NIHVIVO-3828 allows update and graph URI retrieval for non-Sesame SPARQL endpoints and NIHVIVO-3850 fixes IllegalStateException when downloading unmergeable statements
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brianjlowe
parent
4b192ef8eb
commit
e2438d404d
55 changed files with 82 additions and 49 deletions
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@ -180,6 +180,7 @@ public class JenaIngestController extends BaseEditController {
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processRenameResourceRequest(vreq, response, maker, modelType);
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} else if("mergeResult".equals(actionStr)){
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processMergeResultRequest(vreq, response, maker, modelType);
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return;
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}
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else {
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@ -10,16 +10,15 @@ import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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import org.apache.commons.httpclient.HttpException;
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import org.apache.commons.httpclient.HttpClient;
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import org.apache.commons.httpclient.NameValuePair;
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import org.apache.commons.httpclient.methods.ByteArrayRequestEntity;
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import org.apache.commons.httpclient.methods.PostMethod;
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import org.apache.commons.httpclient.methods.RequestEntity;
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import org.apache.commons.io.IOUtils;
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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 org.openrdf.model.Resource;
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import org.openrdf.query.MalformedQueryException;
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import org.openrdf.query.QueryLanguage;
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import org.openrdf.query.Update;
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import org.openrdf.query.UpdateExecutionException;
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import org.openrdf.repository.Repository;
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import org.openrdf.repository.RepositoryConnection;
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import org.openrdf.repository.RepositoryException;
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import org.openrdf.repository.RepositoryResult;
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@ -32,6 +31,7 @@ import com.hp.hpl.jena.query.QueryExecutionFactory;
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import com.hp.hpl.jena.query.QueryFactory;
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import com.hp.hpl.jena.query.QuerySolution;
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import com.hp.hpl.jena.query.ResultSet;
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import com.hp.hpl.jena.query.ResultSetFactory;
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import com.hp.hpl.jena.query.ResultSetFormatter;
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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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@ -48,6 +48,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.ChangeSetImpl;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceImpl;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.ListeningGraph;
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import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
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/*
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* API to write, read, and update Vitro's RDF store, with support
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@ -59,8 +60,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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private static final Log log = LogFactory.getLog(RDFServiceImpl.class);
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private String readEndpointURI;
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private String updateEndpointURI;
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private Repository readRepository;
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private Repository updateRepository;
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private HTTPRepository readRepository;
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private HTTPRepository updateRepository;
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private boolean useSesameContextQuery = true;
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/**
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* Returns an RDFService for a remote repository
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@ -78,7 +80,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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this.updateEndpointURI = updateEndpointURI;
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this.readRepository = new HTTPRepository(readEndpointURI);
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this.updateRepository = new HTTPRepository(updateEndpointURI);
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testConnection();
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}
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@ -332,25 +334,47 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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// graph update API
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@Override
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public List<String> getGraphURIs() throws RDFServiceException {
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List<String> graphNodeList = new ArrayList<String>();
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try {
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RepositoryConnection conn = getWriteConnection();
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if (!this.useSesameContextQuery) {
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return getGraphURIsFromSparqlQuery();
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} else {
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try {
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RepositoryResult<Resource> conResult = conn.getContextIDs();
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while (conResult.hasNext()) {
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Resource res = conResult.next();
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graphNodeList.add(res.stringValue());
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}
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} finally {
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conn.close();
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return getGraphURIsFromSesameContexts();
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} catch (RepositoryException re) {
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this.useSesameContextQuery = false;
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return getGraphURIsFromSparqlQuery();
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}
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} catch (RepositoryException re) {
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throw new RuntimeException(re);
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}
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}
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private List<String> getGraphURIsFromSesameContexts() throws RepositoryException {
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List<String> graphURIs = new ArrayList<String>();
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RepositoryConnection conn = getReadConnection();
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try {
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RepositoryResult<Resource> conResult = conn.getContextIDs();
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while (conResult.hasNext()) {
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Resource res = conResult.next();
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graphURIs.add(res.stringValue());
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}
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} finally {
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conn.close();
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}
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return graphNodeList;
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return graphURIs;
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}
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private List<String> getGraphURIsFromSparqlQuery() throws RDFServiceException {
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List<String> graphURIs = new ArrayList<String>();
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try {
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String graphURIString = "SELECT DISTINCT ?g WHERE { GRAPH ?g { ?s ?p ?o } } ORDER BY ?g";
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ResultSet rs = ResultSetFactory.fromJSON(
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sparqlSelectQuery(graphURIString, RDFService.ResultFormat.JSON));
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while (rs.hasNext()) {
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QuerySolution qs = rs.nextSolution();
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graphURIs.add(qs.getResource("g").getURI());
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}
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} catch (Exception e) {
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throw new RDFServiceException("Unable to list graph URIs", e);
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}
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return graphURIs;
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}
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/**
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@ -416,6 +440,14 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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return updateEndpointURI;
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}
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protected RepositoryConnection getReadConnection() {
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try {
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return this.readRepository.getConnection();
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} catch (RepositoryException e) {
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throw new RuntimeException(e);
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}
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}
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protected RepositoryConnection getWriteConnection() {
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try {
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return this.updateRepository.getConnection();
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@ -424,35 +456,34 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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}
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}
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protected void executeUpdate(String updateString) {
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protected void executeUpdate(String updateString) throws RDFServiceException {
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try {
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RepositoryConnection conn = getWriteConnection();
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try {
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Update u = conn.prepareUpdate(QueryLanguage.SPARQL, updateString);
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u.execute();
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} catch (MalformedQueryException e) {
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throw new RuntimeException(e);
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} catch (UpdateExecutionException e) {
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log.error(e,e);
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log.error("Update command: \n" + updateString);
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throw new RuntimeException(e);
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} finally {
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conn.close();
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HttpClient httpClient = new HttpClient();
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PostMethod meth = new PostMethod(updateEndpointURI);
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meth.addRequestHeader("Content-Type", "application/x-www-form-urlencoded");
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NameValuePair[] body = new NameValuePair[1];
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body[0] = new NameValuePair("update", updateString);
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meth.setRequestBody(body);
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int response = httpClient.executeMethod(meth);
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if (response > 399) {
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log.error("response " + response + " to update. \n");
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log.debug("update string: \n" + updateString);
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throw new RDFServiceException("Unable to perform SPARQL UPDATE");
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}
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} catch (RepositoryException re) {
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throw new RuntimeException(re);
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}
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} catch (Exception e) {
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throw new RDFServiceException("Unable to perform change set update", e);
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}
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}
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public void addModel(Model model, String graphURI) {
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public void addModel(Model model, String graphURI) throws RDFServiceException {
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verbModel(model, graphURI, "INSERT");
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}
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public void deleteModel(Model model, String graphURI) {
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public void deleteModel(Model model, String graphURI) throws RDFServiceException {
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verbModel(model, graphURI, "DELETE");
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}
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private void verbModel(Model model, String graphURI, String verb) {
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private void verbModel(Model model, String graphURI, String verb) throws RDFServiceException {
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Model m = ModelFactory.createDefaultModel();
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int testLimit = 1000;
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StmtIterator stmtIt = model.listStatements();
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@ -481,7 +512,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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}
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}
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protected void addTriple(Triple t, String graphURI) {
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protected void addTriple(Triple t, String graphURI) throws RDFServiceException {
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StringBuffer updateString = new StringBuffer();
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updateString.append("INSERT DATA { ");
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@ -498,7 +529,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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notifyListeners(t, ModelChange.Operation.ADD, graphURI);
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}
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protected void removeTriple(Triple t, String graphURI) {
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protected void removeTriple(Triple t, String graphURI) throws RDFServiceException {
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StringBuffer updateString = new StringBuffer();
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updateString.append("DELETE DATA { ");
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@ -551,7 +582,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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}
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}
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private void performChange(ModelChange modelChange) {
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private void performChange(ModelChange modelChange) throws RDFServiceException {
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Model model = parseModel(modelChange);
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if (modelChange.getOperation() == ModelChange.Operation.ADD) {
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addModel(model, modelChange.getGraphURI());
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@ -563,7 +594,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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}
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}
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private void removeBlankNodesWithSparqlUpdate(Model model, String graphURI) {
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private void removeBlankNodesWithSparqlUpdate(Model model, String graphURI)
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throws RDFServiceException {
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List<Statement> blankNodeStatements = new ArrayList<Statement>();
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StmtIterator stmtIt = model.listStatements();
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while (stmtIt.hasNext()) {
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@ -636,7 +668,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
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}
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}
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private void removeUsingSparqlUpdate(Model model, String graphURI) {
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private void removeUsingSparqlUpdate(Model model, String graphURI) throws RDFServiceException {
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StmtIterator stmtIt = model.listStatements();
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