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Avoid lock on graph uri update in RdfServiceSparql #424

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merged 6 commits into from
Jun 20, 2024
Merged

Avoid lock on graph uri update in RdfServiceSparql #424

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a0a60cd
Avoid lock on graph uri update in rdfServiceSparql
litvinovg Nov 1, 2023
6006581
delete duplicate variable initialization
litvinovg Nov 1, 2023
7b6f2e2
fix identation
litvinovg Nov 3, 2023
e314dca
refact: extracted method to update graph URIs in RDFServiceImpl
litvinovg Nov 3, 2023
ec84b99
style: fixed layout, removed files from checkstyle suppressions
litvinovg Nov 3, 2023
a09ce2c
fix: reset rebuildGraphUriCache flag at start of graphUriRebuild to a…
litvinovg Jun 20, 2024
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141 changes: 64 additions & 77 deletions .../edu/cornell/mannlib/vitro/webapp/rdfservice/filter/SameAsFilteringRDFServiceFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,17 @@
import java.util.Iterator;
import java.util.List;

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.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;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
Expand All @@ -30,27 +38,18 @@
import org.apache.jena.rdf.model.StmtIterator;
import org.apache.jena.vocabulary.OWL;

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.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;

public class SameAsFilteringRDFServiceFactory implements RDFServiceFactory {

private final static Log log = LogFactory.getLog(
SameAsFilteringRDFServiceFactory.class);
private final static Log log = LogFactory.getLog(SameAsFilteringRDFServiceFactory.class);
private RDFServiceFactory f;
private Model sameAsModel;

public SameAsFilteringRDFServiceFactory(RDFServiceFactory rdfServiceFactory) {
this.f = rdfServiceFactory;
try {
InputStream in = f.getRDFService().sparqlConstructQuery("CONSTRUCT { ?s <" + OWL.sameAs.getURI() + "> ?o } WHERE { ?s <" + OWL.sameAs.getURI() + "> ?o } ", ModelSerializationFormat.N3);
InputStream in = f.getRDFService().sparqlConstructQuery(
"CONSTRUCT { ?s <" + OWL.sameAs.getURI() + "> ?o } WHERE { ?s <" + OWL.sameAs.getURI() + "> ?o } ",
ModelSerializationFormat.N3);
sameAsModel = RDFServiceUtils.parseModel(in, ModelSerializationFormat.N3);
} catch (RDFServiceException e) {
throw new RuntimeException(e);
Expand Down Expand Up @@ -98,11 +97,9 @@ public SameAsFilteringRDFService(RDFService rdfService) {
}

@Override
public InputStream sparqlConstructQuery(String query,
RDFService.ModelSerializationFormat resultFormat)
throws RDFServiceException {
Model m = RDFServiceUtils.parseModel(
s.sparqlConstructQuery(query, resultFormat), resultFormat);
public InputStream sparqlConstructQuery(String query, RDFService.ModelSerializationFormat resultFormat)
throws RDFServiceException {
Model m = RDFServiceUtils.parseModel(s.sparqlConstructQuery(query, resultFormat), resultFormat);
Model filtered = ModelFactory.createDefaultModel();
StmtIterator stmtIt = m.listStatements();
while (stmtIt.hasNext()) {
Expand All @@ -112,14 +109,12 @@ public InputStream sparqlConstructQuery(String query,
}
}
ByteArrayOutputStream out = new ByteArrayOutputStream();
filtered.write(out, RDFServiceUtils.getSerializationFormatString(
resultFormat));
filtered.write(out, RDFServiceUtils.getSerializationFormatString(resultFormat));
return new ByteArrayInputStream(out.toByteArray());
}

@Override
public void sparqlConstructQuery(String query, Model model)
throws RDFServiceException {
public void sparqlConstructQuery(String query, Model model) throws RDFServiceException {
Model m = ModelFactory.createDefaultModel();
s.sparqlConstructQuery(query, m);

Expand All @@ -133,11 +128,9 @@ public void sparqlConstructQuery(String query, Model model)
}

@Override
public InputStream sparqlSelectQuery(String query, ResultFormat resultFormat)
throws RDFServiceException {
ResultSet rs = ResultSetFactory.load(
s.sparqlSelectQuery(query, resultFormat),
RDFServiceUtils.getJenaResultSetFormat(resultFormat));
public InputStream sparqlSelectQuery(String query, ResultFormat resultFormat) throws RDFServiceException {
ResultSet rs = ResultSetFactory.load(s.sparqlSelectQuery(query, resultFormat),
RDFServiceUtils.getJenaResultSetFormat(resultFormat));
List<QuerySolution> solutions = new ArrayList<QuerySolution>();
while (rs.hasNext()) {
QuerySolution solution = rs.nextSolution();
Expand All @@ -148,27 +141,26 @@ public InputStream sparqlSelectQuery(String query, ResultFormat resultFormat)
ResultSet resultSet = new FilteredResultSet(solutions, rs);
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
switch (resultFormat) {
case CSV:
ResultSetFormatter.outputAsCSV(outputStream,resultSet);
break;
case TEXT:
ResultSetFormatter.out(outputStream,resultSet);
break;
case JSON:
ResultSetFormatter.outputAsJSON(outputStream, resultSet);
break;
case XML:
ResultSetFormatter.outputAsXML(outputStream, resultSet);
break;
default:
throw new RDFServiceException("unrecognized result format");
case CSV:
ResultSetFormatter.outputAsCSV(outputStream, resultSet);
break;
case TEXT:
ResultSetFormatter.out(outputStream, resultSet);
break;
case JSON:
ResultSetFormatter.outputAsJSON(outputStream, resultSet);
break;
case XML:
ResultSetFormatter.outputAsXML(outputStream, resultSet);
break;
default:
throw new RDFServiceException("unrecognized result format");
}
return new ByteArrayInputStream(outputStream.toByteArray());
}

@Override
public void sparqlSelectQuery(String query, ResultSetConsumer consumer)
throws RDFServiceException {
public void sparqlSelectQuery(String query, ResultSetConsumer consumer) throws RDFServiceException {

s.sparqlSelectQuery(query, new ResultSetConsumer.Chaining(consumer) {
@Override
Expand Down Expand Up @@ -200,13 +192,14 @@ private List<Resource> getSameAsResources(Resource resource) {
if (resource.isAnon()) {
return sameAsResources;
}
String queryStr = "SELECT DISTINCT ?s WHERE { <" + resource.getURI() + "> <" + OWL.sameAs.getURI() + "> ?s } ORDER BY ?s";
try {
String queryStr = "SELECT DISTINCT ?s WHERE { <" + resource.getURI() + "> <" + OWL.sameAs.getURI()
+ "> ?s } ORDER BY ?s";
try {
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.create(query, sameAsModel);
try {
ResultSet rs = qe.execSelect();
//ResultSet rs = JSONInput.fromJSON(s.sparqlSelectQuery(queryStr, ResultFormat.JSON));
// ResultSet rs = JSONInput.fromJSON(s.sparqlSelectQuery(queryStr, ResultFormat.JSON));
while (rs.hasNext()) {
QuerySolution q = rs.next();
Resource res = q.getResource("s");
Expand All @@ -219,14 +212,14 @@ private List<Resource> getSameAsResources(Resource resource) {
qe.close();
}
return sameAsResources;
} catch (/*RDFService*/Exception e) {
} catch (/* RDFService */Exception e) {
throw new RuntimeException(e);
}
}

private boolean isRedundant(QuerySolution q) {
Iterator<String> varIt = q.varNames();
while(varIt.hasNext()) {
while (varIt.hasNext()) {
String varName = varIt.next();
RDFNode n = q.get(varName);
if (n.isResource()) {
Expand All @@ -241,17 +234,14 @@ private boolean isRedundant(QuerySolution q) {
}

@Override
public boolean changeSetUpdate(ChangeSet changeSet)
throws RDFServiceException {
public boolean changeSetUpdate(ChangeSet changeSet) throws RDFServiceException {
return s.changeSetUpdate(changeSet);
}

@Override
public InputStream sparqlDescribeQuery(String query,
ModelSerializationFormat resultFormat)
public InputStream sparqlDescribeQuery(String query, ModelSerializationFormat resultFormat)
throws RDFServiceException {
Model m = RDFServiceUtils.parseModel(
s.sparqlConstructQuery(query, resultFormat), resultFormat);
Model m = RDFServiceUtils.parseModel(s.sparqlConstructQuery(query, resultFormat), resultFormat);
Model filtered = ModelFactory.createDefaultModel();
StmtIterator stmtIt = m.listStatements();
while (stmtIt.hasNext()) {
Expand All @@ -261,8 +251,7 @@ public InputStream sparqlDescribeQuery(String query,
}
}
ByteArrayOutputStream out = new ByteArrayOutputStream();
filtered.write(out, RDFServiceUtils.getSerializationFormatString(
resultFormat));
filtered.write(out, RDFServiceUtils.getSerializationFormatString(resultFormat));
return new ByteArrayInputStream(out.toByteArray());
}

Expand All @@ -282,27 +271,23 @@ public void getGraphMetadata() throws RDFServiceException {
}

@Override
public void serializeAll(OutputStream outputStream)
throws RDFServiceException {
s.serializeAll(outputStream);
}

@Override
public void serializeGraph(String graphURI, OutputStream outputStream)
throws RDFServiceException {
s.serializeGraph(graphURI, outputStream);
}

@Override
public boolean isEquivalentGraph(String graphURI,
InputStream serializedGraph,
ModelSerializationFormat serializationFormat) throws RDFServiceException {
return s.isEquivalentGraph(graphURI, serializedGraph, serializationFormat);
}
public void serializeAll(OutputStream outputStream) throws RDFServiceException {
s.serializeAll(outputStream);
}

@Override
public boolean isEquivalentGraph(String graphURI,
Model graph) throws RDFServiceException {
public void serializeGraph(String graphURI, OutputStream outputStream) throws RDFServiceException {
s.serializeGraph(graphURI, outputStream);
}

@Override
public boolean isEquivalentGraph(String graphURI, InputStream serializedGraph,
ModelSerializationFormat serializationFormat) throws RDFServiceException {
return s.isEquivalentGraph(graphURI, serializedGraph, serializationFormat);
}

@Override
public boolean isEquivalentGraph(String graphURI, Model graph) throws RDFServiceException {
return s.isEquivalentGraph(graphURI, graph);
}

Expand All @@ -316,8 +301,10 @@ public void close() {
s.close();
}

@Override
protected void rebuildGraphUris() {
}

}


}
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