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Cleanup: remove unused imports and unneeded casts.

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This commit is contained in:
j2blake 2013-05-07 13:27:44 -04:00
parent bb2ceaeea3
commit c7b104ca40
39 changed files with 113 additions and 241 deletions
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23
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java
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@ -8,7 +8,6 @@ import java.util.Collection;
import java.util.Collections; import java.util.Collections;
import java.util.Comparator; import java.util.Comparator;
import java.util.HashMap; import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
@ -24,7 +23,6 @@ import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.ontology.OntResource; import com.hp.hpl.jena.ontology.OntResource;
import com.hp.hpl.jena.ontology.ProfileException; import com.hp.hpl.jena.ontology.ProfileException;
import com.hp.hpl.jena.ontology.Restriction; import com.hp.hpl.jena.ontology.Restriction;
import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
import com.hp.hpl.jena.query.Query; import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution; import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory; import com.hp.hpl.jena.query.QueryExecutionFactory;
@ -53,7 +51,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao; import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.InsertException; import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao; 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.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent; 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.dao.jena.pellet.PelletListener;
@ -93,7 +90,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
try { try {
com.hp.hpl.jena.ontology.OntResource ind = ontModel.getOntResource(dataPropertyURI); com.hp.hpl.jena.ontology.OntResource ind = ontModel.getOntResource(dataPropertyURI);
if( ind != null ){ if( ind != null ){
ontModel.add(ind,(Property)DATAPROPERTY_ISEXTERNALID, "TRUE"); ontModel.add(ind, DATAPROPERTY_ISEXTERNALID, "TRUE");
return true; return true;
}else{ }else{
return false; return false;
@ -114,7 +111,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
while(restIt.hasNext()) { while(restIt.hasNext()) {
Resource restRes = restIt.next(); Resource restRes = restIt.next();
if (restRes.canAs(OntResource.class)) { if (restRes.canAs(OntResource.class)) {
OntResource restOntRes = (OntResource) restRes.as(OntResource.class); OntResource restOntRes = restRes.as(OntResource.class);
smartRemove(restOntRes, ontModel); smartRemove(restOntRes, ontModel);
} }
} }
@ -181,7 +178,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
dp.setNamespace(op.getNameSpace()); dp.setNamespace(op.getNameSpace());
dp.setLocalName(op.getLocalName()); dp.setLocalName(op.getLocalName());
OntologyDao oDao=getWebappDaoFactory().getOntologyDao(); OntologyDao oDao=getWebappDaoFactory().getOntologyDao();
Ontology o = (Ontology)oDao.getOntologyByURI(dp.getNamespace()); Ontology o = oDao.getOntologyByURI(dp.getNamespace());
if (o==null) { if (o==null) {
if (!VitroVocabulary.vitroURI.equals(dp.getNamespace())) { if (!VitroVocabulary.vitroURI.equals(dp.getNamespace())) {
log.debug("datapropFromOntProperty(): no ontology object found for the namespace "+dp.getNamespace()); log.debug("datapropFromOntProperty(): no ontology object found for the namespace "+dp.getNamespace());
@ -206,8 +203,8 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
dp.setExample(getPropertyStringValue(op,EXAMPLE_ANNOT)); dp.setExample(getPropertyStringValue(op,EXAMPLE_ANNOT));
dp.setDescription(getPropertyStringValue(op,DESCRIPTION_ANNOT)); dp.setDescription(getPropertyStringValue(op,DESCRIPTION_ANNOT));
dp.setPublicDescription(getPropertyStringValue(op,PUBLIC_DESCRIPTION_ANNOT)); dp.setPublicDescription(getPropertyStringValue(op,PUBLIC_DESCRIPTION_ANNOT));
dp.setDisplayTier(((WebappDaoFactoryJena)getWebappDaoFactory()).getJenaBaseDao().getPropertyNonNegativeIntValue(op, DISPLAY_RANK_ANNOT)); dp.setDisplayTier((getWebappDaoFactory()).getJenaBaseDao().getPropertyNonNegativeIntValue(op, DISPLAY_RANK_ANNOT));
dp.setDisplayLimit(((WebappDaoFactoryJena)getWebappDaoFactory()).getJenaBaseDao().getPropertyNonNegativeIntValue(op, DISPLAY_LIMIT)); dp.setDisplayLimit((getWebappDaoFactory()).getJenaBaseDao().getPropertyNonNegativeIntValue(op, DISPLAY_LIMIT));
//There might be multiple HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT properties, only use the highest //There might be multiple HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT properties, only use the highest
StmtIterator it = op.listProperties(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT); StmtIterator it = op.listProperties(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT);
@ -216,7 +213,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
Statement stmt = it.nextStatement(); Statement stmt = it.nextStatement();
RDFNode obj; RDFNode obj;
if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){ if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){
Resource res = (Resource)obj.as(Resource.class); Resource res = obj.as(Resource.class);
if( res != null && res.getURI() != null ){ if( res != null && res.getURI() != null ){
BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI()); BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI());
if( roleFromModel != null && if( roleFromModel != null &&
@ -235,7 +232,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
Statement stmt = it.nextStatement(); Statement stmt = it.nextStatement();
RDFNode obj; RDFNode obj;
if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){ if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){
Resource res = (Resource)obj.as(Resource.class); Resource res = obj.as(Resource.class);
if( res != null && res.getURI() != null ){ if( res != null && res.getURI() != null ){
BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI()); BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI());
if( roleFromModel != null && if( roleFromModel != null &&
@ -365,7 +362,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
while (restIt.hasNext()) { while (restIt.hasNext()) {
Resource restRes = restIt.next(); Resource restRes = restIt.next();
if (restRes.canAs(Restriction.class)) { if (restRes.canAs(Restriction.class)) {
Restriction rest = (Restriction) restRes.as(Restriction.class); Restriction rest = restRes.as(Restriction.class);
if (rest.isAllValuesFromRestriction()) { if (rest.isAllValuesFromRestriction()) {
AllValuesFromRestriction avfrest = rest.asAllValuesFromRestriction(); AllValuesFromRestriction avfrest = rest.asAllValuesFromRestriction();
if (avfrest.getAllValuesFrom() != null) { if (avfrest.getAllValuesFrom() != null) {
@ -485,7 +482,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
} }
com.hp.hpl.jena.ontology.DatatypeProperty jDataprop = ontModel.createDatatypeProperty(dtp.getURI()); com.hp.hpl.jena.ontology.DatatypeProperty jDataprop = ontModel.createDatatypeProperty(dtp.getURI());
if (dtp.getPublicName() != null && dtp.getPublicName().length() > 0) { if (dtp.getPublicName() != null && dtp.getPublicName().length() > 0) {
jDataprop.setLabel(dtp.getPublicName(), (String) getDefaultLanguage()); jDataprop.setLabel(dtp.getPublicName(), getDefaultLanguage());
} else { } else {
jDataprop.removeAll(RDFS.label); jDataprop.removeAll(RDFS.label);
} }
@ -609,7 +606,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
while (parentNodeIt.hasNext()) { while (parentNodeIt.hasNext()) {
RDFNode parentNode = parentNodeIt.next(); RDFNode parentNode = parentNodeIt.next();
if (parentNode.canAs(Property.class)) { if (parentNode.canAs(Property.class)) {
parentList.add((Property) parentNode.as(Property.class)); parentList.add(parentNode.as(Property.class));
} }
} }
if (parentList.size()==0) { if (parentList.size()==0) {

13
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyStatementDaoJena.java
View file

@ -10,6 +10,9 @@ import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Set; import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.datatypes.TypeMapper; import com.hp.hpl.jena.datatypes.TypeMapper;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntResource; import com.hp.hpl.jena.ontology.OntResource;
@ -27,7 +30,6 @@ import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property; import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory; import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.rdf.model.Statement;
@ -40,14 +42,9 @@ import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement; import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl; import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
import edu.cornell.mannlib.vitro.webapp.beans.Individual; import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.edit.ReorderController;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao; import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary; import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualUpdateEvent; import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualUpdateEvent;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ObjectPropertyStatementDaoJena;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPropertyStatementDao public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPropertyStatementDao
{ {
@ -114,7 +111,7 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
StmtIterator stmtIt = ind.listProperties(); StmtIterator stmtIt = ind.listProperties();
while( stmtIt.hasNext() ) while( stmtIt.hasNext() )
{ {
Statement st = (Statement)stmtIt.next(); Statement st = stmtIt.next();
boolean addToList = /*allowAnyNameSpace ? st.getObject().canAs(Literal.class) :*/ st.getObject().isLiteral() && boolean addToList = /*allowAnyNameSpace ? st.getObject().canAs(Literal.class) :*/ st.getObject().isLiteral() &&
( (
(RDF.value.equals(st.getPredicate()) || VitroVocabulary.value.equals(st.getPredicate().getURI())) (RDF.value.equals(st.getPredicate()) || VitroVocabulary.value.equals(st.getPredicate().getURI()))
@ -210,7 +207,7 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
// do something annoying if we are dealing with a blank node // do something annoying if we are dealing with a blank node
try { try {
getOntModel().enterCriticalSection(Lock.READ); getOntModel().enterCriticalSection(Lock.READ);
OntResource ontRes = (OntResource) getOntModel().createResource( OntResource ontRes = getOntModel().createResource(
new AnonId(entity.getLocalName())).as(OntResource.class); new AnonId(entity.getLocalName())).as(OntResource.class);
if (ontRes == null) { if (ontRes == null) {
return edList; return edList;

8
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyStatementDaoSDB.java
View file

@ -3,7 +3,6 @@
package edu.cornell.mannlib.vitro.webapp.dao.jena; package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collection;
import java.util.List; import java.util.List;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
@ -12,20 +11,15 @@ import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.QueryExecution; import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory; import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory; import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.QuerySolutionMap;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal; import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator; import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.vocabulary.RDF; import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement; import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl; import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
import edu.cornell.mannlib.vitro.webapp.beans.Individual; import edu.cornell.mannlib.vitro.webapp.beans.Individual;
@ -85,7 +79,7 @@ public class DataPropertyStatementDaoSDB extends DataPropertyStatementDaoJena
StmtIterator stmtIt = ind.listProperties(); StmtIterator stmtIt = ind.listProperties();
while( stmtIt.hasNext() ) while( stmtIt.hasNext() )
{ {
Statement st = (Statement)stmtIt.next(); Statement st = stmtIt.next();
boolean addToList = /*allowAnyNameSpace ? st.getObject().canAs(Literal.class) :*/ st.getObject().isLiteral() && boolean addToList = /*allowAnyNameSpace ? st.getObject().canAs(Literal.class) :*/ st.getObject().isLiteral() &&
( (
(RDF.value.equals(st.getPredicate()) || VitroVocabulary.value.equals(st.getPredicate().getURI())) (RDF.value.equals(st.getPredicate()) || VitroVocabulary.value.equals(st.getPredicate().getURI()))

4
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DatatypeDaoJena.java
View file

@ -4,14 +4,10 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap; import java.util.HashMap;
import java.util.HashSet;
import java.util.List; import java.util.List;
import com.hp.hpl.jena.ontology.OntModel;
import edu.cornell.mannlib.vitro.webapp.beans.Datatype; import edu.cornell.mannlib.vitro.webapp.beans.Datatype;
import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao; import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
public class DatatypeDaoJena extends JenaBaseDao implements DatatypeDao { public class DatatypeDaoJena extends JenaBaseDao implements DatatypeDao {

6
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DependentResourceDeleteJena.java
View file

@ -9,7 +9,6 @@ import java.util.List;
import java.util.ListIterator; import java.util.ListIterator;
import java.util.Set; import java.util.Set;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property; import com.hp.hpl.jena.rdf.model.Property;
@ -89,14 +88,13 @@ public class DependentResourceDeleteJena {
* Find all statements where for a given statement in the assertions, * Find all statements where for a given statement in the assertions,
* there is at least one statement in the retractions that has * there is at least one statement in the retractions that has
* the same predicate and object. */ * the same predicate and object. */
@SuppressWarnings("unchecked")
private static List<Statement> getChangedStmts(Model assertions, Model retractions){ private static List<Statement> getChangedStmts(Model assertions, Model retractions){
List<Statement> changedStmts = new LinkedList<Statement>(); List<Statement> changedStmts = new LinkedList<Statement>();
StmtIterator it = assertions.listStatements(); StmtIterator it = assertions.listStatements();
while(it.hasNext()){ while(it.hasNext()){
Statement assertionStmtStatement = it.nextStatement(); Statement assertionStmtStatement = it.nextStatement();
if( assertionStmtStatement.getObject().canAs( Resource.class )){ if( assertionStmtStatement.getObject().canAs( Resource.class )){
Resource asserObj = (Resource) assertionStmtStatement.getObject().as(Resource.class); Resource asserObj = assertionStmtStatement.getObject().as(Resource.class);
StmtIterator retractionStmts = StmtIterator retractionStmts =
retractions.listStatements( retractions.listStatements(
(Resource)null, (Resource)null,
@ -138,7 +136,7 @@ public class DependentResourceDeleteJena {
if( ( obj.canAs(Resource.class) && isPredicateDependencyRelation(stmt.getPredicate(), model) ) if( ( obj.canAs(Resource.class) && isPredicateDependencyRelation(stmt.getPredicate(), model) )
|| ( obj.isAnon() && perviousWasDependentResource ) ){ || ( obj.isAnon() && perviousWasDependentResource ) ){
Resource res = (Resource)obj.as(Resource.class); Resource res = obj.as(Resource.class);
String id = res.isAnon()?res.getId().toString():res.getURI(); String id = res.isAnon()?res.getId().toString():res.getURI();
if( !visitedUris.contains(id) ){ if( !visitedUris.contains(id) ){

3
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DisplayModelDaoJena.java
View file

@ -7,9 +7,7 @@ import java.io.File;
import java.io.FileInputStream; import java.io.FileInputStream;
import java.io.FileOutputStream; import java.io.FileOutputStream;
import java.io.FileReader; import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream;
import java.io.StringReader; import java.io.StringReader;
import java.nio.channels.FileChannel; import java.nio.channels.FileChannel;
@ -22,7 +20,6 @@ import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory; import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.util.FileManager;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayModelDao; import edu.cornell.mannlib.vitro.webapp.dao.DisplayModelDao;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary; import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;

1
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/EmptyReifier.java
View file

@ -2,7 +2,6 @@
package edu.cornell.mannlib.vitro.webapp.dao.jena; package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import org.apache.commons.collections.iterators.EmptyIterator; import org.apache.commons.collections.iterators.EmptyIterator;

20
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoJena.java
View file

@ -146,7 +146,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
if (theClass.isAnon() && theClass.canAs(UnionClass.class)) { if (theClass.isAnon() && theClass.canAs(UnionClass.class)) {
UnionClass u = (UnionClass) theClass.as(UnionClass.class); UnionClass u = theClass.as(UnionClass.class);
for (OntClass operand : u.listOperands().toList()) { for (OntClass operand : u.listOperands().toList()) {
VClass vc = new VClassJena(operand, getWebappDaoFactory()); VClass vc = new VClassJena(operand, getWebappDaoFactory());
ents.addAll(getIndividualsByVClass(vc)); ents.addAll(getIndividualsByVClass(vc));
@ -159,8 +159,8 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
try { try {
while (stmtIt.hasNext()) { while (stmtIt.hasNext()) {
Statement stmt = stmtIt.nextStatement(); Statement stmt = stmtIt.nextStatement();
OntResource ind = (OntResource) stmt.getSubject().as(OntResource.class); OntResource ind = stmt.getSubject().as(OntResource.class);
ents.add(new IndividualJena(ind, (WebappDaoFactoryJena) getWebappDaoFactory())); ents.add(new IndividualJena(ind, getWebappDaoFactory()));
} }
} finally { } finally {
stmtIt.close(); stmtIt.close();
@ -232,7 +232,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
ontModel.getBaseModel().notifyEvent(new IndividualCreationEvent(getWebappDaoFactory().getUserURI(),true,entURI)); ontModel.getBaseModel().notifyEvent(new IndividualCreationEvent(getWebappDaoFactory().getUserURI(),true,entURI));
com.hp.hpl.jena.ontology.Individual ind = ontModel.createIndividual(entURI,cls); com.hp.hpl.jena.ontology.Individual ind = ontModel.createIndividual(entURI,cls);
if (ent.getName() != null) { if (ent.getName() != null) {
ind.setLabel(ent.getName(), (String) getDefaultLanguage()); ind.setLabel(ent.getName(), getDefaultLanguage());
} }
List<VClass> vclasses = ent.getVClasses(false); List<VClass> vclasses = ent.getVClasses(false);
if (vclasses != null) { if (vclasses != null) {
@ -388,7 +388,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
return 1; return 1;
} }
if (res.canAs(OntResource.class)) { if (res.canAs(OntResource.class)) {
OntResource ontRes = (OntResource) res.as(OntResource.class); OntResource ontRes = res.as(OntResource.class);
smartRemove(ontRes, ontModel); smartRemove(ontRes, ontModel);
} else { } else {
ontModel.removeAll(res,null,null); ontModel.removeAll(res,null,null);
@ -420,7 +420,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
OntResource ontRes = (entityURI.startsWith(VitroVocabulary.PSEUDO_BNODE_NS)) OntResource ontRes = (entityURI.startsWith(VitroVocabulary.PSEUDO_BNODE_NS))
? (OntResource) ontModel.createResource(new AnonId(entityURI.substring(VitroVocabulary.PSEUDO_BNODE_NS.length()))).as(OntResource.class) ? (OntResource) ontModel.createResource(new AnonId(entityURI.substring(VitroVocabulary.PSEUDO_BNODE_NS.length()))).as(OntResource.class)
: ontModel.getOntResource(entityURI); : ontModel.getOntResource(entityURI);
Individual ent = new IndividualJena(ontRes, (WebappDaoFactoryJena) getWebappDaoFactory()); Individual ent = new IndividualJena(ontRes, getWebappDaoFactory());
return ent; return ent;
} catch (Exception ex) { } catch (Exception ex) {
return null; return null;
@ -494,7 +494,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
String subUri = ((Resource)sub).getURI(); String subUri = ((Resource)sub).getURI();
if( ! individualsMap.containsKey(subUri)){ if( ! individualsMap.containsKey(subUri)){
com.hp.hpl.jena.ontology.Individual ind = getOntModel().getIndividual(subUri); com.hp.hpl.jena.ontology.Individual ind = getOntModel().getIndividual(subUri);
individualsMap.put(subUri,new IndividualJena(ind, (WebappDaoFactoryJena) getWebappDaoFactory())); individualsMap.put(subUri,new IndividualJena(ind, getWebappDaoFactory()));
} }
} }
@ -519,7 +519,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
String subUri = ((Resource)sub).getURI(); String subUri = ((Resource)sub).getURI();
if( ! individualsMap.containsKey(subUri)){ if( ! individualsMap.containsKey(subUri)){
com.hp.hpl.jena.ontology.Individual ind = getOntModel().getIndividual(subUri); com.hp.hpl.jena.ontology.Individual ind = getOntModel().getIndividual(subUri);
individualsMap.put(subUri,new IndividualJena(ind, (WebappDaoFactoryJena) getWebappDaoFactory())); individualsMap.put(subUri,new IndividualJena(ind, getWebappDaoFactory()));
} }
} }
@ -544,7 +544,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
String subUri = ((Resource)sub).getURI(); String subUri = ((Resource)sub).getURI();
if( ! individualsMap.containsKey(subUri)){ if( ! individualsMap.containsKey(subUri)){
com.hp.hpl.jena.ontology.Individual ind = getOntModel().getIndividual(subUri); com.hp.hpl.jena.ontology.Individual ind = getOntModel().getIndividual(subUri);
individualsMap.put(subUri,new IndividualJena(ind, (WebappDaoFactoryJena) getWebappDaoFactory())); individualsMap.put(subUri,new IndividualJena(ind, getWebappDaoFactory()));
} }
} }
} finally { } finally {
@ -594,7 +594,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
continue; continue;
} }
com.hp.hpl.jena.ontology.Individual ind = getOntModel().getIndividual(st.getURI()); com.hp.hpl.jena.ontology.Individual ind = getOntModel().getIndividual(st.getURI());
inds.add(new IndividualJena(ind, (WebappDaoFactoryJena) getWebappDaoFactory())); inds.add(new IndividualJena(ind, getWebappDaoFactory()));
} }
} finally { } finally {
if( stmts != null ) stmts.close(); if( stmts != null ) stmts.close();

4
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoSDB.java
View file

@ -106,7 +106,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
: ResourceFactory.createResource(vclassURI); : ResourceFactory.createResource(vclassURI);
if (theClass.isAnon() && theClass.canAs(UnionClass.class)) { if (theClass.isAnon() && theClass.canAs(UnionClass.class)) {
UnionClass u = (UnionClass) theClass.as(UnionClass.class); UnionClass u = theClass.as(UnionClass.class);
for (OntClass operand : u.listOperands().toList()) { for (OntClass operand : u.listOperands().toList()) {
VClass vc = new VClassJena(operand, getWebappDaoFactory()); VClass vc = new VClassJena(operand, getWebappDaoFactory());
ents.addAll(getIndividualsByVClass(vc)); ents.addAll(getIndividualsByVClass(vc));
@ -523,7 +523,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
try { try {
ResultSet results = qe.execSelect(); ResultSet results = qe.execSelect();
while (results.hasNext()) { while (results.hasNext()) {
QuerySolution qs = (QuerySolution) results.next(); QuerySolution qs = results.next();
Resource res = (Resource) qs.get("?ent"); Resource res = (Resource) qs.get("?ent");
if (res.getURI() != null) { if (res.getURI() != null) {
individualURIs.add(res.getURI()); individualURIs.add(res.getURI());

14
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualJena.java
View file

@ -254,8 +254,8 @@ public class IndividualJena extends IndividualImpl implements Individual {
if (!s.getSubject().canAs(OntResource.class) || !s.getObject().canAs(OntResource.class)) { if (!s.getSubject().canAs(OntResource.class) || !s.getObject().canAs(OntResource.class)) {
continue; continue;
} }
Individual subj = new IndividualJena((OntResource) s.getSubject().as(OntResource.class), webappDaoFactory); Individual subj = new IndividualJena(s.getSubject().as(OntResource.class), webappDaoFactory);
Individual obj = new IndividualJena((OntResource) s.getObject().as(OntResource.class), webappDaoFactory); Individual obj = new IndividualJena(s.getObject().as(OntResource.class), webappDaoFactory);
ObjectProperty op = webappDaoFactory.getObjectPropertyDao().getObjectPropertyByURI(s.getPredicate().getURI()); ObjectProperty op = webappDaoFactory.getObjectPropertyDao().getObjectPropertyByURI(s.getPredicate().getURI());
if (subj != null && obj != null && op != null) { if (subj != null && obj != null && op != null) {
ObjectPropertyStatement ops = new ObjectPropertyStatementImpl(); ObjectPropertyStatement ops = new ObjectPropertyStatementImpl();
@ -287,7 +287,7 @@ public class IndividualJena extends IndividualImpl implements Individual {
RDFNode value = values.nextNode(); RDFNode value = values.nextNode();
if (value.canAs(OntResource.class)) { if (value.canAs(OntResource.class)) {
relatedIndividuals.add( relatedIndividuals.add(
new IndividualJena((OntResource) value.as(OntResource.class), webappDaoFactory) ); new IndividualJena(value.as(OntResource.class), webappDaoFactory) );
} }
} }
} finally { } finally {
@ -305,7 +305,7 @@ public class IndividualJena extends IndividualImpl implements Individual {
try { try {
RDFNode value = ind.getPropertyValue(ind.getModel().getProperty(propertyURI)); RDFNode value = ind.getPropertyValue(ind.getModel().getProperty(propertyURI));
if (value != null && value.canAs(OntResource.class)) { if (value != null && value.canAs(OntResource.class)) {
return new IndividualJena((OntResource) value.as(OntResource.class), webappDaoFactory); return new IndividualJena(value.as(OntResource.class), webappDaoFactory);
} else { } else {
return null; return null;
} }
@ -582,11 +582,11 @@ public class IndividualJena extends IndividualImpl implements Individual {
int rv = 0; int rv = 0;
try { try {
if( val1 instanceof String ) if( val1 instanceof String )
rv = collator.compare( ((String)val1) , ((String)val2) ); rv = collator.compare(val1 , val2);
//rv = ((String)val1).compareTo((String)val2); //rv = ((String)val1).compareTo((String)val2);
else if( val1 instanceof Date ) { else if( val1 instanceof Date ) {
DateTime dt1 = new DateTime((Date)val1); DateTime dt1 = new DateTime(val1);
DateTime dt2 = new DateTime((Date)val2); DateTime dt2 = new DateTime(val2);
rv = dt1.compareTo(dt2); rv = dt1.compareTo(dt2);
} }
else else

15
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualSDB.java
View file

@ -478,8 +478,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
Individual subj = null; Individual subj = null;
try { try {
subj = new IndividualSDB( subj = new IndividualSDB(
((OntResource) s.getSubject().as(OntResource.class)) s.getSubject().as(OntResource.class).getURI(),
.getURI(),
this.dwf, datasetMode, webappDaoFactory); this.dwf, datasetMode, webappDaoFactory);
} catch (IndividualNotFoundException e) { } catch (IndividualNotFoundException e) {
// leave null subject // leave null subject
@ -487,8 +486,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
Individual obj = null; Individual obj = null;
try { try {
obj = new IndividualSDB( obj = new IndividualSDB(
((OntResource) s.getObject().as(OntResource.class)) s.getObject().as(OntResource.class).getURI(),
.getURI(),
this.dwf, datasetMode, webappDaoFactory); this.dwf, datasetMode, webappDaoFactory);
} catch (IndividualNotFoundException e) { } catch (IndividualNotFoundException e) {
// leave null object // leave null object
@ -548,8 +546,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
if (value.canAs(OntResource.class)) { if (value.canAs(OntResource.class)) {
relatedIndividuals.add( relatedIndividuals.add(
new IndividualSDB( new IndividualSDB(
((OntResource) value.as(OntResource.class)) value.as(OntResource.class).getURI(),
.getURI(),
this.dwf, this.dwf,
datasetMode, datasetMode,
webappDaoFactory) ); webappDaoFactory) );
@ -588,7 +585,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
if (value != null && value.canAs(OntResource.class)) { if (value != null && value.canAs(OntResource.class)) {
try { try {
return new IndividualSDB( return new IndividualSDB(
((OntResource) value.as(OntResource.class)).getURI(), value.as(OntResource.class).getURI(),
dwf, datasetMode, webappDaoFactory); dwf, datasetMode, webappDaoFactory);
} catch (IndividualNotFoundException e) { } catch (IndividualNotFoundException e) {
return null; return null;
@ -1045,8 +1042,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
rv = collator.compare( ((String)val1) , ((String)val2) ); rv = collator.compare( ((String)val1) , ((String)val2) );
//rv = ((String)val1).compareTo((String)val2); //rv = ((String)val1).compareTo((String)val2);
else if( val1 instanceof Date ) { else if( val1 instanceof Date ) {
DateTime dt1 = new DateTime((Date)val1); DateTime dt1 = new DateTime(val1);
DateTime dt2 = new DateTime((Date)val2); DateTime dt2 = new DateTime(val2);
rv = dt1.compareTo(dt2); rv = dt1.compareTo(dt2);
} }
else else

14
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaBaseDao.java
View file

@ -12,7 +12,6 @@ import java.util.Date;
import java.util.HashSet; import java.util.HashSet;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.Set; import java.util.Set;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
@ -23,7 +22,6 @@ import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
import com.hp.hpl.jena.graph.Node; import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.iri.IRI; import com.hp.hpl.jena.iri.IRI;
import com.hp.hpl.jena.iri.IRIFactory; import com.hp.hpl.jena.iri.IRIFactory;
import com.hp.hpl.jena.iri.Violation;
import com.hp.hpl.jena.ontology.DatatypeProperty; import com.hp.hpl.jena.ontology.DatatypeProperty;
import com.hp.hpl.jena.ontology.ObjectProperty; import com.hp.hpl.jena.ontology.ObjectProperty;
import com.hp.hpl.jena.ontology.OntClass; import com.hp.hpl.jena.ontology.OntClass;
@ -749,10 +747,10 @@ public class JenaBaseDao extends JenaBaseDaoCon {
if (label != null && label.length() > 0) { if (label != null && label.length() > 0) {
String existingValue = ontRes.getLabel((String) getDefaultLanguage()); String existingValue = ontRes.getLabel(getDefaultLanguage());
if (existingValue == null || !existingValue.equals(label)) { if (existingValue == null || !existingValue.equals(label)) {
ontRes.setLabel(label, (String) getDefaultLanguage()); ontRes.setLabel(label, getDefaultLanguage());
} }
} else { } else {
ontRes.removeAll(RDFS.label); ontRes.removeAll(RDFS.label);
@ -910,7 +908,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
if (iri.hasViolation(false) ) { if (iri.hasViolation(false) ) {
String errorStr = ("Bad URI: "+ uri + String errorStr = ("Bad URI: "+ uri +
"\nOnly well-formed absolute URIrefs can be included in RDF/XML output: " "\nOnly well-formed absolute URIrefs can be included in RDF/XML output: "
+ ((Violation)iri.violations(false).next()).getShortMessage()); + (iri.violations(false).next()).getShortMessage());
return errorStr; return errorStr;
} else { } else {
return null; return null;
@ -933,7 +931,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
String idStr = vitroURIStr.split("#")[1]; String idStr = vitroURIStr.split("#")[1];
RDFNode rdfNode = ontModel.getRDFNode(Node.createAnon(AnonId.create(idStr))); RDFNode rdfNode = ontModel.getRDFNode(Node.createAnon(AnonId.create(idStr)));
if ( (rdfNode != null) && (rdfNode.canAs(OntClass.class)) ) { if ( (rdfNode != null) && (rdfNode.canAs(OntClass.class)) ) {
cls = (OntClass) rdfNode.as(OntClass.class); cls = rdfNode.as(OntClass.class);
} }
} else { } else {
try { try {
@ -1006,7 +1004,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
StmtIterator stmtIt = getOntModel().listStatements((Resource)null, prop, value); StmtIterator stmtIt = getOntModel().listStatements((Resource)null, prop, value);
while (stmtIt.hasNext()) { while (stmtIt.hasNext()) {
Statement stmt = stmtIt.nextStatement(); Statement stmt = stmtIt.nextStatement();
possibleSubjectSet.add((Resource)stmt.getSubject()); possibleSubjectSet.add(stmt.getSubject());
} }
Iterator<Resource> possibleSubjectIt = possibleSubjectSet.iterator(); Iterator<Resource> possibleSubjectIt = possibleSubjectSet.iterator();
@ -1016,7 +1014,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
boolean hasAlternatePath = false; boolean hasAlternatePath = false;
while (stmtIt.hasNext()) { while (stmtIt.hasNext()) {
Statement stmt = stmtIt.nextStatement(); Statement stmt = stmtIt.nextStatement();
if (stmt.getObject().isResource() && possibleSubjectSet.contains((Resource)stmt.getObject())) { if (stmt.getObject().isResource() && possibleSubjectSet.contains(stmt.getObject())) {
hasAlternatePath = true; hasAlternatePath = true;
break; break;
} }

2
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaChangeListener.java
View file

@ -8,7 +8,6 @@ import java.util.HashSet;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.openjena.riot.RiotException;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelChangedListener; import com.hp.hpl.jena.rdf.model.ModelChangedListener;
@ -17,7 +16,6 @@ import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator; import com.hp.hpl.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener; import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeListener;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.SimpleReasonerSetup; import edu.cornell.mannlib.vitro.webapp.servlet.setup.SimpleReasonerSetup;
/** /**

4
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtils.java
View file

@ -95,7 +95,7 @@ public class JenaModelUtils {
.getRootClasses(); .getRootClasses();
for (Iterator<VClass> rootClassIt = rootClasses.iterator(); for (Iterator<VClass> rootClassIt = rootClasses.iterator();
rootClassIt.hasNext(); ) { rootClassIt.hasNext(); ) {
VClass rootClass = (VClass) rootClassIt.next(); VClass rootClass = rootClassIt.next();
Individual classGroup = modelForClassgroups.createIndividual( Individual classGroup = modelForClassgroups.createIndividual(
wadf.getDefaultNamespace() + "vitroClassGroup" + wadf.getDefaultNamespace() + "vitroClassGroup" +
rootClass.getLocalName(), classGroupClass); rootClass.getLocalName(), classGroupClass);
@ -108,7 +108,7 @@ public class JenaModelUtils {
for (Iterator<String> childIt = myWebappDaoFactory.getVClassDao() for (Iterator<String> childIt = myWebappDaoFactory.getVClassDao()
.getAllSubClassURIs(rootClass.getURI()).iterator(); .getAllSubClassURIs(rootClass.getURI()).iterator();
childIt.hasNext(); ) { childIt.hasNext(); ) {
String childURI = (String) childIt.next(); String childURI = childIt.next();
Resource childClass = modelForClassgroupAnnotations Resource childClass = modelForClassgroupAnnotations
.getResource(childURI); .getResource(childURI);
if (!modelForClassgroupAnnotations.contains( if (!modelForClassgroupAnnotations.contains(

16
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java
View file

@ -90,7 +90,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
p.setNamespace(op.getNameSpace()); p.setNamespace(op.getNameSpace());
p.setLocalName(op.getLocalName()); p.setLocalName(op.getLocalName());
OntologyDao oDao=getWebappDaoFactory().getOntologyDao(); OntologyDao oDao=getWebappDaoFactory().getOntologyDao();
Ontology o = (Ontology)oDao.getOntologyByURI(p.getNamespace()); Ontology o = oDao.getOntologyByURI(p.getNamespace());
if (o==null) { if (o==null) {
if (!VitroVocabulary.vitroURI.equals(p.getNamespace())) { if (!VitroVocabulary.vitroURI.equals(p.getNamespace())) {
log.debug("propertyFromOntProperty(): no ontology object found for the namespace "+p.getNamespace()); log.debug("propertyFromOntProperty(): no ontology object found for the namespace "+p.getNamespace());
@ -178,7 +178,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
Statement stmt = it.nextStatement(); Statement stmt = it.nextStatement();
RDFNode obj; RDFNode obj;
if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){ if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){
Resource res = (Resource)obj.as(Resource.class); Resource res = obj.as(Resource.class);
if( res != null && res.getURI() != null ){ if( res != null && res.getURI() != null ){
BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI()); BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI());
if( roleFromModel != null && if( roleFromModel != null &&
@ -197,7 +197,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
Statement stmt = it.nextStatement(); Statement stmt = it.nextStatement();
RDFNode obj; RDFNode obj;
if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){ if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){
Resource res = (Resource)obj.as(Resource.class); Resource res = obj.as(Resource.class);
if( res != null && res.getURI() != null ){ if( res != null && res.getURI() != null ){
BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI()); BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI());
if( roleFromModel != null && if( roleFromModel != null &&
@ -257,7 +257,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
while (opIt.hasNext()) { while (opIt.hasNext()) {
Resource res = (Resource) opIt.next(); Resource res = (Resource) opIt.next();
if ( (res.canAs(OntProperty.class)) && (!NONUSER_NAMESPACES.contains(res.getNameSpace())) ) { if ( (res.canAs(OntProperty.class)) && (!NONUSER_NAMESPACES.contains(res.getNameSpace())) ) {
props.add(propertyFromOntProperty((OntProperty)res.as(OntProperty.class))); props.add(propertyFromOntProperty(res.as(OntProperty.class)));
} }
} }
} finally { } finally {
@ -296,7 +296,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
while(it.hasNext()){ while(it.hasNext()){
ObjectPropertyStatement objPropertyStmt = (ObjectPropertyStatement)it.next(); ObjectPropertyStatement objPropertyStmt = (ObjectPropertyStatement)it.next();
if (hash.containsKey(objPropertyStmt.getPropertyURI())) { if (hash.containsKey(objPropertyStmt.getPropertyURI())) {
ObjectProperty p = (ObjectProperty) hash.get(objPropertyStmt.getPropertyURI()); ObjectProperty p = hash.get(objPropertyStmt.getPropertyURI());
p.addObjectPropertyStatement(objPropertyStmt); p.addObjectPropertyStatement(objPropertyStmt);
} else { } else {
OntProperty op = getOntModel().getOntProperty(objPropertyStmt.getPropertyURI()); OntProperty op = getOntModel().getOntProperty(objPropertyStmt.getPropertyURI());
@ -601,7 +601,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
while(restIt.hasNext()) { while(restIt.hasNext()) {
Resource restRes = restIt.next(); Resource restRes = restIt.next();
if (restRes.canAs(OntResource.class)) { if (restRes.canAs(OntResource.class)) {
OntResource restOntRes = (OntResource) restRes.as(OntResource.class); OntResource restOntRes = restRes.as(OntResource.class);
smartRemove(restOntRes, ontModel); smartRemove(restOntRes, ontModel);
} }
} }
@ -625,7 +625,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
while(restIt.hasNext()) { while(restIt.hasNext()) {
Resource restRes = restIt.next(); Resource restRes = restIt.next();
if (restRes.canAs(OntResource.class)) { if (restRes.canAs(OntResource.class)) {
OntResource restOntRes = (OntResource) restRes.as(OntResource.class); OntResource restOntRes = restRes.as(OntResource.class);
smartRemove(restOntRes, ontModel); smartRemove(restOntRes, ontModel);
} }
} }
@ -658,7 +658,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
while (propIt.hasNext()) { while (propIt.hasNext()) {
Resource res = (Resource) propIt.next(); Resource res = (Resource) propIt.next();
if (res.canAs(OntProperty.class)) { if (res.canAs(OntProperty.class)) {
com.hp.hpl.jena.ontology.OntProperty op = (com.hp.hpl.jena.ontology.OntProperty) res.as(OntProperty.class); com.hp.hpl.jena.ontology.OntProperty op = res.as(OntProperty.class);
boolean isRoot = false; boolean isRoot = false;
Iterator parentIt = op.listSuperProperties(); Iterator parentIt = op.listSuperProperties();
if (parentIt != null) { if (parentIt != null) {

4
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyStatementDaoJena.java
View file

@ -99,7 +99,7 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
ClosableIterator<Statement> propIt = ind.listProperties(); ClosableIterator<Statement> propIt = ind.listProperties();
try { try {
while (propIt.hasNext()) { while (propIt.hasNext()) {
Statement st = (Statement) propIt.next(); Statement st = propIt.next();
if (st.getObject().isResource() && !(NONUSER_NAMESPACES.contains(st.getPredicate().getNameSpace()))) { if (st.getObject().isResource() && !(NONUSER_NAMESPACES.contains(st.getPredicate().getNameSpace()))) {
try { try {
@ -173,7 +173,7 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
try { try {
int count = 0; int count = 0;
while ( (opsIt.hasNext()) && ((endIndex<0) || (count<endIndex)) ) { while ( (opsIt.hasNext()) && ((endIndex<0) || (count<endIndex)) ) {
Statement stmt = (Statement) opsIt.next(); Statement stmt = opsIt.next();
if (stmt.getObject().isResource()) { if (stmt.getObject().isResource()) {
++count; ++count;
if (startIndex<0 || startIndex<=count) { if (startIndex<0 || startIndex<=count) {

2
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyStatementDaoSDB.java
View file

@ -102,7 +102,7 @@ public class ObjectPropertyStatementDaoSDB extends
ClosableIterator<Statement> propIt = ind.listProperties(); ClosableIterator<Statement> propIt = ind.listProperties();
try { try {
while (propIt.hasNext()) { while (propIt.hasNext()) {
Statement st = (Statement) propIt.next(); Statement st = propIt.next();
if (st.getObject().isResource() && !(NONUSER_NAMESPACES.contains(st.getPredicate().getNameSpace()))) { if (st.getObject().isResource() && !(NONUSER_NAMESPACES.contains(st.getPredicate().getNameSpace()))) {
try { try {
ObjectPropertyStatement objPropertyStmt = new ObjectPropertyStatementImpl(); ObjectPropertyStatement objPropertyStmt = new ObjectPropertyStatementImpl();

3
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/OntologyDaoJena.java
View file

@ -2,10 +2,8 @@
package edu.cornell.mannlib.vitro.webapp.dao.jena; package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.text.Collator;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.HashSet;
import java.util.List; import java.util.List;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
@ -16,7 +14,6 @@ import com.hp.hpl.jena.util.iterator.ClosableIterator;
import edu.cornell.mannlib.vitro.webapp.beans.Ontology; import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao; import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
public class OntologyDaoJena extends JenaBaseDao implements OntologyDao { public class OntologyDaoJena extends JenaBaseDao implements OntologyDao {

1
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PageDaoJena.java
View file

@ -8,7 +8,6 @@ import java.util.HashMap;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.HashMap;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;

13
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyDaoJena.java
View file

@ -34,7 +34,6 @@ import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator; import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.sparql.resultset.ResultSetMem; import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
import com.hp.hpl.jena.util.iterator.ClosableIterator;
import com.hp.hpl.jena.vocabulary.OWL; import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDFS; import com.hp.hpl.jena.vocabulary.RDFS;
@ -151,7 +150,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
List<String> directSubproperties = getSubPropertyURIs(propertyURI); List<String> directSubproperties = getSubPropertyURIs(propertyURI);
Iterator<String> it=directSubproperties.iterator(); Iterator<String> it=directSubproperties.iterator();
while(it.hasNext()){ while(it.hasNext()){
String uri = (String)it.next(); String uri = it.next();
if (!subtree.contains(uri)) { if (!subtree.contains(uri)) {
subtree.add(uri); subtree.add(uri);
getAllSubPropertyURIs(uri,subtree); getAllSubPropertyURIs(uri,subtree);
@ -192,7 +191,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
List<String> directSuperproperties = getSuperPropertyURIs(propertyURI,true); List<String> directSuperproperties = getSuperPropertyURIs(propertyURI,true);
Iterator<String> it=directSuperproperties.iterator(); Iterator<String> it=directSuperproperties.iterator();
while(it.hasNext()){ while(it.hasNext()){
String uri = (String)it.next(); String uri = it.next();
if (!subtree.contains(uri)) { if (!subtree.contains(uri)) {
subtree.add(uri); subtree.add(uri);
getAllSuperPropertyURIs(uri,subtree); getAllSuperPropertyURIs(uri,subtree);
@ -342,13 +341,13 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
if (targetProp != null) { if (targetProp != null) {
StmtIterator stmtIter = ontModel.listStatements((Resource) null, OWL.onProperty, (RDFNode) targetProp); StmtIterator stmtIter = ontModel.listStatements((Resource) null, OWL.onProperty, targetProp);
while (stmtIter.hasNext()) { while (stmtIter.hasNext()) {
Statement statement = stmtIter.next(); Statement statement = stmtIter.next();
if ( statement.getSubject().canAs(OntClass.class) ) { if ( statement.getSubject().canAs(OntClass.class) ) {
classURISet.addAll(getRelatedClasses((OntClass) statement.getSubject().as(OntClass.class))); classURISet.addAll(getRelatedClasses(statement.getSubject().as(OntClass.class)));
} else { } else {
log.warn("getClassesWithRestrictionOnProperty: Unexpected use of onProperty: it is not applied to a class"); log.warn("getClassesWithRestrictionOnProperty: Unexpected use of onProperty: it is not applied to a class");
} }
@ -661,7 +660,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
// TODO: check if restriction is something like // TODO: check if restriction is something like
// maxCardinality 0 or allValuesFrom owl:Nothing, // maxCardinality 0 or allValuesFrom owl:Nothing,
// in which case the property is NOT applicable! // in which case the property is NOT applicable!
Restriction rest = (Restriction) relatedClass.as(Restriction.class); Restriction rest = relatedClass.as(Restriction.class);
OntProperty onProperty = rest.getOnProperty(); OntProperty onProperty = rest.getOnProperty();
if (onProperty != null) { if (onProperty != null) {
Resource[] ranges = new Resource[2]; Resource[] ranges = new Resource[2];
@ -726,7 +725,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
rangeClassURI = PSEUDO_BNODE_NS + rangeRes.getId() rangeClassURI = PSEUDO_BNODE_NS + rangeRes.getId()
.toString(); .toString();
} else { } else {
rangeClassURI = (String) rangeRes.getURI(); rangeClassURI = rangeRes.getURI();
} }
pi.setRangeClassURI(rangeClassURI); pi.setRangeClassURI(rangeClassURI);
VClass range = getWebappDaoFactory().getVClassDao() VClass range = getWebappDaoFactory().getVClassDao()

5
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyGroupDaoJena.java
View file

@ -4,7 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.ListIterator; import java.util.ListIterator;
@ -16,7 +15,6 @@ import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
import com.hp.hpl.jena.ontology.Individual; import com.hp.hpl.jena.ontology.Individual;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec; import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
@ -26,7 +24,6 @@ import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.iterator.ClosableIterator; import com.hp.hpl.jena.util.iterator.ClosableIterator;
import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl; import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Property; import edu.cornell.mannlib.vitro.webapp.beans.Property;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup; import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao; import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
@ -228,7 +225,7 @@ public class PropertyGroupDaoJena extends JenaBaseDao implements PropertyGroupDa
try { try {
Individual groupInd = ontModel.getIndividual(group.getURI()); Individual groupInd = ontModel.getIndividual(group.getURI());
try { try {
groupInd.setLabel(group.getName(), (String) getDefaultLanguage()); groupInd.setLabel(group.getName(), getDefaultLanguage());
} catch (Exception e) { } catch (Exception e) {
log.error("error updating name for "+groupInd.getURI()); log.error("error updating name for "+groupInd.getURI());
} }

12
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyInstanceDaoJena.java
View file

@ -7,27 +7,18 @@ import java.util.Calendar;
import java.util.Collection; import java.util.Collection;
import java.util.Collections; import java.util.Collections;
import java.util.Comparator; import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.Set;
import com.hp.hpl.jena.ontology.ObjectProperty;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntProperty; import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.ontology.Restriction;
import com.hp.hpl.jena.rdf.model.Property; import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory; import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.vocabulary.OWL; import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF; import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.beans.Individual; import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement; import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
@ -35,7 +26,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstanceIface; import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstanceIface;
import edu.cornell.mannlib.vitro.webapp.beans.VClass; import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao; import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualDeletionEvent; import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualDeletionEvent;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualUpdateEvent; import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualUpdateEvent;
public class PropertyInstanceDaoJena extends PropertyDaoJena implements public class PropertyInstanceDaoJena extends PropertyDaoJena implements
@ -58,7 +48,7 @@ public class PropertyInstanceDaoJena extends PropertyDaoJena implements
Property pred = tboxModel.getProperty(propertyURI); Property pred = tboxModel.getProperty(propertyURI);
OntProperty invPred = null; OntProperty invPred = null;
if (pred.canAs(OntProperty.class)) { if (pred.canAs(OntProperty.class)) {
invPred = ((OntProperty)pred.as(OntProperty.class)).getInverse(); invPred = pred.as(OntProperty.class).getInverse();
} }
Resource objRes = ontModel.getResource(objectURI); Resource objRes = ontModel.getResource(objectURI);
if ( (subjRes != null) && (pred != null) && (objRes != null) ) { if ( (subjRes != null) && (pred != null) && (objRes != null) ) {

1
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceDataset.java
View file

@ -8,7 +8,6 @@ import java.util.Iterator;
import com.hp.hpl.jena.graph.Node; import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.query.Dataset; import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.sparql.core.DatasetGraph; import com.hp.hpl.jena.sparql.core.DatasetGraph;

5
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceDatasetGraph.java
View file

@ -10,10 +10,6 @@ import java.util.List;
import com.hp.hpl.jena.graph.Graph; import com.hp.hpl.jena.graph.Graph;
import com.hp.hpl.jena.graph.Node; import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.graph.Triple; import com.hp.hpl.jena.graph.Triple;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution; import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet; import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
@ -21,7 +17,6 @@ import com.hp.hpl.jena.shared.LockMRSW;
import com.hp.hpl.jena.sparql.core.DatasetGraph; import com.hp.hpl.jena.sparql.core.DatasetGraph;
import com.hp.hpl.jena.sparql.core.Quad; import com.hp.hpl.jena.sparql.core.Quad;
import com.hp.hpl.jena.sparql.resultset.JSONInput; import com.hp.hpl.jena.sparql.resultset.JSONInput;
import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
import com.hp.hpl.jena.sparql.util.Context; import com.hp.hpl.jena.sparql.util.Context;
import com.hp.hpl.jena.util.iterator.SingletonIterator; import com.hp.hpl.jena.util.iterator.SingletonIterator;
import com.hp.hpl.jena.util.iterator.WrappedIterator; import com.hp.hpl.jena.util.iterator.WrappedIterator;

1
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceGraphBulkUpdater.java
View file

@ -4,7 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.io.ByteArrayInputStream; import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream; import java.io.ByteArrayOutputStream;
import java.io.InputStream;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;

2
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceModelMaker.java
View file

@ -305,7 +305,7 @@ public class RDFServiceModelMaker implements ModelMaker {
List<String> graphNames = rdfService.getGraphURIs(); List<String> graphNames = rdfService.getGraphURIs();
Iterator<String> nameIt = graphNames.iterator(); Iterator<String> nameIt = graphNames.iterator();
while (nameIt.hasNext()) { while (nameIt.hasNext()) {
String name = (String) nameIt.next(); String name = nameIt.next();
metadataModel.add(dbResource,metadataModel.getProperty( metadataModel.add(dbResource,metadataModel.getProperty(
HAS_NAMED_MODEL_URI),name); HAS_NAMED_MODEL_URI),name);
} }

40
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
View file

@ -98,11 +98,11 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
labelStr += "some values from "; labelStr += "some values from ";
} }
if (fillerRes.canAs(OntClass.class)) { if (fillerRes.canAs(OntClass.class)) {
OntClass avf = (OntClass) fillerRes.as(OntClass.class); OntClass avf = fillerRes.as(OntClass.class);
labelStr += getLabelForClass(avf,withPrefix,forPickList); labelStr += getLabelForClass(avf,withPrefix,forPickList);
} else { } else {
try { try {
labelStr += getLabelOrId( (OntResource) fillerRes.as(OntResource.class)); labelStr += getLabelOrId(fillerRes.as(OntResource.class));
} catch (Exception e) { } catch (Exception e) {
labelStr += "???"; labelStr += "???";
} }
@ -113,9 +113,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
RDFNode fillerNode = hvRest.getHasValue(); RDFNode fillerNode = hvRest.getHasValue();
try { try {
if (fillerNode.isResource()) { if (fillerNode.isResource()) {
labelStr += getLabelOrId((OntResource)fillerNode.as(OntResource.class)); labelStr += getLabelOrId(fillerNode.as(OntResource.class));
} else { } else {
labelStr += ((Literal) fillerNode.as(Literal.class)).getLexicalForm(); labelStr += fillerNode.as(Literal.class).getLexicalForm();
} }
} catch (Exception e) { } catch (Exception e) {
labelStr += "???"; labelStr += "???";
@ -138,10 +138,10 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
String labelStr = "("; String labelStr = "(";
if (cls.isComplementClass()) { if (cls.isComplementClass()) {
labelStr += "not "; labelStr += "not ";
ComplementClass ccls = (ComplementClass) cls.as(ComplementClass.class); ComplementClass ccls = cls.as(ComplementClass.class);
labelStr += getLabelForClass(ccls.getOperand(),withPrefix,forPickList); labelStr += getLabelForClass(ccls.getOperand(),withPrefix,forPickList);
} else if (cls.isIntersectionClass()) { } else if (cls.isIntersectionClass()) {
IntersectionClass icls = (IntersectionClass) cls.as(IntersectionClass.class); IntersectionClass icls = cls.as(IntersectionClass.class);
for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) { for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) {
OntClass operand = (OntClass) operandIt.next(); OntClass operand = (OntClass) operandIt.next();
labelStr += getLabelForClass(operand,withPrefix,forPickList); labelStr += getLabelForClass(operand,withPrefix,forPickList);
@ -150,7 +150,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
} }
} }
} else if (cls.isUnionClass()) { } else if (cls.isUnionClass()) {
UnionClass icls = (UnionClass) cls.as(UnionClass.class); UnionClass icls = cls.as(UnionClass.class);
for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) { for (Iterator operandIt = icls.listOperands(); operandIt.hasNext();) {
OntClass operand = (OntClass) operandIt.next(); OntClass operand = (OntClass) operandIt.next();
labelStr += getLabelForClass(operand,withPrefix,forPickList); labelStr += getLabelForClass(operand,withPrefix,forPickList);
@ -169,7 +169,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
} else { } else {
if (withPrefix || forPickList) { if (withPrefix || forPickList) {
OntologyDao oDao=getWebappDaoFactory().getOntologyDao(); OntologyDao oDao=getWebappDaoFactory().getOntologyDao();
Ontology o = (Ontology)oDao.getOntologyByURI(cls.getNameSpace()); Ontology o = oDao.getOntologyByURI(cls.getNameSpace());
if (o!=null) { if (o!=null) {
if (withPrefix) { if (withPrefix) {
return(o.getPrefix()==null?(o.getName()==null?"unspec:"+getLabelOrId(cls):o.getName()+":"+getLabelOrId(cls)):o.getPrefix()+":"+getLabelOrId(cls)); return(o.getPrefix()==null?(o.getName()==null?"unspec:"+getLabelOrId(cls):o.getName()+":"+getLabelOrId(cls)):o.getPrefix()+":"+getLabelOrId(cls));
@ -208,7 +208,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
while(restIt.hasNext()) { while(restIt.hasNext()) {
Resource restRes = restIt.next(); Resource restRes = restIt.next();
if (restRes.canAs(OntResource.class)) { if (restRes.canAs(OntResource.class)) {
OntResource restOntRes = (OntResource) restRes.as(OntResource.class); OntResource restOntRes = restRes.as(OntResource.class);
smartRemove(restOntRes, ontModel); smartRemove(restOntRes, ontModel);
} }
} }
@ -216,7 +216,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
while(restIt.hasNext()) { while(restIt.hasNext()) {
Resource restRes = restIt.next(); Resource restRes = restIt.next();
if (restRes.canAs(OntResource.class)) { if (restRes.canAs(OntResource.class)) {
OntResource restOntRes = (OntResource) restRes.as(OntResource.class); OntResource restOntRes = restRes.as(OntResource.class);
smartRemove(restOntRes, ontModel); smartRemove(restOntRes, ontModel);
} }
} }
@ -400,7 +400,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
List<String> directSubclasses = getSubClassURIs(classURI); List<String> directSubclasses = getSubClassURIs(classURI);
Iterator<String> it=directSubclasses.iterator(); Iterator<String> it=directSubclasses.iterator();
while(it.hasNext()){ while(it.hasNext()){
String uri = (String)it.next(); String uri = it.next();
if (!subtree.contains(uri)) { if (!subtree.contains(uri)) {
subtree.add(uri); subtree.add(uri);
getAllSubClassURIs(uri,subtree); getAllSubClassURIs(uri,subtree);
@ -423,7 +423,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
while (superClassIt.hasNext()) { while (superClassIt.hasNext()) {
Statement stmt = superClassIt.nextStatement(); Statement stmt = superClassIt.nextStatement();
if (stmt.getObject().canAs(OntResource.class)) { if (stmt.getObject().canAs(OntResource.class)) {
OntResource superRes = (OntResource) stmt.getObject().as(OntResource.class); OntResource superRes = stmt.getObject().as(OntResource.class);
String test = getClassURIStr(superRes); String test = getClassURIStr(superRes);
superclassURIs.add(test); superclassURIs.add(test);
} }
@ -442,7 +442,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
List<String> directSuperclasses = getSuperClassURIs(classURI, true); List<String> directSuperclasses = getSuperClassURIs(classURI, true);
Iterator<String> it=directSuperclasses.iterator(); Iterator<String> it=directSuperclasses.iterator();
while(it.hasNext()){ while(it.hasNext()){
String uri = (String)it.next(); String uri = it.next();
if (!subtree.contains(uri)) { if (!subtree.contains(uri)) {
subtree.add(uri); subtree.add(uri);
getAllSuperClassURIs(uri,subtree); getAllSuperClassURIs(uri,subtree);
@ -459,7 +459,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
while (classIt.hasNext()) { while (classIt.hasNext()) {
try { try {
Individual classInd = classIt.next(); Individual classInd = classIt.next();
OntClass cls = (OntClass) classInd.as(OntClass.class); OntClass cls = classInd.as(OntClass.class);
if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) { if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) {
classes.add(new VClassJena(cls,getWebappDaoFactory())); classes.add(new VClassJena(cls,getWebappDaoFactory()));
} }
@ -724,17 +724,17 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
Statement axStmt = (Statement) axStmtIt.next(); Statement axStmt = (Statement) axStmtIt.next();
OntResource subjOntRes = null; OntResource subjOntRes = null;
if (axStmt.getSubject().canAs(OntResource.class)) { if (axStmt.getSubject().canAs(OntResource.class)) {
subjOntRes = (OntResource) axStmt.getSubject().as(OntResource.class); subjOntRes = axStmt.getSubject().as(OntResource.class);
} }
if ( if (
(subjOntRes != null) && (subjSuperclasses.contains(getClassURIStr(subjOntRes))) && (subjOntRes != null) && (subjSuperclasses.contains(getClassURIStr(subjOntRes))) &&
(axStmt.getPredicate().equals(RDFS.subClassOf) || (axStmt.getPredicate().equals(OWL.equivalentClass))) (axStmt.getPredicate().equals(RDFS.subClassOf) || (axStmt.getPredicate().equals(OWL.equivalentClass)))
) { ) {
if (restRes.canAs(AllValuesFromRestriction.class)) { if (restRes.canAs(AllValuesFromRestriction.class)) {
AllValuesFromRestriction avfRest = (AllValuesFromRestriction) restRes.as(AllValuesFromRestriction.class); AllValuesFromRestriction avfRest = restRes.as(AllValuesFromRestriction.class);
Resource avf = avfRest.getAllValuesFrom(); Resource avf = avfRest.getAllValuesFrom();
if (avf.canAs(OntClass.class)) { if (avf.canAs(OntClass.class)) {
superclass = (OntClass) avfRest.getAllValuesFrom().as(OntClass.class); superclass = avfRest.getAllValuesFrom().as(OntClass.class);
} }
} }
} }
@ -818,8 +818,8 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
while (annotIt.hasNext()) { while (annotIt.hasNext()) {
try { try {
Statement annot = (Statement) annotIt.next(); Statement annot = (Statement) annotIt.next();
Resource cls = (Resource) annot.getSubject(); Resource cls = annot.getSubject();
VClass vcw = (VClass) getVClassByURI(cls.getURI()); VClass vcw = getVClassByURI(cls.getURI());
if (vcw != null) { if (vcw != null) {
boolean classIsInstantiated = false; boolean classIsInstantiated = false;
if (getIndividualCount) { if (getIndividualCount) {
@ -926,7 +926,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
OntClass ontCls = ontModel.createClass(cls.getURI()); OntClass ontCls = ontModel.createClass(cls.getURI());
try { try {
if (cls.getName() != null && cls.getName().length() > 0) { if (cls.getName() != null && cls.getName().length() > 0) {
ontCls.setLabel(cls.getName(), (String) getDefaultLanguage()); ontCls.setLabel(cls.getName(), getDefaultLanguage());
} else { } else {
ontCls.removeAll(RDFS.label); ontCls.removeAll(RDFS.label);
} }

8
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoSDB.java
View file

@ -2,8 +2,6 @@
package edu.cornell.mannlib.vitro.webapp.dao.jena; package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.util.List;
import com.hp.hpl.jena.ontology.AnnotationProperty; import com.hp.hpl.jena.ontology.AnnotationProperty;
import com.hp.hpl.jena.ontology.OntClass; import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.query.Dataset; import com.hp.hpl.jena.query.Dataset;
@ -11,8 +9,6 @@ import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution; import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory; import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory; import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.QuerySolutionMap;
import com.hp.hpl.jena.query.ResultSet; import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.Syntax; import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Literal; import com.hp.hpl.jena.rdf.model.Literal;
@ -64,8 +60,8 @@ public class VClassDaoSDB extends VClassDaoJena {
while (annotIt.hasNext()) { while (annotIt.hasNext()) {
try { try {
Statement annot = (Statement) annotIt.next(); Statement annot = (Statement) annotIt.next();
Resource cls = (Resource) annot.getSubject(); Resource cls = annot.getSubject();
VClass vcw = (VClass) getVClassByURI(cls.getURI()); VClass vcw = getVClassByURI(cls.getURI());
if (vcw != null) { if (vcw != null) {
boolean classIsInstantiated = false; boolean classIsInstantiated = false;
if (getIndividualCount) { if (getIndividualCount) {

3
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassGroupCache.java
View file

@ -4,10 +4,8 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.HashMap; import java.util.HashMap;
import java.util.HashSet;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Set;
import javax.servlet.ServletContext; import javax.servlet.ServletContext;
import javax.servlet.ServletContextEvent; import javax.servlet.ServletContextEvent;
@ -33,7 +31,6 @@ import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.beans.VClass; import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup; import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao; import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary; import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;

13
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassGroupDaoJena.java
View file

@ -14,11 +14,9 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.datatypes.xsd.XSDDatatype; import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
import com.hp.hpl.jena.ontology.DatatypeProperty;
import com.hp.hpl.jena.ontology.Individual; import com.hp.hpl.jena.ontology.Individual;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec; import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory; import com.hp.hpl.jena.rdf.model.ResourceFactory;
@ -32,7 +30,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.InsertException; import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao; import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao; import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch; import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
@ -82,7 +79,7 @@ public class VClassGroupDaoJena extends JenaBaseDao implements VClassGroupDao {
ClosableIterator<Individual> groupIt = getOntModel().listIndividuals(CLASSGROUP); ClosableIterator<Individual> groupIt = getOntModel().listIndividuals(CLASSGROUP);
try { try {
while (groupIt.hasNext()) { while (groupIt.hasNext()) {
Individual groupInd = (Individual) groupIt.next(); Individual groupInd = groupIt.next();
VClassGroup group = groupFromGroupIndividual(groupInd); VClassGroup group = groupFromGroupIndividual(groupInd);
if (group!=null) { if (group!=null) {
groups.add(group); groups.add(group);
@ -94,7 +91,7 @@ public class VClassGroupDaoJena extends JenaBaseDao implements VClassGroupDao {
Collections.sort(groups); Collections.sort(groups);
Iterator<VClassGroup> groupsIt = groups.iterator(); Iterator<VClassGroup> groupsIt = groups.iterator();
while (groupsIt.hasNext()) { while (groupsIt.hasNext()) {
VClassGroup group = (VClassGroup) groupsIt.next(); VClassGroup group = groupsIt.next();
map.put(group.getPublicName(), group); map.put(group.getPublicName(), group);
} }
return map; return map;
@ -140,7 +137,7 @@ public class VClassGroupDaoJena extends JenaBaseDao implements VClassGroupDao {
ClosableIterator<Individual> groupIt = getOntModel().listIndividuals(CLASSGROUP); ClosableIterator<Individual> groupIt = getOntModel().listIndividuals(CLASSGROUP);
try { try {
while (groupIt.hasNext()) { while (groupIt.hasNext()) {
Individual grp = (Individual) groupIt.next(); Individual grp = groupIt.next();
VClassGroup vgrp = groupFromGroupIndividual(grp); VClassGroup vgrp = groupFromGroupIndividual(grp);
if (vgrp != null) { if (vgrp != null) {
groups.add(vgrp); groups.add(vgrp);
@ -247,7 +244,7 @@ public class VClassGroupDaoJena extends JenaBaseDao implements VClassGroupDao {
int removedGroupsCount = 0; int removedGroupsCount = 0;
ListIterator<VClassGroup> it = groups.listIterator(); ListIterator<VClassGroup> it = groups.listIterator();
while(it.hasNext()){ while(it.hasNext()){
VClassGroup group = (VClassGroup) it.next(); VClassGroup group = it.next();
List<VClass> classes = group.getVitroClassList(); List<VClass> classes = group.getVitroClassList();
if( classes == null || classes.size() < 1 ){ if( classes == null || classes.size() < 1 ){
removedGroupsCount++; removedGroupsCount++;
@ -283,7 +280,7 @@ public class VClassGroupDaoJena extends JenaBaseDao implements VClassGroupDao {
try { try {
Individual groupInd = ontModel.getIndividual(vcg.getURI()); Individual groupInd = ontModel.getIndividual(vcg.getURI());
try { try {
groupInd.setLabel(vcg.getPublicName(), (String) getDefaultLanguage()); groupInd.setLabel(vcg.getPublicName(), getDefaultLanguage());
} catch (Exception e) { } catch (Exception e) {
log.error("error updating name for "+groupInd.getURI()); log.error("error updating name for "+groupInd.getURI());
} }

4
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassJena.java
View file

@ -324,7 +324,7 @@ public class VClassJena extends VClass {
Statement stmt = it.nextStatement(); Statement stmt = it.nextStatement();
RDFNode obj; RDFNode obj;
if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){ if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){
Resource res = (Resource)obj.as(Resource.class); Resource res = obj.as(Resource.class);
if( res != null && res.getURI() != null ){ if( res != null && res.getURI() != null ){
BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI()); BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI());
if( roleFromModel != null && if( roleFromModel != null &&
@ -358,7 +358,7 @@ public class VClassJena extends VClass {
Statement stmt = it.nextStatement(); Statement stmt = it.nextStatement();
RDFNode obj; RDFNode obj;
if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){ if( stmt != null && (obj = stmt.getObject()) != null && obj.isURIResource() ){
Resource res = (Resource)obj.as(Resource.class); Resource res = obj.as(Resource.class);
if( res != null && res.getURI() != null ){ if( res != null && res.getURI() != null ){
BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI()); BaseResourceBean.RoleLevel roleFromModel = BaseResourceBean.RoleLevel.getRoleByUri(res.getURI());
if( roleFromModel != null && if( roleFromModel != null &&

3
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VitroJenaSpecialModelMaker.java
View file

@ -2,8 +2,6 @@
package edu.cornell.mannlib.vitro.webapp.dao.jena; package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.util.HashMap;
import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletRequest;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
@ -14,7 +12,6 @@ import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelMaker; import com.hp.hpl.jena.rdf.model.ModelMaker;
import com.hp.hpl.jena.rdf.model.ModelReader; import com.hp.hpl.jena.rdf.model.ModelReader;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.util.iterator.ExtendedIterator; import com.hp.hpl.jena.util.iterator.ExtendedIterator;
/** /**

3
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/WebappDaoFactoryJena.java
View file

@ -11,7 +11,6 @@ import java.util.Set;
import com.hp.hpl.jena.iri.IRI; import com.hp.hpl.jena.iri.IRI;
import com.hp.hpl.jena.iri.IRIFactory; import com.hp.hpl.jena.iri.IRIFactory;
import com.hp.hpl.jena.iri.Violation;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec; import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.ontology.OntResource; import com.hp.hpl.jena.ontology.OntResource;
@ -184,7 +183,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
IRI iri = factory.create( uriStr ); IRI iri = factory.create( uriStr );
if (iri.hasViolation(false) ) { if (iri.hasViolation(false) ) {
validURI = false; validURI = false;
errorMsg += ((Violation)iri.violations(false).next()) errorMsg += (iri.violations(false).next())
.getShortMessage() + " "; .getShortMessage() + " ";
} else if (checkUniqueness) { } else if (checkUniqueness) {
OntModel ontModel = ontModelSelector.getFullModel(); OntModel ontModel = ontModelSelector.getFullModel();

6
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/pellet/ObjectPropertyStatementPatternFactory.java
View file

@ -2,15 +2,9 @@
package edu.cornell.mannlib.vitro.webapp.dao.jena.pellet; package edu.cornell.mannlib.vitro.webapp.dao.jena.pellet;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import com.hp.hpl.jena.rdf.model.Property; import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.ObjectPropertyStatementPattern;
public class ObjectPropertyStatementPatternFactory { public class ObjectPropertyStatementPatternFactory {
//private static Set<ObjectPropertyStatementPattern> patternSet = new HashSet<ObjectPropertyStatementPattern>(); //private static Set<ObjectPropertyStatementPattern> patternSet = new HashSet<ObjectPropertyStatementPattern>();

4
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/pellet/PelletListener.java
View file

@ -320,9 +320,9 @@ public class PelletListener implements ModelChangedListener {
try { try {
if ( ( ((Resource)stmt.getObject()).equals(RDFS.Resource) ) ) { if ( ( ((Resource)stmt.getObject()).equals(RDFS.Resource) ) ) {
reject = true; reject = true;
} else if ( ( ((Resource)stmt.getSubject()).equals(OWL.Nothing) ) ) { } else if ( ( stmt.getSubject().equals(OWL.Nothing) ) ) {
reject = true; reject = true;
} else if ( ( ((Resource)stmt.getObject()).equals(OWL.Nothing) ) ) { } else if ( ( stmt.getObject().equals(OWL.Nothing) ) ) {
reject = true; reject = true;
} }
} catch (Exception e) {} } catch (Exception e) {}

16
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessDataGetterN3Map.java
View file

@ -2,27 +2,11 @@
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils; package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
import java.lang.reflect.Constructor;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map;
import javax.servlet.ServletContext;
import net.sf.json.JSONObject;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessDataGetterN3;
import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.DataGetter;
/* /*
* This class determines what n3 should be returned for a particular data getter and can be overwritten or extended in VIVO. * This class determines what n3 should be returned for a particular data getter and can be overwritten or extended in VIVO.
*/ */

13
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessDataGetterN3Utils.java
View file

@ -4,25 +4,12 @@ package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocess
import java.lang.reflect.Constructor; import java.lang.reflect.Constructor;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map;
import javax.servlet.ServletContext;
import net.sf.json.JSONObject; import net.sf.json.JSONObject;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessDataGetterN3;
import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.DataGetter;
/* /*
* This class determines what n3 should be returned for a particular data getter and can be overwritten or extended in VIVO. * This class determines what n3 should be returned for a particular data getter and can be overwritten or extended in VIVO.
*/ */

33
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/WebappDaoSetup.java
View file

@ -94,17 +94,10 @@ public class WebappDaoSetup extends JenaDataSourceSetupBase
setStartupDataset(dataset, ctx); setStartupDataset(dataset, ctx);
// ABox assertions // ABox assertions
Model aboxAssertions = dataset.getNamedModel( baseOms.setABoxModel(ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL)));
JenaDataSourceSetupBase.JENA_DB_MODEL);
baseOms.setABoxModel(
ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM, aboxAssertions));
// ABox inferences // ABox inferences
Model aboxInferences = dataset.getNamedModel( inferenceOms.setABoxModel(ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, dataset.getNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL)));
JenaDataSourceSetupBase.JENA_INF_MODEL);
inferenceOms.setABoxModel(ModelFactory.createOntologyModel(
OntModelSpec.OWL_MEM, aboxInferences));
// TBox assertions // TBox assertions
try { try {
@ -115,16 +108,12 @@ public class WebappDaoSetup extends JenaDataSourceSetupBase
if (tboxAssertionsDB != null) { if (tboxAssertionsDB != null) {
long startTime = System.currentTimeMillis(); long startTime = System.currentTimeMillis();
System.out.println( log.info("Copying cached tbox assertions into memory");
"Copying cached tbox assertions into memory");
tboxAssertions.add(tboxAssertionsDB); tboxAssertions.add(tboxAssertionsDB);
System.out.println((System.currentTimeMillis() - startTime) log.info((System.currentTimeMillis() - startTime)/ 1000 + " seconds to load tbox assertions");
/ 1000 + " seconds to load tbox assertions"); tboxAssertions.getBaseModel().register(new ModelSynchronizer(tboxAssertionsDB));
} }
tboxAssertions.getBaseModel().register(new ModelSynchronizer(
tboxAssertionsDB));
baseOms.setTBoxModel(tboxAssertions); baseOms.setTBoxModel(tboxAssertions);
} catch (Throwable e) { } catch (Throwable e) {
log.error("Unable to load tbox assertion cache from DB", e); log.error("Unable to load tbox assertion cache from DB", e);
@ -139,15 +128,15 @@ public class WebappDaoSetup extends JenaDataSourceSetupBase
if (tboxInferencesDB != null) { if (tboxInferencesDB != null) {
long startTime = System.currentTimeMillis(); long startTime = System.currentTimeMillis();
System.out.println( log.info(
"Copying cached tbox inferences into memory"); "Copying cached tbox inferences into memory");
tboxInferences.add(tboxInferencesDB); tboxInferences.add(tboxInferencesDB);
System.out.println((System.currentTimeMillis() - startTime) System.out.println((System.currentTimeMillis() - startTime)
/ 1000 + " seconds to load tbox inferences"); / 1000 + " seconds to load tbox inferences");
}
tboxInferences.getBaseModel().register(new ModelSynchronizer( tboxInferences.getBaseModel().register(new ModelSynchronizer(
tboxInferencesDB)); tboxInferencesDB));
}
inferenceOms.setTBoxModel(tboxInferences); inferenceOms.setTBoxModel(tboxInferences);
} catch (Throwable e) { } catch (Throwable e) {
log.error("Unable to load tbox inference cache from DB", e); log.error("Unable to load tbox inference cache from DB", e);
@ -155,7 +144,6 @@ public class WebappDaoSetup extends JenaDataSourceSetupBase
} }
// union ABox // union ABox
Model m = ModelFactory.createUnion( Model m = ModelFactory.createUnion(
baseOms.getABoxModel(), inferenceOms.getABoxModel()); baseOms.getABoxModel(), inferenceOms.getABoxModel());
m = ModelFactory.createModelForGraph( m = ModelFactory.createModelForGraph(
@ -167,8 +155,7 @@ public class WebappDaoSetup extends JenaDataSourceSetupBase
unionOms.setABoxModel(unionABoxModel); unionOms.setABoxModel(unionABoxModel);
// union TBox // union TBox
m = ModelFactory.createUnion( m = ModelFactory.createUnion(baseOms.getTBoxModel(), inferenceOms.getTBoxModel());
baseOms.getTBoxModel(), inferenceOms.getTBoxModel());
m = ModelFactory.createModelForGraph( m = ModelFactory.createModelForGraph(
new SpecialBulkUpdateHandlerGraph( new SpecialBulkUpdateHandlerGraph(
m.getGraph(), m.getGraph(),

12
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/pageDataGetter/IndividualsForClassesDataGetter.java
View file

@ -5,7 +5,6 @@ package edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter;
import java.net.URLEncoder; import java.net.URLEncoder;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap; import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
@ -17,22 +16,11 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.json.JSONObject; import org.json.JSONObject;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.VClass; import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup; import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.IndividualListController;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder; import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.PageDao; import edu.cornell.mannlib.vitro.webapp.dao.PageDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VClassGroupCache; import edu.cornell.mannlib.vitro.webapp.dao.jena.VClassGroupCache;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.VClassGroupTemplateModel; import edu.cornell.mannlib.vitro.webapp.web.templatemodels.VClassGroupTemplateModel;