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NIHVIVO-214

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sjm222 2010-03-23 18:52:31 +00:00
parent 1085a57957
commit e217c5b90f
3 changed files with 316 additions and 91 deletions
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165
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaBaseDao.java
View file

@ -187,10 +187,13 @@ public class JenaBaseDao extends JenaBaseDaoCon {
existingValue = ((Literal)object).getString(); existingValue = ((Literal)object).getString();
} }
} }
if ( (existingValue!=null && value == null) || (existingValue!=null && value != null && !(existingValue.equals(value)) ) ) {
if (value == null || value.length() == 0) {
model.removeAll(res, dataprop, null);
} else if (existingValue == null ) {
model.add(res, dataprop, value, XSDDatatype.XSDstring);
} else if (!existingValue.equals(value)) {
model.removeAll(res, dataprop, null); model.removeAll(res, dataprop, null);
}
if ( (existingValue==null && value != null && value.length()>0) || (existingValue!=null && value != null && value.length()>0 && !(existingValue.equals(value)) ) ) {
model.add(res, dataprop, value, XSDDatatype.XSDstring); model.add(res, dataprop, value, XSDDatatype.XSDstring);
} }
} }
@ -258,11 +261,25 @@ public class JenaBaseDao extends JenaBaseDaoCon {
* convenience method for use with functional datatype properties * convenience method for use with functional datatype properties
*/ */
protected void updatePropertyIntValue(Resource res, Property dataprop, int value, Model model) { protected void updatePropertyIntValue(Resource res, Property dataprop, int value, Model model) {
if (dataprop != null) { if (dataprop != null) {
Integer existingValue = null;
Statement stmt = res.getProperty(dataprop);
if (stmt != null) {
RDFNode object = stmt.getObject();
if (object != null && object.isLiteral()){
existingValue = ((Literal)object).getInt();
}
}
if (existingValue == null ) {
model.add(res, dataprop, Integer.toString(value), XSDDatatype.XSDint);
} else if (existingValue.intValue() != value) {
model.removeAll(res, dataprop, null); model.removeAll(res, dataprop, null);
model.add(res, dataprop, Integer.toString(value), XSDDatatype.XSDint); model.add(res, dataprop, Integer.toString(value), XSDDatatype.XSDint);
} }
} }
}
/** /**
* convenience method * convenience method
@ -292,12 +309,12 @@ public class JenaBaseDao extends JenaBaseDaoCon {
* convenience method for use with functional datatype properties * convenience method for use with functional datatype properties
*/ */
protected void updatePropertyNonNegativeIntValue(Resource res, Property dataprop, int value, Model model) { protected void updatePropertyNonNegativeIntValue(Resource res, Property dataprop, int value, Model model) {
if (dataprop != null) {
model.removeAll(res, dataprop, null); if (value < 0)
if (value>-1) { return;
model.add(res, dataprop, Integer.toString(value), XSDDatatype.XSDint);
} updatePropertyIntValue(res,dataprop,value,model);
}
} }
/** /**
@ -313,10 +330,25 @@ public class JenaBaseDao extends JenaBaseDaoCon {
* convenience method for use with functional properties * convenience method for use with functional properties
*/ */
protected void updatePropertyFloatValue(Resource res, Property dataprop, Float value, Model model) { protected void updatePropertyFloatValue(Resource res, Property dataprop, Float value, Model model) {
if (dataprop != null) { if (dataprop != null) {
Float existingValue = null;
Statement stmt = res.getProperty(dataprop);
if (stmt != null) {
RDFNode object = stmt.getObject();
if (object != null && object.isLiteral()){
existingValue = ((Literal)object).getFloat();
}
}
if (value == null) {
model.removeAll(res, dataprop, null); model.removeAll(res, dataprop, null);
if( value != null ) } else if (existingValue == null ) {
model.add(res, dataprop, Float.toString(value), XSDDatatype.XSDfloat); model.add(res, dataprop, Float.toString(value), XSDDatatype.XSDfloat);
} else if (existingValue != value) {
model.removeAll(res, dataprop, null);
model.add(res, dataprop, Float.toString(value), XSDDatatype.XSDfloat);
}
} }
} }
@ -364,9 +396,24 @@ public class JenaBaseDao extends JenaBaseDaoCon {
protected synchronized void updatePropertyDateValue(Resource res, DatatypeProperty dataprop, Date value, Model model) { protected synchronized void updatePropertyDateValue(Resource res, DatatypeProperty dataprop, Date value, Model model) {
try { try {
if (dataprop != null) { if (dataprop != null) {
if (value == null) {
model.removeAll(res, dataprop, null); model.removeAll(res, dataprop, null);
if (value != null) { } else {
Date existingValue = null;
Statement stmt = res.getProperty(dataprop);
if (stmt != null) {
RDFNode object = stmt.getObject();
if (object != null && object.isLiteral()){
existingValue = (Date)((Literal)object).getValue();
}
}
if (existingValue == null ) {
model.add(res, dataprop, xsdDateFormat.format(value), XSDDatatype.XSDdate); model.add(res, dataprop, xsdDateFormat.format(value), XSDDatatype.XSDdate);
} else if (existingValue != value) {
model.removeAll(res, dataprop, null);
model.add(res, dataprop, xsdDateFormat.format(value), XSDDatatype.XSDdate);
}
} }
} }
} catch (Exception e) { } catch (Exception e) {
@ -443,10 +490,45 @@ public class JenaBaseDao extends JenaBaseDaoCon {
* convenience method for use with functional object properties * convenience method for use with functional object properties
*/ */
protected void updatePropertyResourceURIValue(Resource res, ObjectProperty prop, String objectURI) { protected void updatePropertyResourceURIValue(Resource res, ObjectProperty prop, String objectURI) {
Resource objectRes = getOntModel().getResource(objectURI);
if (prop != null && objectRes != null) { Model model = res.getModel();
res.removeAll(prop);
res.addProperty(prop, objectRes); if (model != null) {
updatePropertyResourceURIValue(res, prop, objectURI, model);
}
}
/**
* convenience method for use with functional properties
*/
protected void updatePropertyResourceURIValue(Resource res, Property prop, String uri, Model model) {
if (prop != null) {
if (uri == null) {
model.removeAll(res, prop, null);
} else {
String badURIErrorStr = checkURI(uri);
if (badURIErrorStr != null) {
log.error(badURIErrorStr);
return;
}
Resource existingValue = null;
Statement stmt = res.getProperty(prop);
if (stmt != null) {
RDFNode object = stmt.getObject();
if (object != null && object.isResource()){
existingValue = (Resource)object;
}
}
if (existingValue == null ) {
model.add(res, prop, model.createResource(uri));
} else if (!(existingValue.getURI()).equals(uri)) {
model.removeAll(res, prop, null);
model.add(res, prop, model.createResource(uri));
}
}
} }
} }
@ -463,12 +545,59 @@ public class JenaBaseDao extends JenaBaseDaoCon {
* convenience method for use with functional object properties * convenience method for use with functional object properties
*/ */
protected void updatePropertyResourceValue(Resource res, Property prop, Resource objectRes) { protected void updatePropertyResourceValue(Resource res, Property prop, Resource objectRes) {
if (prop != null && objectRes != null) {
res.removeAll(prop); Model model = res.getModel();
res.addProperty(prop, objectRes);
if (model != null) {
updatePropertyResourceValue(res, prop, objectRes, model);
}
}
/**
* convenience method for use with functional object properties
*/
protected void updatePropertyResourceValue(Resource res, Property prop, Resource objectRes, Model model) {
if (prop != null) {
if (objectRes == null) {
model.removeAll(res, prop, null);
} else {
Resource existingValue = null;
Statement stmt = res.getProperty(prop);
if (stmt != null) {
RDFNode object = stmt.getObject();
if (object != null && object.isResource()){
existingValue = (Resource)object;
} }
} }
if (existingValue == null ) {
model.add(res, prop, objectRes);
} else if (!existingValue.equals(objectRes)) {
model.removeAll(res, prop, null);
model.add(res, prop, objectRes);
}
}
}
}
/**
* convenience method for updating the RDFS label
*/
protected void updateRDFSLabel(OntClass ontCls, String label) {
if (label != null && label.length() > 0) {
String existingValue = ontCls.getLabel((String) getDefaultLanguage());
if (existingValue == null || !existingValue.equals(label)) {
ontCls.setLabel(label, (String) getDefaultLanguage());
}
} else {
ontCls.removeAll(RDFS.label);
}
}
private String getLabel(String lang, List<RDFNode>labelList) { private String getLabel(String lang, List<RDFNode>labelList) {
Iterator<RDFNode> labelIt = labelList.iterator(); Iterator<RDFNode> labelIt = labelList.iterator();

73
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
View file

@ -885,84 +885,34 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
public void updateVClass(VClass cls, OntModel ontModel) { public void updateVClass(VClass cls, OntModel ontModel) {
ontModel.enterCriticalSection(Lock.WRITE); ontModel.enterCriticalSection(Lock.WRITE);
getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),true)); ontModel.getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),true));
try { try {
OntClass ontCls = ontModel.getOntClass(cls.getURI()); OntClass ontCls = ontModel.getOntClass(cls.getURI());
if (ontCls != null) { if (ontCls != null) {
try { updateRDFSLabel(ontCls, cls.getName());
if (cls.getName() != null && cls.getName().length() > 0) { updatePropertyResourceURIValue(ontCls,IN_CLASSGROUP,cls.getGroupURI(),ontModel);
ontCls.setLabel(cls.getName(), (String) getDefaultLanguage());
} else {
ontCls.removeAll(RDFS.label);
}
} catch (Exception e) {
log.error("error updating label for class "+cls.getURI());
}
if (IN_CLASSGROUP != null) {
try {
if (cls.getGroupURI() != null) {
String badURIErrorStr = checkURI(cls.getGroupURI());
if (badURIErrorStr == null) {
ontCls.addProperty(IN_CLASSGROUP, ResourceFactory.createResource(cls.getGroupURI()));
} else {
log.error(badURIErrorStr);
}
} else {
ontCls.removeAll(IN_CLASSGROUP);
}
} catch (Exception e) {
log.error("error linking class "+cls.getURI()+" to class group");
}
} else {
log.error("vitro:inClassgroup property not found in RBox");
}
updatePropertyStringValue(ontCls,SHORTDEF,cls.getShortDef(),ontModel); updatePropertyStringValue(ontCls,SHORTDEF,cls.getShortDef(),ontModel);
updatePropertyStringValue(ontCls,EXAMPLE_ANNOT,cls.getExample(),ontModel); updatePropertyStringValue(ontCls,EXAMPLE_ANNOT,cls.getExample(),ontModel);
updatePropertyStringValue(ontCls,DESCRIPTION_ANNOT,cls.getDescription(),ontModel); updatePropertyStringValue(ontCls,DESCRIPTION_ANNOT,cls.getDescription(),ontModel);
updatePropertyIntValue(ontCls,DISPLAY_LIMIT,cls.getDisplayLimit(),ontModel); updatePropertyIntValue(ontCls,DISPLAY_LIMIT,cls.getDisplayLimit(),ontModel);
updatePropertyIntValue(ontCls,DISPLAY_RANK_ANNOT,cls.getDisplayRank(),ontModel); updatePropertyIntValue(ontCls,DISPLAY_RANK_ANNOT,cls.getDisplayRank(),ontModel);
updatePropertyFloatValue(ontCls, SEARCH_BOOST_ANNOT, cls.getSearchBoost(), ontModel); updatePropertyFloatValue(ontCls, SEARCH_BOOST_ANNOT, cls.getSearchBoost(), ontModel);
if (HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT != null) {
try { if (cls.getHiddenFromDisplayBelowRoleLevel() != null) {
ontCls.removeAll(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT); updatePropertyResourceURIValue(ontCls,HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT,cls.getHiddenFromDisplayBelowRoleLevel().getURI(),ontModel);
if (cls.getHiddenFromDisplayBelowRoleLevel()!=null) {
String badURIErrorStr = checkURI(cls.getHiddenFromDisplayBelowRoleLevel().getURI());
if (badURIErrorStr == null) {
ontCls.addProperty(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT, ResourceFactory.createResource(cls.getHiddenFromDisplayBelowRoleLevel().getURI()));
} else {
log.error(badURIErrorStr);
}
}
} catch (Exception e) {
log.error("error linking class "+cls.getURI()+" to HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL edit role");
}
} else {
log.error("vitro:hiddenFromDisplayBelowRoleLevelAnnot property not found in RBox");
} }
if (PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT != null) { if (cls.getProhibitedFromUpdateBelowRoleLevel() != null) {
try { updatePropertyResourceURIValue(ontCls,PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT,cls.getProhibitedFromUpdateBelowRoleLevel().getURI(),ontModel);
ontCls.removeAll(PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT);
if (cls.getProhibitedFromUpdateBelowRoleLevel()!=null) {
String badURIErrorStr = checkURI(cls.getProhibitedFromUpdateBelowRoleLevel().getURI());
if (badURIErrorStr == null) {
ontCls.addProperty(PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT, ResourceFactory.createResource(cls.getProhibitedFromUpdateBelowRoleLevel().getURI()));
} else {
log.error(badURIErrorStr);
}
}
} catch (Exception e) {
log.error("error linking class "+cls.getURI()+" to PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL edit role");
}
} else {
log.error("vitro:prohibitedFromUpdateBelowRoleLevelAnnot property not found in RBox");
} }
updatePropertyStringValue(ontCls,PROPERTY_CUSTOMENTRYFORMANNOT,cls.getCustomEntryForm(),ontModel); updatePropertyStringValue(ontCls,PROPERTY_CUSTOMENTRYFORMANNOT,cls.getCustomEntryForm(),ontModel);
updatePropertyStringValue(ontCls,PROPERTY_CUSTOMDISPLAYVIEWANNOT,cls.getCustomDisplayView(),ontModel); updatePropertyStringValue(ontCls,PROPERTY_CUSTOMDISPLAYVIEWANNOT,cls.getCustomDisplayView(),ontModel);
updatePropertyStringValue(ontCls,PROPERTY_CUSTOMSHORTVIEWANNOT,cls.getCustomShortView(),ontModel); updatePropertyStringValue(ontCls,PROPERTY_CUSTOMSHORTVIEWANNOT,cls.getCustomShortView(),ontModel);
updatePropertyStringValue(ontCls,PROPERTY_CUSTOMSEARCHVIEWANNOT,cls.getCustomSearchView(),ontModel); updatePropertyStringValue(ontCls,PROPERTY_CUSTOMSEARCHVIEWANNOT,cls.getCustomSearchView(),ontModel);
} else { } else {
log.error("error: cannot find class "+cls.getURI()+" for updating"); log.error("error: cannot find jena class "+cls.getURI()+" for updating");
} }
} finally { } finally {
getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),false)); getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),false));
@ -970,6 +920,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
} }
} }
private VClass vClassWebappFromOntClass(OntClass cls) { private VClass vClassWebappFromOntClass(OntClass cls) {
VClass vcw = new VClass(); VClass vcw = new VClass();
getOntModel().enterCriticalSection(Lock.READ); getOntModel().enterCriticalSection(Lock.READ);

145
webapp/test/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoTest.java Normal file
View file

@ -0,0 +1,145 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.dao.jena;
import org.junit.Assert;
import org.junit.Test;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
/**
*
*
*/
public class VClassDaoTest {
@Test
// Test that the VClassDaoJena::updateVClass method will only update the jena model for
// those properties in VClass that have a different value from what is already in the
// jena model for that property.
//
// Specifically, VClass should not remove a statement from the model and then add the
// same statement back in. The reason for this is that in vivo the "immutable" properties
// are stored in a sub-model and the user-editable properties are stored in a super-model and
// all updates are performed against the super-model, so removing and then re-adding
// the same statement may result in a change of state (if the statement was in the sub-model
// it will migrate to the super-model) because of the way jena handles additions and
// deletions with respect to super and sub models. This migration of statements may cause
// undesirable behavior in the vivo/vitro application.
public void modelIsolation(){
// 1. create two models and attach one as a sub-model of the other
// 2. populate the sub-model with one statement for each of the 14 properties represented in VClass
// 3. save the state of both the sub-model and the super-model
// 4. populate a VClass object with the data in the (combined) model and call the updateVClass method
// 5. verify that both the sub-model and the super-model are unchanged
String class1URI = "http://test.vivo/AcademicDegree";
OntModel superModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); // this simulates the user-editable ontology in vivo
OntModel subModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); // this simulates the core ontology in vivo
superModel.addSubModel(subModel);
String rdfsLabel = "this is the rdfs label";
String lang = "en-US";
// populate sub-model
OntClass class1 = subModel.createClass(class1URI);
class1.setLabel(rdfsLabel,lang); //rdfs:label
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.IN_CLASSGROUP), subModel.createResource("http://thisIsTheClassGroupURI"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.SHORTDEF), subModel.createTypedLiteral("this is the short definition"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.EXAMPLE_ANNOT), subModel.createTypedLiteral("this is the example - why is this a string?"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.DESCRIPTION_ANNOT), subModel.createTypedLiteral("this is the description"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.DISPLAY_LIMIT), subModel.createTypedLiteral(-1));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.DISPLAY_RANK_ANNOT), subModel.createTypedLiteral(-11));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.SEARCH_BOOST_ANNOT), subModel.createTypedLiteral(2.4f));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT), subModel.createResource("http://vitro.mannlib.cornell.edu/ns/vitro/role#curator"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT), subModel.createResource("http://vitro.mannlib.cornell.edu/ns/vitro/role#selfEditor"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.PROPERTY_CUSTOMENTRYFORMANNOT), subModel.createTypedLiteral("this is the custom entry form annotation"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.PROPERTY_CUSTOMDISPLAYVIEWANNOT), subModel.createTypedLiteral("this is the custom display view annotation"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.PROPERTY_CUSTOMSHORTVIEWANNOT), subModel.createTypedLiteral("this is the custom short view annotation"));
class1.setPropertyValue(subModel.createProperty(VitroVocabulary.PROPERTY_CUSTOMSEARCHVIEWANNOT), subModel.createTypedLiteral("this is the custom search view annotation"));
// Save copies of sub-model and super-model
// uncommment the next two lines to debug failures
//System.out.println("**Before updating VClass:");
//printModels(superModel, subModel);
OntModel origSubModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
origSubModel.add(subModel);
superModel.remove(subModel);
OntModel origSuperModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
origSuperModel.add(superModel);
superModel.add(subModel);
// Populate the VClass with the data in the sub-model and then update the combined model
WebappDaoFactoryJena wdfj = new WebappDaoFactoryJena(superModel);
VClassDaoJena vcdj = (VClassDaoJena) wdfj.getVClassDao();
VClass vClass = vcdj.getVClassByURI(class1URI); // the VClass will be populated with the
// information already in the jena model.
Assert.assertEquals(vClass.getName(), class1.getLabel(lang)); //
vcdj.updateVClass(vClass); // we haven't changed any values here, so
// the models should be unchanged.
// Verify that the sub-model and super-model are both unchanged
// uncommment the next two lines to debug failures
//System.out.println("\n**After updating VClass:");
//printModels(superModel,subModel);
superModel.remove(subModel);
//modtime affects the diff but we don't care about that difference
wipeOutModTime(origSubModel);
wipeOutModTime(origSuperModel);
wipeOutModTime(subModel);
wipeOutModTime(superModel);
Assert.assertTrue(subModel.isIsomorphicWith(origSubModel));
Assert.assertTrue(superModel.isIsomorphicWith(origSuperModel));
}
void printModels(OntModel superModel, OntModel subModel) {
// Detach the submodel for printing to get an accurate
// account of what is in each.
superModel.remove(subModel);
System.out.println("\nThe sub-model has " + subModel.size() + " statements:");
System.out.println("---------------------------------------------------");
subModel.writeAll(System.out,"N3",null);
System.out.println("\nThe super-model has " + superModel.size() + " statements:");
System.out.println("---------------------------------------------------");
superModel.write(System.out,"N3",null);
superModel.addSubModel(subModel);
}
void wipeOutModTime(Model model){
model.removeAll(null, model.createProperty(VitroVocabulary.MODTIME), null);
}
}