various small fixes
This commit is contained in:
brianjlowe
parent
e375dc33f6
commit
1db72b3397
2 changed files with 62 additions and 48 deletions
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@ -2,7 +2,6 @@
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
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import java.net.URLEncoder;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashSet;
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@ -61,7 +60,7 @@ 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.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
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import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
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public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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@ -148,8 +147,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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labelStr += getLabelForClass(ccls.getOperand(),withPrefix,forPickList);
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} else if (cls.isIntersectionClass()) {
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IntersectionClass icls = cls.as(IntersectionClass.class);
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for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) {
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OntClass operand = (OntClass) operandIt.next();
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for (Iterator<? extends OntClass> operandIt =
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icls.listOperands(); operandIt.hasNext();) {
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OntClass operand = operandIt.next();
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labelStr += getLabelForClass(operand,withPrefix,forPickList);
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if (operandIt.hasNext()) {
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labelStr += " and ";
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@ -157,8 +157,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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}
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} else if (cls.isUnionClass()) {
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UnionClass icls = cls.as(UnionClass.class);
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for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) {
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OntClass operand = (OntClass) operandIt.next();
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for (Iterator<? extends OntClass> operandIt =
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icls.listOperands(); operandIt.hasNext();) {
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OntClass operand = operandIt.next();
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labelStr += getLabelForClass(operand,withPrefix,forPickList);
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if (operandIt.hasNext()) {
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labelStr += " or ";
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@ -170,7 +171,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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// BJL23 2009-02-19
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// I'm putting the link markup in because I need it,
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// but obviously we need to factor this out into the display layer.
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return "<a href=\"vclassEdit?uri="+URLEncoder.encode(getClassURIStr(cls),"UTF-8")+"\">[anonymous class]</a>";
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return "<a href=\"vclassEdit?uri=" +
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URLEncoder.encode(getClassURIStr(cls)) +
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"\">[anonymous class]</a>";
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}
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} else {
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if (withPrefix || forPickList) {
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@ -244,8 +247,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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List<String> uriList = new ArrayList<String>();
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getOntModel().enterCriticalSection(Lock.READ);
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try {
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for (Iterator i = ontClass.listDisjointWith(); i.hasNext(); ) {
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OntClass disjointClass = (OntClass) i.next();
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for (Iterator<? extends OntClass> i =
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ontClass.listDisjointWith(); i.hasNext(); ) {
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OntClass disjointClass = i.next();
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uriList.add(getClassURIStr(disjointClass));
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}
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} catch (ProfileException pe) {
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@ -288,10 +292,11 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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getOntModel().enterCriticalSection(Lock.READ);
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try {
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OntClass ontClass = getOntClass(getOntModel(), classURI);
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ClosableIterator equivalentOntClassIt = ontClass.listEquivalentClasses();
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ClosableIterator<OntClass> equivalentOntClassIt = ontClass.listEquivalentClasses();
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try {
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for (Iterator eqOntClassIt = equivalentOntClassIt; eqOntClassIt.hasNext(); ) {
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OntClass eqClass = (OntClass) eqOntClassIt.next();
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for (Iterator<OntClass> eqOntClassIt =
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equivalentOntClassIt; eqOntClassIt.hasNext(); ) {
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OntClass eqClass = eqOntClassIt.next();
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equivalentClassURIs.add(getClassURIStr(eqClass));
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}
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} finally {
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@ -482,10 +487,6 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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return classes;
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}
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private Iterator<OntClass> smarterListHierarchyRootClasses(OntModel ontModel) {
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return smarterListHierarchyRootClasses(ontModel, null);
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}
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/**
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* The basic idea here is that we ignore anonymous superclasses for the purpose
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* of determining whether something is a root class.
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@ -569,16 +570,21 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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OntModel ontModel = getOntModel();
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ontModel.enterCriticalSection(Lock.READ);
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try {
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Iterator<OntClass> ontClassIt = ontModel.listClasses();
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Iterator<Resource> ontClassIt = ontModel.listResourcesWithProperty(
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RDF.type, OWL.Class);
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while (ontClassIt.hasNext()) {
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OntClass ontClass = ontClassIt.next();
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Resource ontClass = ontClassIt.next();
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if (ontologyURI.equals(ontClass.getNameSpace())) {
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boolean root = true;
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StmtIterator superStmtIt = ontModel.listStatements(ontClass, RDFS.subClassOf, (RDFNode) null);
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StmtIterator superStmtIt = ontModel.listStatements(
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ontClass, RDFS.subClassOf, (RDFNode) null);
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try {
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while (superStmtIt.hasNext()) {
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Statement superStmt = superStmtIt.nextStatement();
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if ( superStmt.getObject().isResource() && ontologyURI.equals(((Resource) superStmt.getObject()).getNameSpace()) ) {
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if ( superStmt.getObject().isResource()
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&& ontologyURI.equals(
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((Resource) superStmt.getObject())
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.getNameSpace()) ) {
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root = false;
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break;
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}
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@ -586,8 +592,10 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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} finally {
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superStmtIt.close();
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}
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if (root) {
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ontologyRootClasses.add(new VClassJena(ontClass,getWebappDaoFactory()));
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if (root && ontClass.canAs(OntClass.class)) {
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ontologyRootClasses.add(new VClassJena(
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(OntClass) ontClass.as(OntClass.class),
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getWebappDaoFactory()));
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}
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}
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}
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@ -598,12 +606,12 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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}
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public List <String> getSubClassURIs(String classURI) {
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List subURIs = new ArrayList();
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List<String> subURIs = new ArrayList<String>();
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OntClass superClass = getOntClass(getOntModel(),classURI);
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try {
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Iterator subIt = superClass.listSubClasses(true);
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Iterator<OntClass> subIt = superClass.listSubClasses(true);
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while (subIt.hasNext()) {
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OntClass cls = (OntClass) subIt.next();
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OntClass cls = subIt.next();
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subURIs.add(getClassURIStr(cls));
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}
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} catch (Exception e) {
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@ -617,10 +625,10 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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}
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public List <String> getSuperClassURIs(String classURI, boolean direct) {
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List supURIs = new ArrayList();
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List<String> supURIs = new ArrayList<String>();
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OntClass subClass = getOntClass(getOntModel(), classURI);
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try {
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Iterator supIt = subClass.listSuperClasses(direct);
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Iterator<OntClass> supIt = subClass.listSuperClasses(direct);
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while (supIt.hasNext()) {
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OntClass cls = (OntClass) supIt.next();
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supURIs.add(getClassURIStr(cls));
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@ -717,12 +725,16 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
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OntResource superclass = null;
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if (vclassURI != null) {
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// TODO need a getAllSuperPropertyURIs method in ObjectPropertyDao
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List<String> superproperties = getWebappDaoFactory().getObjectPropertyDao().getSuperPropertyURIs(propertyURI,false);
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List<String> superproperties = getWebappDaoFactory()
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.getObjectPropertyDao()
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.getSuperPropertyURIs(propertyURI, false);
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superproperties.add(propertyURI);
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HashSet<String> subjSuperclasses = new HashSet<String>(getAllSuperClassURIs(vclassURI));
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HashSet<String> subjSuperclasses = new HashSet<String>(
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getAllSuperClassURIs(vclassURI));
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subjSuperclasses.add(vclassURI);
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for (String objectPropertyURI : superproperties) {
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for (Iterator restStmtIt = getOntModel().listStatements(null,OWL.onProperty,getOntModel().getProperty(objectPropertyURI)); restStmtIt.hasNext();) {
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for (Iterator restStmtIt = getOntModel().listStatements(
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null,OWL.onProperty,getOntModel().getProperty(objectPropertyURI)); restStmtIt.hasNext();) {
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Statement restStmt = (Statement) restStmtIt.next();
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Resource restRes = restStmt.getSubject();
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for (Iterator axStmtIt = getOntModel().listStatements(null,null,restRes); axStmtIt.hasNext();) {
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@ -138,23 +138,25 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
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boolean requiredUpdate = ontologyUpdater.updateRequired(ctx);
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try {
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ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
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log.info("Data migration required");
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migrationChangesMade = ontologyUpdater.update(ctx);
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if (tryMigrateDisplay) {
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try {
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migrateDisplayModel(settings);
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log.info("Migrated display model");
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} catch (Exception e) {
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log.warn("unable to successfully update display model: " + e.getMessage());
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}
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}
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// reload the display model since the TBoxUpdater may have
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// modified it
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new ApplicationModelSetup().contextInitialized(sce);
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} catch (Exception ioe) {
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ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
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if(!JenaDataSourceSetupBase.isFirstStartup()) {
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try {
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ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
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log.info("Data migration required");
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migrationChangesMade = ontologyUpdater.update(ctx);
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if (tryMigrateDisplay) {
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try {
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migrateDisplayModel(settings);
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log.info("Migrated display model");
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} catch (Exception e) {
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log.warn("unable to successfully update display model: " + e.getMessage());
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}
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}
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// reload the display model since the TBoxUpdater may have
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// modified it
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new ApplicationModelSetup().contextInitialized(sce);
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} catch (Exception ioe) {
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ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
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}
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}
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SimpleReasoner simpleReasoner = (SimpleReasoner) sce.getServletContext()
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