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incremental development for release 1.2 knowledge base migration.

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This commit is contained in:
sjm222 2010-12-28 15:04:42 +00:00
parent d1f000c772
commit d1394e7b33
2 changed files with 144 additions and 45 deletions
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184
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
View file

@ -119,7 +119,7 @@ public class ABoxUpdater {
*/
public void renameClass(AtomicOntologyChange change) throws IOException {
//logger.log("Processing a class rename from: " + change.getSourceURI() + " to " + change.getDestinationURI());
logger.log("Processing a class rename from: " + change.getSourceURI() + " to " + change.getDestinationURI());
aboxModel.enterCriticalSection(Lock.WRITE);
try {
@ -226,7 +226,7 @@ public class ABoxUpdater {
*/
public void addClass(AtomicOntologyChange change) throws IOException {
//logger.log("Processing a class addition of class " + change.getDestinationURI());
logger.log("Processing a class addition of class " + change.getDestinationURI());
OntClass addedClass = newTboxModel.getOntClass(change.getDestinationURI());
@ -275,25 +275,18 @@ public class ABoxUpdater {
}
}
/**
*
* Update a knowledge base to account for a class deletion in the ontology.
* All references to the deleted class URI in either the subject or the object
* position of a statement are changed to use the closest available parent of
* the deleted class from the previous ontology that remains in the new version
* of the ontology. Note that the closest available parent may be owl:Thing.
* If the deleted class has more than one closest available parent, then
* change individuals that were asserted to be of the deleted class to be
* asserted to be of both parent classes.
*
* Remove all instances of and references to a class in the abox of the knowledge base.
*
* @param change - an AtomicOntologyChange object representing a class
* delete operation.
*
*/
public void deleteClass(AtomicOntologyChange change) throws IOException {
//logger.log("Processing a class deletion of class " + change.getSourceURI());
logger.log("Processing a class deletion of class " + change.getSourceURI());
OntClass deletedClass = oldTboxModel.getOntClass(change.getSourceURI());
@ -302,39 +295,84 @@ public class ABoxUpdater {
return;
}
List<OntClass> classList = deletedClass.listSuperClasses(true).toList();
List<OntClass> namedClassList = new ArrayList<OntClass>();
for (OntClass ontClass : classList) {
if (!ontClass.isAnon()) {
namedClassList.add(ontClass);
}
Model retractions = ModelFactory.createDefaultModel();
// Remove statements where the deleted class is the subject (e.g. statements with vitro annotation properties as the predicate)
aboxModel.enterCriticalSection(Lock.WRITE);
try {
int count = 0;
StmtIterator iter = aboxModel.listStatements(deletedClass, (Property) null, (RDFNode) null);
while (iter.hasNext()) {
Statement oldStatement = iter.next();
count++;
retractions.add(oldStatement);
logChange(oldStatement, false);
}
if (count > 0) {
logger.log("Removed " + count + " subject reference" + ((count > 1) ? "s" : "") + " to the " + deletedClass.getURI() + " class");
}
} finally {
aboxModel.leaveCriticalSection();
}
OntClass parent = (!namedClassList.isEmpty())
? namedClassList.get(0)
: OWL_THING;
OntClass replacementClass = newTboxModel.getOntClass(parent.getURI());
while (replacementClass == null) {
parent = parent.getSuperClass();
if (parent == null) {
replacementClass = OWL_THING;
} else {
replacementClass = newTboxModel.getOntClass(parent.getURI());
}
}
//log summary of changes
logger.log("Class " + deletedClass.getURI() + " has been deleted. Any references to it in the knowledge base have been changed to " + replacementClass.getURI());
// Remove instances of the deleted class
aboxModel.enterCriticalSection(Lock.WRITE);
try {
int count = 0;
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass);
AtomicOntologyChange chg = new AtomicOntologyChange(deletedClass.getURI(), replacementClass.getURI(), AtomicChangeType.RENAME, change.getNotes());
renameClass(chg);
while (iter.hasNext()) {
count++;
Statement typeStmt = iter.next();
retractions.add(typeStmt);
StmtIterator iter2 = aboxModel.listStatements(typeStmt.getSubject(), (Property) null, (RDFNode) null);
while (iter2.hasNext()) {
retractions.add(iter2.next());
}
}
//log summary of changes
if (count > 0) {
logger.log("Removed " + count + " instance" + ((count > 1) ? "s" : "") + " of the " + deletedClass.getURI() + " class.");
}
aboxModel.remove(retractions);
record.recordRetractions(retractions);
} finally {
aboxModel.leaveCriticalSection();
}
// Remove other object references to the deleted class - what would these be? nothing, I think.
aboxModel.enterCriticalSection(Lock.WRITE);
try {
int count = 0;
StmtIterator iter = aboxModel.listStatements((Resource) null, (Property) null, deletedClass);
while (iter.hasNext()) {
count++;
Statement oldStatement = iter.next();
retractions.add(oldStatement);
logChange(oldStatement, false);
}
//log summary of changes
if (count > 0) {
logger.log("Removed " + count + " object reference" + ((count > 1) ? "s" : "") + " to the " + deletedClass.getURI() + " class.");
}
aboxModel.remove(retractions);
record.recordRetractions(retractions);
} finally {
aboxModel.leaveCriticalSection();
}
}
public void processPropertyChanges(List<AtomicOntologyChange> changes) throws IOException {
Iterator<AtomicOntologyChange> propItr = changes.iterator();
while(propItr.hasNext()){
AtomicOntologyChange propChangeObj = propItr.next();
@ -352,6 +390,9 @@ public class ABoxUpdater {
}
private void addProperty(AtomicOntologyChange propObj) throws IOException{
logger.log("Processing a property addition of property " + propObj.getDestinationURI());
OntProperty addedProperty = newTboxModel.getOntProperty (propObj.getDestinationURI());
if (addedProperty == null) {
@ -419,6 +460,8 @@ public class ABoxUpdater {
private void deleteProperty(AtomicOntologyChange propObj) throws IOException{
logger.log("Processing a property deletion of property " + propObj.getSourceURI());
OntProperty deletedProperty = oldTboxModel.getOntProperty(propObj.getSourceURI());
if (deletedProperty == null && "Prop".equals(propObj.getNotes())) {
@ -471,6 +514,8 @@ public class ABoxUpdater {
private void renameProperty(AtomicOntologyChange propObj) throws IOException {
logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
OntProperty oldProperty = oldTboxModel.getOntProperty(propObj.getSourceURI());
OntProperty newProperty = newTboxModel.getOntProperty(propObj.getDestinationURI());
@ -515,10 +560,8 @@ public class ABoxUpdater {
+ " changed to use " +
propObj.getDestinationURI() + " instead.");
}
}
public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {
logChange(oldStatement,false);
logChange(newStatement,true);
@ -530,4 +573,61 @@ public class ABoxUpdater {
" object = " + (statement.getObject().isLiteral() ? ((Literal)statement.getObject()).getLexicalForm()
: ((Resource)statement.getObject()).getURI()));
}
/**
*
* Update a knowledge base to account for a class deletion in the ontology.
* All references to the deleted class URI in either the subject or the object
* position of a statement are changed to use the closest available parent of
* the deleted class from the previous ontology that remains in the new version
* of the ontology. Note that the closest available parent may be owl:Thing.
* If the deleted class has more than one closest available parent, then
* change individuals that were asserted to be of the deleted class to be
* asserted to be of both parent classes.
*
* @param change - an AtomicOntologyChange object representing a class
* delete operation.
*
*/
public void obsolete_deleteClass(AtomicOntologyChange change) throws IOException {
logger.log("Processing a class deletion of class " + change.getSourceURI());
OntClass deletedClass = oldTboxModel.getOntClass(change.getSourceURI());
if (deletedClass == null) {
logger.log("WARNING: didn't find the deleted class " + change.getSourceURI() + " in the old model. Skipping updates for this deletion");
return;
}
List<OntClass> classList = deletedClass.listSuperClasses(true).toList();
List<OntClass> namedClassList = new ArrayList<OntClass>();
for (OntClass ontClass : classList) {
if (!ontClass.isAnon()) {
namedClassList.add(ontClass);
}
}
OntClass parent = (!namedClassList.isEmpty())
? namedClassList.get(0)
: OWL_THING;
OntClass replacementClass = newTboxModel.getOntClass(parent.getURI());
while (replacementClass == null) {
parent = parent.getSuperClass();
if (parent == null) {
replacementClass = OWL_THING;
} else {
replacementClass = newTboxModel.getOntClass(parent.getURI());
}
}
//log summary of changes
logger.log("Class " + deletedClass.getURI() + " has been deleted. Any references to it in the knowledge base have been changed to " + replacementClass.getURI());
AtomicOntologyChange chg = new AtomicOntologyChange(deletedClass.getURI(), replacementClass.getURI(), AtomicChangeType.RENAME, change.getNotes());
renameClass(chg);
}
}

5
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
View file

@ -245,9 +245,8 @@ public class OntologyUpdater {
private void updateTBoxAnnotations() throws IOException {
(new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
settings.getNewTBoxAnnotationsModel(),
settings.getOntModelSelector().getABoxModel(), logger, record))
.updateVitroPropertyDefaultValues();
settings.getNewTBoxAnnotationsModel(),
settings.getOntModelSelector().getABoxModel(), logger, record)).updateVitroPropertyDefaultValues();
}
/**