NIHVIVO-3312 cleanup of WebappDaoFactory
This commit is contained in:
brianjlowe
parent
f093795db1
commit
589f1242c4
8 changed files with 212 additions and 315 deletions
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@ -28,7 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroModelProperties;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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public class VclassEditController extends BaseEditController {
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@ -33,7 +33,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroModelProperties;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
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@ -5,44 +5,22 @@ package edu.cornell.mannlib.vitro.webapp.dao;
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import java.util.HashSet;
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import java.util.Set;
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public class VitroModelProperties {
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public static final int RDF_ABOX_ONLY = 50;
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public static final int RDFS = 100;
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public static final int OWL_FULL = 200;
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public static final int OWL_DL = 202;
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public static final int OWL_LITE = 204;
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public class WebappDaoFactoryConfig {
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private int languageProfile;
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private String[] preferredLanguages;
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private String defaultNamespace;
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private Set<String> nonUserNamespaces;
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public static boolean isOWL(int languageProfile) {
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return ((OWL_FULL <= languageProfile && OWL_LITE >= languageProfile));
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}
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public static boolean isRDFS(int languageProfile) {
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return (languageProfile==100);
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}
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public VitroModelProperties() {
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languageProfile = 200;
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preferredLanguages = new String[1];
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preferredLanguages[0] = null;
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public WebappDaoFactoryConfig() {
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preferredLanguages = new String[3];
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preferredLanguages[0] = "en-US";
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preferredLanguages[1] = "en";
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preferredLanguages[2] = "EN";
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defaultNamespace = "http://vitro.mannlib.cornell.edu/ns/default#";
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nonUserNamespaces = new HashSet<String>();
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nonUserNamespaces.add(VitroVocabulary.vitroURI);
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}
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public int getLanguageProfile() {
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return this.languageProfile;
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}
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public void setLanguageProfile(int languageProfile) {
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this.languageProfile = languageProfile;
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}
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public String[] getPreferredLanguages() {
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return this.preferredLanguages;
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}
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@ -25,11 +25,8 @@ import com.hp.hpl.jena.query.QueryFactory;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.vocabulary.OWL;
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import com.hp.hpl.jena.vocabulary.RDF;
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@ -38,6 +35,7 @@ import com.hp.hpl.jena.vocabulary.RDFS;
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import edu.cornell.mannlib.vitro.webapp.beans.VClass;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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public class JenaModelUtils {
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@ -67,7 +65,10 @@ public class JenaModelUtils {
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SimpleOntModelSelector oms = new SimpleOntModelSelector();
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oms.setTBoxModel(ontModel);
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oms.setApplicationMetadataModel(modelForClassgroups);
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WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena(new SimpleOntModelSelector(ontModel),wadf.getDefaultNamespace(),null,null,null);
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WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
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config.setDefaultNamespace(wadf.getDefaultNamespace());
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WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena(
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new SimpleOntModelSelector(ontModel), config, null);
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OntModel tempModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
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Resource classGroupClass = ResourceFactory.createResource(VitroVocabulary.CLASSGROUP);
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Property inClassGroupProperty = ResourceFactory.createProperty(VitroVocabulary.IN_CLASSGROUP);
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@ -54,6 +54,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
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import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
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@ -72,16 +73,11 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
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protected OntModelSelector ontModelSelector;
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protected String defaultNamespace;
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protected HashSet<String> nonuserNamespaces;
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protected String[] preferredLanguages;
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protected WebappDaoFactoryConfig config;
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protected PelletListener pelletListener;
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protected String userURI;
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protected boolean INCLUDE_TOP_CONCEPT = false;
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protected boolean INCLUDE_BOTTOM_CONCEPT = false;
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private Map<String,String> properties = new HashMap<String,String>();
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@ -91,9 +87,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
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public WebappDaoFactoryJena(WebappDaoFactoryJena base, String userURI) {
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this.ontModelSelector = base.ontModelSelector;
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this.defaultNamespace = base.defaultNamespace;
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this.nonuserNamespaces = base.nonuserNamespaces;
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this.preferredLanguages = base.preferredLanguages;
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this.config = base.config;
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this.userURI = userURI;
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this.dwf = base.dwf;
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}
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@ -101,50 +95,12 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector,
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OntModelSelector baseOntModelSelector,
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OntModelSelector inferenceOntModelSelector,
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String defaultNamespace,
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HashSet<String> nonuserNamespaces,
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String[] preferredLanguages,
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String userURI){
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WebappDaoFactoryConfig config,
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String userURI) {
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this.ontModelSelector = ontModelSelector;
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if (defaultNamespace != null) {
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this.defaultNamespace = defaultNamespace;
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} else {
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initDefaultNamespace();
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}
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if (nonuserNamespaces != null) {
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this.nonuserNamespaces = nonuserNamespaces;
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} else {
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initNonuserNamespaces();
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}
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if (preferredLanguages != null) {
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this.preferredLanguages = preferredLanguages;
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} else {
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initPreferredLanguages();
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}
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this.config = config;
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this.userURI = userURI;
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Model languageUniversalsModel = ModelFactory.createDefaultModel();
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if (INCLUDE_TOP_CONCEPT) {
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Resource top = getTopConcept();
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if (top != null) {
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languageUniversalsModel.add(top, RDF.type,
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this.ontModelSelector.getTBoxModel().getProfile()
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.CLASS());
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}
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}
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if (INCLUDE_BOTTOM_CONCEPT) {
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Resource bottom = getBottomConcept();
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if (bottom != null) {
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languageUniversalsModel.add(bottom, RDF.type,
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this.ontModelSelector.getTBoxModel().getProfile()
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.CLASS());
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}
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}
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if (languageUniversalsModel.size()>0) {
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this.ontModelSelector.getTBoxModel().addSubModel(
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languageUniversalsModel);
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}
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Model assertions = (baseOntModelSelector != null)
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? baseOntModelSelector.getFullModel()
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@ -157,7 +113,46 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
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this.dwf = new StaticDatasetFactory(dataset);
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}
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector,
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WebappDaoFactoryConfig config,
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String userURI) {
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this(ontModelSelector, null, null, config, userURI);
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}
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector,
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WebappDaoFactoryConfig config) {
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this(ontModelSelector, config, null);
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}
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector,
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OntModelSelector baseOntModelSelector,
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OntModelSelector inferenceOntModelSelector,
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WebappDaoFactoryConfig config) {
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this(ontModelSelector,
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baseOntModelSelector,
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inferenceOntModelSelector,
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config,
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null);
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}
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector) {
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this(ontModelSelector, new WebappDaoFactoryConfig(), null);
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}
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public WebappDaoFactoryJena(OntModel ontModel) {
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this(new SimpleOntModelSelector(
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ontModel), new WebappDaoFactoryConfig(), null);
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}
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public OntModelSelector getOntModelSelector() {
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return this.ontModelSelector;
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}
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public OntModel getOntModel() {
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return this.ontModelSelector.getFullModel();
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}
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public static Dataset makeInMemoryDataset(Model assertions,
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Model inferences) {
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DataSource dataset = DatasetFactory.create();
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@ -175,128 +170,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
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dataset.setDefaultModel(union);
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return dataset;
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}
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector,
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String defaultNamespace,
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HashSet<String> nonuserNamespaces,
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String[] preferredLanguages,
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String userURI){
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this(ontModelSelector,
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null,
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null,
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defaultNamespace,
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nonuserNamespaces,
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preferredLanguages,
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userURI);
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}
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector,
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String defaultNamespace,
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HashSet<String> nonuserNamespaces,
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String[] preferredLanguages) {
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this(ontModelSelector,
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defaultNamespace,
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nonuserNamespaces,
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preferredLanguages,
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null);
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}
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector,
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OntModelSelector baseOntModelSelector,
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OntModelSelector inferenceOntModelSelector,
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String defaultNamespace,
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HashSet<String> nonuserNamespaces,
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String[] preferredLanguages){
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this(ontModelSelector,
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baseOntModelSelector,
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inferenceOntModelSelector,
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defaultNamespace,
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nonuserNamespaces,
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preferredLanguages,
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null);
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}
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public WebappDaoFactoryJena(OntModelSelector ontModelSelector) {
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this(ontModelSelector, null, null, null, null, null);
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}
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public WebappDaoFactoryJena(OntModel ontModel,
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String defaultNamespace,
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HashSet<String> nonuserNamespaces,
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String[] preferredLanguages,
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String userURI) {
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this(new SimpleOntModelSelector(ontModel),
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defaultNamespace,
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nonuserNamespaces,
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preferredLanguages,
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userURI);
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}
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public WebappDaoFactoryJena(OntModel ontModel,
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String defaultNamespace,
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HashSet<String> nonuserNamespaces,
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String[] preferredLanguages) {
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this(new SimpleOntModelSelector(ontModel),
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defaultNamespace,
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nonuserNamespaces,
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preferredLanguages,
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null);
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}
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public WebappDaoFactoryJena(OntModel ontModel) {
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this(new SimpleOntModelSelector(
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ontModel), null, null, null, null, null);
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}
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public OntModelSelector getOntModelSelector() {
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return this.ontModelSelector;
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}
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public OntModel getOntModel() {
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return this.ontModelSelector.getFullModel();
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}
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/**
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* Return the current language profile's Top concept as a Jena resource,
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* or null if not applicable. The special case is RDFS, where we use
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* rdfs:Resource as the analog of Top, rather than returning null.
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* @return
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*/
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public Resource getTopConcept() {
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Resource top = null;
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if (this.ontModelSelector.getTBoxModel().getProfile().NAMESPACE()
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.equals(RDFS.getURI())) {
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top = RDFS.Resource;
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} else {
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top = this.ontModelSelector.getTBoxModel().getProfile().THING();
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}
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return top;
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}
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/**
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* Return the current language profile's Bottom concept as a Jena resource,
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* or null if not applicable.
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* @return
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*/
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public Resource getBottomConcept() {
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return this.ontModelSelector.getTBoxModel().getProfile().THING();
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}
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private void initDefaultNamespace() {
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defaultNamespace = "http://vivo.library.cornell.edu/ns/0.1#";
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}
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private void initNonuserNamespaces() {
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nonuserNamespaces = new HashSet<String>();
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nonuserNamespaces.add(VitroVocabulary.vitroURI);
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}
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private void initPreferredLanguages() {
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preferredLanguages = new String[3];
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preferredLanguages[0] = "en-US";
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preferredLanguages[1] = "en";
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preferredLanguages[2] = "EN";
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}
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/* ******************************************** */
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@ -366,15 +239,15 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
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/* **************** accessors ***************** */
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public String getDefaultNamespace() {
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return defaultNamespace;
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return config.getDefaultNamespace();
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}
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public String[] getPreferredLanguages() {
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return this.preferredLanguages;
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return config.getPreferredLanguages();
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}
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public Set<String> getNonuserNamespaces() {
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return nonuserNamespaces;
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return config.getNonUserNamespaces();
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}
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/**
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@ -595,9 +468,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
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//Not sure what this is but will set to equivalence here
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this.ontModelSelector = base.ontModelSelector;
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}
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this.defaultNamespace = base.defaultNamespace;
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this.nonuserNamespaces = base.nonuserNamespaces;
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this.preferredLanguages = base.preferredLanguages;
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this.config = base.config;
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this.userURI = base.userURI;
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this.dwf = base.dwf;
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}
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@ -19,6 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
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import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
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import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
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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.servlet.setup.JenaDataSourceSetupBase;
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public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
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@ -30,7 +31,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
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* For use when any database connection associated with the Dataset
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* is managed externally
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*/
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public WebappDaoFactorySDB(OntModelSelector ontModelSelector, Dataset dataset) {
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public WebappDaoFactorySDB(OntModelSelector ontModelSelector,
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Dataset dataset) {
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super(ontModelSelector);
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this.dwf = new StaticDatasetFactory(dataset);
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}
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@ -41,10 +43,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
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*/
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public WebappDaoFactorySDB(OntModelSelector ontModelSelector,
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Dataset dataset,
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String defaultNamespace,
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HashSet<String> nonuserNamespaces,
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String[] preferredLanguages) {
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super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
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WebappDaoFactoryConfig config) {
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super(ontModelSelector, config);
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this.dwf = new StaticDatasetFactory(dataset);
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}
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@ -55,10 +55,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
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public WebappDaoFactorySDB(OntModelSelector ontModelSelector,
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BasicDataSource bds,
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StoreDesc storeDesc,
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String defaultNamespace,
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HashSet<String> nonuserNamespaces,
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String[] preferredLanguages) {
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super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
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WebappDaoFactoryConfig config) {
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super(ontModelSelector, config);
|
||||
this.dwf = new ReconnectingDatasetFactory(bds, storeDesc);
|
||||
}
|
||||
|
||||
|
|
@ -69,11 +67,9 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
|
|||
public WebappDaoFactorySDB(OntModelSelector ontModelSelector,
|
||||
BasicDataSource bds,
|
||||
StoreDesc storeDesc,
|
||||
String defaultNamespace,
|
||||
HashSet<String> nonuserNamespaces,
|
||||
String[] preferredLanguages,
|
||||
WebappDaoFactoryConfig config,
|
||||
SDBDatasetMode datasetMode) {
|
||||
super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
|
||||
super(ontModelSelector, config);
|
||||
this.dwf = new ReconnectingDatasetFactory(bds, storeDesc);
|
||||
this.datasetMode = datasetMode;
|
||||
}
|
||||
|
|
@ -82,9 +78,7 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
|
|||
public WebappDaoFactorySDB(WebappDaoFactorySDB base, String userURI) {
|
||||
super(base.ontModelSelector);
|
||||
this.ontModelSelector = base.ontModelSelector;
|
||||
this.defaultNamespace = base.defaultNamespace;
|
||||
this.nonuserNamespaces = base.nonuserNamespaces;
|
||||
this.preferredLanguages = base.preferredLanguages;
|
||||
this.config = base.config;
|
||||
this.userURI = userURI;
|
||||
this.dwf = base.dwf;
|
||||
}
|
||||
|
|
@ -125,7 +119,6 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
|
|||
}
|
||||
|
||||
public WebappDaoFactory getUserAwareDaoFactory(String userURI) {
|
||||
// TODO: put the user-aware factories in a hashmap so we don't keep re-creating them
|
||||
return new WebappDaoFactorySDB(this, userURI);
|
||||
}
|
||||
|
||||
|
|
@ -174,7 +167,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
|
|||
private BasicDataSource _bds;
|
||||
private StoreDesc _storeDesc;
|
||||
|
||||
public ReconnectingDatasetFactory(BasicDataSource bds, StoreDesc storeDesc) {
|
||||
public ReconnectingDatasetFactory(BasicDataSource bds,
|
||||
StoreDesc storeDesc) {
|
||||
_bds = bds;
|
||||
_storeDesc = storeDesc;
|
||||
}
|
||||
|
|
@ -187,7 +181,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
|
|||
Dataset dataset = SDBFactory.connectDataset(store);
|
||||
return new DatasetWrapper(dataset, conn);
|
||||
} catch (SQLException sqe) {
|
||||
throw new RuntimeException("Unable to connect to database", sqe);
|
||||
throw new RuntimeException(
|
||||
"Unable to connect to database", sqe);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ import com.hp.hpl.jena.sdb.sql.SDBConnection;
|
|||
|
||||
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
|
||||
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
|
||||
|
|
@ -103,8 +104,9 @@ public class WebappDaoFactorySDBPrep implements Filter {
|
|||
store = SDBFactory.connectStore(conn, storeDesc);
|
||||
dataset = SDBFactory.connectDataset(store);
|
||||
VitroRequest vreq = new VitroRequest((HttpServletRequest) request);
|
||||
wadf =
|
||||
new WebappDaoFactorySDB(oms, dataset, defaultNamespace, null, null);
|
||||
WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
|
||||
config.setDefaultNamespace(defaultNamespace);
|
||||
wadf = new WebappDaoFactorySDB(oms, dataset, config);
|
||||
vreq.setWebappDaoFactory(wadf);
|
||||
vreq.setFullWebappDaoFactory(wadf);
|
||||
vreq.setDataset(dataset);
|
||||
|
|
|
|||
|
|
@ -43,6 +43,7 @@ import com.hp.hpl.jena.vocabulary.RDF;
|
|||
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
|
||||
|
|
@ -54,7 +55,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
|
|||
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
|
||||
|
||||
public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements javax.servlet.ServletContextListener {
|
||||
public class JenaDataSourceSetup extends JenaDataSourceSetupBase
|
||||
implements javax.servlet.ServletContextListener {
|
||||
|
||||
private static final Log log = LogFactory.getLog(JenaDataSourceSetup.class);
|
||||
|
||||
|
|
@ -120,38 +122,57 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
}
|
||||
}
|
||||
|
||||
// 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.
|
||||
// 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.
|
||||
// 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));
|
||||
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));
|
||||
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 time out issues like the
|
||||
// ABox models do (and so don't need the extra step to make them listenable).
|
||||
|
||||
// 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);
|
||||
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");
|
||||
System.out.println(
|
||||
"Copying cached tbox assertions into memory");
|
||||
tboxAssertions.add(tboxAssertionsDB);
|
||||
System.out.println((System.currentTimeMillis()-startTime)/1000+" seconds to load tbox assertions");
|
||||
System.out.println((System.currentTimeMillis() - startTime)
|
||||
/ 1000 + " seconds to load tbox assertions");
|
||||
}
|
||||
|
||||
tboxAssertions.getBaseModel().register(new ModelSynchronizer(tboxAssertionsDB));
|
||||
tboxAssertions.getBaseModel().register(new ModelSynchronizer(
|
||||
tboxAssertionsDB));
|
||||
baseOms.setTBoxModel(tboxAssertions);
|
||||
} catch (Throwable e) {
|
||||
log.error("Unable to load tbox assertion cache from DB", e);
|
||||
|
|
@ -159,56 +180,80 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
|
||||
// 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);
|
||||
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");
|
||||
System.out.println(
|
||||
"Copying cached tbox inferences into memory");
|
||||
tboxInferences.add(tboxInferencesDB);
|
||||
System.out.println((System.currentTimeMillis()-startTime)/1000+" seconds to load tbox inferences");
|
||||
System.out.println((System.currentTimeMillis() - startTime)
|
||||
/ 1000 + " seconds to load tbox inferences");
|
||||
}
|
||||
|
||||
tboxInferences.getBaseModel().register(new ModelSynchronizer(tboxInferencesDB));
|
||||
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()));
|
||||
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()));
|
||||
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);
|
||||
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");
|
||||
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));
|
||||
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)));
|
||||
applicationMetadataModel.add(
|
||||
InitialJenaModelUtils.loadInitialModel(
|
||||
ctx, getDefaultNamespace(ctx)));
|
||||
|
||||
} else if (applicationMetadataModelDB.size() == 0) {
|
||||
repairAppMetadataModel(applicationMetadataModel, aboxAssertions, aboxInferences);
|
||||
repairAppMetadataModel(
|
||||
applicationMetadataModel, aboxAssertions,
|
||||
aboxInferences);
|
||||
}
|
||||
|
||||
baseOms.setApplicationMetadataModel(applicationMetadataModel);
|
||||
inferenceOms.setApplicationMetadataModel(baseOms.getApplicationMetadataModel());
|
||||
unionOms.setApplicationMetadataModel(baseOms.getApplicationMetadataModel());
|
||||
inferenceOms.setApplicationMetadataModel(
|
||||
baseOms.getApplicationMetadataModel());
|
||||
unionOms.setApplicationMetadataModel(
|
||||
baseOms.getApplicationMetadataModel());
|
||||
|
||||
} catch (Throwable e) {
|
||||
log.error("Unable to load application metadata model cache from DB", e);
|
||||
log.error("Unable to load application metadata model cache from DB"
|
||||
, e);
|
||||
}
|
||||
|
||||
checkForNamespaceMismatch( baseOms.getApplicationMetadataModel(), ctx );
|
||||
|
|
@ -220,31 +265,28 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
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()));
|
||||
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,
|
||||
getDefaultNamespace(ctx),
|
||||
null,
|
||||
null,
|
||||
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()));
|
||||
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,
|
||||
getDefaultNamespace(ctx),
|
||||
null,
|
||||
null,
|
||||
inferenceOms, bds, storeDesc, config,
|
||||
WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
|
||||
ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
|
||||
|
||||
|
|
@ -252,23 +294,19 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
DB_ONT_MODEL_SPEC, makeDBModel(
|
||||
bds, WebappDaoFactorySDB.UNION_GRAPH,
|
||||
DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx));
|
||||
//OntModel masterUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
|
||||
// ModelFactory.createUnion(unionABoxModel, unionTBoxModel));
|
||||
unionOms.setFullModel(masterUnion);
|
||||
ctx.setAttribute("jenaOntModel", masterUnion);
|
||||
WebappDaoFactory wadf = new WebappDaoFactorySDB(unionOms, bds, storeDesc, getDefaultNamespace(ctx), null, null);
|
||||
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
|
||||
|
||||
//log.info("Setting up namespace mapper");
|
||||
|
||||
//NamespaceMapper namespaceMapper = new NamespaceMapperJena(masterUnion, masterUnion, defaultNamespace);
|
||||
//ctx.setAttribute("NamespaceMapper", namespaceMapper);
|
||||
//unionOms.getFullModel().getBaseModel().register(namespaceMapper);
|
||||
ModelContext.setUnionOntModelSelector(unionOms, ctx);
|
||||
// assertions and inferences
|
||||
ModelContext.setBaseOntModelSelector(baseOms, ctx);
|
||||
// assertions
|
||||
ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);
|
||||
// inferences
|
||||
|
||||
ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
|
||||
|
||||
|
|
@ -352,7 +390,7 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
}
|
||||
|
||||
|
||||
/* ====================================================================== */
|
||||
/* ===================================================================== */
|
||||
|
||||
|
||||
@Override
|
||||
|
|
@ -360,7 +398,8 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
// Nothing to do.
|
||||
}
|
||||
|
||||
private OntModel ontModelFromContextAttribute(ServletContext ctx, String attribute) {
|
||||
private OntModel ontModelFromContextAttribute(ServletContext ctx,
|
||||
String attribute) {
|
||||
OntModel ontModel;
|
||||
Object attributeValue = ctx.getAttribute(attribute);
|
||||
if (attributeValue != null && attributeValue instanceof OntModel) {
|
||||
|
|
@ -387,7 +426,8 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
}
|
||||
}
|
||||
|
||||
private void loadDataFromFilesystem(OntModelSelector baseOms, ServletContext ctx) {
|
||||
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());
|
||||
|
|
@ -398,7 +438,9 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
+ " seconds to read RDF files ");
|
||||
}
|
||||
|
||||
private static void getTBoxModel(Model fullModel, Model submodels, Model tboxModel) {
|
||||
private static void getTBoxModel(Model fullModel,
|
||||
Model submodels,
|
||||
Model tboxModel) {
|
||||
|
||||
JenaModelUtils modelUtils = new JenaModelUtils();
|
||||
|
||||
|
|
@ -421,7 +463,9 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
/*
|
||||
* 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) {
|
||||
private static void copyDifference(Model model1,
|
||||
Model model2,
|
||||
Model model3) {
|
||||
|
||||
StmtIterator iter = model1.listStatements();
|
||||
|
||||
|
|
@ -502,16 +546,17 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
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.
|
||||
// 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);
|
||||
OntModel submodels = ModelFactory.createOntologyModel(
|
||||
MEM_ONT_MODEL_SPEC);
|
||||
readOntologyFilesInPathSet(SUBMODELS, ctx, submodels);
|
||||
|
||||
Model tboxAssertions = SDBFactory.connectNamedModel(
|
||||
|
|
@ -540,10 +585,12 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
|
||||
// Set up the application metadata model
|
||||
Model applicationMetadataModel = SDBFactory.connectNamedModel(
|
||||
store, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
|
||||
store,
|
||||
JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
|
||||
getAppMetadata(memModel, applicationMetadataModel);
|
||||
log.info("During initial SDB setup, created an application metadata model of size "
|
||||
+ applicationMetadataModel.size());
|
||||
log.info("During initial SDB setup, created an application " +
|
||||
"metadata model of size " +
|
||||
applicationMetadataModel.size());
|
||||
|
||||
// remove application metadata from ABox model
|
||||
aboxAssertions.remove(applicationMetadataModel);
|
||||
|
|
@ -583,7 +630,10 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
|
|||
// even if the store exists, it may be empty
|
||||
|
||||
try {
|
||||
return (SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL)).size() > 0;
|
||||
return (SDBFactory.connectNamedModel(
|
||||
store,
|
||||
JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL))
|
||||
.size() > 0;
|
||||
} catch (Exception e) {
|
||||
return false;
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue