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startup listener refactoring for RDF API

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This commit is contained in:
brianjlowe 2012-06-12 19:55:18 +00:00
parent 068a4d9931
commit 94a34e274b
15 changed files with 481 additions and 2057 deletions
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6
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/VitroRequest.java
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@ -114,15 +114,15 @@ public class VitroRequest extends HttpServletRequestWrapper {
public WebappDaoFactory getAssertionsWebappDaoFactory() { public WebappDaoFactory getAssertionsWebappDaoFactory() {
Object webappDaoFactoryAttr = _req.getSession().getAttribute("assertionsWebappDaoFactory"); Object webappDaoFactoryAttr = _req.getSession().getAttribute("assertionsWebappDaoFactory");
if (webappDaoFactoryAttr instanceof WebappDaoFactory) { if (webappDaoFactoryAttr instanceof WebappDaoFactory) {
log.info("Returning assertionsWebappDaoFactory from session"); log.debug("Returning assertionsWebappDaoFactory from session");
return (WebappDaoFactory) webappDaoFactoryAttr; return (WebappDaoFactory) webappDaoFactoryAttr;
} else { } else {
webappDaoFactoryAttr = getAttribute("assertionsWebappDaoFactory"); webappDaoFactoryAttr = getAttribute("assertionsWebappDaoFactory");
if (webappDaoFactoryAttr instanceof WebappDaoFactory) { if (webappDaoFactoryAttr instanceof WebappDaoFactory) {
log.info("returning assertionsWebappDaoFactory from request attribute"); log.debug("returning assertionsWebappDaoFactory from request attribute");
return (WebappDaoFactory) webappDaoFactoryAttr; return (WebappDaoFactory) webappDaoFactoryAttr;
} else { } else {
log.info("Returning assertionsWebappDaoFactory from context"); log.debug("Returning assertionsWebappDaoFactory from context");
return (WebappDaoFactory) _req.getSession().getServletContext().getAttribute("assertionsWebappDaoFactory"); return (WebappDaoFactory) _req.getSession().getServletContext().getAttribute("assertionsWebappDaoFactory");
} }

4
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
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@ -74,7 +74,7 @@ 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.VitroJenaSDBModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker; import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent; import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.WebappDaoSDBSetup; import edu.cornell.mannlib.vitro.webapp.servlet.setup.WebappDaoSetup;
import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils; import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils; import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult; import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils.MergeResult;
@ -943,7 +943,7 @@ public class JenaIngestController extends BaseEditController {
log.debug("Connecting to DB at "+jdbcUrl); log.debug("Connecting to DB at "+jdbcUrl);
StoreDesc storeDesc = new StoreDesc(LayoutType.LayoutTripleNodesHash,dbTypeObj) ; StoreDesc storeDesc = new StoreDesc(LayoutType.LayoutTripleNodesHash,dbTypeObj) ;
ServletContext ctx = vreq.getSession().getServletContext(); ServletContext ctx = vreq.getSession().getServletContext();
BasicDataSource bds = WebappDaoSDBSetup.makeBasicDataSource( BasicDataSource bds = WebappDaoSetup.makeBasicDataSource(
driver, jdbcUrl, username, password, ctx); driver, jdbcUrl, username, password, ctx);
try { try {
VitroJenaSDBModelMaker vsmm = new VitroJenaSDBModelMaker(storeDesc, bds); VitroJenaSDBModelMaker vsmm = new VitroJenaSDBModelMaker(storeDesc, bds);

10
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ModelContext.java
View file

@ -111,16 +111,6 @@ public class ModelContext {
log.error(e,e); log.error(e,e);
} }
// ModelContext.getJenaOntModel(ctx).register(ml);
// ModelContext.getBaseOntModel(ctx).register(ml);
// ModelContext.getInferenceOntModel(ctx).register(ml);
// ModelContext.getUnionOntModelSelector(ctx).getABoxModel().register(ml);
// ModelContext.getBaseOntModelSelector(ctx).getABoxModel().register(ml);
// ModelContext.getBaseOntModelSelector(ctx).getApplicationMetadataModel().register(ml);
// ModelContext.getInferenceOntModelSelector(ctx).getABoxModel().register(ml);
// ModelContext.getBaseOntModelSelector(ctx).getTBoxModel().register(ml);
} }
public static OntModel getDisplayModel(ServletContext ctx){ public static OntModel getDisplayModel(ServletContext ctx){

6
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/StandardModelSelector.java
View file

@ -29,13 +29,13 @@ public class StandardModelSelector implements ModelSelector {
} }
} }
if(sessionOntModel != null && sessionOntModel instanceof OntModel ) { if(sessionOntModel != null && sessionOntModel instanceof OntModel ) {
log.info("++++++++++ using OntModelSelector from session"); log.debug("using OntModelSelector from session");
return (OntModel)sessionOntModel; return (OntModel)sessionOntModel;
} else if (vreq.getOntModelSelector() != null) { } else if (vreq.getOntModelSelector() != null) {
log.info("++++++++++ using OntModelSelector from request"); log.debug("using OntModelSelector from request");
return vreq.getOntModelSelector().getABoxModel(); return vreq.getOntModelSelector().getABoxModel();
} else { } else {
log.info("++++++++++ using OntModelSelector from context"); log.debug("using OntModelSelector from context");
return ((OntModelSelector) context return ((OntModelSelector) context
.getAttribute("unionOntModelSelector")).getABoxModel(); .getAttribute("unionOntModelSelector")).getABoxModel();
} }

6
webapp/src/edu/cornell/mannlib/vitro/webapp/filters/WebappDaoFactorySDBPrep.java
View file

@ -41,6 +41,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDataset;
import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDatasetGraph; import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlDatasetGraph;
import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraphMultilingual; import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraphMultilingual;
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB; import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils; import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
@ -110,9 +111,14 @@ public class WebappDaoFactorySDBPrep implements Filter {
RDFService rdfService = factory.getRDFService(); RDFService rdfService = factory.getRDFService();
Dataset dataset = new RDFServiceDataset(rdfService); Dataset dataset = new RDFServiceDataset(rdfService);
wadf = new WebappDaoFactorySDB(rdfService, oms, config); wadf = new WebappDaoFactorySDB(rdfService, oms, config);
WebappDaoFactory assertions = new WebappDaoFactorySDB(
rdfService, oms, config, SDBDatasetMode.ASSERTIONS_ONLY);
vreq.setWebappDaoFactory(wadf); vreq.setWebappDaoFactory(wadf);
vreq.setAssertionsWebappDaoFactory(assertions);
vreq.setFullWebappDaoFactory(wadf); vreq.setFullWebappDaoFactory(wadf);
vreq.setDataset(dataset); vreq.setDataset(dataset);
vreq.setOntModelSelector(oms);
vreq.setJenaOntModel(ModelFactory.createOntologyModel( vreq.setJenaOntModel(ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM, dataset.getDefaultModel())); OntModelSpec.OWL_MEM, dataset.getDefaultModel()));

10
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sdb/RDFServiceSDB.java
View file

@ -99,6 +99,10 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
try { try {
if (transaction) { if (transaction) {
conn.getTransactionHandler().begin(); conn.getTransactionHandler().begin();
} else {
for (Object o : changeSet.getPreChangeEvents()) {
this.notifyListenersOfEvent(o);
}
} }
while (csIt.hasNext()) { while (csIt.hasNext()) {
ModelChange modelChange = csIt.next(); ModelChange modelChange = csIt.next();
@ -124,10 +128,10 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
dataset.getLock().leaveCriticalSection(); dataset.getLock().leaveCriticalSection();
} }
} }
for (Object o : changeSet.getPreChangeEvents()) {
this.notifyListenersOfEvent(o);
}
if (transaction) { if (transaction) {
for (Object o : changeSet.getPreChangeEvents()) {
this.notifyListenersOfEvent(o);
}
conn.getTransactionHandler().commit(); conn.getTransactionHandler().commit();
} }
for (Object o : changeSet.getPostChangeEvents()) { for (Object o : changeSet.getPostChangeEvents()) {

4
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java
View file

@ -77,9 +77,7 @@ public class FileGraphSetup implements ServletContextListener {
log.error(errMsg); log.error(errMsg);
throw new ClassCastException(errMsg); throw new ClassCastException(errMsg);
} catch (Throwable t) { } catch (Throwable t) {
System.out.println("Throwable in listener " + this.getClass().getName()); log.error(t, t);
log.error(t);
t.printStackTrace();
} finally { } finally {
OntDocumentManager.getInstance().setProcessImports(false); OntDocumentManager.getInstance().setProcessImports(false);
} }

673
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetup.java
View file

@ -1,673 +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.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
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.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;
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.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.VitroJenaModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
public class JenaDataSourceSetup 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);
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 = 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));
// WebappDaoFactory baseWadf = new WebappDaoFactorySDB(
// baseOms, bds, storeDesc, 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(
// inferenceOms, bds, storeDesc, config,
// WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
// ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
// OntModel masterUnion = 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);
ModelMaker 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.
}
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);
}
}

3
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupBase.java
View file

@ -75,7 +75,6 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
public static String APPPATH = BASE+"app/"; public static String APPPATH = BASE+"app/";
//these files are loaded everytime the system starts up //these files are loaded everytime the system starts up
public static String APPPATH_LOAD = APPPATH + "menuload/"; public static String APPPATH_LOAD = APPPATH + "menuload/";
protected static String SUBMODELS = "/WEB-INF/submodels/";
//All files in this directory will be reloaded every startup //All files in this directory will be reloaded every startup
//and attached as sub-models to the displayOntModel. //and attached as sub-models to the displayOntModel.
@ -430,7 +429,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
} else if (TripleStoreType.SDB.equals(type)) { } else if (TripleStoreType.SDB.equals(type)) {
StoreDesc storeDesc = new StoreDesc( StoreDesc storeDesc = new StoreDesc(
LayoutType.LayoutTripleNodesHash, DatabaseType.fetch(dbtypeStr)); LayoutType.LayoutTripleNodesHash, DatabaseType.fetch(dbtypeStr));
BasicDataSource bds = WebappDaoSDBSetup.makeBasicDataSource( BasicDataSource bds = WebappDaoSetup.makeBasicDataSource(
getDbDriverClassName(ctx), jdbcUrl, username, password, ctx); getDbDriverClassName(ctx), jdbcUrl, username, password, ctx);
bds.setMaxActive(4); // for now, the SDB model makers should not use more bds.setMaxActive(4); // for now, the SDB model makers should not use more
// than a small handful of connections // than a small handful of connections

239
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ModelSetup.java
View file

@ -1,239 +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 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.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
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 edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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.OntModelSelectorImpl;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase.TripleStoreType;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
/**
* Setup the ABox, TBox, inference and Union models.
* Also setup the OntModelSelectors.
*/
public class ModelSetup extends JenaDataSourceSetupBase
implements javax.servlet.ServletContextListener {
private static final Log log = LogFactory.getLog(ModelSetup.class);
@Override
public void contextInitialized(ServletContextEvent sce) {
ServletContext ctx = sce.getServletContext();
StartupStatus ss = StartupStatus.getBean(ctx);
BasicDataSource bds = getApplicationDataSource(ctx);
if( bds == null ){
ss.fatal(this, "A DataSource must be setup before ModelSetup "+
"is run. Make sure that JenaPersistentDataSourceSetup runs before "+
"ModelSetup.");
return;
}
setupModels(ctx,ss,bds);
}
private void setupModels(ServletContext ctx, StartupStatus ss, BasicDataSource bds){
log.info("Setting up model makers and union models");
///////////////////////////////////////////////////////////////
//set up the OntModelSelectors
OntModelSelectorImpl baseOms = new OntModelSelectorImpl();
OntModelSelectorImpl inferenceOms = new OntModelSelectorImpl();
OntModelSelectorImpl unionOms = new OntModelSelectorImpl();
//Put OntModelSelectorImpl objs into the context
ModelContext.setOntModelSelector(unionOms, ctx);
ModelContext.setUnionOntModelSelector(unionOms, ctx);
// assertions and inferences
ModelContext.setBaseOntModelSelector(baseOms, ctx);
// assertions
ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);
// inferences
//add userAccountsModel to OntModelSelectors
OntModel userAccountsModel = ontModelFromContextAttribute(
ctx, "userAccountsOntModel");
baseOms.setUserAccountsModel(userAccountsModel);
inferenceOms.setUserAccountsModel(userAccountsModel);
unionOms.setUserAccountsModel(userAccountsModel);
//add display to OntModelSelectors
OntModel displayModel = ontModelFromContextAttribute(
ctx,DISPLAY_ONT_MODEL);
baseOms.setDisplayModel(displayModel);
inferenceOms.setDisplayModel(displayModel);
unionOms.setDisplayModel(displayModel);
// 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);
}
// create TBox + ABox union models
OntModel baseUnion = ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM,
ModelFactory.createUnion(baseOms.getABoxModel(),
baseOms.getTBoxModel()));
baseOms.setFullModel(baseUnion);
ModelContext.setBaseOntModel(baseOms.getFullModel(), ctx);
log.info("Model makers and union set up");
}
@Override
public void contextDestroyed(ServletContextEvent arg0) {
// nothing to do.
}
}

683
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFServiceSetup.java
View file

@ -1,12 +1,7 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */ /* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.servlet.setup; 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.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import javax.servlet.ServletContext; import javax.servlet.ServletContext;
import javax.servlet.ServletContextEvent; import javax.servlet.ServletContextEvent;
@ -15,21 +10,6 @@ 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.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.SDB; import com.hp.hpl.jena.sdb.SDB;
import com.hp.hpl.jena.sdb.SDBFactory; import com.hp.hpl.jena.sdb.SDBFactory;
import com.hp.hpl.jena.sdb.Store; import com.hp.hpl.jena.sdb.Store;
@ -38,601 +18,79 @@ import com.hp.hpl.jena.sdb.sql.SDBConnection;
import com.hp.hpl.jena.sdb.store.DatabaseType; import com.hp.hpl.jena.sdb.store.DatabaseType;
import com.hp.hpl.jena.sdb.store.LayoutType; import com.hp.hpl.jena.sdb.store.LayoutType;
import com.hp.hpl.jena.sdb.util.StoreUtils; 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.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.RDFServiceModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory; 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;
public class RDFServiceSetup extends JenaDataSourceSetupBase public class RDFServiceSetup extends JenaDataSourceSetupBase
implements javax.servlet.ServletContextListener { implements javax.servlet.ServletContextListener {
private static final Log log = LogFactory.getLog(RDFServiceSetup.class);
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 { @Override
public void contextDestroyed(ServletContextEvent arg0) {
OntModelSelectorImpl baseOms = new OntModelSelectorImpl(); // nothing to do
OntModelSelectorImpl inferenceOms = new OntModelSelectorImpl(); }
OntModelSelectorImpl unionOms = new OntModelSelectorImpl();
@Override
OntModel userAccountsModel = ontModelFromContextAttribute( public void contextInitialized(ServletContextEvent sce) {
ctx, "userAccountsOntModel"); ServletContext ctx = sce.getServletContext();
baseOms.setUserAccountsModel(userAccountsModel); StartupStatus ss = StartupStatus.getBean(ctx);
inferenceOms.setUserAccountsModel(userAccountsModel); try {
unionOms.setUserAccountsModel(userAccountsModel); String endpointURI = ConfigurationProperties.getBean(sce).getProperty(
"VitroConnection.DataSource.endpointURI");
OntModel displayModel = ontModelFromContextAttribute( if (endpointURI != null) {
ctx,DISPLAY_ONT_MODEL); useEndpoint(endpointURI, ctx);
baseOms.setDisplayModel(displayModel); } else {
inferenceOms.setDisplayModel(displayModel); useSDB(ctx, ss);
unionOms.setDisplayModel(displayModel); }
} catch (SQLException e) {
// SDB setup ss.fatal(this, "Exception in RDFServiceSetup", e);
}
}
private void useEndpoint(String endpointURI, ServletContext ctx) {
RDFService rdfService = new RDFServiceSparql(endpointURI);
RDFServiceFactory rdfServiceFactory = new RDFServiceFactorySingle(rdfService);
RDFServiceUtils.setRDFServiceFactory(ctx, rdfServiceFactory);
}
private void useSDB(ServletContext ctx, StartupStatus ss) throws SQLException {
BasicDataSource bds = getApplicationDataSource(ctx);
if( bds == null ){
ss.fatal(this, "A DataSource must be setup before SDBSetup "+
"is run. Make sure that JenaPersistentDataSourceSetup runs before "+
"SDBSetup.");
return;
}
// union default graph // union default graph
SDB.getContext().set(SDB.unionDefaultGraph, true) ; SDB.getContext().set(SDB.unionDefaultGraph, true) ;
//
StoreDesc storeDesc = makeStoreDesc(ctx); StoreDesc storeDesc = makeStoreDesc(ctx);
// setApplicationStoreDesc(storeDesc, ctx); setApplicationStoreDesc(storeDesc, ctx);
//
BasicDataSource bds = getApplicationDataSource(ctx); Store store = connectStore(bds, storeDesc);
// if (bds == null) { setApplicationStore(store, ctx);
// bds = makeDataSourceFromConfigurationProperties(ctx);
// setApplicationDataSource(bds, ctx); if (!isSetUp(store)) {
// } JenaPersistentDataSourceSetup.thisIsFirstStartup();
setupSDB(ctx, store);
}
// Store store = connectStore(bds, storeDesc);
// setApplicationStore(store, ctx);
//okay let's make a graph-backed model
RDFService rdfService = new RDFServiceSDB(bds, storeDesc); RDFService rdfService = new RDFServiceSDB(bds, storeDesc);
RDFServiceFactory rdfServiceFactory = new RDFServiceFactorySingle(rdfService); RDFServiceFactory rdfServiceFactory = new RDFServiceFactorySingle(rdfService);
RDFServiceUtils.setRDFServiceFactory(ctx, rdfServiceFactory); RDFServiceUtils.setRDFServiceFactory(ctx, rdfServiceFactory);
// Graph g = new RDFServiceGraph(rdfService);
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);
baseOms.setABoxModel(
ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM, aboxAssertions));
// ABox inferences
Model aboxInferences = dataset.getNamedModel(
JenaDataSourceSetupBase.JENA_INF_MODEL);
inferenceOms.setABoxModel(ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM, aboxInferences));
// 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"); log.info("SDB store ready for use");
makeModelMakerFromConnectionProperties(TripleStoreType.RDB, ctx);
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
setVitroJenaModelMaker(vjmm, ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
RDFServiceModelMaker vsmm = new RDFServiceModelMaker(rdfServiceFactory);
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. * Tests whether an SDB store has been formatted and populated for use.
@ -656,25 +114,26 @@ public class RDFServiceSetup extends JenaDataSourceSetupBase
} }
} }
private static final String STOREDESC_ATTR = "storeDesc"; public static StoreDesc makeStoreDesc(ServletContext ctx) {
private static final String STORE_ATTR = "kbStore"; String layoutStr = ConfigurationProperties.getBean(ctx).getProperty(
"VitroConnection.DataSource.sdb.layout", "layout2/hash");
public static void setApplicationStoreDesc(StoreDesc storeDesc, String dbtypeStr = ConfigurationProperties.getBean(ctx).getProperty(
ServletContext ctx) { "VitroConnection.DataSource.dbtype", "MySQL");
ctx.setAttribute(STOREDESC_ATTR, storeDesc); return new StoreDesc(
LayoutType.fetch(layoutStr),
DatabaseType.fetch(dbtypeStr) );
} }
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);
}
}
public static Store connectStore(BasicDataSource bds, StoreDesc storeDesc)
throws SQLException {
SDBConnection conn = new SDBConnection(bds.getConnection());
return SDBFactory.connectStore(conn, storeDesc);
}
protected static void setupSDB(ServletContext ctx, Store store) {
log.info("Initializing SDB store");
store.getTableFormatter().create();
store.getTableFormatter().truncate();
}
}

231
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SDBSetup.java
View file

@ -1,231 +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 java.sql.SQLException;
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.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
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 edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
public class SDBSetup extends JenaDataSourceSetupBase
implements javax.servlet.ServletContextListener {
private static final Log log = LogFactory.getLog(SDBSetup.class);
@Override
public void contextDestroyed(ServletContextEvent arg0) {
// nothing to do
}
@Override
public void contextInitialized(ServletContextEvent sce) {
ServletContext ctx = sce.getServletContext();
StartupStatus ss = StartupStatus.getBean(ctx);
try {
setupSDB(ctx, ss);
log.info("SDB store ready for use");
} catch (SQLException e) {
ss.fatal(this, "Exception in setupSDB", e);
}
}
private void setupSDB(ServletContext ctx, StartupStatus ss) throws SQLException {
BasicDataSource bds = getApplicationDataSource(ctx);
if( bds == null ){
ss.fatal(this, "A DataSource must be setup before SDBSetup "+
"is run. Make sure that JenaPersistentDataSourceSetup runs before "+
"SDBSetup.");
return;
}
// union default graph
SDB.getContext().set(SDB.unionDefaultGraph, true) ;
StoreDesc storeDesc = makeStoreDesc(ctx);
setApplicationStoreDesc(storeDesc, ctx);
Store store = connectStore(bds, storeDesc);
setApplicationStore(store, ctx);
if (!isSetUp(store)) {
JenaPersistentDataSourceSetup.thisIsFirstStartup();
setupSDB(ctx, store);
}
}
/**
* 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;
}
}
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);
}
protected static void setupSDB(ServletContext ctx, Store store) {
setupSDB(ctx, store, ModelFactory.createDefaultModel(),
ModelFactory.createDefaultModel());
}
protected static void setupSDB(ServletContext ctx, Store store,
Model memModel, Model inferenceModel) {
log.info("Initializing SDB store");
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.");
}
}
/*
* 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;
}
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;
}
}

273
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.servlet.setup;
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.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;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.sdb.StoreDesc;
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.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.VitroModelSource;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
/**
* Primarily sets up webapp DAO factories.
*/
public class WebappDaoSDBSetup extends JenaDataSourceSetupBase
implements javax.servlet.ServletContextListener {
private static final Log log = LogFactory.getLog(WebappDaoSDBSetup.class);
@Override
public void contextInitialized(ServletContextEvent sce) {
ServletContext ctx = sce.getServletContext();
StartupStatus ss = StartupStatus.getBean(ctx);
try {
long startTime = System.currentTimeMillis();
setUpJenaDataSource(ctx, ss);
log.info((System.currentTimeMillis() - startTime) / 1000 +
" seconds to set up SDB store");
//TODO remove this temporary development scaffolding
if (true || ConfigurationProperties.getBean(sce).getProperty(
"VitroConnection.DataSource.endpointURI") != null) {
(new RDFServiceSetup()).contextInitialized(sce);
}
} 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, StartupStatus ss) throws SQLException {
BasicDataSource bds = getApplicationDataSource(ctx);
if( bds == null ){
ss.fatal(this, "A DataSource must be setup before "+ WebappDaoSDBSetup.class.getName() +
"is run. Make sure that JenaPersistentDataSourceSetup runs before "+
WebappDaoSDBSetup.class.getName() );
return;
}
//Get the OntModelSelectors
OntModelSelectorImpl baseOms =
(OntModelSelectorImpl) ModelContext.getBaseOntModelSelector(ctx);
OntModelSelectorImpl inferenceOms =
(OntModelSelectorImpl) ModelContext.getInferenceOntModelSelector(ctx);
OntModelSelectorImpl unionOms =
(OntModelSelectorImpl) ModelContext.getUnionOntModelSelector(ctx);
///////////////////////////////////////////////////////////////
// Check for namespace mismatch
checkForNamespaceMismatch( baseOms.getApplicationMetadataModel(), ctx );
ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
///////////////////////////////////////////////////////////////
// first startup?
if (isFirstStartup()) {
loadDataFromFilesystem(baseOms, ctx);
}
log.info("Setting up DAO factories");
///////////////////////////////////////////////////////////////
//create assertions webapp DAO factory
StoreDesc storeDesc = getApplicationStoreDesc(ctx);
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
config.setDefaultNamespace(getDefaultNamespace(ctx));
// WebappDaoFactory baseWadf = new WebappDaoFactorySDB(
// baseOms, bds, storeDesc, config,
// WebappDaoFactorySDB.SDBDatasetMode.ASSERTIONS_ONLY);
// ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
///////////////////////////////////////////////////////////////
//create inference webapp DAO factory
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);
///////////////////////////////////////////////////////////////
//create default union webapp DAO factory
// OntModel masterUnion = 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);
makeModelMakerFromConnectionProperties(TripleStoreType.RDB, ctx);
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
setVitroJenaModelMaker(vjmm, ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
ModelMaker 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("DAOs 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.
}
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.info("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 ");
}
}

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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.query.Dataset;
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;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.sdb.StoreDesc;
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.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.RDFServiceModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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.RDFServiceFactory;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase.TripleStoreType;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
/**
* Primarily sets up webapp DAO factories.
*/
public class WebappDaoSetup extends JenaDataSourceSetupBase
implements javax.servlet.ServletContextListener {
private static final Log log = LogFactory.getLog(WebappDaoSetup.class);
@Override
public void contextInitialized(ServletContextEvent sce) {
ServletContext ctx = sce.getServletContext();
StartupStatus ss = StartupStatus.getBean(ctx);
try {
long startTime = System.currentTimeMillis();
setUpJenaDataSource(ctx, ss);
log.info((System.currentTimeMillis() - startTime) / 1000 +
" seconds to set up models and DAO factories");
} 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, StartupStatus ss) {
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);
RDFServiceFactory rdfServiceFactory = RDFServiceUtils.getRDFServiceFactory(ctx);
RDFService rdfService = rdfServiceFactory.getRDFService();
Dataset dataset = new RDFServiceDataset(rdfService);
setStartupDataset(dataset, ctx);
// ABox assertions
Model aboxAssertions = dataset.getNamedModel(
JenaDataSourceSetupBase.JENA_DB_MODEL);
baseOms.setABoxModel(
ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM, aboxAssertions));
// ABox inferences
Model aboxInferences = dataset.getNamedModel(
JenaDataSourceSetupBase.JENA_INF_MODEL);
inferenceOms.setABoxModel(ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM, aboxInferences));
// 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)));
}
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));
makeModelMakerFromConnectionProperties(TripleStoreType.RDB, ctx);
VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
setVitroJenaModelMaker(vjmm, ctx);
makeModelMakerFromConnectionProperties(TripleStoreType.SDB, ctx);
RDFServiceModelMaker vsmm = new RDFServiceModelMaker(rdfServiceFactory);
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.
}
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.info("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 ");
}
}

5
webapp/web/WEB-INF/resources/startup_listeners.txt
View file

@ -16,13 +16,12 @@ edu.cornell.mannlib.vitro.webapp.email.FreemarkerEmailFactory$Setup
### this listener must be run before SDBSetup, all models setups and WebappDaoSetup ### ### this listener must be run before SDBSetup, all models setups and WebappDaoSetup ###
edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaPersistentDataSourceSetup edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaPersistentDataSourceSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.SDBSetup edu.cornell.mannlib.vitro.webapp.servlet.setup.RDFServiceSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.ApplicationModelSetup edu.cornell.mannlib.vitro.webapp.servlet.setup.ApplicationModelSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.UserModelSetup edu.cornell.mannlib.vitro.webapp.servlet.setup.UserModelSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.ModelSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.WebappDaoSDBSetup edu.cornell.mannlib.vitro.webapp.servlet.setup.WebappDaoSetup
edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase