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NIHVIVO-3974 preventing reproduction of axioms with blank nodes in filegraphs and NIHVIVO-3958 applying query syntax leniency to RDFServiceSparql

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This commit is contained in:
brianjlowe 2012-09-27 20:55:18 +00:00
parent daf3018ed8
commit b9cd04f0fa
5 changed files with 47 additions and 37 deletions
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27
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceImpl.java
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@ -3,6 +3,7 @@
package edu.cornell.mannlib.vitro.webapp.rdfservice.impl;
import java.io.ByteArrayInputStream;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.CopyOnWriteArrayList;
@ -13,7 +14,11 @@ 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.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.ModelFactory;
import com.hp.hpl.jena.rdf.model.Statement;
@ -31,7 +36,7 @@ public abstract class RDFServiceImpl implements RDFService {
private static final Log log = LogFactory.getLog(RDFServiceImpl.class);
protected static final String BNODE_ROOT_QUERY =
"SELECT ?s WHERE { ?s ?p ?o OPTIONAL { ?ss ?pp ?s } FILTER (!isBlank(?s) || !bound(?ss)) }";
"SELECT DISTINCT ?s WHERE { ?s ?p ?o OPTIONAL { ?ss ?pp ?s } FILTER (!isBlank(?s) || !bound(?ss)) }";
protected String defaultWriteGraphURI;
protected List<ChangeListener> registeredListeners = new CopyOnWriteArrayList<ChangeListener>();
@ -261,4 +266,24 @@ public abstract class RDFServiceImpl implements RDFService {
result[1] = nonBlankNodeModel;
return result;
}
protected Query createQuery(String queryString) {
List<Syntax> syntaxes = Arrays.asList(
Syntax.defaultQuerySyntax, Syntax.syntaxSPARQL_11,
Syntax.syntaxSPARQL_10, Syntax.syntaxSPARQL, Syntax.syntaxARQ);
Query q = null;
Iterator<Syntax> syntaxIt = syntaxes.iterator();
while (q == null) {
Syntax syntax = syntaxIt.next();
try {
q = QueryFactory.create(queryString, syntax);
} catch (QueryParseException e) {
if (!syntaxIt.hasNext()) {
throw(e);
}
}
}
return q;
}
}

19
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java
View file

@ -359,25 +359,6 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
super.notifyListeners(triple, operation, graphURI);
}
protected Query createQuery(String queryString) {
List<Syntax> syntaxes = Arrays.asList(
Syntax.defaultQuerySyntax, Syntax.syntaxSPARQL_11,
Syntax.syntaxSPARQL_10, Syntax.syntaxSPARQL, Syntax.syntaxARQ);
Query q = null;
Iterator<Syntax> syntaxIt = syntaxes.iterator();
while (q == null) {
Syntax syntax = syntaxIt.next();
try {
q = QueryFactory.create(queryString, syntax);
} catch (QueryParseException e) {
if (!syntaxIt.hasNext()) {
throw(e);
}
}
}
return q;
}
protected QueryExecution createQueryExecution(String queryString, Query q, Dataset d) {
return QueryExecutionFactory.create(q, d);
}

15
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java
View file

@ -13,9 +13,7 @@ import java.util.List;
import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.MultiThreadedHttpConnectionManager;
import org.apache.commons.httpclient.NameValuePair;
import org.apache.commons.httpclient.methods.ByteArrayRequestEntity;
import org.apache.commons.httpclient.methods.PostMethod;
import org.apache.commons.httpclient.methods.RequestEntity;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -49,7 +47,6 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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.jena.ListeningGraph;
import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
/*
* API to write, read, and update Vitro's RDF store, with support
@ -223,7 +220,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
RDFServiceImpl.ModelSerializationFormat resultFormat) throws RDFServiceException {
Model model = ModelFactory.createDefaultModel();
Query query = QueryFactory.create(queryStr);
Query query = createQuery(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(readEndpointURI, query);
try {
@ -253,7 +250,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
RDFServiceImpl.ModelSerializationFormat resultFormat) throws RDFServiceException {
Model model = ModelFactory.createDefaultModel();
Query query = QueryFactory.create(queryStr);
Query query = createQuery(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(readEndpointURI, query);
try {
@ -281,7 +278,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
@Override
public InputStream sparqlSelectQuery(String queryStr, RDFService.ResultFormat resultFormat) throws RDFServiceException {
Query query = QueryFactory.create(queryStr);
Query query = createQuery(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(readEndpointURI, query);
try {
@ -323,7 +320,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
@Override
public boolean sparqlAskQuery(String queryStr) throws RDFServiceException {
Query query = QueryFactory.create(queryStr);
Query query = createQuery(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(readEndpointURI, query);
try {
@ -582,7 +579,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
@Override
protected boolean sparqlSelectQueryHasResults(String queryStr) throws RDFServiceException {
Query query = QueryFactory.create(queryStr);
Query query = createQuery(queryStr);
QueryExecution qe = QueryExecutionFactory.sparqlService(readEndpointURI, query);
try {
@ -638,6 +635,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
Model blankNodeModel = ModelFactory.createDefaultModel();
blankNodeModel.add(blankNodeStatements);
log.debug("update model size " + model.size());
log.debug("blank node model size " + blankNodeModel.size());

17
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java
View file

@ -19,7 +19,6 @@ import javax.servlet.ServletContextListener;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntDocumentManager;
import com.hp.hpl.jena.ontology.OntDocumentManager;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
@ -29,7 +28,8 @@ import com.hp.hpl.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
// This ContextListener must run after the JenaDataSourceSetup ContextListener
@ -50,9 +50,11 @@ public class FileGraphSetup implements ServletContextListener {
try {
ServletContext ctx = sce.getServletContext();
OntDocumentManager.getInstance().setProcessImports(true);
baseOms = ModelContext.getBaseOntModelSelector(sce.getServletContext());
Dataset dataset = JenaDataSourceSetupBase.getStartupDataset(sce.getServletContext());
RDFServiceModelMaker maker = new RDFServiceModelMaker(RDFServiceUtils.getRDFServiceFactory(ctx));
// ABox files
Set<String> pathSet = sce.getServletContext().getResourcePaths(PATH_ROOT + ABOX);
@ -61,7 +63,7 @@ public class FileGraphSetup implements ServletContextListener {
if (pathSet != null) {
OntModel aboxBaseModel = baseOms.getABoxModel();
aboxChanged = readGraphs(sce, pathSet, dataset, ABOX, aboxBaseModel);
aboxChanged = readGraphs(sce, pathSet, maker, ABOX, aboxBaseModel);
}
// TBox files
@ -71,7 +73,7 @@ public class FileGraphSetup implements ServletContextListener {
if (pathSet != null) {
OntModel tboxBaseModel = baseOms.getTBoxModel();
tboxChanged = readGraphs(sce, pathSet, dataset, TBOX, tboxBaseModel);
tboxChanged = readGraphs(sce, pathSet, maker, TBOX, tboxBaseModel);
}
} catch (ClassCastException cce) {
String errMsg = "Unable to cast servlet context attribute to the appropriate type " + cce.getLocalizedMessage();
@ -105,7 +107,7 @@ public class FileGraphSetup implements ServletContextListener {
* Note: no connection needs to be maintained between the in-memory copy of the
* graph and the DB copy.
*/
public boolean readGraphs(ServletContextEvent sce, Set<String> pathSet, Dataset dataset, String type, OntModel baseModel) {
public boolean readGraphs(ServletContextEvent sce, Set<String> pathSet, RDFServiceModelMaker dataset, String type, OntModel baseModel) {
int count = 0;
@ -169,10 +171,9 @@ public class FileGraphSetup implements ServletContextListener {
* Otherwise, if a graph with the given name is in the DB and is isomorphic with
* the graph that was read from the files system, then do nothing.
*/
public boolean updateGraphInDB(Dataset dataset, Model fileModel, String type, String path) {
public boolean updateGraphInDB(RDFServiceModelMaker dataset, Model fileModel, String type, String path) {
String graphURI = pathToURI(path,type);
Model dbModel = dataset.getNamedModel(graphURI);
Model dbModel = dataset.getModel(graphURI);
boolean modelChanged = false;
boolean isIsomorphic = dbModel.isIsomorphicWith(fileModel);

4
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaOutputUtils.java
View file

@ -28,6 +28,10 @@ public class JenaOutputUtils {
Map<String,String> prefixes = new HashMap<String,String>();
List<Ontology> ontologies = wadf.getOntologyDao().getAllOntologies();
// apparently this is null if empty
if (ontologies == null) {
return;
}
Iterator<Ontology> iter = ontologies.iterator();
String namespace = null;
String prefix = null;