diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
index 1d168eb63..67dc61ea4 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
@@ -2,7 +2,6 @@
package edu.cornell.mannlib.vitro.webapp.dao.jena;
-import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
@@ -61,7 +60,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
+import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
public class VClassDaoJena extends JenaBaseDao implements VClassDao {
@@ -148,8 +147,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
labelStr += getLabelForClass(ccls.getOperand(),withPrefix,forPickList);
} else if (cls.isIntersectionClass()) {
IntersectionClass icls = cls.as(IntersectionClass.class);
- for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) {
- OntClass operand = (OntClass) operandIt.next();
+ for (Iterator operandIt =
+ icls.listOperands(); operandIt.hasNext();) {
+ OntClass operand = operandIt.next();
labelStr += getLabelForClass(operand,withPrefix,forPickList);
if (operandIt.hasNext()) {
labelStr += " and ";
@@ -157,8 +157,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
}
} else if (cls.isUnionClass()) {
UnionClass icls = cls.as(UnionClass.class);
- for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) {
- OntClass operand = (OntClass) operandIt.next();
+ for (Iterator operandIt =
+ icls.listOperands(); operandIt.hasNext();) {
+ OntClass operand = operandIt.next();
labelStr += getLabelForClass(operand,withPrefix,forPickList);
if (operandIt.hasNext()) {
labelStr += " or ";
@@ -170,7 +171,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
// BJL23 2009-02-19
// I'm putting the link markup in because I need it,
// but obviously we need to factor this out into the display layer.
- return "[anonymous class]";
+ return "[anonymous class]";
}
} else {
if (withPrefix || forPickList) {
@@ -244,8 +247,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
List uriList = new ArrayList();
getOntModel().enterCriticalSection(Lock.READ);
try {
- for (Iterator i = ontClass.listDisjointWith(); i.hasNext(); ) {
- OntClass disjointClass = (OntClass) i.next();
+ for (Iterator i =
+ ontClass.listDisjointWith(); i.hasNext(); ) {
+ OntClass disjointClass = i.next();
uriList.add(getClassURIStr(disjointClass));
}
} catch (ProfileException pe) {
@@ -288,10 +292,11 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
getOntModel().enterCriticalSection(Lock.READ);
try {
OntClass ontClass = getOntClass(getOntModel(), classURI);
- ClosableIterator equivalentOntClassIt = ontClass.listEquivalentClasses();
+ ClosableIterator equivalentOntClassIt = ontClass.listEquivalentClasses();
try {
- for (Iterator eqOntClassIt = equivalentOntClassIt; eqOntClassIt.hasNext(); ) {
- OntClass eqClass = (OntClass) eqOntClassIt.next();
+ for (Iterator eqOntClassIt =
+ equivalentOntClassIt; eqOntClassIt.hasNext(); ) {
+ OntClass eqClass = eqOntClassIt.next();
equivalentClassURIs.add(getClassURIStr(eqClass));
}
} finally {
@@ -482,10 +487,6 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
return classes;
}
- private Iterator smarterListHierarchyRootClasses(OntModel ontModel) {
- return smarterListHierarchyRootClasses(ontModel, null);
- }
-
/**
* The basic idea here is that we ignore anonymous superclasses for the purpose
* of determining whether something is a root class.
@@ -569,16 +570,21 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
OntModel ontModel = getOntModel();
ontModel.enterCriticalSection(Lock.READ);
try {
- Iterator ontClassIt = ontModel.listClasses();
+ Iterator ontClassIt = ontModel.listResourcesWithProperty(
+ RDF.type, OWL.Class);
while (ontClassIt.hasNext()) {
- OntClass ontClass = ontClassIt.next();
+ Resource ontClass = ontClassIt.next();
if (ontologyURI.equals(ontClass.getNameSpace())) {
boolean root = true;
- StmtIterator superStmtIt = ontModel.listStatements(ontClass, RDFS.subClassOf, (RDFNode) null);
+ StmtIterator superStmtIt = ontModel.listStatements(
+ ontClass, RDFS.subClassOf, (RDFNode) null);
try {
while (superStmtIt.hasNext()) {
Statement superStmt = superStmtIt.nextStatement();
- if ( superStmt.getObject().isResource() && ontologyURI.equals(((Resource) superStmt.getObject()).getNameSpace()) ) {
+ if ( superStmt.getObject().isResource()
+ && ontologyURI.equals(
+ ((Resource) superStmt.getObject())
+ .getNameSpace()) ) {
root = false;
break;
}
@@ -586,8 +592,10 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
} finally {
superStmtIt.close();
}
- if (root) {
- ontologyRootClasses.add(new VClassJena(ontClass,getWebappDaoFactory()));
+ if (root && ontClass.canAs(OntClass.class)) {
+ ontologyRootClasses.add(new VClassJena(
+ (OntClass) ontClass.as(OntClass.class),
+ getWebappDaoFactory()));
}
}
}
@@ -598,12 +606,12 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
}
public List getSubClassURIs(String classURI) {
- List subURIs = new ArrayList();
+ List subURIs = new ArrayList();
OntClass superClass = getOntClass(getOntModel(),classURI);
try {
- Iterator subIt = superClass.listSubClasses(true);
+ Iterator subIt = superClass.listSubClasses(true);
while (subIt.hasNext()) {
- OntClass cls = (OntClass) subIt.next();
+ OntClass cls = subIt.next();
subURIs.add(getClassURIStr(cls));
}
} catch (Exception e) {
@@ -617,10 +625,10 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
}
public List getSuperClassURIs(String classURI, boolean direct) {
- List supURIs = new ArrayList();
+ List supURIs = new ArrayList();
OntClass subClass = getOntClass(getOntModel(), classURI);
try {
- Iterator supIt = subClass.listSuperClasses(direct);
+ Iterator supIt = subClass.listSuperClasses(direct);
while (supIt.hasNext()) {
OntClass cls = (OntClass) supIt.next();
supURIs.add(getClassURIStr(cls));
@@ -717,12 +725,16 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
OntResource superclass = null;
if (vclassURI != null) {
// TODO need a getAllSuperPropertyURIs method in ObjectPropertyDao
- List superproperties = getWebappDaoFactory().getObjectPropertyDao().getSuperPropertyURIs(propertyURI,false);
+ List superproperties = getWebappDaoFactory()
+ .getObjectPropertyDao()
+ .getSuperPropertyURIs(propertyURI, false);
superproperties.add(propertyURI);
- HashSet subjSuperclasses = new HashSet(getAllSuperClassURIs(vclassURI));
+ HashSet subjSuperclasses = new HashSet(
+ getAllSuperClassURIs(vclassURI));
subjSuperclasses.add(vclassURI);
for (String objectPropertyURI : superproperties) {
- for (Iterator restStmtIt = getOntModel().listStatements(null,OWL.onProperty,getOntModel().getProperty(objectPropertyURI)); restStmtIt.hasNext();) {
+ for (Iterator restStmtIt = getOntModel().listStatements(
+ null,OWL.onProperty,getOntModel().getProperty(objectPropertyURI)); restStmtIt.hasNext();) {
Statement restStmt = (Statement) restStmtIt.next();
Resource restRes = restStmt.getSubject();
for (Iterator axStmtIt = getOntModel().listStatements(null,null,restRes); axStmtIt.hasNext();) {
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
index d02bbeceb..d68ca6433 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
@@ -138,24 +138,26 @@ public class UpdateKnowledgeBase implements ServletContextListener {
KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
boolean requiredUpdate = ontologyUpdater.updateRequired(ctx);
- try {
- ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
- log.info("Data migration required");
- migrationChangesMade = ontologyUpdater.update(ctx);
- if (tryMigrateDisplay) {
- try {
- migrateDisplayModel(settings);
- log.info("Migrated display model");
- } catch (Exception e) {
- log.warn("unable to successfully update display model: " + e.getMessage());
- }
- }
- // reload the display model since the TBoxUpdater may have
- // modified it
- new ApplicationModelSetup().contextInitialized(sce);
- } catch (Exception ioe) {
- ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
- }
+ if(!JenaDataSourceSetupBase.isFirstStartup()) {
+ try {
+ ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
+ log.info("Data migration required");
+ migrationChangesMade = ontologyUpdater.update(ctx);
+ if (tryMigrateDisplay) {
+ try {
+ migrateDisplayModel(settings);
+ log.info("Migrated display model");
+ } catch (Exception e) {
+ log.warn("unable to successfully update display model: " + e.getMessage());
+ }
+ }
+ // reload the display model since the TBoxUpdater may have
+ // modified it
+ new ApplicationModelSetup().contextInitialized(sce);
+ } catch (Exception ioe) {
+ ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
+ }
+ }
SimpleReasoner simpleReasoner = (SimpleReasoner) sce.getServletContext()
.getAttribute(SimpleReasoner.class.getName());