Ingest Tools using RDFService
This commit is contained in:
brianjlowe
parent
f55916b8d8
commit
068a4d9931
8 changed files with 259 additions and 1412 deletions
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@ -69,6 +69,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
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import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker;
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@ -206,13 +207,13 @@ public class JenaIngestController extends BaseEditController {
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}
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}
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private void processRDBModelsRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
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private void processRDBModelsRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
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VitroJenaModelMaker vjmm = (VitroJenaModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
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ModelMaker vjmm = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
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vreq.getSession().setAttribute("vitroJenaModelMaker", vjmm);
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vreq.getSession().setAttribute("vitroJenaModelMaker", vjmm);
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showModelList(vreq, vjmm, "rdb");
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showModelList(vreq, vjmm, "rdb");
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}
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}
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private void processSDBModelsRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
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private void processSDBModelsRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
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VitroJenaSDBModelMaker vsmm = (VitroJenaSDBModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
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ModelMaker vsmm = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
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vreq.getSession().setAttribute("vitroJenaModelMaker", vsmm);
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vreq.getSession().setAttribute("vitroJenaModelMaker", vsmm);
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showModelList(vreq, vsmm, "sdb");
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showModelList(vreq, vsmm, "sdb");
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}
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}
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@ -714,7 +715,7 @@ public class JenaIngestController extends BaseEditController {
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? ((VitroJenaSpecialModelMaker) maker).getInnerModelMaker()
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? ((VitroJenaSpecialModelMaker) maker).getInnerModelMaker()
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: maker;
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: maker;
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if (modelType == null) {
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if (modelType == null) {
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if (maker instanceof VitroJenaSDBModelMaker) {
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if (maker instanceof RDFServiceModelMaker) {
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modelType = "sdb";
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modelType = "sdb";
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} else {
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} else {
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modelType = "rdb";
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modelType = "rdb";
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@ -0,0 +1,244 @@
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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 java.text.Collator;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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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.GraphMaker;
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import com.hp.hpl.jena.query.Dataset;
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import com.hp.hpl.jena.query.Query;
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import com.hp.hpl.jena.query.QueryExecution;
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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.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.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.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.sdb.SDBFactory;
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import com.hp.hpl.jena.sdb.Store;
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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 com.hp.hpl.jena.vocabulary.RDFS;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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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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public class RDFServiceModelMaker implements ModelMaker {
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private final static Log log = LogFactory.getLog(VitroJenaSDBModelMaker.class);
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private RDFServiceFactory rdfServiceFactory;
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public static final String METADATA_MODEL_URI =
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"http://vitro.mannlib.cornell.edu/ns/vitro/sdb/metadata";
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public static final String HAS_NAMED_MODEL_URI =
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"http://vitro.mannlib.cornell.edu/ns/vitro/sdb/hasNamedModel";
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private Resource sdbResource; // a resource representing the SDB database
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public RDFServiceModelMaker(RDFServiceFactory rdfServiceFactory) {
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this.rdfServiceFactory = rdfServiceFactory;
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}
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protected RDFService getRDFService() {
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return rdfServiceFactory.getRDFService();
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}
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Model getMetadataModel() {
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return getModel(METADATA_MODEL_URI);
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}
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public void close() {
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// n.a.
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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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try {
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metadataModel.add(
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sdbResource,metadataModel.getProperty(
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HAS_NAMED_MODEL_URI), modelName);
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} finally {
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metadataModel.close();
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}
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return model;
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}
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public Model createModel(String arg0, boolean arg1) {
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// TODO Figure out if we can offer a "create if not found" option using SDB
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return createModel(arg0);
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}
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public GraphMaker getGraphMaker() {
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throw new UnsupportedOperationException(
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"GraphMaker not supported by " + this.getClass().getName());
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}
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public boolean hasModel(String arg0) {
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Model metadataModel = getMetadataModel();
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try {
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StmtIterator stmtIt = metadataModel.listStatements(
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sdbResource, metadataModel.getProperty(
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HAS_NAMED_MODEL_URI), arg0);
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try {
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return stmtIt.hasNext();
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} finally {
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if (stmtIt != null) {
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stmtIt.close();
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}
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}
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} finally {
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metadataModel.close();
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}
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}
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public ExtendedIterator<String> listModels() {
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Model metadataModel = getMetadataModel();
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try {
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return listModelNames(metadataModel);
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} finally {
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metadataModel.close();
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}
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}
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private ExtendedIterator<String> listModelNames(Model metadataModel) {
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Set<String> modelNameSet = new HashSet<String>();
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Iterator<RDFNode> metadataNameIt = metadataModel.listObjectsOfProperty(
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metadataModel.getProperty(HAS_NAMED_MODEL_URI));
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while (metadataNameIt.hasNext()) {
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RDFNode rdfNode = metadataNameIt.next();
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if (rdfNode.isLiteral()) {
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modelNameSet.add(((Literal) rdfNode).getLexicalForm());
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}
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}
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RDFService service = getRDFService();
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try {
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modelNameSet.addAll(service.getGraphURIs());
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} catch (RDFServiceException e) {
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throw new RuntimeException(e);
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} finally {
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service.close();
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}
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List<String> modelNameList = new ArrayList<String>();
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modelNameList.addAll(modelNameSet);
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Collections.sort(modelNameList, Collator.getInstance());
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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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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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}
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}
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public void removeModel(String arg0) {
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Model m = getModel(arg0);
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m.removeAll(null,null,null);
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Model metadataModel = getMetadataModel();
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try {
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metadataModel.remove(sdbResource, metadataModel.getProperty(
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HAS_NAMED_MODEL_URI),metadataModel.createLiteral(arg0));
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} finally {
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metadataModel.close();
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}
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}
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public Model addDescription(Model arg0, Resource arg1) {
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throw new UnsupportedOperationException(
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"addDescription not supported by " + this.getClass().getName());
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}
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public Model createModelOver(String arg0) {
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throw new UnsupportedOperationException(
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"createModelOver not supported by " + this.getClass().getName());
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}
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public Model getDescription() {
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throw new UnsupportedOperationException(
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"createModelOver not supported by " + this.getClass().getName());
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}
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public Model getDescription(Resource arg0) {
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throw new UnsupportedOperationException(
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"getDescription not supported by "+this.getClass().getName());
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}
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public Model openModel() {
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RDFService service = getRDFService();
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try {
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Dataset dataset = new RDFServiceDataset(service);
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return dataset.getDefaultModel();
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} finally {
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service.close();
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}
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}
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public Model createDefaultModel() {
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return openModel();
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}
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public Model createFreshModel() {
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throw new UnsupportedOperationException(
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"createFreshModel not supported by " + this.getClass().getName());
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}
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/**
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* @deprecated
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*/
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public Model createModel() {
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return openModel();
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}
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/**
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* @deprecated
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*/
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public Model getModel() {
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return openModel();
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}
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public Model openModel(String arg0) {
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return openModel();
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}
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public Model openModelIfPresent(String arg0) {
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return (this.hasModel(arg0))
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? openModel(arg0, false)
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: null;
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}
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public Model getModel(String modelName) {
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return openModel(modelName, true);
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}
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public Model getModel(String arg0, ModelReader arg1) {
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throw new UnsupportedOperationException(
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"getModel(String, ModelReader) not supported by " +
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this.getClass().getName());
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}
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}
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@ -24,6 +24,7 @@ import com.hp.hpl.jena.query.QueryFactory;
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import com.hp.hpl.jena.query.Syntax;
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import com.hp.hpl.jena.query.Syntax;
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import com.hp.hpl.jena.rdf.model.Model;
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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.ModelFactory;
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import com.hp.hpl.jena.rdf.model.ModelMaker;
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import com.hp.hpl.jena.rdf.model.ResIterator;
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import com.hp.hpl.jena.rdf.model.ResIterator;
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import com.hp.hpl.jena.rdf.model.Resource;
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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.ResourceFactory;
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@ -44,7 +45,6 @@ import com.hp.hpl.jena.vocabulary.RDF;
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import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
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import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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@ -52,9 +52,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
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import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
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import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
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@ -68,14 +66,6 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase
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ServletContext ctx = sce.getServletContext();
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ServletContext ctx = sce.getServletContext();
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StartupStatus ss = StartupStatus.getBean(ctx);
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StartupStatus ss = StartupStatus.getBean(ctx);
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// temporary scaffolding in the rdfapi dev branch
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// TODO remove me
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if (ConfigurationProperties.getBean(ctx).getProperty(
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"VitroConnection.DataSource.endpointURI") != null) {
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(new JenaDataSourceSetupSparql2()).contextInitialized(sce);
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return;
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}
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try {
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try {
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long startTime = System.currentTimeMillis();
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long startTime = System.currentTimeMillis();
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setUpJenaDataSource(ctx);
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setUpJenaDataSource(ctx);
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@ -331,7 +321,7 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase
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VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
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VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
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setVitroJenaModelMaker(vjmm, ctx);
|
setVitroJenaModelMaker(vjmm, ctx);
|
||||||
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
||||||
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
|
ModelMaker vsmm = getVitroJenaSDBModelMaker();
|
||||||
setVitroJenaSDBModelMaker(vsmm, ctx);
|
setVitroJenaSDBModelMaker(vsmm, ctx);
|
||||||
|
|
||||||
//bdc34: I have no reason for vsmm vs vjmm.
|
//bdc34: I have no reason for vsmm vs vjmm.
|
||||||
|
|
|
||||||
|
|
@ -26,6 +26,7 @@ import com.hp.hpl.jena.query.QueryFactory;
|
||||||
import com.hp.hpl.jena.query.Syntax;
|
import com.hp.hpl.jena.query.Syntax;
|
||||||
import com.hp.hpl.jena.rdf.model.Model;
|
import com.hp.hpl.jena.rdf.model.Model;
|
||||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||||
|
import com.hp.hpl.jena.rdf.model.ModelMaker;
|
||||||
import com.hp.hpl.jena.sdb.Store;
|
import com.hp.hpl.jena.sdb.Store;
|
||||||
import com.hp.hpl.jena.sdb.StoreDesc;
|
import com.hp.hpl.jena.sdb.StoreDesc;
|
||||||
import com.hp.hpl.jena.sdb.store.DatabaseType;
|
import com.hp.hpl.jena.sdb.store.DatabaseType;
|
||||||
|
|
@ -405,7 +406,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
|
||||||
}
|
}
|
||||||
|
|
||||||
private static VitroJenaModelMaker vjmm = null;
|
private static VitroJenaModelMaker vjmm = null;
|
||||||
private static VitroJenaSDBModelMaker vsmm = null;
|
private static ModelMaker vsmm = null;
|
||||||
private static VitroModelSource vms = null;
|
private static VitroModelSource vms = null;
|
||||||
private static final String sdbModelMaker = "vitroJenaSDBModelMaker";
|
private static final String sdbModelMaker = "vitroJenaSDBModelMaker";
|
||||||
private static final String rdbModelMaker = "vitroJenaModelMaker";
|
private static final String rdbModelMaker = "vitroJenaModelMaker";
|
||||||
|
|
@ -486,7 +487,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
|
||||||
ctx.setAttribute(rdbModelMaker, vjmm);
|
ctx.setAttribute(rdbModelMaker, vjmm);
|
||||||
}
|
}
|
||||||
|
|
||||||
public static void setVitroJenaSDBModelMaker(VitroJenaSDBModelMaker vsmm,
|
public static void setVitroJenaSDBModelMaker(ModelMaker vsmm,
|
||||||
ServletContext ctx){
|
ServletContext ctx){
|
||||||
ctx.setAttribute(sdbModelMaker, vsmm);
|
ctx.setAttribute(sdbModelMaker, vsmm);
|
||||||
}
|
}
|
||||||
|
|
@ -511,7 +512,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
|
||||||
return vjmm;
|
return vjmm;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected VitroJenaSDBModelMaker getVitroJenaSDBModelMaker(){
|
protected ModelMaker getVitroJenaSDBModelMaker(){
|
||||||
return vsmm;
|
return vsmm;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1,698 +0,0 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.vitro.webapp.servlet.setup;
|
|
||||||
|
|
||||||
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.DISPLAY_ONT_MODEL;
|
|
||||||
|
|
||||||
import java.sql.SQLException;
|
|
||||||
import java.util.ArrayList;
|
|
||||||
import java.util.List;
|
|
||||||
|
|
||||||
import javax.servlet.ServletContext;
|
|
||||||
import javax.servlet.ServletContextEvent;
|
|
||||||
|
|
||||||
import org.apache.commons.dbcp.BasicDataSource;
|
|
||||||
import org.apache.commons.logging.Log;
|
|
||||||
import org.apache.commons.logging.LogFactory;
|
|
||||||
|
|
||||||
import com.hp.hpl.jena.graph.Graph;
|
|
||||||
import com.hp.hpl.jena.ontology.OntModel;
|
|
||||||
import com.hp.hpl.jena.ontology.OntModelSpec;
|
|
||||||
import com.hp.hpl.jena.query.Dataset;
|
|
||||||
import com.hp.hpl.jena.query.DatasetFactory;
|
|
||||||
import com.hp.hpl.jena.query.Query;
|
|
||||||
import com.hp.hpl.jena.query.QueryExecution;
|
|
||||||
import com.hp.hpl.jena.query.QueryExecutionFactory;
|
|
||||||
import com.hp.hpl.jena.query.QueryFactory;
|
|
||||||
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.ResIterator;
|
|
||||||
import com.hp.hpl.jena.rdf.model.Resource;
|
|
||||||
import com.hp.hpl.jena.rdf.model.ResourceFactory;
|
|
||||||
import com.hp.hpl.jena.rdf.model.Statement;
|
|
||||||
import com.hp.hpl.jena.rdf.model.StmtIterator;
|
|
||||||
import com.hp.hpl.jena.sdb.SDB;
|
|
||||||
import com.hp.hpl.jena.sdb.SDBFactory;
|
|
||||||
import com.hp.hpl.jena.sdb.Store;
|
|
||||||
import com.hp.hpl.jena.sdb.StoreDesc;
|
|
||||||
import com.hp.hpl.jena.sdb.sql.SDBConnection;
|
|
||||||
import com.hp.hpl.jena.sdb.store.DatabaseType;
|
|
||||||
import com.hp.hpl.jena.sdb.store.LayoutType;
|
|
||||||
import com.hp.hpl.jena.sdb.util.StoreUtils;
|
|
||||||
import com.hp.hpl.jena.shared.Lock;
|
|
||||||
import com.hp.hpl.jena.util.ResourceUtils;
|
|
||||||
import com.hp.hpl.jena.util.iterator.ClosableIterator;
|
|
||||||
import com.hp.hpl.jena.vocabulary.RDF;
|
|
||||||
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
|
|
||||||
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.OntModelSelectorImpl;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.SingleContentOntModelSelector;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDatasetGraph;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
|
||||||
|
|
||||||
public class JenaDataSourceSetupSparql extends JenaDataSourceSetupBase
|
|
||||||
implements javax.servlet.ServletContextListener {
|
|
||||||
|
|
||||||
private static final Log log = LogFactory.getLog(JenaDataSourceSetupSparql.class);
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public void contextInitialized(ServletContextEvent sce) {
|
|
||||||
ServletContext ctx = sce.getServletContext();
|
|
||||||
StartupStatus ss = StartupStatus.getBean(ctx);
|
|
||||||
|
|
||||||
try {
|
|
||||||
long startTime = System.currentTimeMillis();
|
|
||||||
setUpJenaDataSource(ctx);
|
|
||||||
log.info((System.currentTimeMillis() - startTime) / 1000 +
|
|
||||||
" seconds to set up SDB store");
|
|
||||||
} catch (SQLException sqle) {
|
|
||||||
// SQL exceptions are fatal and should halt startup
|
|
||||||
log.error("Error using SQL database; startup aborted.", sqle);
|
|
||||||
ss.fatal(this, "Error using SQL database; startup aborted.", sqle);
|
|
||||||
} catch (Throwable t) {
|
|
||||||
log.error("Throwable in " + this.getClass().getName(), t);
|
|
||||||
ss.fatal(this, "Throwable in " + this.getClass().getName(), t);
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
private void setUpJenaDataSource(ServletContext ctx) throws SQLException {
|
|
||||||
|
|
||||||
OntModelSelector baseOms = new OntModelSelectorImpl();
|
|
||||||
OntModelSelector inferenceOms = new OntModelSelectorImpl();
|
|
||||||
OntModelSelector unionOms = new OntModelSelectorImpl();
|
|
||||||
|
|
||||||
OntModel userAccountsModel = ontModelFromContextAttribute(
|
|
||||||
ctx, "userAccountsOntModel");
|
|
||||||
// baseOms.setUserAccountsModel(userAccountsModel);
|
|
||||||
// inferenceOms.setUserAccountsModel(userAccountsModel);
|
|
||||||
// unionOms.setUserAccountsModel(userAccountsModel);
|
|
||||||
|
|
||||||
OntModel displayModel = ontModelFromContextAttribute(
|
|
||||||
ctx,DISPLAY_ONT_MODEL);
|
|
||||||
// baseOms.setDisplayModel(displayModel);
|
|
||||||
// inferenceOms.setDisplayModel(displayModel);
|
|
||||||
// unionOms.setDisplayModel(displayModel);
|
|
||||||
|
|
||||||
//okay let's make a graph-backed model
|
|
||||||
String endpointURI = ConfigurationProperties.getBean(
|
|
||||||
ctx).getProperty("VitroConnection.DataSource.endpointURI");
|
|
||||||
|
|
||||||
Graph g = new SparqlGraph(endpointURI);
|
|
||||||
Dataset dataset = DatasetFactory.create(new SparqlDatasetGraph(endpointURI));
|
|
||||||
setStartupDataset(dataset, ctx);
|
|
||||||
|
|
||||||
Model m = ModelFactory.createModelForGraph(g);
|
|
||||||
OntModel om = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, m);
|
|
||||||
baseOms = new SingleContentOntModelSelector(om, displayModel, userAccountsModel);
|
|
||||||
inferenceOms = baseOms;
|
|
||||||
unionOms = baseOms;
|
|
||||||
|
|
||||||
// SDB setup
|
|
||||||
|
|
||||||
// union default graph
|
|
||||||
SDB.getContext().set(SDB.unionDefaultGraph, true) ;
|
|
||||||
|
|
||||||
StoreDesc storeDesc = makeStoreDesc(ctx);
|
|
||||||
setApplicationStoreDesc(storeDesc, ctx);
|
|
||||||
|
|
||||||
BasicDataSource bds = getApplicationDataSource(ctx);
|
|
||||||
if (bds == null) {
|
|
||||||
bds = makeDataSourceFromConfigurationProperties(ctx);
|
|
||||||
setApplicationDataSource(bds, ctx);
|
|
||||||
}
|
|
||||||
|
|
||||||
Store store = connectStore(bds, storeDesc);
|
|
||||||
setApplicationStore(store, ctx);
|
|
||||||
|
|
||||||
// if (!isSetUp(store)) {
|
|
||||||
// log.info("Initializing SDB store");
|
|
||||||
// if (isFirstStartup()) {
|
|
||||||
// setupSDB(ctx, store);
|
|
||||||
// } else {
|
|
||||||
// migrateToSDBFromExistingRDBStore(ctx, store);
|
|
||||||
// }
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// // The code below, which sets up the OntModelSelectors, controls whether
|
|
||||||
// // each model is maintained in memory, in the DB, or both while the
|
|
||||||
// // application is running.
|
|
||||||
//
|
|
||||||
// // Populate the three OntModelSelectors (BaseOntModel = assertions,
|
|
||||||
// // InferenceOntModel = inferences and JenaOntModel = union of assertions
|
|
||||||
// // and inferences) with the post-SDB-conversion models.
|
|
||||||
//
|
|
||||||
// // ABox assertions
|
|
||||||
// Model aboxAssertions = makeDBModel(
|
|
||||||
// bds, JenaDataSourceSetupBase.JENA_DB_MODEL, DB_ONT_MODEL_SPEC,
|
|
||||||
// TripleStoreType.SDB, ctx);
|
|
||||||
// Model listenableAboxAssertions = ModelFactory.createUnion(
|
|
||||||
// aboxAssertions, ModelFactory.createDefaultModel());
|
|
||||||
// baseOms.setABoxModel(
|
|
||||||
// ModelFactory.createOntologyModel(
|
|
||||||
// OntModelSpec.OWL_MEM, listenableAboxAssertions));
|
|
||||||
//
|
|
||||||
// // ABox inferences
|
|
||||||
// Model aboxInferences = makeDBModel(
|
|
||||||
// bds, JenaDataSourceSetupBase.JENA_INF_MODEL, DB_ONT_MODEL_SPEC,
|
|
||||||
// TripleStoreType.SDB, ctx);
|
|
||||||
// Model listenableAboxInferences = ModelFactory.createUnion(
|
|
||||||
// aboxInferences, ModelFactory.createDefaultModel());
|
|
||||||
// inferenceOms.setABoxModel(ModelFactory.createOntologyModel(
|
|
||||||
// OntModelSpec.OWL_MEM, listenableAboxInferences));
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// // Since the TBox models are in memory, they do not have timeout issues
|
|
||||||
// // like the like the ABox models do (and so don't need the extra step
|
|
||||||
// // to make them listenable.)
|
|
||||||
//
|
|
||||||
// // TBox assertions
|
|
||||||
// try {
|
|
||||||
// Model tboxAssertionsDB = makeDBModel(
|
|
||||||
// bds, JENA_TBOX_ASSERTIONS_MODEL, DB_ONT_MODEL_SPEC,
|
|
||||||
// TripleStoreType.SDB, ctx);
|
|
||||||
// OntModel tboxAssertions = ModelFactory.createOntologyModel(
|
|
||||||
// MEM_ONT_MODEL_SPEC);
|
|
||||||
//
|
|
||||||
// if (tboxAssertionsDB != null) {
|
|
||||||
// long startTime = System.currentTimeMillis();
|
|
||||||
// System.out.println(
|
|
||||||
// "Copying cached tbox assertions into memory");
|
|
||||||
// tboxAssertions.add(tboxAssertionsDB);
|
|
||||||
// System.out.println((System.currentTimeMillis() - startTime)
|
|
||||||
// / 1000 + " seconds to load tbox assertions");
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// tboxAssertions.getBaseModel().register(new ModelSynchronizer(
|
|
||||||
// tboxAssertionsDB));
|
|
||||||
// baseOms.setTBoxModel(tboxAssertions);
|
|
||||||
// } catch (Throwable e) {
|
|
||||||
// log.error("Unable to load tbox assertion cache from DB", e);
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// // TBox inferences
|
|
||||||
// try {
|
|
||||||
// Model tboxInferencesDB = makeDBModel(
|
|
||||||
// bds, JENA_TBOX_INF_MODEL, DB_ONT_MODEL_SPEC,
|
|
||||||
// TripleStoreType.SDB, ctx);
|
|
||||||
// OntModel tboxInferences = ModelFactory.createOntologyModel(
|
|
||||||
// MEM_ONT_MODEL_SPEC);
|
|
||||||
//
|
|
||||||
// if (tboxInferencesDB != null) {
|
|
||||||
// long startTime = System.currentTimeMillis();
|
|
||||||
// System.out.println(
|
|
||||||
// "Copying cached tbox inferences into memory");
|
|
||||||
// tboxInferences.add(tboxInferencesDB);
|
|
||||||
// System.out.println((System.currentTimeMillis() - startTime)
|
|
||||||
// / 1000 + " seconds to load tbox inferences");
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// tboxInferences.getBaseModel().register(new ModelSynchronizer(
|
|
||||||
// tboxInferencesDB));
|
|
||||||
// inferenceOms.setTBoxModel(tboxInferences);
|
|
||||||
// } catch (Throwable e) {
|
|
||||||
// log.error("Unable to load tbox inference cache from DB", e);
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// // union ABox
|
|
||||||
// OntModel unionABoxModel = ModelFactory.createOntologyModel(
|
|
||||||
// MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(
|
|
||||||
// baseOms.getABoxModel(), inferenceOms.getABoxModel()));
|
|
||||||
// unionOms.setABoxModel(unionABoxModel);
|
|
||||||
//
|
|
||||||
// // union TBox
|
|
||||||
// OntModel unionTBoxModel = ModelFactory.createOntologyModel(
|
|
||||||
// MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(
|
|
||||||
// baseOms.getTBoxModel(), inferenceOms.getTBoxModel()));
|
|
||||||
// unionOms.setTBoxModel(unionTBoxModel);
|
|
||||||
//
|
|
||||||
//
|
|
||||||
// // Application metadata model is cached in memory.
|
|
||||||
// try {
|
|
||||||
//
|
|
||||||
// Model applicationMetadataModelDB = makeDBModel(
|
|
||||||
// bds, JENA_APPLICATION_METADATA_MODEL, DB_ONT_MODEL_SPEC,
|
|
||||||
// TripleStoreType.SDB, ctx);
|
|
||||||
// OntModel applicationMetadataModel =
|
|
||||||
// ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
|
|
||||||
//
|
|
||||||
// long startTime = System.currentTimeMillis();
|
|
||||||
// System.out.println(
|
|
||||||
// "Copying cached application metadata model into memory");
|
|
||||||
// applicationMetadataModel.add(applicationMetadataModelDB);
|
|
||||||
// System.out.println((System.currentTimeMillis() - startTime)
|
|
||||||
// / 1000 + " seconds to load application metadata model " +
|
|
||||||
// "assertions of size " + applicationMetadataModel.size());
|
|
||||||
// applicationMetadataModel.getBaseModel().register(
|
|
||||||
// new ModelSynchronizer(applicationMetadataModelDB));
|
|
||||||
//
|
|
||||||
// if (isFirstStartup()) {
|
|
||||||
// applicationMetadataModel.add(
|
|
||||||
// InitialJenaModelUtils.loadInitialModel(
|
|
||||||
// ctx, getDefaultNamespace(ctx)));
|
|
||||||
//
|
|
||||||
// } else if (applicationMetadataModelDB.size() == 0) {
|
|
||||||
// repairAppMetadataModel(
|
|
||||||
// applicationMetadataModel, aboxAssertions,
|
|
||||||
// aboxInferences);
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// baseOms.setApplicationMetadataModel(applicationMetadataModel);
|
|
||||||
// inferenceOms.setApplicationMetadataModel(
|
|
||||||
// baseOms.getApplicationMetadataModel());
|
|
||||||
// unionOms.setApplicationMetadataModel(
|
|
||||||
// baseOms.getApplicationMetadataModel());
|
|
||||||
//
|
|
||||||
// } catch (Throwable e) {
|
|
||||||
// log.error("Unable to load application metadata model cache from DB"
|
|
||||||
// , e);
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// checkForNamespaceMismatch( baseOms.getApplicationMetadataModel(), ctx );
|
|
||||||
//
|
|
||||||
// if (isFirstStartup()) {
|
|
||||||
// loadDataFromFilesystem(baseOms, ctx);
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// log.info("Setting up union models and DAO factories");
|
|
||||||
//
|
|
||||||
// // create TBox + ABox union models and set up webapp DAO factories
|
|
||||||
// OntModel baseUnion = ModelFactory.createOntologyModel(
|
|
||||||
// OntModelSpec.OWL_MEM,
|
|
||||||
// ModelFactory.createUnion(baseOms.getABoxModel(),
|
|
||||||
// baseOms.getTBoxModel()));
|
|
||||||
// baseOms.setFullModel(baseUnion);
|
|
||||||
ModelContext.setBaseOntModel(baseOms.getFullModel(), ctx);
|
|
||||||
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
|
|
||||||
config.setDefaultNamespace(getDefaultNamespace(ctx));
|
|
||||||
// revert this
|
|
||||||
WebappDaoFactory baseWadf = new WebappDaoFactoryJena(
|
|
||||||
baseOms, config
|
|
||||||
);
|
|
||||||
ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
|
|
||||||
|
|
||||||
OntModel inferenceUnion = ModelFactory.createOntologyModel(
|
|
||||||
OntModelSpec.OWL_MEM,
|
|
||||||
ModelFactory.createUnion(
|
|
||||||
inferenceOms.getABoxModel(),
|
|
||||||
inferenceOms.getTBoxModel()));
|
|
||||||
// inferenceOms.setFullModel(inferenceUnion);
|
|
||||||
// ModelContext.setInferenceOntModel(inferenceOms.getFullModel(), ctx);
|
|
||||||
// WebappDaoFactory infWadf = new WebappDaoFactorySDB(
|
|
||||||
// inferenceOms, bds, storeDesc, config,
|
|
||||||
// WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
|
|
||||||
// ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
|
|
||||||
|
|
||||||
OntModel masterUnion = unionOms.getFullModel();
|
|
||||||
|
|
||||||
// ModelFactory.createOntologyModel(
|
|
||||||
// DB_ONT_MODEL_SPEC, makeDBModel(
|
|
||||||
// bds, WebappDaoFactorySDB.UNION_GRAPH,
|
|
||||||
// DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx));
|
|
||||||
|
|
||||||
// unionOms.setFullModel(masterUnion);
|
|
||||||
ctx.setAttribute("jenaOntModel", masterUnion);
|
|
||||||
// WebappDaoFactory wadf = new WebappDaoFactorySDB(
|
|
||||||
// unionOms, bds, storeDesc, config);
|
|
||||||
// ctx.setAttribute("webappDaoFactory",wadf);
|
|
||||||
|
|
||||||
ModelContext.setOntModelSelector(unionOms, ctx);
|
|
||||||
ModelContext.setUnionOntModelSelector(unionOms, ctx);
|
|
||||||
// assertions and inferences
|
|
||||||
ModelContext.setBaseOntModelSelector(baseOms, ctx);
|
|
||||||
// assertions
|
|
||||||
ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);
|
|
||||||
// inferences
|
|
||||||
|
|
||||||
ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
|
|
||||||
|
|
||||||
log.info("SDB store ready for use");
|
|
||||||
|
|
||||||
makeModelMakerFromConnectionProperties(TripleStoreType.RDB, ctx);
|
|
||||||
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
|
|
||||||
setVitroJenaModelMaker(vjmm, ctx);
|
|
||||||
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
|
||||||
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
|
|
||||||
setVitroJenaSDBModelMaker(vsmm, ctx);
|
|
||||||
|
|
||||||
//bdc34: I have no reason for vsmm vs vjmm.
|
|
||||||
//I don't know what are the implications of this choice.
|
|
||||||
setVitroModelSource( new VitroModelSource(vsmm,ctx), ctx);
|
|
||||||
|
|
||||||
log.info("Model makers set up");
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* If we find a "portal1" portal (and we should), its URI should use the
|
|
||||||
* default namespace.
|
|
||||||
*/
|
|
||||||
private void checkForNamespaceMismatch(OntModel model, ServletContext ctx) {
|
|
||||||
String expectedNamespace = getDefaultNamespace(ctx);
|
|
||||||
|
|
||||||
List<Resource> portals = getPortal1s(model);
|
|
||||||
|
|
||||||
if(!portals.isEmpty() && noPortalForNamespace(
|
|
||||||
portals, expectedNamespace)) {
|
|
||||||
// There really should be only one portal 1, but if there happen to
|
|
||||||
// be multiple, just arbitrarily pick the first in the list.
|
|
||||||
Resource portal = portals.get(0);
|
|
||||||
String oldNamespace = portal.getNameSpace();
|
|
||||||
renamePortal(portal, expectedNamespace, model);
|
|
||||||
StartupStatus ss = StartupStatus.getBean(ctx);
|
|
||||||
ss.warning(this, "\nThe default namespace has been changed \n" +
|
|
||||||
"from " + oldNamespace +
|
|
||||||
"\nto " + expectedNamespace + ".\n" +
|
|
||||||
"The application will function normally, but " +
|
|
||||||
"any individuals in the \n" + oldNamespace + " " +
|
|
||||||
"namespace will need to have their URIs \n" +
|
|
||||||
"changed in order to be served as linked data. " +
|
|
||||||
"You can use the Ingest Tools \nto change the " +
|
|
||||||
"URIs for a batch of resources.");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private List<Resource> getPortal1s(Model model) {
|
|
||||||
List<Resource> portals = new ArrayList<Resource>();
|
|
||||||
try {
|
|
||||||
model.enterCriticalSection(Lock.READ);
|
|
||||||
ResIterator portalIt = model.listResourcesWithProperty(
|
|
||||||
RDF.type, PORTAL);
|
|
||||||
while (portalIt.hasNext()) {
|
|
||||||
Resource portal = portalIt.nextResource();
|
|
||||||
if ("portal1".equals(portal.getLocalName())) {
|
|
||||||
portals.add(portal);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
} finally {
|
|
||||||
model.leaveCriticalSection();
|
|
||||||
}
|
|
||||||
return portals;
|
|
||||||
}
|
|
||||||
|
|
||||||
private boolean noPortalForNamespace(List<Resource> portals,
|
|
||||||
String expectedNamespace) {
|
|
||||||
for (Resource portal : portals) {
|
|
||||||
if(expectedNamespace.equals(portal.getNameSpace())) {
|
|
||||||
return false;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return true;
|
|
||||||
}
|
|
||||||
|
|
||||||
private void renamePortal(Resource portal, String namespace, Model model) {
|
|
||||||
model.enterCriticalSection(Lock.WRITE);
|
|
||||||
try {
|
|
||||||
ResourceUtils.renameResource(
|
|
||||||
portal, namespace + portal.getLocalName());
|
|
||||||
} finally {
|
|
||||||
model.leaveCriticalSection();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/* ===================================================================== */
|
|
||||||
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public void contextDestroyed(ServletContextEvent sce) {
|
|
||||||
// Nothing to do.
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
protected OntModel ontModelFromContextAttribute(ServletContext ctx,
|
|
||||||
String attribute) {
|
|
||||||
OntModel ontModel;
|
|
||||||
Object attributeValue = ctx.getAttribute(attribute);
|
|
||||||
if (attributeValue != null && attributeValue instanceof OntModel) {
|
|
||||||
ontModel = (OntModel) attributeValue;
|
|
||||||
} else {
|
|
||||||
ontModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
|
|
||||||
ctx.setAttribute(attribute, ontModel);
|
|
||||||
}
|
|
||||||
return ontModel;
|
|
||||||
}
|
|
||||||
|
|
||||||
private boolean isEmpty(Model model) {
|
|
||||||
ClosableIterator<Statement> closeIt = model.listStatements(
|
|
||||||
null, RDF.type, ResourceFactory.createResource(
|
|
||||||
VitroVocabulary.PORTAL));
|
|
||||||
try {
|
|
||||||
if (closeIt.hasNext()) {
|
|
||||||
return false;
|
|
||||||
} else {
|
|
||||||
return true;
|
|
||||||
}
|
|
||||||
} finally {
|
|
||||||
closeIt.close();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private void loadDataFromFilesystem(OntModelSelector baseOms,
|
|
||||||
ServletContext ctx) {
|
|
||||||
Long startTime = System.currentTimeMillis();
|
|
||||||
log.debug("Initializing models from RDF files");
|
|
||||||
readOntologyFilesInPathSet(USER_ABOX_PATH, ctx, baseOms.getABoxModel());
|
|
||||||
readOntologyFilesInPathSet(USER_TBOX_PATH, ctx, baseOms.getTBoxModel());
|
|
||||||
readOntologyFilesInPathSet(
|
|
||||||
USER_APPMETA_PATH, ctx, baseOms.getApplicationMetadataModel());
|
|
||||||
log.debug(((System.currentTimeMillis() - startTime) / 1000)
|
|
||||||
+ " seconds to read RDF files ");
|
|
||||||
}
|
|
||||||
|
|
||||||
private static void getTBoxModel(Model fullModel,
|
|
||||||
Model submodels,
|
|
||||||
Model tboxModel) {
|
|
||||||
|
|
||||||
JenaModelUtils modelUtils = new JenaModelUtils();
|
|
||||||
|
|
||||||
Model tempModel = ModelFactory.createUnion(fullModel, submodels);
|
|
||||||
Model tempTBoxModel = modelUtils.extractTBox(tempModel);
|
|
||||||
|
|
||||||
// copy intersection of tempTBoxModel and fullModel to tboxModel.
|
|
||||||
StmtIterator iter = tempTBoxModel.listStatements();
|
|
||||||
|
|
||||||
while (iter.hasNext()) {
|
|
||||||
Statement stmt = iter.next();
|
|
||||||
if (fullModel.contains(stmt)) {
|
|
||||||
tboxModel.add(stmt);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Copy all statements from model 1 that are not in model 2 to model 3.
|
|
||||||
*/
|
|
||||||
private static void copyDifference(Model model1,
|
|
||||||
Model model2,
|
|
||||||
Model model3) {
|
|
||||||
|
|
||||||
StmtIterator iter = model1.listStatements();
|
|
||||||
|
|
||||||
while (iter.hasNext()) {
|
|
||||||
Statement stmt = iter.next();
|
|
||||||
if (!model2.contains(stmt)) {
|
|
||||||
model3.add(stmt);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected static void getAppMetadata(Model source, Model target) {
|
|
||||||
|
|
||||||
String amdQuery = "DESCRIBE ?x WHERE { " +
|
|
||||||
"{?x a <" + VitroVocabulary.PORTAL +"> } UNION " +
|
|
||||||
"{?x a <" + VitroVocabulary.PROPERTYGROUP +"> } UNION " +
|
|
||||||
"{?x a <" + VitroVocabulary.CLASSGROUP +"> } } ";
|
|
||||||
|
|
||||||
try {
|
|
||||||
Query q = QueryFactory.create(amdQuery, Syntax.syntaxARQ);
|
|
||||||
QueryExecution qe = QueryExecutionFactory.create(q, source);
|
|
||||||
qe.execDescribe(target);
|
|
||||||
} catch (Exception e) {
|
|
||||||
log.error("unable to create the application metadata model",e);
|
|
||||||
}
|
|
||||||
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected static void repairAppMetadataModel(Model applicationMetadataModel,
|
|
||||||
Model aboxAssertions,
|
|
||||||
Model aboxInferences) {
|
|
||||||
|
|
||||||
log.info("Moving application metadata from ABox to dedicated model");
|
|
||||||
getAppMetadata(aboxAssertions, applicationMetadataModel);
|
|
||||||
getAppMetadata(aboxInferences, applicationMetadataModel);
|
|
||||||
aboxAssertions.remove(applicationMetadataModel);
|
|
||||||
aboxInferences.remove(applicationMetadataModel);
|
|
||||||
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
public static StoreDesc makeStoreDesc(ServletContext ctx) {
|
|
||||||
String layoutStr = ConfigurationProperties.getBean(ctx).getProperty(
|
|
||||||
"VitroConnection.DataSource.sdb.layout", "layout2/hash");
|
|
||||||
String dbtypeStr = ConfigurationProperties.getBean(ctx).getProperty(
|
|
||||||
"VitroConnection.DataSource.dbtype", "MySQL");
|
|
||||||
return new StoreDesc(
|
|
||||||
LayoutType.fetch(layoutStr),
|
|
||||||
DatabaseType.fetch(dbtypeStr) );
|
|
||||||
}
|
|
||||||
|
|
||||||
public static Store connectStore(BasicDataSource bds, StoreDesc storeDesc)
|
|
||||||
throws SQLException {
|
|
||||||
SDBConnection conn = new SDBConnection(bds.getConnection()) ;
|
|
||||||
return SDBFactory.connectStore(conn, storeDesc);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static void setupSDB(ServletContext ctx, Store store) {
|
|
||||||
setupSDB(ctx,
|
|
||||||
store,
|
|
||||||
ModelFactory.createDefaultModel(),
|
|
||||||
ModelFactory.createDefaultModel());
|
|
||||||
}
|
|
||||||
|
|
||||||
public static void setupSDB(ServletContext ctx,
|
|
||||||
Store store,
|
|
||||||
Model memModel,
|
|
||||||
Model inferenceModel) {
|
|
||||||
|
|
||||||
store.getTableFormatter().create();
|
|
||||||
store.getTableFormatter().truncate();
|
|
||||||
|
|
||||||
store.getTableFormatter().dropIndexes(); // improve load performance
|
|
||||||
|
|
||||||
try {
|
|
||||||
|
|
||||||
// This is a one-time copy of stored KB data - from a Jena RDB store
|
|
||||||
// to a Jena SDB store. In the process, we will also separate out
|
|
||||||
// the TBox from the Abox; these are in the same graph in pre-1.2
|
|
||||||
// VIVO versions and will now be stored and maintained in separate
|
|
||||||
// models. Access to the Jena RDB data is through the
|
|
||||||
// OntModelSelectors that have been set up earlier in the current
|
|
||||||
// session by JenaPersistentDataSourceSetup.java. In the code
|
|
||||||
// below, note that the current getABoxModel() methods on the
|
|
||||||
// OntModelSelectors return a graph with both ABox and TBox data.
|
|
||||||
|
|
||||||
OntModel submodels = ModelFactory.createOntologyModel(
|
|
||||||
MEM_ONT_MODEL_SPEC);
|
|
||||||
readOntologyFilesInPathSet(SUBMODELS, ctx, submodels);
|
|
||||||
|
|
||||||
Model tboxAssertions = SDBFactory.connectNamedModel(
|
|
||||||
store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
|
|
||||||
// initially putting the results in memory so we have a
|
|
||||||
// cheaper way of computing the difference when we copy the ABox
|
|
||||||
Model memTboxAssertions = ModelFactory.createDefaultModel();
|
|
||||||
getTBoxModel(memModel, submodels, memTboxAssertions);
|
|
||||||
tboxAssertions.add(memTboxAssertions);
|
|
||||||
|
|
||||||
Model tboxInferences = SDBFactory.connectNamedModel(
|
|
||||||
store, JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL);
|
|
||||||
// initially putting the results in memory so we have a
|
|
||||||
// cheaper way of computing the difference when we copy the ABox
|
|
||||||
Model memTboxInferences = ModelFactory.createDefaultModel();
|
|
||||||
getTBoxModel(inferenceModel, submodels, memTboxInferences);
|
|
||||||
tboxInferences.add(memTboxInferences);
|
|
||||||
|
|
||||||
Model aboxAssertions = SDBFactory.connectNamedModel(
|
|
||||||
store, JenaDataSourceSetupBase.JENA_DB_MODEL);
|
|
||||||
copyDifference(memModel, memTboxAssertions, aboxAssertions);
|
|
||||||
|
|
||||||
Model aboxInferences = SDBFactory.connectNamedModel(
|
|
||||||
store, JenaDataSourceSetupBase.JENA_INF_MODEL);
|
|
||||||
copyDifference(inferenceModel, memTboxInferences, aboxInferences);
|
|
||||||
|
|
||||||
// Set up the application metadata model
|
|
||||||
Model applicationMetadataModel = SDBFactory.connectNamedModel(
|
|
||||||
store,
|
|
||||||
JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
|
|
||||||
getAppMetadata(memModel, applicationMetadataModel);
|
|
||||||
log.info("During initial SDB setup, created an application " +
|
|
||||||
"metadata model of size " +
|
|
||||||
applicationMetadataModel.size());
|
|
||||||
|
|
||||||
// remove application metadata from ABox model
|
|
||||||
aboxAssertions.remove(applicationMetadataModel);
|
|
||||||
aboxInferences.remove(applicationMetadataModel);
|
|
||||||
|
|
||||||
// Make sure the reasoner takes into account the newly-set-up data.
|
|
||||||
SimpleReasonerSetup.setRecomputeRequired(ctx);
|
|
||||||
|
|
||||||
} finally {
|
|
||||||
log.info("Adding indexes to SDB database tables.");
|
|
||||||
store.getTableFormatter().addIndexes();
|
|
||||||
log.info("Indexes created.");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private void migrateToSDBFromExistingRDBStore(ServletContext ctx,
|
|
||||||
Store store) {
|
|
||||||
Model rdbAssertionsModel = makeDBModelFromConfigurationProperties(
|
|
||||||
JENA_DB_MODEL, DB_ONT_MODEL_SPEC, ctx);
|
|
||||||
Model rdbInferencesModel = makeDBModelFromConfigurationProperties(
|
|
||||||
JENA_INF_MODEL, DB_ONT_MODEL_SPEC, ctx);
|
|
||||||
setupSDB(ctx, store, rdbAssertionsModel, rdbInferencesModel);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Tests whether an SDB store has been formatted and populated for use.
|
|
||||||
* @param store
|
|
||||||
* @return
|
|
||||||
*/
|
|
||||||
private boolean isSetUp(Store store) throws SQLException {
|
|
||||||
if (!(StoreUtils.isFormatted(store))) {
|
|
||||||
return false;
|
|
||||||
}
|
|
||||||
|
|
||||||
// even if the store exists, it may be empty
|
|
||||||
|
|
||||||
try {
|
|
||||||
return (SDBFactory.connectNamedModel(
|
|
||||||
store,
|
|
||||||
JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL))
|
|
||||||
.size() > 0;
|
|
||||||
} catch (Exception e) {
|
|
||||||
return false;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private static final String STOREDESC_ATTR = "storeDesc";
|
|
||||||
private static final String STORE_ATTR = "kbStore";
|
|
||||||
|
|
||||||
public static void setApplicationStoreDesc(StoreDesc storeDesc,
|
|
||||||
ServletContext ctx) {
|
|
||||||
ctx.setAttribute(STOREDESC_ATTR, storeDesc);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static StoreDesc getApplicationStoreDesc(ServletContext ctx) {
|
|
||||||
return (StoreDesc) ctx.getAttribute(STOREDESC_ATTR);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static void setApplicationStore(Store store,
|
|
||||||
ServletContext ctx) {
|
|
||||||
ctx.setAttribute(STORE_ATTR, store);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static Store getApplicationStore(ServletContext ctx) {
|
|
||||||
return (Store) ctx.getAttribute(STORE_ATTR);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
@ -1,686 +0,0 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.vitro.webapp.servlet.setup;
|
|
||||||
|
|
||||||
import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.DISPLAY_ONT_MODEL;
|
|
||||||
|
|
||||||
import java.sql.SQLException;
|
|
||||||
import java.util.ArrayList;
|
|
||||||
import java.util.List;
|
|
||||||
|
|
||||||
import javax.servlet.ServletContext;
|
|
||||||
import javax.servlet.ServletContextEvent;
|
|
||||||
|
|
||||||
import org.apache.commons.dbcp.BasicDataSource;
|
|
||||||
import org.apache.commons.logging.Log;
|
|
||||||
import org.apache.commons.logging.LogFactory;
|
|
||||||
|
|
||||||
import com.hp.hpl.jena.graph.Graph;
|
|
||||||
import com.hp.hpl.jena.ontology.OntModel;
|
|
||||||
import com.hp.hpl.jena.ontology.OntModelSpec;
|
|
||||||
import com.hp.hpl.jena.query.Dataset;
|
|
||||||
import com.hp.hpl.jena.query.Query;
|
|
||||||
import com.hp.hpl.jena.query.QueryExecution;
|
|
||||||
import com.hp.hpl.jena.query.QueryExecutionFactory;
|
|
||||||
import com.hp.hpl.jena.query.QueryFactory;
|
|
||||||
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.ResIterator;
|
|
||||||
import com.hp.hpl.jena.rdf.model.Resource;
|
|
||||||
import com.hp.hpl.jena.rdf.model.ResourceFactory;
|
|
||||||
import com.hp.hpl.jena.rdf.model.Statement;
|
|
||||||
import com.hp.hpl.jena.rdf.model.StmtIterator;
|
|
||||||
import com.hp.hpl.jena.sdb.SDBFactory;
|
|
||||||
import com.hp.hpl.jena.sdb.Store;
|
|
||||||
import com.hp.hpl.jena.sdb.StoreDesc;
|
|
||||||
import com.hp.hpl.jena.sdb.sql.SDBConnection;
|
|
||||||
import com.hp.hpl.jena.sdb.store.DatabaseType;
|
|
||||||
import com.hp.hpl.jena.sdb.store.LayoutType;
|
|
||||||
import com.hp.hpl.jena.sdb.util.StoreUtils;
|
|
||||||
import com.hp.hpl.jena.shared.Lock;
|
|
||||||
import com.hp.hpl.jena.util.ResourceUtils;
|
|
||||||
import com.hp.hpl.jena.util.iterator.ClosableIterator;
|
|
||||||
import com.hp.hpl.jena.vocabulary.RDF;
|
|
||||||
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.sparql.RDFServiceSparql;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
|
|
||||||
|
|
||||||
public class JenaDataSourceSetupSparql2 extends JenaDataSourceSetupBase
|
|
||||||
implements javax.servlet.ServletContextListener {
|
|
||||||
|
|
||||||
private static final Log log = LogFactory.getLog(JenaDataSourceSetup.class);
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public void contextInitialized(ServletContextEvent sce) {
|
|
||||||
ServletContext ctx = sce.getServletContext();
|
|
||||||
StartupStatus ss = StartupStatus.getBean(ctx);
|
|
||||||
|
|
||||||
try {
|
|
||||||
long startTime = System.currentTimeMillis();
|
|
||||||
setUpJenaDataSource(ctx);
|
|
||||||
log.info((System.currentTimeMillis() - startTime) / 1000 +
|
|
||||||
" seconds to set up SDB store");
|
|
||||||
} catch (SQLException sqle) {
|
|
||||||
// SQL exceptions are fatal and should halt startup
|
|
||||||
log.error("Error using SQL database; startup aborted.", sqle);
|
|
||||||
ss.fatal(this, "Error using SQL database; startup aborted.", sqle);
|
|
||||||
} catch (Throwable t) {
|
|
||||||
log.error("Throwable in " + this.getClass().getName(), t);
|
|
||||||
ss.fatal(this, "Throwable in " + this.getClass().getName(), t);
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
private void setUpJenaDataSource(ServletContext ctx) throws SQLException {
|
|
||||||
|
|
||||||
OntModelSelectorImpl baseOms = new OntModelSelectorImpl();
|
|
||||||
OntModelSelectorImpl inferenceOms = new OntModelSelectorImpl();
|
|
||||||
OntModelSelectorImpl unionOms = new OntModelSelectorImpl();
|
|
||||||
|
|
||||||
OntModel userAccountsModel = ontModelFromContextAttribute(
|
|
||||||
ctx, "userAccountsOntModel");
|
|
||||||
baseOms.setUserAccountsModel(userAccountsModel);
|
|
||||||
inferenceOms.setUserAccountsModel(userAccountsModel);
|
|
||||||
unionOms.setUserAccountsModel(userAccountsModel);
|
|
||||||
|
|
||||||
OntModel displayModel = ontModelFromContextAttribute(
|
|
||||||
ctx,DISPLAY_ONT_MODEL);
|
|
||||||
baseOms.setDisplayModel(displayModel);
|
|
||||||
inferenceOms.setDisplayModel(displayModel);
|
|
||||||
unionOms.setDisplayModel(displayModel);
|
|
||||||
|
|
||||||
// SDB setup
|
|
||||||
|
|
||||||
// union default graph
|
|
||||||
// SDB.getContext().set(SDB.unionDefaultGraph, true) ;
|
|
||||||
//
|
|
||||||
// StoreDesc storeDesc = makeStoreDesc(ctx);
|
|
||||||
// setApplicationStoreDesc(storeDesc, ctx);
|
|
||||||
//
|
|
||||||
// BasicDataSource bds = getApplicationDataSource(ctx);
|
|
||||||
// if (bds == null) {
|
|
||||||
// bds = makeDataSourceFromConfigurationProperties(ctx);
|
|
||||||
// setApplicationDataSource(bds, ctx);
|
|
||||||
// }
|
|
||||||
|
|
||||||
// Store store = connectStore(bds, storeDesc);
|
|
||||||
// setApplicationStore(store, ctx);
|
|
||||||
|
|
||||||
//okay let's make a graph-backed model
|
|
||||||
String endpointURI = ConfigurationProperties.getBean(
|
|
||||||
ctx).getProperty("VitroConnection.DataSource.endpointURI");
|
|
||||||
|
|
||||||
Graph g = new SparqlGraph(endpointURI);
|
|
||||||
|
|
||||||
RDFService rdfService = new RDFServiceSparql(endpointURI);
|
|
||||||
Dataset dataset = new RDFServiceDataset(rdfService);
|
|
||||||
setStartupDataset(dataset, ctx);
|
|
||||||
|
|
||||||
// setStartupDataset(SDBFactory.connectDataset(store), ctx);
|
|
||||||
|
|
||||||
// if (!isSetUp(store)) {
|
|
||||||
// log.info("Initializing SDB store");
|
|
||||||
// if (isFirstStartup()) {
|
|
||||||
// setupSDB(ctx, store);
|
|
||||||
// } else {
|
|
||||||
// migrateToSDBFromExistingRDBStore(ctx, store);
|
|
||||||
// }
|
|
||||||
// }
|
|
||||||
|
|
||||||
// The code below, which sets up the OntModelSelectors, controls whether
|
|
||||||
// each model is maintained in memory, in the DB, or both while the
|
|
||||||
// application is running.
|
|
||||||
|
|
||||||
// Populate the three OntModelSelectors (BaseOntModel = assertions,
|
|
||||||
// InferenceOntModel = inferences and JenaOntModel = union of assertions
|
|
||||||
// and inferences) with the post-SDB-conversion models.
|
|
||||||
|
|
||||||
// ABox assertions
|
|
||||||
Model aboxAssertions = dataset.getNamedModel(
|
|
||||||
JenaDataSourceSetupBase.JENA_DB_MODEL);
|
|
||||||
Model listenableAboxAssertions = ModelFactory.createUnion(
|
|
||||||
aboxAssertions, ModelFactory.createDefaultModel());
|
|
||||||
baseOms.setABoxModel(
|
|
||||||
ModelFactory.createOntologyModel(
|
|
||||||
OntModelSpec.OWL_MEM, listenableAboxAssertions));
|
|
||||||
|
|
||||||
// ABox inferences
|
|
||||||
Model aboxInferences = dataset.getNamedModel(
|
|
||||||
JenaDataSourceSetupBase.JENA_INF_MODEL);
|
|
||||||
Model listenableAboxInferences = ModelFactory.createUnion(
|
|
||||||
aboxInferences, ModelFactory.createDefaultModel());
|
|
||||||
inferenceOms.setABoxModel(ModelFactory.createOntologyModel(
|
|
||||||
OntModelSpec.OWL_MEM, listenableAboxInferences));
|
|
||||||
|
|
||||||
|
|
||||||
// Since the TBox models are in memory, they do not have timeout issues
|
|
||||||
// like the like the ABox models do (and so don't need the extra step
|
|
||||||
// to make them listenable.)
|
|
||||||
|
|
||||||
// TBox assertions
|
|
||||||
try {
|
|
||||||
Model tboxAssertionsDB = dataset.getNamedModel(
|
|
||||||
JENA_TBOX_ASSERTIONS_MODEL);
|
|
||||||
OntModel tboxAssertions = ModelFactory.createOntologyModel(
|
|
||||||
MEM_ONT_MODEL_SPEC);
|
|
||||||
|
|
||||||
if (tboxAssertionsDB != null) {
|
|
||||||
long startTime = System.currentTimeMillis();
|
|
||||||
System.out.println(
|
|
||||||
"Copying cached tbox assertions into memory");
|
|
||||||
tboxAssertions.add(tboxAssertionsDB);
|
|
||||||
System.out.println((System.currentTimeMillis() - startTime)
|
|
||||||
/ 1000 + " seconds to load tbox assertions");
|
|
||||||
}
|
|
||||||
|
|
||||||
tboxAssertions.getBaseModel().register(new ModelSynchronizer(
|
|
||||||
tboxAssertionsDB));
|
|
||||||
|
|
||||||
baseOms.setTBoxModel(tboxAssertions);
|
|
||||||
} catch (Throwable e) {
|
|
||||||
log.error("Unable to load tbox assertion cache from DB", e);
|
|
||||||
}
|
|
||||||
|
|
||||||
// TBox inferences
|
|
||||||
try {
|
|
||||||
Model tboxInferencesDB = dataset.getNamedModel(JENA_TBOX_INF_MODEL);
|
|
||||||
OntModel tboxInferences = ModelFactory.createOntologyModel(
|
|
||||||
MEM_ONT_MODEL_SPEC);
|
|
||||||
|
|
||||||
if (tboxInferencesDB != null) {
|
|
||||||
long startTime = System.currentTimeMillis();
|
|
||||||
System.out.println(
|
|
||||||
"Copying cached tbox inferences into memory");
|
|
||||||
tboxInferences.add(tboxInferencesDB);
|
|
||||||
System.out.println((System.currentTimeMillis() - startTime)
|
|
||||||
/ 1000 + " seconds to load tbox inferences");
|
|
||||||
}
|
|
||||||
|
|
||||||
tboxInferences.getBaseModel().register(new ModelSynchronizer(
|
|
||||||
tboxInferencesDB));
|
|
||||||
inferenceOms.setTBoxModel(tboxInferences);
|
|
||||||
} catch (Throwable e) {
|
|
||||||
log.error("Unable to load tbox inference cache from DB", e);
|
|
||||||
}
|
|
||||||
|
|
||||||
// union ABox
|
|
||||||
OntModel unionABoxModel = ModelFactory.createOntologyModel(
|
|
||||||
MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(
|
|
||||||
baseOms.getABoxModel(), inferenceOms.getABoxModel()));
|
|
||||||
unionOms.setABoxModel(unionABoxModel);
|
|
||||||
|
|
||||||
// union TBox
|
|
||||||
OntModel unionTBoxModel = ModelFactory.createOntologyModel(
|
|
||||||
MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(
|
|
||||||
baseOms.getTBoxModel(), inferenceOms.getTBoxModel()));
|
|
||||||
unionOms.setTBoxModel(unionTBoxModel);
|
|
||||||
|
|
||||||
|
|
||||||
// Application metadata model is cached in memory.
|
|
||||||
try {
|
|
||||||
|
|
||||||
Model applicationMetadataModelDB = dataset.getNamedModel(
|
|
||||||
JENA_APPLICATION_METADATA_MODEL);
|
|
||||||
OntModel applicationMetadataModel =
|
|
||||||
ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
|
|
||||||
|
|
||||||
long startTime = System.currentTimeMillis();
|
|
||||||
System.out.println(
|
|
||||||
"Copying cached application metadata model into memory");
|
|
||||||
applicationMetadataModel.add(applicationMetadataModelDB);
|
|
||||||
System.out.println((System.currentTimeMillis() - startTime)
|
|
||||||
/ 1000 + " seconds to load application metadata model " +
|
|
||||||
"assertions of size " + applicationMetadataModel.size());
|
|
||||||
applicationMetadataModel.getBaseModel().register(
|
|
||||||
new ModelSynchronizer(applicationMetadataModelDB));
|
|
||||||
|
|
||||||
if (applicationMetadataModel.size()== 0 /* isFirstStartup() */) {
|
|
||||||
applicationMetadataModel.add(
|
|
||||||
InitialJenaModelUtils.loadInitialModel(
|
|
||||||
ctx, getDefaultNamespace(ctx)));
|
|
||||||
|
|
||||||
}
|
|
||||||
// else if (applicationMetadataModelDB.size() == 0) {
|
|
||||||
// repairAppMetadataModel(
|
|
||||||
// applicationMetadataModel, aboxAssertions,
|
|
||||||
// aboxInferences);
|
|
||||||
// }
|
|
||||||
|
|
||||||
baseOms.setApplicationMetadataModel(applicationMetadataModel);
|
|
||||||
inferenceOms.setApplicationMetadataModel(
|
|
||||||
baseOms.getApplicationMetadataModel());
|
|
||||||
unionOms.setApplicationMetadataModel(
|
|
||||||
baseOms.getApplicationMetadataModel());
|
|
||||||
|
|
||||||
} catch (Throwable e) {
|
|
||||||
log.error("Unable to load application metadata model cache from DB"
|
|
||||||
, e);
|
|
||||||
}
|
|
||||||
|
|
||||||
checkForNamespaceMismatch( baseOms.getApplicationMetadataModel(), ctx );
|
|
||||||
|
|
||||||
if (isFirstStartup()) {
|
|
||||||
loadDataFromFilesystem(baseOms, ctx);
|
|
||||||
}
|
|
||||||
|
|
||||||
log.info("Setting up union models and DAO factories");
|
|
||||||
|
|
||||||
// create TBox + ABox union models and set up webapp DAO factories
|
|
||||||
OntModel baseUnion = ModelFactory.createOntologyModel(
|
|
||||||
OntModelSpec.OWL_MEM,
|
|
||||||
ModelFactory.createUnion(baseOms.getABoxModel(),
|
|
||||||
baseOms.getTBoxModel()));
|
|
||||||
baseOms.setFullModel(baseUnion);
|
|
||||||
ModelContext.setBaseOntModel(baseOms.getFullModel(), ctx);
|
|
||||||
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
|
|
||||||
config.setDefaultNamespace(getDefaultNamespace(ctx));
|
|
||||||
WebappDaoFactory baseWadf = new WebappDaoFactorySDB(
|
|
||||||
rdfService, baseOms, config,
|
|
||||||
WebappDaoFactorySDB.SDBDatasetMode.ASSERTIONS_ONLY);
|
|
||||||
ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
|
|
||||||
|
|
||||||
OntModel inferenceUnion = ModelFactory.createOntologyModel(
|
|
||||||
OntModelSpec.OWL_MEM,
|
|
||||||
ModelFactory.createUnion(
|
|
||||||
inferenceOms.getABoxModel(),
|
|
||||||
inferenceOms.getTBoxModel()));
|
|
||||||
inferenceOms.setFullModel(inferenceUnion);
|
|
||||||
ModelContext.setInferenceOntModel(inferenceOms.getFullModel(), ctx);
|
|
||||||
WebappDaoFactory infWadf = new WebappDaoFactorySDB(
|
|
||||||
rdfService, inferenceOms, config,
|
|
||||||
WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
|
|
||||||
ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
|
|
||||||
|
|
||||||
OntModel masterUnion = ModelFactory.createOntologyModel(
|
|
||||||
DB_ONT_MODEL_SPEC, dataset.getDefaultModel());
|
|
||||||
unionOms.setFullModel(masterUnion);
|
|
||||||
ctx.setAttribute("jenaOntModel", masterUnion);
|
|
||||||
WebappDaoFactory wadf = new WebappDaoFactorySDB(
|
|
||||||
rdfService, unionOms, config);
|
|
||||||
ctx.setAttribute("webappDaoFactory",wadf);
|
|
||||||
|
|
||||||
ModelContext.setOntModelSelector(unionOms, ctx);
|
|
||||||
ModelContext.setUnionOntModelSelector(unionOms, ctx);
|
|
||||||
// assertions and inferences
|
|
||||||
ModelContext.setBaseOntModelSelector(baseOms, ctx);
|
|
||||||
// assertions
|
|
||||||
ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);
|
|
||||||
// inferences
|
|
||||||
|
|
||||||
ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
|
|
||||||
|
|
||||||
log.info("SDB store ready for use");
|
|
||||||
|
|
||||||
makeModelMakerFromConnectionProperties(TripleStoreType.RDB, ctx);
|
|
||||||
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
|
|
||||||
setVitroJenaModelMaker(vjmm, ctx);
|
|
||||||
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
|
||||||
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
|
|
||||||
setVitroJenaSDBModelMaker(vsmm, ctx);
|
|
||||||
|
|
||||||
//bdc34: I have no reason for vsmm vs vjmm.
|
|
||||||
//I don't know what are the implications of this choice.
|
|
||||||
setVitroModelSource( new VitroModelSource(vsmm,ctx), ctx);
|
|
||||||
|
|
||||||
log.info("Model makers set up");
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* If we find a "portal1" portal (and we should), its URI should use the
|
|
||||||
* default namespace.
|
|
||||||
*/
|
|
||||||
private void checkForNamespaceMismatch(OntModel model, ServletContext ctx) {
|
|
||||||
String expectedNamespace = getDefaultNamespace(ctx);
|
|
||||||
|
|
||||||
List<Resource> portals = getPortal1s(model);
|
|
||||||
|
|
||||||
if(!portals.isEmpty() && noPortalForNamespace(
|
|
||||||
portals, expectedNamespace)) {
|
|
||||||
// There really should be only one portal 1, but if there happen to
|
|
||||||
// be multiple, just arbitrarily pick the first in the list.
|
|
||||||
Resource portal = portals.get(0);
|
|
||||||
String oldNamespace = portal.getNameSpace();
|
|
||||||
renamePortal(portal, expectedNamespace, model);
|
|
||||||
StartupStatus ss = StartupStatus.getBean(ctx);
|
|
||||||
ss.warning(this, "\nThe default namespace has been changed \n" +
|
|
||||||
"from " + oldNamespace +
|
|
||||||
"\nto " + expectedNamespace + ".\n" +
|
|
||||||
"The application will function normally, but " +
|
|
||||||
"any individuals in the \n" + oldNamespace + " " +
|
|
||||||
"namespace will need to have their URIs \n" +
|
|
||||||
"changed in order to be served as linked data. " +
|
|
||||||
"You can use the Ingest Tools \nto change the " +
|
|
||||||
"URIs for a batch of resources.");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private List<Resource> getPortal1s(Model model) {
|
|
||||||
List<Resource> portals = new ArrayList<Resource>();
|
|
||||||
try {
|
|
||||||
model.enterCriticalSection(Lock.READ);
|
|
||||||
ResIterator portalIt = model.listResourcesWithProperty(
|
|
||||||
RDF.type, PORTAL);
|
|
||||||
while (portalIt.hasNext()) {
|
|
||||||
Resource portal = portalIt.nextResource();
|
|
||||||
if ("portal1".equals(portal.getLocalName())) {
|
|
||||||
portals.add(portal);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
} finally {
|
|
||||||
model.leaveCriticalSection();
|
|
||||||
}
|
|
||||||
return portals;
|
|
||||||
}
|
|
||||||
|
|
||||||
private boolean noPortalForNamespace(List<Resource> portals,
|
|
||||||
String expectedNamespace) {
|
|
||||||
for (Resource portal : portals) {
|
|
||||||
if(expectedNamespace.equals(portal.getNameSpace())) {
|
|
||||||
return false;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return true;
|
|
||||||
}
|
|
||||||
|
|
||||||
private void renamePortal(Resource portal, String namespace, Model model) {
|
|
||||||
model.enterCriticalSection(Lock.WRITE);
|
|
||||||
try {
|
|
||||||
ResourceUtils.renameResource(
|
|
||||||
portal, namespace + portal.getLocalName());
|
|
||||||
} finally {
|
|
||||||
model.leaveCriticalSection();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/* ===================================================================== */
|
|
||||||
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public void contextDestroyed(ServletContextEvent sce) {
|
|
||||||
// Nothing to do.
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
protected OntModel ontModelFromContextAttribute(ServletContext ctx,
|
|
||||||
String attribute) {
|
|
||||||
OntModel ontModel;
|
|
||||||
Object attributeValue = ctx.getAttribute(attribute);
|
|
||||||
if (attributeValue != null && attributeValue instanceof OntModel) {
|
|
||||||
ontModel = (OntModel) attributeValue;
|
|
||||||
} else {
|
|
||||||
ontModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
|
|
||||||
ctx.setAttribute(attribute, ontModel);
|
|
||||||
}
|
|
||||||
return ontModel;
|
|
||||||
}
|
|
||||||
|
|
||||||
private boolean isEmpty(Model model) {
|
|
||||||
ClosableIterator<Statement> closeIt = model.listStatements(
|
|
||||||
null, RDF.type, ResourceFactory.createResource(
|
|
||||||
VitroVocabulary.PORTAL));
|
|
||||||
try {
|
|
||||||
if (closeIt.hasNext()) {
|
|
||||||
return false;
|
|
||||||
} else {
|
|
||||||
return true;
|
|
||||||
}
|
|
||||||
} finally {
|
|
||||||
closeIt.close();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private void loadDataFromFilesystem(OntModelSelector baseOms,
|
|
||||||
ServletContext ctx) {
|
|
||||||
Long startTime = System.currentTimeMillis();
|
|
||||||
log.debug("Initializing models from RDF files");
|
|
||||||
readOntologyFilesInPathSet(USER_ABOX_PATH, ctx, baseOms.getABoxModel());
|
|
||||||
readOntologyFilesInPathSet(USER_TBOX_PATH, ctx, baseOms.getTBoxModel());
|
|
||||||
readOntologyFilesInPathSet(
|
|
||||||
USER_APPMETA_PATH, ctx, baseOms.getApplicationMetadataModel());
|
|
||||||
log.debug(((System.currentTimeMillis() - startTime) / 1000)
|
|
||||||
+ " seconds to read RDF files ");
|
|
||||||
}
|
|
||||||
|
|
||||||
private static void getTBoxModel(Model fullModel,
|
|
||||||
Model submodels,
|
|
||||||
Model tboxModel) {
|
|
||||||
|
|
||||||
JenaModelUtils modelUtils = new JenaModelUtils();
|
|
||||||
|
|
||||||
Model tempModel = ModelFactory.createUnion(fullModel, submodels);
|
|
||||||
Model tempTBoxModel = modelUtils.extractTBox(tempModel);
|
|
||||||
|
|
||||||
// copy intersection of tempTBoxModel and fullModel to tboxModel.
|
|
||||||
StmtIterator iter = tempTBoxModel.listStatements();
|
|
||||||
|
|
||||||
while (iter.hasNext()) {
|
|
||||||
Statement stmt = iter.next();
|
|
||||||
if (fullModel.contains(stmt)) {
|
|
||||||
tboxModel.add(stmt);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Copy all statements from model 1 that are not in model 2 to model 3.
|
|
||||||
*/
|
|
||||||
private static void copyDifference(Model model1,
|
|
||||||
Model model2,
|
|
||||||
Model model3) {
|
|
||||||
|
|
||||||
StmtIterator iter = model1.listStatements();
|
|
||||||
|
|
||||||
while (iter.hasNext()) {
|
|
||||||
Statement stmt = iter.next();
|
|
||||||
if (!model2.contains(stmt)) {
|
|
||||||
model3.add(stmt);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected static void getAppMetadata(Model source, Model target) {
|
|
||||||
|
|
||||||
String amdQuery = "DESCRIBE ?x WHERE { " +
|
|
||||||
"{?x a <" + VitroVocabulary.PORTAL +"> } UNION " +
|
|
||||||
"{?x a <" + VitroVocabulary.PROPERTYGROUP +"> } UNION " +
|
|
||||||
"{?x a <" + VitroVocabulary.CLASSGROUP +"> } } ";
|
|
||||||
|
|
||||||
try {
|
|
||||||
Query q = QueryFactory.create(amdQuery, Syntax.syntaxARQ);
|
|
||||||
QueryExecution qe = QueryExecutionFactory.create(q, source);
|
|
||||||
qe.execDescribe(target);
|
|
||||||
} catch (Exception e) {
|
|
||||||
log.error("unable to create the application metadata model",e);
|
|
||||||
}
|
|
||||||
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected static void repairAppMetadataModel(Model applicationMetadataModel,
|
|
||||||
Model aboxAssertions,
|
|
||||||
Model aboxInferences) {
|
|
||||||
|
|
||||||
log.info("Moving application metadata from ABox to dedicated model");
|
|
||||||
getAppMetadata(aboxAssertions, applicationMetadataModel);
|
|
||||||
getAppMetadata(aboxInferences, applicationMetadataModel);
|
|
||||||
aboxAssertions.remove(applicationMetadataModel);
|
|
||||||
aboxInferences.remove(applicationMetadataModel);
|
|
||||||
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
public static StoreDesc makeStoreDesc(ServletContext ctx) {
|
|
||||||
String layoutStr = ConfigurationProperties.getBean(ctx).getProperty(
|
|
||||||
"VitroConnection.DataSource.sdb.layout", "layout2/hash");
|
|
||||||
String dbtypeStr = ConfigurationProperties.getBean(ctx).getProperty(
|
|
||||||
"VitroConnection.DataSource.dbtype", "MySQL");
|
|
||||||
return new StoreDesc(
|
|
||||||
LayoutType.fetch(layoutStr),
|
|
||||||
DatabaseType.fetch(dbtypeStr) );
|
|
||||||
}
|
|
||||||
|
|
||||||
public static Store connectStore(BasicDataSource bds, StoreDesc storeDesc)
|
|
||||||
throws SQLException {
|
|
||||||
SDBConnection conn = new SDBConnection(bds.getConnection()) ;
|
|
||||||
return SDBFactory.connectStore(conn, storeDesc);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static void setupSDB(ServletContext ctx, Store store) {
|
|
||||||
setupSDB(ctx,
|
|
||||||
store,
|
|
||||||
ModelFactory.createDefaultModel(),
|
|
||||||
ModelFactory.createDefaultModel());
|
|
||||||
}
|
|
||||||
|
|
||||||
public static void setupSDB(ServletContext ctx,
|
|
||||||
Store store,
|
|
||||||
Model memModel,
|
|
||||||
Model inferenceModel) {
|
|
||||||
|
|
||||||
store.getTableFormatter().create();
|
|
||||||
store.getTableFormatter().truncate();
|
|
||||||
|
|
||||||
store.getTableFormatter().dropIndexes(); // improve load performance
|
|
||||||
|
|
||||||
try {
|
|
||||||
|
|
||||||
// This is a one-time copy of stored KB data - from a Jena RDB store
|
|
||||||
// to a Jena SDB store. In the process, we will also separate out
|
|
||||||
// the TBox from the Abox; these are in the same graph in pre-1.2
|
|
||||||
// VIVO versions and will now be stored and maintained in separate
|
|
||||||
// models. Access to the Jena RDB data is through the
|
|
||||||
// OntModelSelectors that have been set up earlier in the current
|
|
||||||
// session by JenaPersistentDataSourceSetup.java. In the code
|
|
||||||
// below, note that the current getABoxModel() methods on the
|
|
||||||
// OntModelSelectors return a graph with both ABox and TBox data.
|
|
||||||
|
|
||||||
OntModel submodels = ModelFactory.createOntologyModel(
|
|
||||||
MEM_ONT_MODEL_SPEC);
|
|
||||||
readOntologyFilesInPathSet(SUBMODELS, ctx, submodels);
|
|
||||||
|
|
||||||
Model tboxAssertions = SDBFactory.connectNamedModel(
|
|
||||||
store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
|
|
||||||
// initially putting the results in memory so we have a
|
|
||||||
// cheaper way of computing the difference when we copy the ABox
|
|
||||||
Model memTboxAssertions = ModelFactory.createDefaultModel();
|
|
||||||
getTBoxModel(memModel, submodels, memTboxAssertions);
|
|
||||||
tboxAssertions.add(memTboxAssertions);
|
|
||||||
|
|
||||||
Model tboxInferences = SDBFactory.connectNamedModel(
|
|
||||||
store, JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL);
|
|
||||||
// initially putting the results in memory so we have a
|
|
||||||
// cheaper way of computing the difference when we copy the ABox
|
|
||||||
Model memTboxInferences = ModelFactory.createDefaultModel();
|
|
||||||
getTBoxModel(inferenceModel, submodels, memTboxInferences);
|
|
||||||
tboxInferences.add(memTboxInferences);
|
|
||||||
|
|
||||||
Model aboxAssertions = SDBFactory.connectNamedModel(
|
|
||||||
store, JenaDataSourceSetupBase.JENA_DB_MODEL);
|
|
||||||
copyDifference(memModel, memTboxAssertions, aboxAssertions);
|
|
||||||
|
|
||||||
Model aboxInferences = SDBFactory.connectNamedModel(
|
|
||||||
store, JenaDataSourceSetupBase.JENA_INF_MODEL);
|
|
||||||
copyDifference(inferenceModel, memTboxInferences, aboxInferences);
|
|
||||||
|
|
||||||
// Set up the application metadata model
|
|
||||||
Model applicationMetadataModel = SDBFactory.connectNamedModel(
|
|
||||||
store,
|
|
||||||
JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
|
|
||||||
getAppMetadata(memModel, applicationMetadataModel);
|
|
||||||
log.info("During initial SDB setup, created an application " +
|
|
||||||
"metadata model of size " +
|
|
||||||
applicationMetadataModel.size());
|
|
||||||
|
|
||||||
// remove application metadata from ABox model
|
|
||||||
aboxAssertions.remove(applicationMetadataModel);
|
|
||||||
aboxInferences.remove(applicationMetadataModel);
|
|
||||||
|
|
||||||
// Make sure the reasoner takes into account the newly-set-up data.
|
|
||||||
SimpleReasonerSetup.setRecomputeRequired(ctx);
|
|
||||||
|
|
||||||
} finally {
|
|
||||||
log.info("Adding indexes to SDB database tables.");
|
|
||||||
store.getTableFormatter().addIndexes();
|
|
||||||
log.info("Indexes created.");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private void migrateToSDBFromExistingRDBStore(ServletContext ctx,
|
|
||||||
Store store) {
|
|
||||||
Model rdbAssertionsModel = makeDBModelFromConfigurationProperties(
|
|
||||||
JENA_DB_MODEL, DB_ONT_MODEL_SPEC, ctx);
|
|
||||||
Model rdbInferencesModel = makeDBModelFromConfigurationProperties(
|
|
||||||
JENA_INF_MODEL, DB_ONT_MODEL_SPEC, ctx);
|
|
||||||
setupSDB(ctx, store, rdbAssertionsModel, rdbInferencesModel);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Tests whether an SDB store has been formatted and populated for use.
|
|
||||||
* @param store
|
|
||||||
* @return
|
|
||||||
*/
|
|
||||||
private boolean isSetUp(Store store) throws SQLException {
|
|
||||||
if (!(StoreUtils.isFormatted(store))) {
|
|
||||||
return false;
|
|
||||||
}
|
|
||||||
|
|
||||||
// even if the store exists, it may be empty
|
|
||||||
|
|
||||||
try {
|
|
||||||
return (SDBFactory.connectNamedModel(
|
|
||||||
store,
|
|
||||||
JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL))
|
|
||||||
.size() > 0;
|
|
||||||
} catch (Exception e) {
|
|
||||||
return false;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private static final String STOREDESC_ATTR = "storeDesc";
|
|
||||||
private static final String STORE_ATTR = "kbStore";
|
|
||||||
|
|
||||||
public static void setApplicationStoreDesc(StoreDesc storeDesc,
|
|
||||||
ServletContext ctx) {
|
|
||||||
ctx.setAttribute(STOREDESC_ATTR, storeDesc);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static StoreDesc getApplicationStoreDesc(ServletContext ctx) {
|
|
||||||
return (StoreDesc) ctx.getAttribute(STOREDESC_ATTR);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static void setApplicationStore(Store store,
|
|
||||||
ServletContext ctx) {
|
|
||||||
ctx.setAttribute(STORE_ATTR, store);
|
|
||||||
}
|
|
||||||
|
|
||||||
public static Store getApplicationStore(ServletContext ctx) {
|
|
||||||
return (Store) ctx.getAttribute(STORE_ATTR);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
@ -15,7 +15,6 @@ import org.apache.commons.dbcp.BasicDataSource;
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
|
||||||
import com.hp.hpl.jena.graph.Graph;
|
|
||||||
import com.hp.hpl.jena.ontology.OntModel;
|
import com.hp.hpl.jena.ontology.OntModel;
|
||||||
import com.hp.hpl.jena.ontology.OntModelSpec;
|
import com.hp.hpl.jena.ontology.OntModelSpec;
|
||||||
import com.hp.hpl.jena.query.Dataset;
|
import com.hp.hpl.jena.query.Dataset;
|
||||||
|
|
@ -54,9 +53,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
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||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
||||||
|
|
@ -64,7 +62,6 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle;
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle;
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.sdb.RDFServiceSDB;
|
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.sdb.RDFServiceSDB;
|
||||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.sparql.RDFServiceSparql;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
||||||
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
|
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
|
||||||
|
|
||||||
|
|
@ -330,7 +327,7 @@ public class RDFServiceSetup extends JenaDataSourceSetupBase
|
||||||
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
|
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
|
||||||
setVitroJenaModelMaker(vjmm, ctx);
|
setVitroJenaModelMaker(vjmm, ctx);
|
||||||
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
||||||
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
|
RDFServiceModelMaker vsmm = new RDFServiceModelMaker(rdfServiceFactory);
|
||||||
setVitroJenaSDBModelMaker(vsmm, ctx);
|
setVitroJenaSDBModelMaker(vsmm, ctx);
|
||||||
|
|
||||||
//bdc34: I have no reason for vsmm vs vjmm.
|
//bdc34: I have no reason for vsmm vs vjmm.
|
||||||
|
|
|
||||||
|
|
@ -17,6 +17,7 @@ import com.hp.hpl.jena.ontology.OntModel;
|
||||||
import com.hp.hpl.jena.ontology.OntModelSpec;
|
import com.hp.hpl.jena.ontology.OntModelSpec;
|
||||||
import com.hp.hpl.jena.rdf.model.Model;
|
import com.hp.hpl.jena.rdf.model.Model;
|
||||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||||
|
import com.hp.hpl.jena.rdf.model.ModelMaker;
|
||||||
import com.hp.hpl.jena.rdf.model.ResIterator;
|
import com.hp.hpl.jena.rdf.model.ResIterator;
|
||||||
import com.hp.hpl.jena.rdf.model.Resource;
|
import com.hp.hpl.jena.rdf.model.Resource;
|
||||||
import com.hp.hpl.jena.rdf.model.ResourceFactory;
|
import com.hp.hpl.jena.rdf.model.ResourceFactory;
|
||||||
|
|
@ -29,15 +30,12 @@ import com.hp.hpl.jena.vocabulary.RDF;
|
||||||
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
|
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
|
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
|
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
|
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.OntModelSelector;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
|
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
|
||||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
|
|
@ -152,7 +150,7 @@ public class WebappDaoSDBSetup extends JenaDataSourceSetupBase
|
||||||
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
|
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
|
||||||
setVitroJenaModelMaker(vjmm, ctx);
|
setVitroJenaModelMaker(vjmm, ctx);
|
||||||
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
|
||||||
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
|
ModelMaker vsmm = getVitroJenaSDBModelMaker();
|
||||||
setVitroJenaSDBModelMaker(vsmm, ctx);
|
setVitroJenaSDBModelMaker(vsmm, ctx);
|
||||||
|
|
||||||
//bdc34: I have no reason for vsmm vs vjmm.
|
//bdc34: I have no reason for vsmm vs vjmm.
|
||||||
|
|
|
||||||
Loading…
Add table
Reference in a new issue