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Ingest Tools using RDFService

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This commit is contained in:
brianjlowe 2012-06-12 14:26:11 +00:00
parent f55916b8d8
commit 068a4d9931
8 changed files with 259 additions and 1412 deletions
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7
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
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@ -69,6 +69,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
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.VitroJenaSpecialModelMaker;
@ -206,13 +207,13 @@ public class JenaIngestController extends BaseEditController {
}
private void processRDBModelsRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
VitroJenaModelMaker vjmm = (VitroJenaModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
ModelMaker vjmm = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker");
vreq.getSession().setAttribute("vitroJenaModelMaker", vjmm);
showModelList(vreq, vjmm, "rdb");
}
private void processSDBModelsRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
VitroJenaSDBModelMaker vsmm = (VitroJenaSDBModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
ModelMaker vsmm = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
vreq.getSession().setAttribute("vitroJenaModelMaker", vsmm);
showModelList(vreq, vsmm, "sdb");
}
@ -714,7 +715,7 @@ public class JenaIngestController extends BaseEditController {
? ((VitroJenaSpecialModelMaker) maker).getInnerModelMaker()
: maker;
if (modelType == null) {
if (maker instanceof VitroJenaSDBModelMaker) {
if (maker instanceof RDFServiceModelMaker) {
modelType = "sdb";
} else {
modelType = "rdb";

244
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceModelMaker.java Normal file
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@ -0,0 +1,244 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.text.Collator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.graph.GraphMaker;
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.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelMaker;
import com.hp.hpl.jena.rdf.model.ModelReader;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
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.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.util.iterator.WrappedIterator;
import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
public class RDFServiceModelMaker implements ModelMaker {
private final static Log log = LogFactory.getLog(VitroJenaSDBModelMaker.class);
private RDFServiceFactory rdfServiceFactory;
public static final String METADATA_MODEL_URI =
"http://vitro.mannlib.cornell.edu/ns/vitro/sdb/metadata";
public static final String HAS_NAMED_MODEL_URI =
"http://vitro.mannlib.cornell.edu/ns/vitro/sdb/hasNamedModel";
private Resource sdbResource; // a resource representing the SDB database
public RDFServiceModelMaker(RDFServiceFactory rdfServiceFactory) {
this.rdfServiceFactory = rdfServiceFactory;
}
protected RDFService getRDFService() {
return rdfServiceFactory.getRDFService();
}
Model getMetadataModel() {
return getModel(METADATA_MODEL_URI);
}
public void close() {
// n.a.
}
public Model createModel(String modelName) {
Model model = getModel(modelName);
Model metadataModel = getMetadataModel();
try {
metadataModel.add(
sdbResource,metadataModel.getProperty(
HAS_NAMED_MODEL_URI), modelName);
} finally {
metadataModel.close();
}
return model;
}
public Model createModel(String arg0, boolean arg1) {
// TODO Figure out if we can offer a "create if not found" option using SDB
return createModel(arg0);
}
public GraphMaker getGraphMaker() {
throw new UnsupportedOperationException(
"GraphMaker not supported by " + this.getClass().getName());
}
public boolean hasModel(String arg0) {
Model metadataModel = getMetadataModel();
try {
StmtIterator stmtIt = metadataModel.listStatements(
sdbResource, metadataModel.getProperty(
HAS_NAMED_MODEL_URI), arg0);
try {
return stmtIt.hasNext();
} finally {
if (stmtIt != null) {
stmtIt.close();
}
}
} finally {
metadataModel.close();
}
}
public ExtendedIterator<String> listModels() {
Model metadataModel = getMetadataModel();
try {
return listModelNames(metadataModel);
} finally {
metadataModel.close();
}
}
private ExtendedIterator<String> listModelNames(Model metadataModel) {
Set<String> modelNameSet = new HashSet<String>();
Iterator<RDFNode> metadataNameIt = metadataModel.listObjectsOfProperty(
metadataModel.getProperty(HAS_NAMED_MODEL_URI));
while (metadataNameIt.hasNext()) {
RDFNode rdfNode = metadataNameIt.next();
if (rdfNode.isLiteral()) {
modelNameSet.add(((Literal) rdfNode).getLexicalForm());
}
}
RDFService service = getRDFService();
try {
modelNameSet.addAll(service.getGraphURIs());
} catch (RDFServiceException e) {
throw new RuntimeException(e);
} finally {
service.close();
}
List<String> modelNameList = new ArrayList<String>();
modelNameList.addAll(modelNameSet);
Collections.sort(modelNameList, Collator.getInstance());
return WrappedIterator.create(modelNameList.iterator());
}
public Model openModel(String arg0, boolean arg1) {
RDFService service = getRDFService();
try {
Dataset dataset = new RDFServiceDataset(service);
return dataset.getNamedModel(arg0);
} finally {
service.close();
}
}
public void removeModel(String arg0) {
Model m = getModel(arg0);
m.removeAll(null,null,null);
Model metadataModel = getMetadataModel();
try {
metadataModel.remove(sdbResource, metadataModel.getProperty(
HAS_NAMED_MODEL_URI),metadataModel.createLiteral(arg0));
} finally {
metadataModel.close();
}
}
public Model addDescription(Model arg0, Resource arg1) {
throw new UnsupportedOperationException(
"addDescription not supported by " + this.getClass().getName());
}
public Model createModelOver(String arg0) {
throw new UnsupportedOperationException(
"createModelOver not supported by " + this.getClass().getName());
}
public Model getDescription() {
throw new UnsupportedOperationException(
"createModelOver not supported by " + this.getClass().getName());
}
public Model getDescription(Resource arg0) {
throw new UnsupportedOperationException(
"getDescription not supported by "+this.getClass().getName());
}
public Model openModel() {
RDFService service = getRDFService();
try {
Dataset dataset = new RDFServiceDataset(service);
return dataset.getDefaultModel();
} finally {
service.close();
}
}
public Model createDefaultModel() {
return openModel();
}
public Model createFreshModel() {
throw new UnsupportedOperationException(
"createFreshModel not supported by " + this.getClass().getName());
}
/**
* @deprecated
*/
public Model createModel() {
return openModel();
}
/**
* @deprecated
*/
public Model getModel() {
return openModel();
}
public Model openModel(String arg0) {
return openModel();
}
public Model openModelIfPresent(String arg0) {
return (this.hasModel(arg0))
? openModel(arg0, false)
: null;
}
public Model getModel(String modelName) {
return openModel(modelName, true);
}
public Model getModel(String arg0, ModelReader arg1) {
throw new UnsupportedOperationException(
"getModel(String, ModelReader) not supported by " +
this.getClass().getName());
}
}

16
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetup.java
View file

@ -24,6 +24,7 @@ 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.ModelMaker;
import com.hp.hpl.jena.rdf.model.ResIterator;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
@ -44,7 +45,6 @@ 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;
@ -52,9 +52,7 @@ 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.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.startup.StartupStatus;
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
@ -67,15 +65,7 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase
public void contextInitialized(ServletContextEvent sce) {
ServletContext ctx = sce.getServletContext();
StartupStatus ss = StartupStatus.getBean(ctx);
// temporary scaffolding in the rdfapi dev branch
// TODO remove me
if (ConfigurationProperties.getBean(ctx).getProperty(
"VitroConnection.DataSource.endpointURI") != null) {
(new JenaDataSourceSetupSparql2()).contextInitialized(sce);
return;
}
try {
long startTime = System.currentTimeMillis();
setUpJenaDataSource(ctx);
@ -331,7 +321,7 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
setVitroJenaModelMaker(vjmm, ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
ModelMaker vsmm = getVitroJenaSDBModelMaker();
setVitroJenaSDBModelMaker(vsmm, ctx);
//bdc34: I have no reason for vsmm vs vjmm.

7
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupBase.java
View file

@ -26,6 +26,7 @@ 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.ModelMaker;
import com.hp.hpl.jena.sdb.Store;
import com.hp.hpl.jena.sdb.StoreDesc;
import com.hp.hpl.jena.sdb.store.DatabaseType;
@ -405,7 +406,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
}
private static VitroJenaModelMaker vjmm = null;
private static VitroJenaSDBModelMaker vsmm = null;
private static ModelMaker vsmm = null;
private static VitroModelSource vms = null;
private static final String sdbModelMaker = "vitroJenaSDBModelMaker";
private static final String rdbModelMaker = "vitroJenaModelMaker";
@ -486,7 +487,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
ctx.setAttribute(rdbModelMaker, vjmm);
}
public static void setVitroJenaSDBModelMaker(VitroJenaSDBModelMaker vsmm,
public static void setVitroJenaSDBModelMaker(ModelMaker vsmm,
ServletContext ctx){
ctx.setAttribute(sdbModelMaker, vsmm);
}
@ -511,7 +512,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
return vjmm;
}
protected VitroJenaSDBModelMaker getVitroJenaSDBModelMaker(){
protected ModelMaker getVitroJenaSDBModelMaker(){
return vsmm;
}

698
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupSparql.java
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@ -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);
}
}

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webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupSparql2.java
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@ -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);
}
}

7
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFServiceSetup.java
View file

@ -15,7 +15,6 @@ 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;
@ -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.OntModelSelectorImpl;
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;
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;
@ -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.RDFServiceUtils;
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.utils.jena.InitialJenaModelUtils;
@ -330,7 +327,7 @@ public class RDFServiceSetup extends JenaDataSourceSetupBase
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
setVitroJenaModelMaker(vjmm, ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
RDFServiceModelMaker vsmm = new RDFServiceModelMaker(rdfServiceFactory);
setVitroJenaSDBModelMaker(vsmm, ctx);
//bdc34: I have no reason for vsmm vs vjmm.

6
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/WebappDaoSDBSetup.java
View file

@ -17,6 +17,7 @@ import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.rdf.model.Model;
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.Resource;
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.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.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.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.startup.StartupStatus;
/**
@ -152,7 +150,7 @@ public class WebappDaoSDBSetup extends JenaDataSourceSetupBase
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
setVitroJenaModelMaker(vjmm, ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
ModelMaker vsmm = getVitroJenaSDBModelMaker();
setVitroJenaSDBModelMaker(vsmm, ctx);
//bdc34: I have no reason for vsmm vs vjmm.