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NIHVIVO-264

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sjm222 2010-04-02 12:43:15 +00:00
parent b3f0695ced
commit 3b64ea8986
1 changed files with 29 additions and 21 deletions
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50
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
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@ -3,12 +3,12 @@
package edu.cornell.mannlib.vitro.webapp.ontology.update; package edu.cornell.mannlib.vitro.webapp.ontology.update;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import com.hp.hpl.jena.ontology.OntClass; 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.OntModelSpec;
import com.hp.hpl.jena.ontology.OntProperty; import com.hp.hpl.jena.ontology.OntProperty;
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;
@ -26,7 +26,6 @@ import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType; import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
/** /**
* Performs knowledge base updates to the abox to align with a new ontology version * Performs knowledge base updates to the abox to align with a new ontology version
* *
@ -128,7 +127,9 @@ public class ABoxUpdater {
// Change class references in the subjects of statements // Change class references in the subjects of statements
StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null); StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null);
// TODO - catch and report exceptions in adding and removing from the model //log summary of changes
logger.log("Changing " + iter.toList().size() + " subject referernces to the " + oldClass.getURI() + " class to be " + newClass.getURI());
while (iter.hasNext()) { while (iter.hasNext()) {
Statement oldStatement = iter.next(); Statement oldStatement = iter.next();
Statement newStatement = ResourceFactory.createStatement(newClass, oldStatement.getPredicate(), oldStatement.getObject()); Statement newStatement = ResourceFactory.createStatement(newClass, oldStatement.getPredicate(), oldStatement.getObject());
@ -137,17 +138,20 @@ public class ABoxUpdater {
logChange(oldStatement, false); logChange(oldStatement, false);
logChange(newStatement,true); logChange(newStatement,true);
} }
// Change class references in the objects of statements // Change class references in the objects of statements
iter = aboxModel.listStatements((Resource) null, (Property) null, oldClass); iter = aboxModel.listStatements((Resource) null, (Property) null, oldClass);
// TODO - catch and report exceptions in adding and removing from the model
//log summary of changes
logger.log("Changing " + iter.toList().size() + " object referernces to the " + oldClass.getURI() + " class to be " + newClass.getURI());
while (iter.hasNext()) { while (iter.hasNext()) {
Statement oldStatement = iter.next(); Statement oldStatement = iter.next();
Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), oldStatement.getPredicate(), newClass); Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), oldStatement.getPredicate(), newClass);
retractions.add(oldStatement); retractions.add(oldStatement);
additions.add(newStatement); additions.add(newStatement);
//TODO - worried about logging changes before the changes are already made //TODO - worried about logging changes before the changes have actually been made
// in the model // in the model
logChanges(oldStatement, newStatement); logChanges(oldStatement, newStatement);
} }
@ -165,11 +169,11 @@ public class ABoxUpdater {
/** /**
* *
* Examine a knowledge based on a class addition to the ontology, and * Examine a knowledge based on a class addition to the ontology and
* add messages to the change log indicating where manual review is * add messages to the change log indicating where manual review is
* recommended. If the added class has a parent in the new ontology * recommended. If the added class has a direct parent in the new ontology
* that is not OWL.Thing, and if the knowledge base contains individuals * that is not OWL.Thing, and if the knowledge base contains individuals
* asserted to be in the parent class, then log message recommending * asserted to be in the parent class, then log a message recommending
* review of those individuals to see whether they are of the new * review of those individuals to see whether they are of the new
* class type. * class type.
* *
@ -182,11 +186,11 @@ public class ABoxUpdater {
OntClass addedClass = newTboxModel.getOntClass(change.getDestinationURI()); OntClass addedClass = newTboxModel.getOntClass(change.getDestinationURI());
if (addedClass == null) { if (addedClass == null) {
// TODO - log logger.logError(this.getClass().getName() + " : addClass - didn't find the added class " + change.getSourceURI() + " in the new model.");
return; return;
} }
ExtendedIterator<OntClass> classIter = addedClass.listSuperClasses(); ExtendedIterator<OntClass> classIter = addedClass.listSuperClasses(true);
while (classIter.hasNext()) { while (classIter.hasNext()) {
OntClass parentOfAddedClass = classIter.next(); OntClass parentOfAddedClass = classIter.next();
@ -204,6 +208,7 @@ public class ABoxUpdater {
indList += "\n\t" + stmt.getSubject().getURI(); indList += "\n\t" + stmt.getSubject().getURI();
} }
//TODO - take out the detailed logging after our internal testing is completed.
logger.log("There are " + count + " individuals in the model that are of type " + parentOfAddedClass.getURI() + "," + logger.log("There are " + count + " individuals in the model that are of type " + parentOfAddedClass.getURI() + "," +
" and a new subclass of that class has been added: " + addedClass.getURI() + ". " + " and a new subclass of that class has been added: " + addedClass.getURI() + ". " +
"Please review the following individuals to see whether they should be of type: " + addedClass.getURI() + ":" + "Please review the following individuals to see whether they should be of type: " + addedClass.getURI() + ":" +
@ -215,13 +220,14 @@ public class ABoxUpdater {
/** /**
* *
* Update a knowledge base to account for a class deletion from the ontology. * 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 * 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 * 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 * the deleted class from the previous ontology that remains in the new version
* of the ontology. If the deleted class has more than one closest available parent, * of the ontology. Note that the closest available parent may be owl:Thing.
* then no change is made to the knowledge base, and message indicating that manual * If the deleted class has more than one closest available parent, then
* review is necessary is added to the change log. * 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 * @param change - an AtomicOntologyChange object representing a class
* delete operation. * delete operation.
@ -232,13 +238,11 @@ public class ABoxUpdater {
OntClass deletedClass = oldTboxModel.getOntClass(change.getSourceURI()); OntClass deletedClass = oldTboxModel.getOntClass(change.getSourceURI());
if (deletedClass == null) { if (deletedClass == null) {
logger.logError(this.getClass().getName() + " : deleteClass - didn't find the deleted class " + change.getSourceURI() + " in the old model."); logger.logError(this.getClass().getName() + " : deleteClass - didn't find the deleted class " +
change.getSourceURI() + " in the old model.");
return; return;
} }
//TODO - what if there are multiple parents? maybe
// in that case don't do the rename, but rather
// log a message that they will have to review?
OntClass parent = deletedClass.getSuperClass(); OntClass parent = deletedClass.getSuperClass();
OntClass replacementClass = newTboxModel.getOntClass(parent.getURI()); OntClass replacementClass = newTboxModel.getOntClass(parent.getURI());
@ -246,7 +250,11 @@ public class ABoxUpdater {
parent = parent.getSuperClass(); parent = parent.getSuperClass();
replacementClass = newTboxModel.getOntClass(parent.getURI()); 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 will be changed to " +
replacementClass.getURI());
AtomicOntologyChange chg = new AtomicOntologyChange(deletedClass.getURI(), replacementClass.getURI(), AtomicChangeType.RENAME); AtomicOntologyChange chg = new AtomicOntologyChange(deletedClass.getURI(), replacementClass.getURI(), AtomicChangeType.RENAME);
renameClass(chg); renameClass(chg);
} }