VIVO-82 Refactoring WebappDaoSetup to clarify the model setup.
This commit is contained in:
j2blake
parent
6123f41d95
commit
0e34b459e5
1 changed files with 146 additions and 217 deletions
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@ -3,6 +3,8 @@
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package edu.cornell.mannlib.vitro.webapp.servlet.setup;
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package edu.cornell.mannlib.vitro.webapp.servlet.setup;
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import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.DISPLAY_ONT_MODEL;
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import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.DISPLAY_ONT_MODEL;
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import static edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode.ASSERTIONS_ONLY;
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import static edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY;
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import java.util.ArrayList;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.List;
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@ -13,6 +15,8 @@ import javax.servlet.ServletContextEvent;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.graph.BulkUpdateHandler;
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import com.hp.hpl.jena.graph.Graph;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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import com.hp.hpl.jena.query.Dataset;
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import com.hp.hpl.jena.query.Dataset;
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@ -20,19 +24,14 @@ import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.ResIterator;
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import com.hp.hpl.jena.rdf.model.ResIterator;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.util.ResourceUtils;
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import com.hp.hpl.jena.util.ResourceUtils;
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import com.hp.hpl.jena.util.iterator.ClosableIterator;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDF;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
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@ -59,202 +58,96 @@ public class WebappDaoSetup extends JenaDataSourceSetupBase
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ServletContext ctx = sce.getServletContext();
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ServletContext ctx = sce.getServletContext();
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StartupStatus ss = StartupStatus.getBean(ctx);
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StartupStatus ss = StartupStatus.getBean(ctx);
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try {
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long begin = System.currentTimeMillis();
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long startTime = System.currentTimeMillis();
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setUpJenaDataSource(ctx);
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setUpJenaDataSource(ctx, ss);
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ss.info(this, secondsSince(begin) + " seconds to set up models and DAO factories");
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log.info((System.currentTimeMillis() - startTime) / 1000 +
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" seconds to set up models and DAO factories");
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} catch (Throwable t) {
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log.error("Throwable in " + this.getClass().getName(), t);
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ss.fatal(this, "Throwable in " + this.getClass().getName(), t);
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}
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}
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}
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private void setUpJenaDataSource(ServletContext ctx) {
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private void setUpJenaDataSource(ServletContext ctx, StartupStatus ss) {
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OntModelSelectorImpl baseOms = new OntModelSelectorImpl();
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OntModelSelectorImpl inferenceOms = new OntModelSelectorImpl();
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OntModelSelectorImpl unionOms = new OntModelSelectorImpl();
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OntModel userAccountsModel = ontModelFromContextAttribute(
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ctx, "userAccountsOntModel");
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baseOms.setUserAccountsModel(userAccountsModel);
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inferenceOms.setUserAccountsModel(userAccountsModel);
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unionOms.setUserAccountsModel(userAccountsModel);
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OntModel displayModel = ontModelFromContextAttribute(
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ctx,DISPLAY_ONT_MODEL);
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baseOms.setDisplayModel(displayModel);
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inferenceOms.setDisplayModel(displayModel);
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unionOms.setDisplayModel(displayModel);
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RDFServiceFactory rdfServiceFactory = RDFServiceUtils.getRDFServiceFactory(ctx);
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RDFServiceFactory rdfServiceFactory = RDFServiceUtils.getRDFServiceFactory(ctx);
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RDFService rdfService = rdfServiceFactory.getRDFService();
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RDFService rdfService = rdfServiceFactory.getRDFService();
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Dataset dataset = new RDFServiceDataset(rdfService);
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Dataset dataset = new RDFServiceDataset(rdfService);
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setStartupDataset(dataset, ctx);
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setStartupDataset(dataset, ctx);
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// ABox assertions
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OntModel applicationMetadataModel = createdMemoryMappedModel(dataset, JENA_APPLICATION_METADATA_MODEL, "application metadata model");
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baseOms.setABoxModel(ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL)));
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if (applicationMetadataModel.size()== 0) {
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// ABox inferences
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inferenceOms.setABoxModel(ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dataset.getNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL)));
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// TBox assertions
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try {
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Model tboxAssertionsDB = dataset.getNamedModel(
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JENA_TBOX_ASSERTIONS_MODEL);
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OntModel tboxAssertions = ModelFactory.createOntologyModel(
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MEM_ONT_MODEL_SPEC);
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if (tboxAssertionsDB != null) {
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long startTime = System.currentTimeMillis();
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log.info("Copying cached tbox assertions into memory");
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tboxAssertions.add(tboxAssertionsDB);
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log.info((System.currentTimeMillis() - startTime)/ 1000 + " seconds to load tbox assertions");
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tboxAssertions.getBaseModel().register(new ModelSynchronizer(tboxAssertionsDB));
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}
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baseOms.setTBoxModel(tboxAssertions);
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} catch (Throwable e) {
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log.error("Unable to load tbox assertion cache from DB", e);
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throw new RuntimeException(e);
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}
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// TBox inferences
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try {
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Model tboxInferencesDB = dataset.getNamedModel(JENA_TBOX_INF_MODEL);
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OntModel tboxInferences = ModelFactory.createOntologyModel(
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MEM_ONT_MODEL_SPEC);
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if (tboxInferencesDB != null) {
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long startTime = System.currentTimeMillis();
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log.info(
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"Copying cached tbox inferences into memory");
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tboxInferences.add(tboxInferencesDB);
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System.out.println((System.currentTimeMillis() - startTime)
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/ 1000 + " seconds to load tbox inferences");
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tboxInferences.getBaseModel().register(new ModelSynchronizer(
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tboxInferencesDB));
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}
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inferenceOms.setTBoxModel(tboxInferences);
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} catch (Throwable e) {
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log.error("Unable to load tbox inference cache from DB", e);
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throw new RuntimeException(e);
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}
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// union ABox
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Model m = ModelFactory.createUnion(
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baseOms.getABoxModel(), inferenceOms.getABoxModel());
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m = ModelFactory.createModelForGraph(
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new SpecialBulkUpdateHandlerGraph(
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m.getGraph(),
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baseOms.getABoxModel().getGraph().getBulkUpdateHandler()));
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OntModel unionABoxModel = ModelFactory.createOntologyModel(
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MEM_ONT_MODEL_SPEC, m);
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unionOms.setABoxModel(unionABoxModel);
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// union TBox
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m = ModelFactory.createUnion(baseOms.getTBoxModel(), inferenceOms.getTBoxModel());
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m = ModelFactory.createModelForGraph(
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new SpecialBulkUpdateHandlerGraph(
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m.getGraph(),
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baseOms.getTBoxModel().getGraph().getBulkUpdateHandler()));
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OntModel unionTBoxModel = ModelFactory.createOntologyModel(
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MEM_ONT_MODEL_SPEC, m);
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unionOms.setTBoxModel(unionTBoxModel);
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// Application metadata model is cached in memory.
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try {
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Model applicationMetadataModelDB = dataset.getNamedModel(
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JENA_APPLICATION_METADATA_MODEL);
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OntModel applicationMetadataModel =
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ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
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long startTime = System.currentTimeMillis();
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System.out.println(
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"Copying cached application metadata model into memory");
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applicationMetadataModel.add(applicationMetadataModelDB);
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System.out.println((System.currentTimeMillis() - startTime)
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/ 1000 + " seconds to load application metadata model " +
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"assertions of size " + applicationMetadataModel.size());
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applicationMetadataModel.getBaseModel().register(
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new ModelSynchronizer(applicationMetadataModelDB));
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if (applicationMetadataModel.size()== 0 /* isFirstStartup() */) {
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JenaDataSourceSetupBase.thisIsFirstStartup();
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JenaDataSourceSetupBase.thisIsFirstStartup();
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applicationMetadataModel.add(
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InitialJenaModelUtils.loadInitialModel(
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ctx, getDefaultNamespace(ctx)));
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}
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}
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baseOms.setApplicationMetadataModel(applicationMetadataModel);
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OntModel userAccountsModel = ontModelFromContextAttribute(ctx, "userAccountsOntModel");
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inferenceOms.setApplicationMetadataModel(
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OntModel displayModel = ontModelFromContextAttribute(ctx,DISPLAY_ONT_MODEL);
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baseOms.getApplicationMetadataModel());
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OntModel baseABoxModel = createNamedModelFromDataset(dataset, JENA_DB_MODEL);
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unionOms.setApplicationMetadataModel(
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OntModel inferenceABoxModel = createNamedModelFromDataset(dataset, JENA_INF_MODEL);
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baseOms.getApplicationMetadataModel());
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OntModel baseTBoxModel = createdMemoryMappedModel(dataset, JENA_TBOX_ASSERTIONS_MODEL, "tbox assertions");
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OntModel inferenceTBoxModel = createdMemoryMappedModel(dataset, JENA_TBOX_INF_MODEL, "tbox inferences");
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} catch (Throwable e) {
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OntModel unionABoxModel = createCombinedBulkUpdatingModel(baseABoxModel, inferenceABoxModel);
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log.error("Unable to load application metadata model cache from DB"
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OntModel unionTBoxModel = createCombinedBulkUpdatingModel(baseTBoxModel, inferenceTBoxModel);
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, e);
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throw new RuntimeException(e);
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}
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checkForNamespaceMismatch( baseOms.getApplicationMetadataModel(), ctx );
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if (isFirstStartup()) {
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if (isFirstStartup()) {
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loadDataFromFilesystem(baseOms, ctx);
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loadInitialApplicationMetadataModel(applicationMetadataModel, ctx);
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loadDataFromFilesystem(baseABoxModel, baseTBoxModel, applicationMetadataModel, ctx);
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}
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}
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log.info("Setting up union models and DAO factories");
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log.info("Setting up union models");
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OntModel baseFullModel = createCombinedBulkUpdatingModel(baseABoxModel, baseTBoxModel);
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OntModel inferenceFullModel = createCombinedModel(inferenceABoxModel, inferenceTBoxModel);
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OntModel unionFullModel = ModelFactory.createOntologyModel(DB_ONT_MODEL_SPEC, dataset.getDefaultModel());
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// create TBox + ABox union models and set up webapp DAO factories
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ModelContext.setBaseOntModel(baseFullModel, ctx);
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Model baseDynamicUnion = ModelFactory.createUnion(baseOms.getABoxModel(),
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ModelContext.setInferenceOntModel(inferenceFullModel, ctx);
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baseOms.getTBoxModel());
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baseDynamicUnion = ModelFactory.createModelForGraph(
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new SpecialBulkUpdateHandlerGraph(
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baseDynamicUnion.getGraph(),
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baseOms.getABoxModel().getGraph().getBulkUpdateHandler()) );
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OntModel baseUnion = ModelFactory.createOntologyModel(
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OntModelSpec.OWL_MEM, baseDynamicUnion);
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baseOms.setFullModel(baseUnion);
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ModelContext.setBaseOntModel(baseOms.getFullModel(), ctx);
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WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
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config.setDefaultNamespace(getDefaultNamespace(ctx));
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WebappDaoFactory baseWadf = new WebappDaoFactorySDB(
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rdfService, baseOms, config,
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WebappDaoFactorySDB.SDBDatasetMode.ASSERTIONS_ONLY);
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ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
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OntModel inferenceUnion = ModelFactory.createOntologyModel(
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checkForNamespaceMismatch( applicationMetadataModel, ctx );
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OntModelSpec.OWL_MEM,
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ModelFactory.createUnion(
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inferenceOms.getABoxModel(),
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inferenceOms.getTBoxModel()));
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inferenceOms.setFullModel(inferenceUnion);
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ModelContext.setInferenceOntModel(inferenceOms.getFullModel(), ctx);
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WebappDaoFactory infWadf = new WebappDaoFactorySDB(
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rdfService, inferenceOms, config,
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WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
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ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
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OntModel masterUnion = ModelFactory.createOntologyModel(
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OntModelSelectorImpl baseOms = new OntModelSelectorImpl();
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DB_ONT_MODEL_SPEC, dataset.getDefaultModel());
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baseOms.setApplicationMetadataModel(applicationMetadataModel);
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unionOms.setFullModel(masterUnion);
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baseOms.setUserAccountsModel(userAccountsModel);
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ctx.setAttribute("jenaOntModel", masterUnion);
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baseOms.setDisplayModel(displayModel);
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WebappDaoFactory wadf = new WebappDaoFactorySDB(
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baseOms.setABoxModel(baseABoxModel);
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rdfService, unionOms, config);
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baseOms.setTBoxModel(baseTBoxModel);
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ctx.setAttribute("webappDaoFactory",wadf);
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baseOms.setFullModel(baseFullModel);
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OntModelSelectorImpl inferenceOms = new OntModelSelectorImpl();
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inferenceOms.setApplicationMetadataModel(applicationMetadataModel);
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inferenceOms.setUserAccountsModel(userAccountsModel);
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inferenceOms.setDisplayModel(displayModel);
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inferenceOms.setABoxModel(inferenceABoxModel);
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inferenceOms.setTBoxModel(inferenceTBoxModel);
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inferenceOms.setFullModel(inferenceFullModel);
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OntModelSelectorImpl unionOms = new OntModelSelectorImpl();
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unionOms.setApplicationMetadataModel(applicationMetadataModel);
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unionOms.setUserAccountsModel(userAccountsModel);
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unionOms.setDisplayModel(displayModel);
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unionOms.setABoxModel(unionABoxModel);
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unionOms.setTBoxModel(unionTBoxModel);
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unionOms.setFullModel(unionFullModel);
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ModelContext.setOntModelSelector(unionOms, ctx);
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ModelContext.setOntModelSelector(unionOms, ctx);
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ModelContext.setUnionOntModelSelector(unionOms, ctx);
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ModelContext.setUnionOntModelSelector(unionOms, ctx); // assertions and inferences
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// assertions and inferences
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ModelContext.setBaseOntModelSelector(baseOms, ctx); // assertions
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ModelContext.setBaseOntModelSelector(baseOms, ctx);
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ModelContext.setInferenceOntModelSelector(inferenceOms, ctx); // inferences
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// assertions
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ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);
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// inferences
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log.info("Setting up DAO factories");
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ctx.setAttribute("jenaOntModel", unionFullModel);
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WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
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config.setDefaultNamespace(getDefaultNamespace(ctx));
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WebappDaoFactory baseWadf = new WebappDaoFactorySDB(rdfService, baseOms, config, ASSERTIONS_ONLY);
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ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
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WebappDaoFactory infWadf = new WebappDaoFactorySDB(rdfService, inferenceOms, config, INFERENCES_ONLY);
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ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
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WebappDaoFactory wadf = new WebappDaoFactorySDB(rdfService, unionOms, config);
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ctx.setAttribute("webappDaoFactory",wadf);
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log.info("Model makers set up");
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ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
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ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
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@ -269,7 +162,52 @@ public class WebappDaoSetup extends JenaDataSourceSetupBase
|
||||||
//I don't know what are the implications of this choice.
|
//I don't know what are the implications of this choice.
|
||||||
setVitroModelSource( new VitroModelSource(vsmm,ctx), ctx);
|
setVitroModelSource( new VitroModelSource(vsmm,ctx), ctx);
|
||||||
|
|
||||||
log.info("Model makers set up");
|
}
|
||||||
|
|
||||||
|
private OntModel createNamedModelFromDataset(Dataset dataset, String name) {
|
||||||
|
return ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dataset.getNamedModel(name));
|
||||||
|
}
|
||||||
|
|
||||||
|
private OntModel createdMemoryMappedModel(Dataset dataset, String name, String label) {
|
||||||
|
try {
|
||||||
|
Model dbModel = dataset.getNamedModel(name);
|
||||||
|
OntModel memoryModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
|
||||||
|
|
||||||
|
if (dbModel != null) {
|
||||||
|
long begin = System.currentTimeMillis();
|
||||||
|
log.info("Copying cached " + label + " into memory");
|
||||||
|
memoryModel.add(dbModel);
|
||||||
|
log.info(secondsSince(begin) + " seconds to load " + label);
|
||||||
|
memoryModel.getBaseModel().register(new ModelSynchronizer(dbModel));
|
||||||
|
}
|
||||||
|
return memoryModel;
|
||||||
|
} catch (Throwable e) {
|
||||||
|
throw new RuntimeException("Unable to load " + label + " from DB", e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private OntModel createCombinedModel(OntModel oneModel, OntModel otherModel) {
|
||||||
|
return ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
|
||||||
|
ModelFactory.createUnion(oneModel, otherModel));
|
||||||
|
}
|
||||||
|
|
||||||
|
private OntModel createCombinedBulkUpdatingModel(OntModel baseModel,
|
||||||
|
OntModel otherModel) {
|
||||||
|
BulkUpdateHandler bulkUpdateHandler = baseModel.getGraph().getBulkUpdateHandler();
|
||||||
|
Graph unionGraph = ModelFactory.createUnion(baseModel, otherModel).getGraph();
|
||||||
|
Model unionModel = ModelFactory.createModelForGraph(
|
||||||
|
new SpecialBulkUpdateHandlerGraph(unionGraph, bulkUpdateHandler));
|
||||||
|
return ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC, unionModel);
|
||||||
|
}
|
||||||
|
|
||||||
|
private void loadInitialApplicationMetadataModel(OntModel applicationMetadataModel,
|
||||||
|
ServletContext ctx) {
|
||||||
|
try {
|
||||||
|
applicationMetadataModel.add(
|
||||||
|
InitialJenaModelUtils.loadInitialModel(ctx, getDefaultNamespace(ctx)));
|
||||||
|
} catch (Throwable e) {
|
||||||
|
throw new RuntimeException("Unable to load application metadata model cache from DB", e);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -343,42 +281,33 @@ public class WebappDaoSetup extends JenaDataSourceSetupBase
|
||||||
|
|
||||||
/* ===================================================================== */
|
/* ===================================================================== */
|
||||||
|
|
||||||
|
private long secondsSince(long startTime) {
|
||||||
@Override
|
return (System.currentTimeMillis() - startTime) / 1000;
|
||||||
public void contextDestroyed(ServletContextEvent sce) {
|
|
||||||
// Nothing to do.
|
|
||||||
}
|
}
|
||||||
|
|
||||||
private boolean isEmpty(Model model) {
|
private void loadDataFromFilesystem(OntModel baseABoxModel, OntModel baseTBoxModel, OntModel applicationMetadataModel,
|
||||||
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) {
|
ServletContext ctx) {
|
||||||
Long startTime = System.currentTimeMillis();
|
Long startTime = System.currentTimeMillis();
|
||||||
log.info("Initializing models from RDF files");
|
log.info("Initializing models from RDF files");
|
||||||
|
|
||||||
readOntologyFilesInPathSet(USER_ABOX_PATH, ctx, baseOms.getABoxModel());
|
readOntologyFilesInPathSet(USER_ABOX_PATH, ctx, baseABoxModel);
|
||||||
readOntologyFilesInPathSet(USER_TBOX_PATH, ctx, baseOms.getTBoxModel());
|
readOntologyFilesInPathSet(USER_TBOX_PATH, ctx, baseTBoxModel);
|
||||||
readOntologyFilesInPathSet(
|
readOntologyFilesInPathSet(USER_APPMETA_PATH, ctx, applicationMetadataModel);
|
||||||
USER_APPMETA_PATH, ctx, baseOms.getApplicationMetadataModel());
|
|
||||||
|
|
||||||
log.debug(((System.currentTimeMillis() - startTime) / 1000)
|
log.debug(((System.currentTimeMillis() - startTime) / 1000)
|
||||||
+ " seconds to read RDF files ");
|
+ " seconds to read RDF files ");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ===================================================================== */
|
||||||
|
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void contextDestroyed(ServletContextEvent sce) {
|
||||||
|
// Nothing to do.
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
Loading…
Add table
Reference in a new issue