NIHVIVO-1735 and NIHVIVO-1753 bugfixes for baseOntModel setup and initial reasoning
This commit is contained in:
bjl23
parent
58027d5d95
commit
6883148154
3 changed files with 308 additions and 259 deletions
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@ -16,7 +16,6 @@ import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.ontology.Individual;
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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.query.Dataset;
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import com.hp.hpl.jena.rdf.model.Literal;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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@ -28,7 +27,6 @@ import com.hp.hpl.jena.sdb.Store;
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import com.hp.hpl.jena.sdb.StoreDesc;
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import com.hp.hpl.jena.sdb.sql.SDBConnection;
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import com.hp.hpl.jena.sdb.store.DatabaseType;
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import com.hp.hpl.jena.sdb.store.DatasetStore;
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import com.hp.hpl.jena.sdb.store.LayoutType;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.util.iterator.ClosableIterator;
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@ -41,12 +39,12 @@ 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.jena.JenaBaseDaoCon;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelectorImpl;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
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import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase.TripleStoreType;
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import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
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import edu.cornell.mannlib.vitro.webapp.utils.jena.NamespaceMapperJena;
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@ -70,8 +68,6 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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sce.getServletContext().setAttribute("jenaOntModel",memModel);
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}
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memModel.addSubModel((new JenaBaseDaoCon()).getConstModel()); // add the vitro tbox to the model
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OntModel inferenceModel = ontModelFromContextAttribute(sce.getServletContext(), "inferenceOntModel");
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OntModel userAccountsModel = ontModelFromContextAttribute(sce.getServletContext(), "userAccountsOntModel");
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@ -79,22 +75,11 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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checkMainModelForUserAccounts(memModel, userAccountsModel);
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}
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OntModel unionModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(memModel, inferenceModel));
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OntModelSelectorImpl baseOms = new OntModelSelectorImpl();
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baseOms.setApplicationMetadataModel(memModel);
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baseOms.setTBoxModel(memModel);
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baseOms.setFullModel(memModel);
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OntModelSelectorImpl inferenceOms = new OntModelSelectorImpl();
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inferenceOms.setABoxModel(inferenceModel);
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inferenceOms.setTBoxModel(inferenceModel);
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inferenceOms.setFullModel(inferenceModel);
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OntModelSelectorImpl unionOms = new OntModelSelectorImpl();
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unionOms.setApplicationMetadataModel(unionModel);
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unionOms.setTBoxModel(unionModel);
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unionOms.setFullModel(unionModel);
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baseOms.setUserAccountsModel(userAccountsModel);
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inferenceOms.setUserAccountsModel(userAccountsModel);
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@ -120,56 +105,16 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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this.setApplicationDataSource(bds, sce.getServletContext());
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SDBConnection conn = new SDBConnection(bds.getConnection()) ;
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Store store = SDBFactory.connectStore(conn, storeDesc);
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try {
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// a test query to see if the store is formatted
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SDBFactory.connectDefaultModel(store).contains(OWL.Thing, RDF.type, OWL.Nothing);
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} catch (Exception e) { // unformatted store
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sce.getServletContext().setAttribute("kbStore", store);
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if (!isSetUp(store)) {
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log.debug("Non-SDB system detected. Setting up SDB store");
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store.getTableFormatter().create();
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store.getTableFormatter().truncate();
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// This is a one-time copy of stored KB data - from a Jena RDB store
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// to a Jena SDB store. In the process, we will also separate out the
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// TBox from the Abox; these are in the same graph in pre 1.2 VIVO
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// versions and will now be stored and maintained in separate models
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// Access to the Jena RDB data is through the OntModelSelectors that have
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// been set up earlier in the current session by
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// JenaPersistentDataSourceSetup.java
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// In the code below, note that the current getABoxModel() methods on
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// the OntModelSelectors return a graph with both ABox and TBox data.
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OntModel submodels = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
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readOntologyFilesInPathSet(SUBMODELS, sce.getServletContext(), submodels);
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Model tboxAssertions = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
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// initially putting the results in memory so we have a
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// cheaper way of computing the difference when we copy the ABox
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Model memTboxAssertions = ModelFactory.createDefaultModel();
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getTBoxModel(memModel, submodels, memTboxAssertions);
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tboxAssertions.add(memTboxAssertions);
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Model tboxInferences = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL);
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// initially putting the results in memory so we have a
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// cheaper way of computing the difference when we copy the ABox
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Model memTboxInferences = ModelFactory.createDefaultModel();
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getTBoxModel(inferenceModel, submodels, memTboxInferences);
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tboxInferences.add(memTboxInferences);
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Model aboxAssertions = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_DB_MODEL);
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copyDifference(memModel, memTboxAssertions, aboxAssertions);
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Model aboxInferences = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_INF_MODEL);
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copyDifference(inferenceModel, memTboxInferences, aboxInferences);
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setupSDB(sce.getServletContext(), store, memModel, inferenceModel);
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}
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// The code below, which sets up the OntModelSelectors, controls whether each
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// model is maintained in memory, in the DB, or both while the application
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// is running.
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}
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sce.getServletContext().setAttribute("kbStore", store);
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//store.getTableFormatter().dropIndexes();
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//store.getTableFormatter().addIndexes();
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// Populate the three OntModelSelectors (BaseOntModel=assertions, InferenceOntModel=inferences
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// and JenaOntModel=union of assertions and inferences) with the post-SDB-conversion models.
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@ -231,25 +176,32 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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OntModel unionTBoxModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(baseOms.getTBoxModel(), inferenceOms.getTBoxModel()));
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unionOms.setTBoxModel(unionTBoxModel);
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Dataset dataset = DatasetStore.create(store);
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//String queryStr = "CONSTRUCT { ?s ?p ?o } \n" +
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// "WHERE { GRAPH ?g { ?s ?p ?o } } ";
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//Query query = QueryFactory.create(queryStr);
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//QueryExecution qe = QueryExecutionFactory.create(query, dataset);
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//log.info("Test query returned " + qe.execConstruct().size() + " statements");
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// add the vitro ontologies to the tbox models
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OntModel vitroTBoxModel = (new JenaBaseDaoCon()).getConstModel();
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baseOms.getTBoxModel().addSubModel(vitroTBoxModel);
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inferenceOms.getTBoxModel().addSubModel(vitroTBoxModel);
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unionOms.getTBoxModel().addSubModel(vitroTBoxModel);
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sce.getServletContext().setAttribute("baseOntModel", memModel);
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// create TBox + ABox union models and set up webapp DAO factories
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OntModel baseUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
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ModelFactory.createUnion(baseOms.getABoxModel(), baseOms.getTBoxModel()));
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baseOms.setFullModel(baseUnion);
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ModelContext.setBaseOntModel(baseOms.getFullModel(), sce.getServletContext());
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WebappDaoFactory baseWadf = new WebappDaoFactorySDB(baseOms, bds, storeDesc, defaultNamespace, null, null);
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//WebappDaoFactory baseWadf = new WebappDaoFactorySDB(baseOms, dataset, defaultNamespace, null, null);
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sce.getServletContext().setAttribute("assertionsWebappDaoFactory",baseWadf);
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sce.getServletContext().setAttribute("inferenceOntModel", inferenceModel);
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OntModel inferenceUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
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ModelFactory.createUnion(inferenceOms.getABoxModel(), inferenceOms.getTBoxModel()));
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inferenceOms.setFullModel(inferenceUnion);
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ModelContext.setInferenceOntModel(inferenceOms.getFullModel(), sce.getServletContext());
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WebappDaoFactory infWadf = new WebappDaoFactorySDB(inferenceOms, bds, storeDesc, defaultNamespace, null, null);
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//WebappDaoFactory infWadf = new WebappDaoFactorySDB(inferenceOms, dataset, defaultNamespace, null, null);
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sce.getServletContext().setAttribute("deductionsWebappDaoFactory", infWadf);
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OntModel masterUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
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ModelFactory.createUnion(unionABoxModel, unionTBoxModel));
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unionOms.setFullModel(masterUnion);
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sce.getServletContext().setAttribute("jenaOntModel", masterUnion);
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WebappDaoFactory wadf = new WebappDaoFactorySDB(unionOms, bds, storeDesc, defaultNamespace, null, null);
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//WebappDaoFactory wadf = new WebappDaoFactorySDB(unionOms, dataset, defaultNamespace, null, null);
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@ -259,14 +211,18 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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sce.getServletContext().setAttribute("baseOntModelSelector", baseOms); //assertions
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sce.getServletContext().setAttribute("inferenceOntModelSelector", inferenceOms); //inferences
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// use "full" models as the legacy application metadata models
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baseOms.setApplicationMetadataModel(baseOms.getFullModel());
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inferenceOms.setApplicationMetadataModel(inferenceOms.getFullModel());
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unionOms.setApplicationMetadataModel(unionOms.getFullModel());
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ApplicationBean appBean = getApplicationBeanFromOntModel(memModel,wadf);
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ApplicationBean appBean = getApplicationBeanFromOntModel(unionOms.getFullModel(),wadf);
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if (appBean != null) {
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sce.getServletContext().setAttribute("applicationBean", appBean);
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}
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if (isEmpty(memModel)) {
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loadDataFromFilesystem(memModel, sce.getServletContext());
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if (isEmpty(unionOms.getFullModel())) {
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loadDataFromFilesystem(unionOms.getFullModel(), sce.getServletContext());
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}
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if (userAccountsModel.size() == 0) {
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@ -276,11 +232,11 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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}
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}
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ensureEssentialInterfaceData(memModel, sce, wadf);
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ensureEssentialInterfaceData(unionOms.getFullModel(), sce, wadf);
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NamespaceMapper namespaceMapper = new NamespaceMapperJena(unionModel, unionModel, defaultNamespace);
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NamespaceMapper namespaceMapper = new NamespaceMapperJena(masterUnion, masterUnion, defaultNamespace);
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sce.getServletContext().setAttribute("NamespaceMapper", namespaceMapper);
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memModel.getBaseModel().register(namespaceMapper);
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unionOms.getFullModel().getBaseModel().register(namespaceMapper);
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sce.getServletContext().setAttribute("defaultNamespace", defaultNamespace);
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@ -310,9 +266,9 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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List<String> portalURIs = new ArrayList<String>();
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try {
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model.enterCriticalSection(Lock.READ);
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Iterator portalIt = model.listIndividuals(PORTAL);
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Iterator<Individual> portalIt = model.listIndividuals(PORTAL);
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while (portalIt.hasNext()) {
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portalURIs.add( ((Individual)portalIt.next()).getURI() );
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portalURIs.add( portalIt.next().getURI() );
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}
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} finally {
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model.leaveCriticalSection();
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@ -339,7 +295,8 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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}
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private ApplicationBean getApplicationBeanFromOntModel(OntModel ontModel,WebappDaoFactory wadf) {
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ClosableIterator appIt = ontModel.listIndividuals(ResourceFactory.createResource(VitroVocabulary.APPLICATION));
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ClosableIterator<Individual> appIt = ontModel.listIndividuals(
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ResourceFactory.createResource(VitroVocabulary.APPLICATION));
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try {
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if (appIt.hasNext()) {
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Individual appInd = (Individual) appIt.next();
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@ -367,7 +324,8 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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private void ensureEssentialInterfaceData(OntModel memModel, ServletContextEvent sce, WebappDaoFactory wadf) {
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Model essentialInterfaceData = null;
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ClosableIterator portalIt = memModel.listIndividuals(memModel.getResource(VitroVocabulary.PORTAL));
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ClosableIterator<Individual> portalIt = memModel.listIndividuals(
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memModel.getResource(VitroVocabulary.PORTAL));
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try {
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if (!portalIt.hasNext()) {
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log.debug("Loading initial site configuration");
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@ -423,7 +381,7 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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}
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private boolean isEmpty(Model model) {
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ClosableIterator closeIt = model.listStatements();
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ClosableIterator<Statement> closeIt = model.listStatements();
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try {
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if (closeIt.hasNext()) {
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return false;
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@ -445,7 +403,7 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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ontModel.add(initialDataModel);
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}
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private void getTBoxModel(Model fullModel, Model submodels, Model tboxModel) {
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private static void getTBoxModel(Model fullModel, Model submodels, Model tboxModel) {
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JenaModelUtils modelUtils = new JenaModelUtils();
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@ -468,7 +426,7 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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/*
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* Copy all statements from model 1 that are not in model 2 to model 3.
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*/
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private void copyDifference(Model model1, Model model2, Model model3) {
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private static void copyDifference(Model model1, Model model2, Model model3) {
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StmtIterator iter = model1.listStatements();
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@ -481,4 +439,67 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
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return;
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}
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public static void setupSDB(ServletContext ctx,
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Store store,
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Model memModel,
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Model inferenceModel) {
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store.getTableFormatter().create();
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store.getTableFormatter().truncate();
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// This is a one-time copy of stored KB data - from a Jena RDB store
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// to a Jena SDB store. In the process, we will also separate out the
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// TBox from the Abox; these are in the same graph in pre 1.2 VIVO
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// versions and will now be stored and maintained in separate models
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// Access to the Jena RDB data is through the OntModelSelectors that have
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// been set up earlier in the current session by
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// JenaPersistentDataSourceSetup.java
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// In the code below, note that the current getABoxModel() methods on
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// the OntModelSelectors return a graph with both ABox and TBox data.
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OntModel submodels = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
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readOntologyFilesInPathSet(SUBMODELS, ctx, submodels);
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Model tboxAssertions = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
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// initially putting the results in memory so we have a
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// cheaper way of computing the difference when we copy the ABox
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Model memTboxAssertions = ModelFactory.createDefaultModel();
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getTBoxModel(memModel, submodels, memTboxAssertions);
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tboxAssertions.add(memTboxAssertions);
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Model tboxInferences = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL);
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// initially putting the results in memory so we have a
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// cheaper way of computing the difference when we copy the ABox
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Model memTboxInferences = ModelFactory.createDefaultModel();
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getTBoxModel(inferenceModel, submodels, memTboxInferences);
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tboxInferences.add(memTboxInferences);
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Model aboxAssertions = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_DB_MODEL);
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copyDifference(memModel, memTboxAssertions, aboxAssertions);
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Model aboxInferences = SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_INF_MODEL);
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copyDifference(inferenceModel, memTboxInferences, aboxInferences);
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// Make sure the reasoner takes into account the newly-set-up data.
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SimpleReasonerSetup.setRecomputeRequired(ctx);
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}
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/**
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* Tests whether an SDB store has been formatted for use.
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* @param store
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* @return
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*/
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private boolean isSetUp(Store store) {
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try {
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// a test query to see if the store is formatted
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SDBFactory.connectDefaultModel(store).contains(
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OWL.Thing, RDF.type, OWL.Nothing);
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return true;
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} catch (Exception e) { // unformatted store
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return false;
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}
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}
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}
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@ -105,6 +105,23 @@ public class SimpleReasonerSetup implements ServletContextListener {
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// the simple reasoner will register itself as a listener to the ABox assertions
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SimpleReasoner simpleReasoner = new SimpleReasoner(unionOms.getTBoxModel(), assertionsOms.getABoxModel(), inferencesOms.getABoxModel(), rebuildModel, scratchModel);
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if (isRecomputeRequired(sce.getServletContext())) {
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log.info("ABox inference recompute required");
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int sleeps = 0;
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while (sleeps < 1000 && pelletListener.isReasoning()) {
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if ((sleeps % 30) == 0) {
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log.info("Waiting for initial TBox reasoning to complete");
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}
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Thread.sleep(100);
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sleeps++;
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}
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simpleReasoner.recompute();
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}
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assertionsOms.getTBoxModel().register(new SimpleReasonerTBoxListener(simpleReasoner));
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sce.getServletContext().setAttribute("simpleReasoner",simpleReasoner);
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@ -120,4 +137,15 @@ public class SimpleReasonerSetup implements ServletContextListener {
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// nothing to do
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}
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private static final String RECOMPUTE_REQUIRED_ATTR =
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SimpleReasonerSetup.class.getName() + ".recomputeRequired";
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public static void setRecomputeRequired(ServletContext ctx) {
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ctx.setAttribute(RECOMPUTE_REQUIRED_ATTR, true);
|
||||
}
|
||||
|
||||
private static boolean isRecomputeRequired(ServletContext ctx) {
|
||||
return (ctx.getAttribute(RECOMPUTE_REQUIRED_ATTR) != null);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -39,8 +39,8 @@ SELECT ?geoLocation ?label
|
|||
WHERE
|
||||
{
|
||||
GRAPH ?g {
|
||||
?geoLocation rdf:type core:GeographicLocation .
|
||||
OPTIONAL { ?geoLocation rdfs:label ?label } .
|
||||
?geoLocation rdf:type core:GeographicLocation
|
||||
OPTIONAL { GRAPH ?h { ?geoLocation rdfs:label ?label } }
|
||||
}
|
||||
}
|
||||
LIMIT 20
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue