NIHVIVO-3871 blank node handling from ingest tools
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stellamit
parent
ae8319dd5a
commit
809ff432b6
4 changed files with 244 additions and 13 deletions
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@ -0,0 +1,147 @@
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
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import java.util.ArrayList;
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import java.util.List;
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import com.hp.hpl.jena.graph.BulkUpdateHandler;
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import com.hp.hpl.jena.graph.Capabilities;
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import com.hp.hpl.jena.graph.Graph;
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import com.hp.hpl.jena.graph.GraphEventManager;
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import com.hp.hpl.jena.graph.GraphStatisticsHandler;
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import com.hp.hpl.jena.graph.Node;
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import com.hp.hpl.jena.graph.Reifier;
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import com.hp.hpl.jena.graph.TransactionHandler;
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import com.hp.hpl.jena.graph.Triple;
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import com.hp.hpl.jena.graph.TripleMatch;
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import com.hp.hpl.jena.graph.query.QueryHandler;
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import com.hp.hpl.jena.shared.AddDeniedException;
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import com.hp.hpl.jena.shared.DeleteDeniedException;
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import com.hp.hpl.jena.shared.PrefixMapping;
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import com.hp.hpl.jena.util.iterator.ExtendedIterator;
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import com.hp.hpl.jena.util.iterator.WrappedIterator;
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public class BlankNodeFilteringGraph implements Graph {
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private Graph graph;
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public BlankNodeFilteringGraph(Graph graph) {
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this.graph = graph;
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}
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@Override
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public void add(Triple t) throws AddDeniedException {
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if (!t.getSubject().isBlank() && !t.getObject().isBlank()) {
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graph.add(t);
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}
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}
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@Override
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public void close() {
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graph.close();
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}
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@Override
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public boolean contains(Node arg0, Node arg1, Node arg2) {
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return graph.contains(arg0, arg1, arg2);
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}
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@Override
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public boolean contains(Triple arg0) {
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return graph.contains(arg0);
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}
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@Override
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public void delete(Triple t) throws DeleteDeniedException {
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if (!t.getSubject().isBlank() && !t.getObject().isBlank()) {
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graph.delete(t);
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} ;
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}
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@Override
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public boolean dependsOn(Graph arg0) {
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return graph.dependsOn(arg0);
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}
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@Override
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public ExtendedIterator<Triple> find(Node subject, Node predicate, Node object) {
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List<Triple> nbTripList = new ArrayList<Triple>();
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ExtendedIterator<Triple> triples = graph.find(subject, predicate, object);
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while (triples.hasNext()) {
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Triple triple = triples.next();
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if (!triple.getSubject().isBlank() && !triple.getObject().isBlank()) {
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nbTripList.add(triple);
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}
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}
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return WrappedIterator.create(nbTripList.iterator());
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}
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@Override
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public ExtendedIterator<Triple> find(TripleMatch tripleMatch) {
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Triple t = tripleMatch.asTriple();
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return find(t.getSubject(), t.getPredicate(), t.getObject());
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}
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@Override
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public BulkUpdateHandler getBulkUpdateHandler() {
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return graph.getBulkUpdateHandler();
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}
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@Override
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public Capabilities getCapabilities() {
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return graph.getCapabilities();
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}
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@Override
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public GraphEventManager getEventManager() {
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return graph.getEventManager();
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}
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@Override
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public PrefixMapping getPrefixMapping() {
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return graph.getPrefixMapping();
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}
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@Override
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public Reifier getReifier() {
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return graph.getReifier();
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}
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@Override
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public GraphStatisticsHandler getStatisticsHandler() {
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return graph.getStatisticsHandler();
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}
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@Override
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public TransactionHandler getTransactionHandler() {
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return graph.getTransactionHandler();
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}
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@Override
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public boolean isClosed() {
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return graph.isClosed();
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}
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@Override
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public boolean isEmpty() {
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return graph.isEmpty();
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}
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@Override
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public boolean isIsomorphicWith(Graph arg0) {
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return graph.isIsomorphicWith(arg0);
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}
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@Override
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public QueryHandler queryHandler() {
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return graph.queryHandler();
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}
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@Override
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public int size() {
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return graph.size();
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}
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}
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@ -0,0 +1,36 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.rdf.listeners.StatementListener;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.Statement;
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public class BlankNodeStatementListener extends StatementListener {
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private static final Log log = LogFactory.getLog(BlankNodeStatementListener.class);
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private Model bnodeModel;
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public BlankNodeStatementListener(Model bnodeModel) {
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this.bnodeModel = bnodeModel;
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}
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@Override
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public void addedStatement(Statement stmt) {
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if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
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bnodeModel.add(stmt);
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}
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}
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@Override
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public void removedStatement(Statement stmt) {
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if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
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bnodeModel.remove(stmt);
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}
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}
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}
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@ -47,7 +47,7 @@ public class RDFServiceGraph implements GraphWithPerform {
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private RDFService rdfService;
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private String graphURI;
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private static final Log log = LogFactory.getLog(SparqlGraph.class);
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private static final Log log = LogFactory.getLog(RDFServiceGraph.class);
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private BulkUpdateHandler bulkUpdateHandler;
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private PrefixMapping prefixMapping = new PrefixMappingImpl();
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@ -13,20 +13,25 @@ import java.util.Set;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.graph.BulkUpdateHandler;
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import com.hp.hpl.jena.graph.Graph;
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import com.hp.hpl.jena.graph.GraphMaker;
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import com.hp.hpl.jena.query.Dataset;
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import com.hp.hpl.jena.rdf.model.Literal;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.ModelMaker;
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import com.hp.hpl.jena.rdf.model.ModelReader;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.util.iterator.ExtendedIterator;
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import com.hp.hpl.jena.util.iterator.WrappedIterator;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
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@ -72,12 +77,20 @@ public class RDFServiceModelMaker implements ModelMaker {
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}
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public Model createModel(String modelName) {
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Model model = getModel(modelName);
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Model metadataModel = getMetadataModel();
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Literal modelNameLiteral = ResourceFactory.createPlainLiteral(modelName);
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Statement metadataStatment = ResourceFactory.createStatement(dbResource,metadataModel.getProperty(
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HAS_NAMED_MODEL_URI), modelNameLiteral);
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// to get around blank node filtering on BlankNodeFiltering graph
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List<Statement> stmtList = new ArrayList<Statement>();
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stmtList.add(metadataStatment);
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try {
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metadataModel.add(
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dbResource,metadataModel.getProperty(
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HAS_NAMED_MODEL_URI), modelName);
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metadataModel.add(stmtList);
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} finally {
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metadataModel.close();
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}
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@ -150,14 +163,49 @@ public class RDFServiceModelMaker implements ModelMaker {
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return WrappedIterator.create(modelNameList.iterator());
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}
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public Model openModel(String arg0, boolean arg1) {
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RDFService service = getRDFService();
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public Model openModel(String graph, boolean arg1) {
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RDFService rdfService = getRDFService();
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String bnodeQuery = "construct { ?s ?p ?o } where { ";
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bnodeQuery += (graph != null) ? "graph <" + graph + "> {" : "";
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bnodeQuery += "?s ?p ?o filter (isBlank(?s) || isBlank(?o)) }";
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bnodeQuery += (graph != null) ? "}" : "";
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Model bnodeModel = ModelFactory.createDefaultModel();
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long start = System.currentTimeMillis();
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try {
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Dataset dataset = new RDFServiceDataset(service);
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return dataset.getNamedModel(arg0);
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} finally {
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service.close();
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bnodeModel.read(rdfService.sparqlConstructQuery(bnodeQuery, ModelSerializationFormat.N3), null, "N3");
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log.debug("constructed a model of blank nodes of size: " + bnodeModel.size() + " for graph " + graph);
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} catch (RDFServiceException se) {
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log.error("Error trying to create blank node model.", se);
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return null;
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} catch (Exception e) {
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log.error("error trying to create a blank node model: " + e.getMessage());
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return null;
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}
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long timeElapsedMillis = System.currentTimeMillis() - start;
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log.debug("msecs to find blank nodes for graph " + graph + " " + timeElapsedMillis);
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Model model = null;
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try {
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Dataset dataset = new RDFServiceDataset(rdfService);
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model = dataset.getNamedModel(graph);
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} finally {
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rdfService.close();
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}
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Graph bnodeFilteringGraph = new BlankNodeFilteringGraph(model.getGraph());
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Model bnodeFilteringModel = ModelFactory.createModelForGraph(bnodeFilteringGraph);
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BulkUpdateHandler bulkUpdateHandler = model.getGraph().getBulkUpdateHandler();
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Model unionModel = ModelFactory.createUnion(bnodeFilteringModel, bnodeModel);
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Graph specialGraph = new SpecialBulkUpdateHandlerGraph(unionModel.getGraph(), bulkUpdateHandler);
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Model specialUnionModel = ModelFactory.createModelForGraph(specialGraph);
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bnodeFilteringModel.register(new BlankNodeStatementListener(bnodeModel));
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return specialUnionModel;
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}
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public void removeModel(String arg0) {
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