register(listener);
}
if (Operation.ADD.equals(modelChange.getOperation())) {
tempModel.read(modelChange.getSerializedModel(), null,
RDFServiceUtils.getSerializationFormatString(
modelChange.getSerializationFormat()));
} else if (Operation.REMOVE.equals(modelChange.getOperation())) {
tempModel.remove(RDFServiceUtils.parseModel(
modelChange.getSerializedModel(),
modelChange.getSerializationFormat()));
}
while (jenaIter.hasNext()) {
tempModel.unregister(jenaIter.next());
}
}
public void notifyListenersOfEvent(Object event) {
Iterator<ChangeListener> iter = registeredListeners.iterator();
while (iter.hasNext()) {
ChangeListener listener = iter.next();
// TODO what is the graphURI parameter for?
listener.notifyEvent(null, event);
}
Iterator<ModelChangedListener> jenaIter = registeredJenaListeners.iterator();
while (jenaIter.hasNext()) {
ModelChangedListener listener = jenaIter.next();
listener.notifyEvent(null, event);
}
}
protected boolean isPreconditionSatisfied(String query,

236
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/ListeningGraph.java
View file

@ -1,236 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.graph.BulkUpdateHandler;
import com.hp.hpl.jena.graph.Capabilities;
import com.hp.hpl.jena.graph.Graph;
import com.hp.hpl.jena.graph.GraphEventManager;
import com.hp.hpl.jena.graph.GraphStatisticsHandler;
import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.graph.TransactionHandler;
import com.hp.hpl.jena.graph.Triple;
import com.hp.hpl.jena.graph.TripleMatch;
import com.hp.hpl.jena.graph.impl.GraphWithPerform;
import com.hp.hpl.jena.graph.impl.SimpleBulkUpdateHandler;
import com.hp.hpl.jena.graph.impl.SimpleEventManager;
import com.hp.hpl.jena.shared.AddDeniedException;
import com.hp.hpl.jena.shared.DeleteDeniedException;
import com.hp.hpl.jena.shared.PrefixMapping;
import com.hp.hpl.jena.shared.impl.PrefixMappingImpl;
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.util.iterator.WrappedIterator;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ModelChange;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceImpl;
import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
public class ListeningGraph implements GraphWithPerform {
private static final Log log = LogFactory.getLog(ListeningGraph.class);
private RDFServiceImpl rdfServiceImpl;
private String graphURI;
private BulkUpdateHandler bulkUpdateHandler;
private GraphEventManager eventManager;
private PrefixMapping prefixMapping = new PrefixMappingImpl();
public ListeningGraph(String graphURI, RDFServiceImpl rdfServiceImpl) {
this.graphURI = graphURI;
this.rdfServiceImpl = rdfServiceImpl;
}
@Override
public void add(Triple triple) throws AddDeniedException {
performAdd(triple);
}
@Override
public void performAdd(Triple triple) throws AddDeniedException {
if (log.isDebugEnabled()) {
log.debug("adding " + triple + " to " + graphURI);
}
this.rdfServiceImpl.notifyListeners(triple, ModelChange.Operation.ADD, graphURI);
}
@Override
public void delete(Triple triple) throws DeleteDeniedException {
performDelete(triple);
}
@Override
public void performDelete(Triple triple) throws DeleteDeniedException {
if (log.isDebugEnabled()) {
log.debug("deleting " + triple + " from " + graphURI);
}
this.rdfServiceImpl.notifyListeners(triple, ModelChange.Operation.REMOVE, graphURI);
}
@Override
public void close() {
// Nothing to close.
}
@Override
public boolean contains(Triple arg0) {
return contains(arg0.getSubject(), arg0.getPredicate(), arg0.getObject());
}
@Override
public boolean contains(Node subject, Node predicate, Node object) {
return false;
}
@Override
public boolean dependsOn(Graph arg0) {
return false; // who knows?
}
@Override
public ExtendedIterator<Triple> find(TripleMatch arg0) {
Triple t = arg0.asTriple();
return find(t.getSubject(), t.getPredicate(), t.getObject());
}
@Override
public ExtendedIterator<Triple> find(Node subject, Node predicate, Node object) {
List<Triple> triplist = new ArrayList<Triple>();
return WrappedIterator.create(triplist.iterator());
}
@Override
public void clear() {
for (Triple t: find(null, null, null).toList()) {
delete(t);
}
}
@Override
public void remove(Node subject, Node predicate, Node object) {
for (Triple t: find(subject, predicate, object).toList()) {
delete(t);
}
}
@Override
@Deprecated
public BulkUpdateHandler getBulkUpdateHandler() {
if (this.bulkUpdateHandler == null) {
this.bulkUpdateHandler = new SimpleBulkUpdateHandler(this);
}
return this.bulkUpdateHandler;
}
@Override
public Capabilities getCapabilities() {
return capabilities;
}
@Override
public GraphEventManager getEventManager() {
if (eventManager == null) {
eventManager = new SimpleEventManager(this);
}
return eventManager;
}
@Override
public PrefixMapping getPrefixMapping() {
return prefixMapping;
}
@Override
public GraphStatisticsHandler getStatisticsHandler() {
return null;
}
@Override
public TransactionHandler getTransactionHandler() {
return null;
}
@Override
public boolean isClosed() {
return false;
}
@Override
public boolean isEmpty() {
return !contains(null, null, null);
}
@Override
public boolean isIsomorphicWith(Graph arg0) {
throw new UnsupportedOperationException("isIsomorphicWith() not supported " +
"by SPARQL graphs");
}
@Override
public int size() {
int size = find(null, null, null).toList().size();
return size;
}
private final static Capabilities capabilities = new Capabilities() {
@Override
public boolean addAllowed() {
return false;
}
@Override
public boolean addAllowed(boolean everyTriple) {
return false;
}
@Override
public boolean canBeEmpty() {
return true;
}
@Override
public boolean deleteAllowed() {
return false;
}
@Override
public boolean deleteAllowed(boolean everyTriple) {
return false;
}
@Override
public boolean findContractSafe() {
return true;
}
@Override
public boolean handlesLiteralTyping() {
return true;
}
@Override
public boolean iteratorRemoveAllowed() {
return false;
}
@Override
public boolean sizeAccurate() {
return true;
}
};
@Override
public String toString() {
return "ListeningGraph["+ToString.hashHex(this)
+ ", " + rdfServiceImpl
+ ", " + ToString.modelName(graphURI) + "]";
}
}

10
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java
View file

@ -91,16 +91,6 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
}
}
protected void notifyListenersOfChanges(ChangeSet changeSet)
throws IOException {
for (ModelChange modelChange: changeSet.getModelChanges()) {
modelChange.getSerializedModel().reset();
Model model = ModelFactory.createModelForGraph(
new ListeningGraph(modelChange.getGraphURI(), this));
operateOnModel(model, modelChange, null);
}
}
protected void notifyListenersOfPostChangeEvents(ChangeSet changeSet) {
for (Object o : changeSet.getPostChangeEvents()) {
this.notifyListenersOfEvent(o);

19
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/model/RDFServiceModel.java
View file

@ -12,14 +12,12 @@ import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.DatasetFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
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.impl.jena.ListeningGraph;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena;
public class RDFServiceModel extends RDFServiceJena implements RDFService {
@ -102,14 +100,15 @@ public class RDFServiceModel extends RDFServiceJena implements RDFService {
}
// notify listeners of triple changes
csIt = changeSet.getModelChanges().iterator();
while (csIt.hasNext()) {
ModelChange modelChange = csIt.next();
modelChange.getSerializedModel().reset();
Model model = ModelFactory.createModelForGraph(
new ListeningGraph(modelChange.getGraphURI(), this));
operateOnModel(model, modelChange, null);
}
notifyListenersOfChanges(changeSet);
// csIt = changeSet.getModelChanges().iterator();
// while (csIt.hasNext()) {
// ModelChange modelChange = csIt.next();
// modelChange.getSerializedModel().reset();
// Model model = ModelFactory.createModelForGraph(
// new ListeningGraph(modelChange.getGraphURI(), this));
// operateOnModel(model, modelChange, null);
// }
for (Object o : changeSet.getPostChangeEvents()) {
this.notifyListenersOfEvent(o);

17
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/sdb/RDFServiceFactorySDB.java
View file

@ -7,6 +7,7 @@ import javax.sql.DataSource;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import com.hp.hpl.jena.sdb.StoreDesc;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
@ -41,6 +42,10 @@ public class RDFServiceFactorySDB implements RDFServiceFactory {
.getRegisteredListeners() ) {
rdfService.registerListener(cl);
}
for (ModelChangedListener cl : ((RDFServiceSDB) longTermRDFService)
.getRegisteredJenaModelChangedListeners() ) {
rdfService.registerJenaModelChangedListener(cl);
}
return rdfService;
} catch (Exception e) {
log.error(e,e);
@ -60,4 +65,16 @@ public class RDFServiceFactorySDB implements RDFServiceFactory {
this.longTermRDFService.unregisterListener(changeListener);
}
@Override
public void registerJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
this.longTermRDFService.registerJenaModelChangedListener(changeListener);
}
@Override
public void unregisterJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
this.longTermRDFService.unregisterJenaModelChangedListener(changeListener);
}
}

18
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/sdb/RDFServiceSDB.java
View file

@ -2,10 +2,9 @@
package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.sdb;
import java.io.IOException;
import java.sql.Connection;
import java.sql.SQLException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.sql.DataSource;
@ -23,6 +22,8 @@ import com.hp.hpl.jena.sdb.sql.SDBConnection;
import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
import edu.cornell.mannlib.vitro.webapp.dao.jena.StaticDatasetFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
@ -76,20 +77,19 @@ public class RDFServiceSDB extends RDFServiceJena implements RDFService {
SDBConnection sdbConn = getSDBConnection();
Dataset dataset = getDataset(sdbConn);
try {
insureThatInputStreamsAreResettable(changeSet);
} catch (IOException e) {
throw new RuntimeException(e);
}
try {
beginTransaction(sdbConn);
notifyListenersOfPreChangeEvents(changeSet);
applyChangeSetToModel(changeSet, dataset);
commitTransaction(sdbConn);
notifyListenersOfChanges(changeSet);
notifyListenersOfPostChangeEvents(changeSet);
return true;
} catch (Exception e) {
log.error(e, e);
@ -140,10 +140,6 @@ public class RDFServiceSDB extends RDFServiceJena implements RDFService {
}
}
private static final Pattern OPTIONAL_PATTERN = Pattern.compile("optional", Pattern.CASE_INSENSITIVE);
private static final Pattern GRAPH_PATTERN = Pattern.compile("graph", Pattern.CASE_INSENSITIVE);
@Override
protected QueryExecution createQueryExecution(String queryString, Query q, Dataset d) {
return QueryExecutionFactory.create(q, d);

14
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/logging/LoggingRDFService.java
View file

@ -7,6 +7,8 @@ import java.io.OutputStream;
import java.util.List;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
@ -163,6 +165,18 @@ public class LoggingRDFService implements RDFService {
innerService.unregisterListener(changeListener);
}
@Override
public void registerJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
innerService.registerJenaModelChangedListener(changeListener);
}
@Override
public void unregisterJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
innerService.unregisterJenaModelChangedListener(changeListener);
}
@Override
public ChangeSet manufactureChangeSet() {
return innerService.manufactureChangeSet();

14
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/logging/LoggingRDFServiceFactory.java
View file

@ -2,6 +2,8 @@
package edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
@ -40,6 +42,18 @@ public class LoggingRDFServiceFactory implements RDFServiceFactory {
factory.unregisterListener(changeListener);
}
@Override
public void registerJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
factory.registerJenaModelChangedListener(changeListener);
}
@Override
public void unregisterJenaModelChangedListener(ModelChangedListener changeListener)
throws RDFServiceException {
factory.unregisterJenaModelChangedListener(changeListener);
}
@Override
public String toString() {
return "LoggingRDFServiceFactory[factory=" + factory + "]";

113
api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java
View file

@ -16,8 +16,6 @@ import java.util.Iterator;
import java.util.List;
import java.util.concurrent.ConcurrentLinkedQueue;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.utils.http.HttpClientFactory;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -65,10 +63,11 @@ 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.ChangeSetImpl;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceImpl;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.ListeningGraph;
import edu.cornell.mannlib.vitro.webapp.utils.http.HttpClientFactory;
import edu.cornell.mannlib.vitro.webapp.utils.sparql.ResultSetIterators.ResultSetQuadsIterator;
import edu.cornell.mannlib.vitro.webapp.utils.sparql.ResultSetIterators.ResultSetTriplesIterator;
@ -83,7 +82,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
protected String readEndpointURI;
protected String updateEndpointURI;
// the number of triples to be
private static final int CHUNK_SIZE = 1000; // added/removed in a single
private static final int CHUNK_SIZE = 5000; // added/removed in a single
// SPARQL UPDATE
protected HttpClient httpClient;
@ -174,6 +173,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
}
try {
for (Object o : changeSet.getPreChangeEvents()) {
this.notifyListenersOfEvent(o);
}
@ -189,28 +189,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
performChange(modelChange);
}
// notify listeners of triple changes
csIt = changeSet.getModelChanges().iterator();
while (csIt.hasNext()) {
ModelChange modelChange = csIt.next();
modelChange.getSerializedModel().reset();
Model model = ModelFactory.createModelForGraph(
new ListeningGraph(modelChange.getGraphURI(), this));
if (modelChange.getOperation() == ModelChange.Operation.ADD) {
model.read(modelChange.getSerializedModel(), null,
getSerializationFormatString(
modelChange.getSerializationFormat()));
} else if (modelChange.getOperation() == ModelChange.Operation.REMOVE){
Model temp = ModelFactory.createDefaultModel();
temp.read(modelChange.getSerializedModel(), null,
getSerializationFormatString(
modelChange.getSerializationFormat()));
model.remove(temp);
} else {
log.error("Unsupported model change type " +
modelChange.getOperation().getClass().getName());
}
}
notifyListenersOfChanges(changeSet);
for (Object o : changeSet.getPostChangeEvents()) {
this.notifyListenersOfEvent(o);
@ -468,7 +447,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
*/
@Override
public void getGraphMetadata() throws RDFServiceException {
throw new UnsupportedOperationException();
}
/**
@ -549,7 +528,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
public void addModel(Model model, String graphURI) throws RDFServiceException {
try {
long start = System.currentTimeMillis();
verbModel(model, graphURI, "INSERT");
log.info((System.currentTimeMillis() - start) + " ms to insert " + model.size() + " triples");
} finally {
rebuildGraphURICache = true;
}
@ -591,45 +572,45 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
}
}
protected void addTriple(Triple t, String graphURI) throws RDFServiceException {
try {
StringBuffer updateString = new StringBuffer();
updateString.append("INSERT DATA { ");
updateString.append((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "");
updateString.append(sparqlNodeUpdate(t.getSubject(), ""));
updateString.append(" ");
updateString.append(sparqlNodeUpdate(t.getPredicate(), ""));
updateString.append(" ");
updateString.append(sparqlNodeUpdate(t.getObject(), ""));
updateString.append(" }");
updateString.append((graphURI != null) ? " } " : "");
executeUpdate(updateString.toString());
notifyListeners(t, ModelChange.Operation.ADD, graphURI);
} finally {
rebuildGraphURICache = true;
}
}
protected void removeTriple(Triple t, String graphURI) throws RDFServiceException {
try {
StringBuffer updateString = new StringBuffer();
updateString.append("DELETE DATA { ");
updateString.append((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "");
updateString.append(sparqlNodeUpdate(t.getSubject(), ""));
updateString.append(" ");
updateString.append(sparqlNodeUpdate(t.getPredicate(), ""));
updateString.append(" ");
updateString.append(sparqlNodeUpdate(t.getObject(), ""));
updateString.append(" }");
updateString.append((graphURI != null) ? " } " : "");
executeUpdate(updateString.toString());
notifyListeners(t, ModelChange.Operation.REMOVE, graphURI);
} finally {
rebuildGraphURICache = true;
}
}
// protected void addTriple(Triple t, String graphURI) throws RDFServiceException {
// try {
// StringBuffer updateString = new StringBuffer();
// updateString.append("INSERT DATA { ");
// updateString.append((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "");
// updateString.append(sparqlNodeUpdate(t.getSubject(), ""));
// updateString.append(" ");
// updateString.append(sparqlNodeUpdate(t.getPredicate(), ""));
// updateString.append(" ");
// updateString.append(sparqlNodeUpdate(t.getObject(), ""));
// updateString.append(" }");
// updateString.append((graphURI != null) ? " } " : "");
//
// executeUpdate(updateString.toString());
// notifyListeners(t, ModelChange.Operation.ADD, graphURI);
// } finally {
// rebuildGraphURICache = true;
// }
// }
//
// protected void removeTriple(Triple t, String graphURI) throws RDFServiceException {
// try {
// StringBuffer updateString = new StringBuffer();
// updateString.append("DELETE DATA { ");
// updateString.append((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "");
// updateString.append(sparqlNodeUpdate(t.getSubject(), ""));
// updateString.append(" ");
// updateString.append(sparqlNodeUpdate(t.getPredicate(), ""));
// updateString.append(" ");
// updateString.append(sparqlNodeUpdate(t.getObject(), ""));
// updateString.append(" }");
// updateString.append((graphURI != null) ? " } " : "");
//
// executeUpdate(updateString.toString());
// notifyListeners(t, ModelChange.Operation.REMOVE, graphURI);
// } finally {
// rebuildGraphURICache = true;
// }
// }
@Override
protected boolean isPreconditionSatisfied(String query,

144
api/src/main/java/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java
View file

@ -10,14 +10,11 @@ import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Queue;
import java.util.Set;
import com.hp.hpl.jena.rdf.model.NodeIterator;
import com.hp.hpl.jena.rdf.model.Property;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -31,6 +28,8 @@ import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.NodeIterator;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
@ -47,6 +46,7 @@ import edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
public class ABoxRecomputer {
@ -62,7 +62,7 @@ public class ABoxRecomputer {
private volatile boolean recomputing = false;
private boolean stopRequested = false;
private final int BATCH_SIZE = 100;
private final int BATCH_SIZE = 500;
private final int REPORTING_INTERVAL = 1000;
/**
@ -92,7 +92,7 @@ public class ABoxRecomputer {
}
/**
* Recompute all inferences.
* Recompute all individuals
*/
public void recompute() {
synchronized (lock1) {
@ -109,11 +109,16 @@ public class ABoxRecomputer {
// This allows the indexer to optimize behaviour whilst paused
searchIndexer.rebuildIndex();
}
log.info("Recomputing ABox inferences.");
log.info("Finding individuals in ABox.");
Queue<String>individualURIs = this.getAllIndividualURIs();
log.info("Recomputing inferences for " + individualURIs.size() + " individuals");
// Create a type cache for this execution and pass it to the recompute function
// Ensures that caches are only valid for the length of one recompute
recomputeABox(new TypeCaches());
recomputeIndividuals(individualURIs, new TypeCaches());
log.info("Finished recomputing inferences");
} finally {
if (searchIndexer != null) {
if(searchIndexer != null) {
searchIndexer.unpause();
}
synchronized (lock1) {
@ -122,30 +127,56 @@ public class ABoxRecomputer {
}
}
/*
* Recompute the entire ABox inference graph.
/**
* Recompute inferences for specified collection of individual URIs,
* or all URIs if parameter is null
*/
protected void recomputeABox(TypeCaches caches) {
log.info("Recomputing ABox inferences.");
log.info("Finding individuals in ABox.");
Collection<String> individuals = this.getAllIndividualURIs();
log.info("Recomputing inferences for " + individuals.size() + " individuals");
public void recompute(Queue<String> individualURIs) {
boolean sizableRecompute = (individualURIs.size() > 20);
try {
if(sizableRecompute && searchIndexer != null) {
searchIndexer.pause();
}
recomputeIndividuals(individualURIs);
} finally {
if (sizableRecompute && searchIndexer != null) {
searchIndexer.unpause();
}
}
}
/*
* Recompute the ABox inference graph for the specified collection of
* individual URIs
*/
private void recomputeIndividuals(Queue<String> individuals) {
recomputeIndividuals(individuals, new TypeCaches());
}
/*
* Recompute the ABox inference graph for the specified collection of
* individual URIs
*/
protected void recomputeIndividuals(Queue<String> individuals, TypeCaches caches) {
if (individuals == null) {
return;
}
long start = System.currentTimeMillis();
int size = individuals.size();
int numInds = 0;
Model rebuildModel = ModelFactory.createDefaultModel();
Model additionalInferences = ModelFactory.createDefaultModel();
List<String> individualsInBatch = new ArrayList<String>();
Iterator<String> individualIt = individuals.iterator();
while (individualIt.hasNext()) {
String individualURI = individualIt.next();
while (!individuals.isEmpty()) {
String individualURI = individuals.poll();
try {
additionalInferences.add(recomputeIndividual(
individualURI, rebuildModel, caches));
individualURI, rebuildModel, caches, individuals));
numInds++;
individualsInBatch.add(individualURI);
boolean batchFilled = (numInds % BATCH_SIZE) == 0;
boolean reportingInterval = (numInds % REPORTING_INTERVAL) == 0;
if (batchFilled || !individualIt.hasNext()) {
if (batchFilled || individuals.isEmpty()) {
log.debug(rebuildModel.size() + " total inferences");
updateInferenceModel(rebuildModel, individualsInBatch);
rebuildModel.removeAll();
@ -153,11 +184,11 @@ public class ABoxRecomputer {
}
if (reportingInterval) {
log.info("Still recomputing inferences ("
+ numInds + "/" + individuals.size() + " individuals)");
+ numInds + "/" + size + " individuals)");
log.info((System.currentTimeMillis() - start) / numInds + " ms per individual");
}
if (stopRequested) {
log.info("a stopRequested signal was received during recomputeABox. Halting Processing.");
log.info("a stopRequested signal was received during recomputeIndividuals. Halting Processing.");
return;
}
} catch (Exception e) {
@ -165,7 +196,7 @@ public class ABoxRecomputer {
}
}
if(additionalInferences.size() > 0) {
log.info("Writing additional inferences generated by reasoner plugins.");
log.debug("Writing additional inferences generated by reasoner plugins.");
ChangeSet change = rdfService.manufactureChangeSet();
change.addAddition(makeN3InputStream(additionalInferences),
RDFService.ModelSerializationFormat.N3, ModelNames.ABOX_INFERENCES);
@ -175,20 +206,20 @@ public class ABoxRecomputer {
log.error("Unable to write additional inferences from reasoner plugins", e);
}
}
log.info("Finished recomputing inferences");
}
private static final boolean RUN_PLUGINS = true;
private static final boolean SKIP_PLUGINS = !RUN_PLUGINS;
private Model recomputeIndividual(String individualURI,
Model rebuildModel, TypeCaches caches) throws RDFServiceException {
Model rebuildModel, TypeCaches caches, Collection<String> individualQueue)
throws RDFServiceException {
long start = System.currentTimeMillis();
Model assertions = getAssertions(individualURI);
log.trace((System.currentTimeMillis() - start) + " ms to get assertions.");
log.debug((System.currentTimeMillis() - start) + " ms to get assertions.");
long prevRebuildSize = (simpleReasoner.getSameAsEnabled()) ? rebuildModel.size() : 0;
Model additionalInferences = recomputeIndividual(
individualURI, null, assertions, rebuildModel, caches, RUN_PLUGINS);
if (simpleReasoner.getSameAsEnabled()) {
Set<String> sameAsInds = getSameAsIndividuals(individualURI);
for (String sameAsInd : sameAsInds) {
@ -201,10 +232,18 @@ public class ABoxRecomputer {
Resource indRes = ResourceFactory.createResource(individualURI);
Resource sameAsIndRes = ResourceFactory.createResource(sameAsInd);
if(!assertions.contains(indRes, OWL.sameAs, sameAsIndRes)) {
if(!rebuildModel.contains(indRes, OWL.sameAs, sameAsIndRes)) {
individualQueue.add(sameAsInd);
rebuildModel.add(indRes, OWL.sameAs, sameAsIndRes);
}
}
}
if(rebuildModel.size() - prevRebuildSize > 0) {
for (String sameAsInd : sameAsInds) {
individualQueue.add(sameAsInd);
}
}
}
return additionalInferences;
}
@ -330,7 +369,6 @@ public class ABoxRecomputer {
mostSpecificTypes = getMostSpecificTypes(individual, assertedTypes);
caches.cacheMostSpecificTypes(key, mostSpecificTypes);
}
return mostSpecificTypes;
}
@ -343,6 +381,8 @@ public class ABoxRecomputer {
" FILTER NOT EXISTS { \n" +
" <" + individual.getURI() + "> a ?type2 . \n" +
" ?type2 <" + RDFS.subClassOf.getURI() + "> ?type. \n" +
" FILTER (?type != ?type2) \n" +
" FILTER NOT EXISTS { ?type <" + OWL.equivalentClass + "> ?type2 } \n" +
" } \n" +
" FILTER NOT EXISTS { \n" +
" <" + individual.getURI() + "> <" + VitroVocabulary.MOST_SPECIFIC_TYPE + "> ?type \n" +
@ -395,8 +435,8 @@ public class ABoxRecomputer {
/*
* Get the URIs for all individuals in the system
*/
protected Collection<String> getAllIndividualURIs() {
HashSet<String> individualURIs = new HashSet<String>();
protected Queue<String> getAllIndividualURIs() {
Queue<String> individualURIs = new IndividualURIQueue<String>();
List<String> classList = new ArrayList<String>();
tboxModel.enterCriticalSection(Lock.READ);
try {
@ -420,7 +460,7 @@ public class ABoxRecomputer {
return individualURIs;
}
protected void getIndividualURIs(String queryString, Set<String> individuals) {
protected void getIndividualURIs(String queryString, Queue<String> individuals) {
int batchSize = 50000;
int offset = 0;
boolean done = false;
@ -507,7 +547,7 @@ public class ABoxRecomputer {
return new ByteArrayInputStream(out.toByteArray());
}
private Set<String> getSameAsIndividuals(String individualURI) {
public Set<String> getSameAsIndividuals(String individualURI) {
HashSet<String> sameAsInds = new HashSet<String>();
sameAsInds.add(individualURI);
getSameAsIndividuals(individualURI, sameAsInds);
@ -519,14 +559,18 @@ public class ABoxRecomputer {
try {
final List<String> addedURIs = new ArrayList<String>();
StringBuilder builder = new StringBuilder();
builder.append("SELECT\n")
.append(" ?object\n")
.append("WHERE\n")
.append("{\n")
.append("WHERE {\n")
.append(" GRAPH ?g { \n")
.append(" {\n")
.append(" <" + individualUri + "> <" + OWL.sameAs + "> ?object .\n")
.append(" } UNION {\n")
.append(" ?object <" + OWL.sameAs + "> <" + individualUri + "> .\n")
.append(" }\n")
.append(" } \n")
.append(" FILTER (?g != <" + ModelNames.ABOX_INFERENCES + ">)\n")
.append("}\n");
rdfService.sparqlSelectQuery(builder.toString(), new ResultSetConsumer() {
@Override
protected void processQuerySolution(QuerySolution qs) {
@ -537,37 +581,11 @@ public class ABoxRecomputer {
}
}
});
for (String indUri : addedURIs) {
getSameAsIndividuals(indUri, sameAsInds);
}
addedURIs.clear();
builder = new StringBuilder();
builder.append("SELECT\n")
.append(" ?subject\n")
.append("WHERE\n")
.append("{\n")
.append(" ?subject <" + OWL.sameAs + "> <" + individualUri + "> .\n")
.append("}\n");
rdfService.sparqlSelectQuery(builder.toString(), new ResultSetConsumer() {
@Override
protected void processQuerySolution(QuerySolution qs) {
Resource object = qs.getResource("subject");
if (object != null && !sameAsInds.contains(object.getURI())) {
sameAsInds.add(object.getURI());
addedURIs.add(object.getURI());
}
}
});
for (String indUri : addedURIs) {
getSameAsIndividuals(indUri, sameAsInds);
}
} catch (RDFServiceException e) {
log.error(e,e);
}
}

143
api/src/main/java/edu/cornell/mannlib/vitro/webapp/reasoner/IndividualURIQueue.java Normal file
View file

@ -0,0 +1,143 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.reasoner;
import java.util.Collection;
import java.util.Iterator;
import java.util.Queue;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ConcurrentLinkedQueue;
public class IndividualURIQueue<E> implements Queue<E> {
private ConcurrentLinkedQueue<E> q = new ConcurrentLinkedQueue<E>();
private ConcurrentHashMap<E, Boolean> m = new ConcurrentHashMap<E, Boolean>();
@Override
public synchronized boolean addAll(Collection<? extends E> c) {
boolean changed = false;
for (E e : c) {
if(!m.containsKey(e)) {
m.put(e, Boolean.TRUE);
q.add(e);
changed = true;
}
}
return changed;
}
@Override
public synchronized void clear() {
m.clear();
q.clear();
}
@Override
public boolean contains(Object o) {
return m.contains(o);
}
@Override
public boolean containsAll(Collection<?> c) {
boolean contains = true;
for(Object e : c) {
contains |= m.contains(e);
}
return contains;
}
@Override
public boolean isEmpty() {
return q.isEmpty();
}
@Override
public Iterator<E> iterator() {
return q.iterator();
}
@Override
public synchronized boolean remove(Object o) {
m.remove(o);
return q.remove(o);
}
@Override
public synchronized boolean removeAll(Collection<?> c) {
for (Object e : c) {
m.remove(e);
}
return q.removeAll(c);
}
@Override
public synchronized boolean retainAll(Collection<?> c) {
boolean changed = false;
Iterator<E> it = m.keySet().iterator();
while(it.hasNext()) {
E e = it.next();
if(!c.contains(e)) {
m.remove(e);
q.remove(e);
changed = true;
}
}
return changed;
}
@Override
public int size() {
return m.size();
}
@Override
public Object[] toArray() {
return q.toArray();
}
@Override
public <T> T[] toArray(T[] a) {
return q.toArray(a);
}
@Override
public synchronized boolean add(E e) {
if(m.containsKey(e)) {
return false;
} else {
m.put(e, Boolean.TRUE);
q.add(e);
return true;
}
}
@Override
public E element() {
return q.element();
}
@Override
public boolean offer(E e) {
return q.offer(e);
}
@Override
public E peek() {
return q.peek();
}
@Override
public synchronized E poll() {
E e = q.poll();
m.remove(e);
return e;
}
@Override
public synchronized E remove() {
E e = q.remove();
m.remove(e);
return e;
}
}

758
api/src/main/java/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -2,12 +2,11 @@
package edu.cornell.mannlib.vitro.webapp.reasoner;
import static edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread.WorkLevel.WORKING;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Queue;
import java.util.Set;
import java.util.concurrent.CopyOnWriteArrayList;
@ -23,7 +22,9 @@ import com.hp.hpl.jena.query.DatasetFactory;
import com.hp.hpl.jena.rdf.listeners.StatementListener;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.NodeIterator;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResIterator;
@ -37,18 +38,17 @@ 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.dao.jena.ABoxJenaChangeListener;
import edu.cornell.mannlib.vitro.webapp.dao.jena.CumulativeDeltaModeler;
import edu.cornell.mannlib.vitro.webapp.dao.jena.DifferenceGraph;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames;
import edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
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.adapters.VitroModelFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
/**
* Allows for real-time incremental materialization or retraction of RDFS-
@ -57,7 +57,8 @@ import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
* @author sjm222
*/
public class SimpleReasoner extends StatementListener {
public class SimpleReasoner extends StatementListener
implements ModelChangedListener, ChangeListener {
private static final Log log = LogFactory.getLog(SimpleReasoner.class);
@ -75,18 +76,8 @@ public class SimpleReasoner extends StatementListener {
VitroModelFactory.createOntologyModel())
.createAnnotationProperty(mostSpecificTypePropertyURI);
// DeltaComputer
private CumulativeDeltaModeler aBoxDeltaModeler1 = null;
private CumulativeDeltaModeler aBoxDeltaModeler2 = null;
private int batchMode = 0; // values: 0, 1 and 2
// Recomputer
private ABoxRecomputer recomputer = null;
private boolean stopRequested = false;
private List<ReasonerPlugin> pluginList = new CopyOnWriteArrayList<ReasonerPlugin>();
private boolean doSameAs = true;
/**
@ -122,17 +113,13 @@ public class SimpleReasoner extends StatementListener {
tboxModel.getGraph())));
this.inferenceModel = inferenceModel;
this.batchMode = 0;
aBoxDeltaModeler1 = new CumulativeDeltaModeler();
aBoxDeltaModeler2 = new CumulativeDeltaModeler();
recomputer = new ABoxRecomputer(tboxModel, aboxModel, rdfService, this, searchIndexer);
stopRequested = false;
if (rdfService == null) {
aboxModel.register(this);
} else {
try {
rdfService.registerListener(new ABoxJenaChangeListener(this));
rdfService.registerListener(this);
} catch (RDFServiceException e) {
throw new RuntimeException("Unable to register change listener", e);
}
@ -154,15 +141,10 @@ public class SimpleReasoner extends StatementListener {
this.inferenceModel = inferenceModel;
this.fullModel = VitroModelFactory.createUnion(aboxModel,
VitroModelFactory.createOntologyModel(inferenceModel));
aBoxDeltaModeler1 = new CumulativeDeltaModeler();
aBoxDeltaModeler2 = new CumulativeDeltaModeler();
this.batchMode = 0;
stopRequested = false;
Dataset ds = DatasetFactory.createMem();
ds.addNamedModel(ModelNames.ABOX_ASSERTIONS, aboxModel);
ds.addNamedModel(ModelNames.ABOX_INFERENCES, inferenceModel);
ds.addNamedModel(ModelNames.TBOX_ASSERTIONS, tboxModel);
ds.setDefaultModel(ModelFactory.createUnion(fullModel, tboxModel));
recomputer = new ABoxRecomputer(tboxModel, aboxModel, new RDFServiceModel(ds), this, searchIndexer);
}
@ -183,6 +165,21 @@ public class SimpleReasoner extends StatementListener {
return this.doSameAs;
}
public void notifyModelChange(ModelChange modelChange) {
if(isABoxInferenceGraph(modelChange.getGraphURI())
|| isTBoxGraph(modelChange.getGraphURI())) {
return;
}
Queue<String> individualURIs = new IndividualURIQueue<String>();
Model m = RDFServiceUtils.parseModel(modelChange.getSerializedModel(),
modelChange.getSerializationFormat());
StmtIterator sit = m.listStatements();
while(sit.hasNext()) {
queueRelevantIndividuals(sit.nextStatement(), individualURIs);
}
recomputeIndividuals(individualURIs);
}
/*
* Performs incremental ABox reasoning based
* on the addition of a new statement
@ -190,21 +187,8 @@ public class SimpleReasoner extends StatementListener {
*/
@Override
public void addedStatement(Statement stmt) {
try {
if (stmt.getPredicate().equals(RDF.type)) {
addedABoxTypeAssertion(stmt, inferenceModel, new HashSet<String>());
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
} else if ( doSameAs && stmt.getPredicate().equals(OWL.sameAs)) {
addedABoxSameAsAssertion(stmt, inferenceModel);
} else {
addedABoxAssertion(stmt, inferenceModel);
}
doPlugins(ModelUpdate.Operation.ADD,stmt);
} catch (Exception e) { // don't stop the edit if there's an exception
log.error("Exception while computing inferences: " + e.getMessage());
}
listenToStatement(stmt, new IndividualURIQueue<String>());
}
/*
@ -214,31 +198,42 @@ public class SimpleReasoner extends StatementListener {
*/
@Override
public void removedStatement(Statement stmt) {
try {
handleRemovedStatement(stmt);
} catch (Exception e) { // don't stop the edit if there's an exception
log.error("Exception while retracting inferences: ", e);
doPlugins(ModelUpdate.Operation.RETRACT,stmt);
Queue<String> individualURIs = new IndividualURIQueue<String>();
if(doSameAs && OWL.sameAs.equals(stmt.getPredicate())) {
if (stmt.getSubject().isURIResource()) {
individualURIs.addAll(this.recomputer.getSameAsIndividuals(
stmt.getSubject().getURI()));
}
if (stmt.getObject().isURIResource()) {
individualURIs.addAll(this.recomputer.getSameAsIndividuals(
stmt.getObject().asResource().getURI()));
}
}
listenToStatement(stmt, individualURIs);
}
private void listenToStatement(Statement stmt, Queue<String> individualURIs) {
queueRelevantIndividuals(stmt, individualURIs);
recomputeIndividuals(individualURIs);
}
private void queueRelevantIndividuals(Statement stmt, Queue<String> individualURIs) {
if(stmt.getSubject().isURIResource()) {
individualURIs.add(stmt.getSubject().getURI());
}
if(stmt.getObject().isURIResource() && !(RDF.type.equals(stmt.getPredicate()))) {
individualURIs.add(stmt.getObject().asResource().getURI());
}
}
/*
* Synchronized part of removedStatement. Interacts with DeltaComputer.
*/
protected synchronized void handleRemovedStatement(Statement stmt) {
if (batchMode == 1) {
aBoxDeltaModeler1.removedStatement(stmt);
} else if (batchMode == 2) {
aBoxDeltaModeler2.removedStatement(stmt);
} else { // batchMode == 0
if (stmt.getPredicate().equals(RDF.type)) {
removedABoxTypeAssertion(stmt, inferenceModel);
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
} else if ( doSameAs && stmt.getPredicate().equals(OWL.sameAs)) {
removedABoxSameAsAssertion(stmt, inferenceModel);
} else {
removedABoxAssertion(stmt, inferenceModel);
}
doPlugins(ModelUpdate.Operation.RETRACT,stmt);
private void recomputeIndividuals(Queue<String> individualURIs) {
long start = System.currentTimeMillis();
int size = individualURIs.size();
recomputer.recompute(individualURIs);
if(size > 2) {
log.info((System.currentTimeMillis() - start) + " ms to recompute "
+ size + " individuals");
}
}
@ -364,201 +359,6 @@ public class SimpleReasoner extends StatementListener {
changedTBoxStatement(stmt, false);
}
protected void addedABoxTypeAssertion(Statement stmt,
Model inferenceModel,
HashSet<String> unknownTypes) {
addedABoxTypeAssertion(stmt, inferenceModel, unknownTypes, true);
}
/**
* Performs incremental reasoning based on a new type assertion
* added to the ABox (assertion that an individual is of a certain
* type).
*
* If it is added that B is of type A, then for each superclass of
* A assert that B is of that type.
*/
protected void addedABoxTypeAssertion(Statement stmt,
Model inferenceModel,
HashSet<String> unknownTypes,
boolean checkRedundancy) {
tboxModel.enterCriticalSection(Lock.READ);
try {
Resource cls = null;
if ( (stmt.getObject().asResource()).getURI() != null ) {
cls = tboxModel.getResource(stmt.getObject().asResource().getURI());
if (cls != null) {
List<Resource> parents = getParents(cls,tboxModel);
Iterator<Resource> parentIt = parents.iterator();
if (parentIt.hasNext()) {
while (parentIt.hasNext()) {
Resource parentClass = parentIt.next();
// VIVO doesn't materialize statements that assert anonymous types
// for individuals. Also, sharing an identical anonymous node is
// not allowed in owl-dl. picklist population code looks at qualities
// of classes not individuals.
if (parentClass.isAnon()) continue;
Statement infStmt =
ResourceFactory.createStatement(stmt.getSubject(),
RDF.type, parentClass);
addInference(infStmt, inferenceModel, true, checkRedundancy);
}
}
} else {
if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) {
if (!unknownTypes.contains(stmt.getObject().asResource().getURI())) {
unknownTypes.add(stmt.getObject().asResource().getURI());
log.warn("Didn't find the target class (the object of an added " +
"rdf:type statement) in the TBox: " +
(stmt.getObject().asResource()).getURI() +
". No class subsumption reasoning will be done " +
"based on type assertions of this type.");
}
}
}
} else {
log.debug("The object of this rdf:type assertion has a null URI, no reasoning"
+ " will be done based on this assertion: " + stmtString(stmt));
return;
}
} finally {
tboxModel.leaveCriticalSection();
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
/**
* If it is removed that B is of type A, then for each superclass of A remove
* the inferred statement that B is of that type UNLESS it is otherwise entailed
* that B is of that type.
*
*/
protected void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
removedABoxTypeAssertion(stmt, inferenceModel, null);
}
/**
* If it is removed that B is of type A, then for each superclass of A remove
* the inferred statement that B is of that type UNLESS it is otherwise entailed
* that B is of that type.
*
* remainingTypeURIs is an optional list of asserted type URIs for the subject of
* stmt, and may be null. Supplying a precompiled list can yield performance
* improvement when this method is called repeatedly for the same subject.
*
*/
protected void removedABoxTypeAssertion(Statement stmt,
Model inferenceModel,
List<String> remainingTypeURIs) {
tboxModel.enterCriticalSection(Lock.READ);
try {
Resource cls = null;
if ( (stmt.getObject().asResource()).getURI() != null ) {
cls = tboxModel.getResource(stmt.getObject().asResource().getURI());
if (cls != null) {
if (entailedType(stmt.getSubject(),cls)) {
addInference(stmt,inferenceModel,true);
}
List<Resource> parents = getParents(cls,tboxModel);
Iterator<Resource> parentIt = parents.iterator();
while (parentIt.hasNext()) {
Resource parentClass = parentIt.next();
// VIVO doesn't materialize statements that assert anonymous types
// for individuals. Also, sharing an identical anonymous node is
// not allowed in owl-dl. picklist population code looks at qualities
// of classes not individuals.
if (parentClass.isAnon()) continue;
List<String> typeURIs = (remainingTypeURIs == null)
? getRemainingAssertedTypeURIs(stmt.getSubject()) : remainingTypeURIs;
if (entailedType(stmt.getSubject(),parentClass, typeURIs)) {
continue; // if a type is still entailed without the
}
// removed statement, then don't remove it
// from the inferences
Statement infStmt =
ResourceFactory.createStatement(stmt.getSubject(), RDF.type, parentClass);
removeInference(infStmt,inferenceModel,true,false);
}
} else {
log.warn("Didn't find target class (the object of the removed rdf:type"
+ "statement) in the TBox: "
+ ((Resource)stmt.getObject()).getURI() + ". No class subsumption"
+" reasoning will be performed based on the removal of this assertion.");
}
} else {
log.warn("The object of this rdf:type assertion has a null URI: "
+ stmtString(stmt));
}
} catch (Exception e) {
log.warn("exception while removing abox type assertions: " + e.getMessage());
} finally {
tboxModel.leaveCriticalSection();
}
}
/**
* Performs incremental property-based reasoning.
*
* Retracts inferences based on the owl:inverseOf relationship.
*
* If it is removed that x prop1 y, and prop2 is an inverseOf prop1
* then remove y prop2 x from the inference graph, unless it is
* otherwise entailed by the assertions graph independently of
* this removed statement.
*/
protected void removedABoxAssertion(Statement stmt, Model inferenceModel) {
if (!stmt.getObject().isLiteral()) {
List<OntProperty> inverseProperties = getInverseProperties(stmt);
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
while (inverseIter.hasNext()) {
OntProperty inverseProp = inverseIter.next();
Statement infStmt = ResourceFactory.createStatement(
stmt.getObject().asResource(), inverseProp, stmt.getSubject());
removeInference(infStmt,inferenceModel);
}
}
if( doSameAs )
doSameAsForRemovedABoxAssertion( stmt, inferenceModel );
// if a statement has been removed that is otherwise entailed,
// add it to the inference graph.
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (entailedStatement(stmt) && !inferenceModel.contains(stmt)) {
inferenceModel.add(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
/**
* If it is added that B is a subClass of A, then for each
* individual that is typed as B, either in the ABox or in the
@ -718,240 +518,6 @@ public class SimpleReasoner extends StatementListener {
return sameIndividuals;
}
/**
* Materializes inferences based on the owl:sameAs relationship.
*
* If it is added that x owl:sameAs y, then all asserted and inferred
* statements about x will become inferred about y if they are not already
* asserted about y, and vice versa.
*/
protected void addedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
Resource subject = null;
Resource object = null;
if (stmt.getSubject().isResource()) {
subject = stmt.getSubject().asResource();
if (tboxModel.containsResource(subject) || subject.isAnon()) {
log.debug("the subject of this sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the subject of this sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
if (stmt.getObject().isResource()) {
object = stmt.getObject().asResource();
if (tboxModel.containsResource(object) || object.isAnon()) {
log.debug("the object of this sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the object of this sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
Statement opposite = ResourceFactory.createStatement(object, OWL.sameAs, subject);
addInference(opposite,inferenceModel,true);
generateSameAsInferences(subject, object, inferenceModel);
generateSameAsInferences(object, subject, inferenceModel);
}
/**
* Materializes inferences based on the owl:sameAs relationship.
*
* If it is removed that x is sameAs y, then remove y sameAs x from
* the inference graph and then recompute the inferences for x and
* y based on their respective assertions.
* that x owl:sameAs y, then all asserted and inferred
*/
protected void removedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
Resource subject = null;
Resource object = null;
if (stmt.getSubject().isResource()) {
subject = stmt.getSubject().asResource();
if (tboxModel.containsResource(subject) || subject.isAnon()) {
log.debug("the subject of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the subject of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
if (stmt.getObject().isResource()) {
object = stmt.getObject().asResource();
if (tboxModel.containsResource(object) || object.isAnon()) {
log.debug("the object of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the object of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
List<Resource> sameIndividuals = getSameIndividuals(subject,inferenceModel);
sameIndividuals.addAll(getSameIndividuals(object, inferenceModel));
Iterator<Resource> sIter1 = sameIndividuals.iterator();
while (sIter1.hasNext()) {
removeInferencesForIndividual(sIter1.next(), inferenceModel);
}
Iterator<Resource> sIter2 = sameIndividuals.iterator();
while (sIter2.hasNext()) {
computeInferencesForIndividual(sIter2.next(), inferenceModel);
}
}
protected void doSameAsForAddedABoxAssertion(Statement stmt, Model inferenceModel){
List<Resource> sameIndividuals =
getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) {
Resource subject = sameIter.next();
Statement sameStmt =
ResourceFactory.createStatement(subject,stmt.getPredicate(),stmt.getObject());
addInference(sameStmt,inferenceModel, doSameAs);
}
}
/**
* Materializes inferences based on the owl:inverseOf relationship.
* and owl:sameAs
*
* If it is added that x prop1 y, and prop2 is an inverseOf prop1
* then add y prop2 x to the inference graph, if it is not already in
* the assertions graph.
*
*/
protected void addedABoxAssertion(Statement stmt, Model inferenceModel) {
if (!stmt.getObject().isLiteral()) {
List<OntProperty> inverseProperties = getInverseProperties(stmt);
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
while (inverseIter.hasNext()) {
Property inverseProp = inverseIter.next();
Statement infStmt = ResourceFactory.createStatement(
stmt.getObject().asResource(), inverseProp, stmt.getSubject());
addInference(infStmt, inferenceModel, true);
}
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
if(doSameAs) {
doSameAsForAddedABoxAssertion( stmt, inferenceModel);
}
}
void doSameAsForRemovedABoxAssertion(Statement stmt, Model inferenceModel){
List<Resource> sameIndividuals =
getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) {
Statement stmtSame =
ResourceFactory.createStatement(sameIter.next(),
stmt.getPredicate(),
stmt.getObject());
removeInference(stmtSame,inferenceModel,false,true);
}
}
protected void generateSameAsInferences(Resource ind1, Resource ind2, Model inferenceModel) {
OntModel unionModel = VitroModelFactory.createOntologyModel();
unionModel.addSubModel(aboxModel);
unionModel.addSubModel(inferenceModel);
aboxModel.enterCriticalSection(Lock.READ);
try {
Iterator<Statement> iter =
unionModel.listStatements(ind1, (Property) null, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (stmt.getObject() == null) continue;
Statement infStmt =
ResourceFactory.createStatement(ind2,stmt.getPredicate(),stmt.getObject());
addInference(infStmt, inferenceModel,true);
}
} finally {
aboxModel.leaveCriticalSection();
}
return;
}
/**
* Remove inferences for individual
*/
protected void removeInferencesForIndividual(Resource ind, Model inferenceModel) {
Model individualInferences = ModelFactory.createDefaultModel();
inferenceModel.enterCriticalSection(Lock.READ);
try {
Iterator<Statement> iter =
inferenceModel.listStatements(ind, (Property) null, (RDFNode) null);
while (iter.hasNext()) {
individualInferences.add(iter.next());
}
} finally {
inferenceModel.leaveCriticalSection();
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
inferenceModel.remove(individualInferences);
} finally {
inferenceModel.leaveCriticalSection();
}
return;
}
/**
* compute inferences for individual
*/
protected void computeInferencesForIndividual(Resource ind, Model inferenceModel) {
Iterator<Statement> iter = null;
aboxModel.enterCriticalSection(Lock.WRITE);
try {
iter = aboxModel.listStatements(ind, (Property) null, (RDFNode) null);
} finally {
aboxModel.leaveCriticalSection();
}
while (iter.hasNext()) {
Statement stmt = iter.next();
addedStatement(stmt);
}
return;
}
/**
* Returns true if it is entailed by class subsumption that
* subject is of type cls; otherwise returns false.
@ -1087,7 +653,6 @@ public class SimpleReasoner extends StatementListener {
*/
protected boolean entailedStatement(Statement stmt) {
//TODO think about checking class subsumption here (for convenience)
// Inverse properties
List<OntProperty> inverses = getInverseProperties(stmt);
Iterator<OntProperty> iIter = inverses.iterator();
@ -1564,209 +1129,34 @@ public class SimpleReasoner extends StatementListener {
if (recomputer != null) {
recomputer.setStopRequested();
}
this.stopRequested = true;
}
// DeltaComputer
/**
* Asynchronous reasoning mode (DeltaComputer) is used in the case of batch removals.
* Asynchronous reasoning mode (DeltaComputer) no longer used
* in the case of batch removals.
*/
public boolean isABoxReasoningAsynchronous() {
if (batchMode > 0) {
return true;
} else {
return false;
}
boolean isABoxInferenceGraph(String graphURI) {
return ModelNames.ABOX_INFERENCES.equals(graphURI);
}
private volatile boolean deltaComputerProcessing = false;
private int eventCount = 0;
boolean isTBoxGraph(String graphURI) {
return ( ModelNames.TBOX_ASSERTIONS.equals(graphURI)
|| ModelNames.TBOX_INFERENCES.equals(graphURI)
|| (graphURI != null && graphURI.contains("tbox")) );
}
@Override
public void notifyEvent(String string, Object event) {
// don't care
}
@Override
public void notifyEvent(Model model, Object event) {
if (event instanceof BulkUpdateEvent) {
handleBulkUpdateEvent(event);
}
}
public synchronized void handleBulkUpdateEvent(Object event) {
if (event instanceof BulkUpdateEvent) {
if (((BulkUpdateEvent) event).getBegin()) {
log.info("received a bulk update begin event");
if (deltaComputerProcessing) {
eventCount++;
log.info("received a bulk update begin event while processing in asynchronous mode. Event count = " + eventCount);
return;
} else {
batchMode = 1;
if (aBoxDeltaModeler1.getRetractions().size() > 0) {
log.warn("Unexpected condition: the aBoxDeltaModeler1 retractions model was not empty when entering batch mode.");
}
if (aBoxDeltaModeler2.getRetractions().size() > 0) {
log.warn("Unexpected condition: the aBoxDeltaModeler2 retractions model was not empty when entering batch mode.");
}
log.info("initializing batch mode 1");
}
} else {
log.info("received a bulk update end event");
if (!deltaComputerProcessing) {
deltaComputerProcessing = true;
VitroBackgroundThread thread = new VitroBackgroundThread(new DeltaComputer(),
"SimpleReasoner.DeltaComputer");
thread.setWorkLevel(WORKING);
thread.start();
} else {
eventCount--;
log.info("received a bulk update end event while currently processing in aynchronous mode. Event count = " + eventCount);
}
}
}
}
private synchronized boolean switchBatchModes() {
if (batchMode == 1) {
aBoxDeltaModeler2.getRetractions().removeAll();
if (aBoxDeltaModeler1.getRetractions().size() > 0) {
batchMode = 2;
log.info("entering batch mode " + batchMode);
} else {
deltaComputerProcessing = false;
if (eventCount == 0) {
batchMode = 0;
}
}
} else if (batchMode == 2) {
aBoxDeltaModeler1.getRetractions().removeAll();
if (aBoxDeltaModeler2.getRetractions().size() > 0) {
batchMode = 1;
log.info("entering batch mode " + batchMode);
} else {
deltaComputerProcessing = false;
if (eventCount == 0) {
batchMode = 0;
}
}
} else {
log.warn("unexpected condition, invoked when batchMode is neither 1 nor 2. batchMode = " + batchMode);
deltaComputerProcessing = false;
}
return deltaComputerProcessing;
}
private class DeltaComputer extends Thread {
public DeltaComputer() {
}
@Override
public void run() {
log.info("starting DeltaComputer.run");
boolean abort = false;
Model retractions = ModelFactory.createDefaultModel();
String qualifier = "";
while (deltaComputerProcessing && !stopRequested) {
if (switchBatchModes()) {
if (batchMode == 1) {
qualifier = "2";
retractions = aBoxDeltaModeler2.getRetractions();
} else if (batchMode == 2) {
qualifier = "1";
retractions = aBoxDeltaModeler1.getRetractions();
}
} else {
break;
}
retractions.enterCriticalSection(Lock.READ);
int num = 0;
try {
log.info("started computing inferences for batch " + qualifier + " updates");
ResIterator subIt = retractions.listSubjects();
while (subIt.hasNext()) {
Resource subj = subIt.nextResource();
StmtIterator iter = retractions.listStatements(
subj, null, (RDFNode) null);
boolean typesModified = false;
try {
List<String> typeURIs = null;
while (iter.hasNext() && !stopRequested) {
Statement stmt = iter.next();
num++;
try {
if (stmt.getPredicate().equals(RDF.type)) {
typesModified = true;
if (typeURIs == null) {
typeURIs = getRemainingAssertedTypeURIs(stmt.getSubject());
}
removedABoxTypeAssertion(stmt, inferenceModel, typeURIs);
} else if (doSameAs && stmt.getPredicate().equals(OWL.sameAs)) {
removedABoxSameAsAssertion(stmt, inferenceModel);
} else {
removedABoxAssertion(stmt, inferenceModel);
}
doPlugins(ModelUpdate.Operation.RETRACT,stmt);
} catch (NullPointerException npe) {
abort = true;
break;
} catch (Exception e) {
log.error("exception in batch mode ",e);
}
if ((num % 6000) == 0) {
log.info("still computing inferences for batch " + qualifier + " update...");
}
if (stopRequested) {
log.info("a stopRequested signal was received during DeltaComputer.run. Halting Processing.");
return;
}
}
} finally {
iter.close();
if (typesModified) {
setMostSpecificTypes(subj, inferenceModel, new HashSet<String>());
}
}
}
} finally {
retractions.removeAll();
retractions.leaveCriticalSection();
}
if (stopRequested) {
log.info("a stopRequested signal was received during DeltaComputer.run. Halting Processing.");
deltaComputerProcessing = false;
return;
}
if (abort) {
log.error("a NullPointerException was received while computing inferences in batch " + qualifier + " mode. Halting inference computation.");
deltaComputerProcessing = false;
return;
}
log.info("finished computing inferences for batch " + qualifier + " updates");
log.debug("\t--> processed " + num + " statements");
}
log.info("ending DeltaComputer.run. batchMode = " + batchMode);
}
// don't care
}
/**

77
api/src/main/java/edu/cornell/mannlib/vitro/webapp/searchindex/IndexingChangeListener.java
View file

@ -2,6 +2,9 @@
package edu.cornell.mannlib.vitro.webapp.searchindex;
import static edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer.Event.Type.REBUILD_REQUESTED;
import static edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer.Event.Type.START_REBUILD;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
@ -16,18 +19,17 @@ import org.apache.jena.riot.tokens.Tokenizer;
import org.apache.jena.riot.tokens.TokenizerFactory;
import com.hp.hpl.jena.graph.Triple;
import com.hp.hpl.jena.rdf.listeners.StatementListener;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
import edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer;
import edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer.Event;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
import static edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer.Event.Type.*;
/**
* When a change is heard, wait for an interval to see if more changes come in.
* When changes stop coming in for a specified interval, send what has
@ -52,8 +54,8 @@ import static edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndex
* which is semantically equivalent to the original, and add that to the list
* instead. The original statement is released.
*/
public class IndexingChangeListener implements ChangeListener,
SearchIndexer.Listener {
public class IndexingChangeListener extends StatementListener
implements ModelChangedListener, SearchIndexer.Listener {
private static final Log log = LogFactory
.getLog(IndexingChangeListener.class);
@ -105,16 +107,16 @@ public class IndexingChangeListener implements ChangeListener,
}
@Override
public void addedStatement(String serializedTriple, String graphURI) {
public void addedStatement(Statement stmt) {
if (!rebuildScheduled) {
noteChange(parseTriple(serializedTriple));
noteChange(stmt);
}
}
@Override
public void removedStatement(String serializedTriple, String graphURI) {
public void removedStatement(Statement stmt) {
if (!rebuildScheduled) {
noteChange(parseTriple(serializedTriple));
noteChange(stmt);
}
}
@ -122,7 +124,7 @@ public class IndexingChangeListener implements ChangeListener,
* We only care about events that signal the end of an edit operation.
*/
@Override
public void notifyEvent(String graphURI, Object event) {
public void notifyEvent(Model model, Object event) {
if ((event instanceof EditEvent)) {
EditEvent editEvent = (EditEvent) event;
if (!editEvent.getBegin()) { // editEvent is the end of an edit
@ -135,34 +137,33 @@ public class IndexingChangeListener implements ChangeListener,
}
}
// TODO avoid duplication with JenaChangeListener
private Statement parseTriple(String serializedTriple) {
try {
// Use RiotReader to parse a Triple
// NB A Triple can be serialized correctly with: FmtUtils.stringForTriple(triple, PrefixMapping.Factory.create()) + " .";'
Tokenizer tokenizer = TokenizerFactory.makeTokenizerString(serializedTriple);
Iterator<Triple> it = RiotReader.createParserNTriples(tokenizer, null);
if (it.hasNext()) {
Triple triple = it.next();
if (it.hasNext()) {
log.warn("More than one triple parsed from change event: '" + serializedTriple + "'");
}
// Use the retained defaultModel instance to convert the Triple to a Statement
// This does not add the Statement to the Model, so the Statement can be disposed when unused
// And whilst the Model is attached to the Statement, using a single instance means only one Model
// is created and attached to all of the Statements created by this instance
return defaultModel.asStatement(triple);
} else {
throw new RuntimeException("no triple parsed from change event: '" + serializedTriple + "'");
}
} catch (RuntimeException riot) {
log.error("Failed to parse triple " + serializedTriple, riot);
throw riot;
}
}
// private Statement parseTriple(String serializedTriple) {
// try {
// // Use RiotReader to parse a Triple
// // NB A Triple can be serialized correctly with: FmtUtils.stringForTriple(triple, PrefixMapping.Factory.create()) + " .";'
// Tokenizer tokenizer = TokenizerFactory.makeTokenizerString(serializedTriple);
// Iterator<Triple> it = RiotReader.createParserNTriples(tokenizer, null);
//
// if (it.hasNext()) {
// Triple triple = it.next();
//
// if (it.hasNext()) {
// log.warn("More than one triple parsed from change event: '" + serializedTriple + "'");
// }
//
// // Use the retained defaultModel instance to convert the Triple to a Statement
// // This does not add the Statement to the Model, so the Statement can be disposed when unused
// // And whilst the Model is attached to the Statement, using a single instance means only one Model
// // is created and attached to all of the Statements created by this instance
// return defaultModel.asStatement(triple);
// } else {
// throw new RuntimeException("no triple parsed from change event: '" + serializedTriple + "'");
// }
// } catch (RuntimeException riot) {
// log.error("Failed to parse triple " + serializedTriple, riot);
// throw riot;
// }
// }
// ----------------------------------------------------------------------
// helper classes

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/searchindex/SearchIndexerSetup.java
View file

@ -55,7 +55,7 @@ public class SearchIndexerSetup implements ServletContextListener {
listener = new IndexingChangeListener(searchIndexer);
listenerWrapper = new DeveloperDisabledChangeListener(listener,
Key.SEARCH_INDEX_SUPPRESS_MODEL_CHANGE_LISTENER);
RDFServiceUtils.getRDFServiceFactory(ctx).registerListener(
RDFServiceUtils.getRDFServiceFactory(ctx).registerJenaModelChangedListener(
listenerWrapper);
this.history = new IndexHistory();
@ -78,7 +78,7 @@ public class SearchIndexerSetup implements ServletContextListener {
searchIndexer.removeListener(this.history);
try {
RDFServiceUtils.getRDFServiceFactory(ctx).unregisterListener(
RDFServiceUtils.getRDFServiceFactory(ctx).unregisterJenaModelChangedListener(
listenerWrapper);
} catch (RDFServiceException e) {
log.warn("Failed to unregister the indexing listener.");

25
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/developer/listeners/DeveloperDisabledChangeListener.java
View file

@ -2,7 +2,11 @@
package edu.cornell.mannlib.vitro.webapp.utils.developer.listeners;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import com.hp.hpl.jena.rdf.listeners.StatementListener;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener;
import com.hp.hpl.jena.rdf.model.Statement;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings;
import edu.cornell.mannlib.vitro.webapp.utils.developer.Key;
@ -11,11 +15,12 @@ import edu.cornell.mannlib.vitro.webapp.utils.developer.Key;
*
* Set the flag and this becomes opaque, passing no events through.
*/
public class DeveloperDisabledChangeListener implements ChangeListener {
private final ChangeListener inner;
public class DeveloperDisabledChangeListener extends StatementListener
implements ModelChangedListener {
private final ModelChangedListener inner;
private final Key disablingKey;
public DeveloperDisabledChangeListener(ChangeListener inner,
public DeveloperDisabledChangeListener(ModelChangedListener inner,
Key disablingKey) {
this.inner = inner;
this.disablingKey = disablingKey;
@ -30,23 +35,23 @@ public class DeveloperDisabledChangeListener implements ChangeListener {
// ----------------------------------------------------------------------
@Override
public void addedStatement(String serializedTriple, String graphURI) {
public void addedStatement(Statement stmt) {
if (isEnabled()) {
inner.addedStatement(serializedTriple, graphURI);
inner.addedStatement(stmt);
}
}
@Override
public void removedStatement(String serializedTriple, String graphURI) {
public void removedStatement(Statement stmt) {
if (isEnabled()) {
inner.removedStatement(serializedTriple, graphURI);
inner.removedStatement(stmt);
}
}
@Override
public void notifyEvent(String graphURI, Object event) {
public void notifyEvent(Model model, Object event) {
if (isEnabled()) {
inner.notifyEvent(graphURI, event);
inner.notifyEvent(model, event);
}
}

90
api/src/test/java/edu/cornell/mannlib/vitro/webapp/controller/api/SparqlUpdateApiTest.java Normal file
View file

@ -0,0 +1,90 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.controller.api;
import static org.junit.Assert.*;
import java.io.StringReader;
import junit.framework.Assert;
import org.junit.Before;
import org.junit.Test;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.DatasetFactory;
import com.hp.hpl.jena.query.ReadWrite;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.update.GraphStore;
import com.hp.hpl.jena.update.GraphStoreFactory;
import com.hp.hpl.jena.update.UpdateAction;
import com.hp.hpl.jena.update.UpdateFactory;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
/**
* Test that the SparqlQueryApiExecutor can handle all query types and all
* formats.
*/
public class SparqlUpdateApiTest extends AbstractTestClass {
private final String GRAPH_URI = "http://example.org/graph";
private final String updateStr1 =
"INSERT DATA { GRAPH <" + GRAPH_URI + "> { \n" +
" <http://here.edu/n1> a <http://here.edu/Class1> . \n" +
"} } ; \n" +
"INSERT { GRAPH <" + GRAPH_URI + "> { \n " +
" ?x a <http://here.edu/Class2> . \n " +
"} } WHERE { \n" +
" GRAPH <" + GRAPH_URI + "> { ?x a <http://here.edu/Class1> } \n " +
"}";
private final String result1 =
"<http://here.edu/n1> a <http://here.edu/Class1> . \n" +
"<http://here.edu/n1> a <http://here.edu/Class2> ." ;
// look at how the SimpleReasoner is set up.
private Model model;
private RDFService rdfService;
@Before
public void setup() {
model = ModelFactory.createDefaultModel();
Dataset ds = DatasetFactory.createMem();
ds.addNamedModel(GRAPH_URI, model);
rdfService = new RDFServiceModel(ds);
}
// ----------------------------------------------------------------------
// Tests
// ----------------------------------------------------------------------
@Test
public void nullRdfService() throws Exception {
model.removeAll();
Model desiredResults = ModelFactory.createDefaultModel();
desiredResults.read(new StringReader(result1), null, "N3");
Dataset ds = new RDFServiceDataset(rdfService);
GraphStore graphStore = GraphStoreFactory.create(ds);
try {
if(ds.supportsTransactions()) {
ds.begin(ReadWrite.WRITE);
System.out.println("yep");
}
UpdateAction.execute(UpdateFactory.create(updateStr1), graphStore);
} finally {
if(ds.supportsTransactions()) {
ds.commit();
ds.end();
}
}
assertEquals("updateStr1 yields result1", desiredResults.toString(), model.toString());
}
}