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NIHVIVO-257

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sjm222 2010-04-01 19:42:44 +00:00
parent 495093638b
commit 3c582af305
1 changed files with 79 additions and 16 deletions
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95
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java
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@ -6,12 +6,15 @@ import java.io.IOException;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.NodeIterator;
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.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock;
/**
* Performs knowledge base updates to the tbox to align with a new ontology version
@ -58,22 +61,34 @@ public class TBoxUpdater {
* knowledge base to be updated are provided in the class constructor and are
* referenced via class level variables.
*
* If the default value (i.e. the value that is provided in the vivo-core-
* annotations files) of a vitro annotation property has been changed for a vivo
* core class, and that default value has not been changed in the site knowledge
* base, then update the value in the site knowledge base to be the new default.
* Also, if a new vitro annotation property setting (i.e. either an existing
* setting applied to an existing class where it wasn't applied before, or
* an existing setting applied to a new class) has been applied to a vivo
* core class then copy that new property statement into the site model.
*
* Writes to the change log file, the error log file, and the incremental change
* knowledge base.
*
* Note: as specified, this method for now assume that no new vitro annotation
* properties have been introduced. This should be updated for future versions.
*/
public void updateVitroPropertyDefaultValues() throws IOException {
/* For each statement in the previous version of the ontology, look for a statement
with the same subject and predicate in the current version, and if the object of
the statement has changed then examine the site model to see if it needs to be
updated. If the site model has *not* changed the object of the statement as it appears
in the previous version, then update it to be the value as it appears in the current
version.
If the site has updated the value of a class property for which the default has
changed, log a message suggesting that they review the setting.
*/
siteModel.enterCriticalSection(Lock.WRITE);
try {
Model additions = ModelFactory.createDefaultModel();
Model retractions = ModelFactory.createDefaultModel();
// Update defaults values for vitro annotation properties in the site model
// if the default has changed in the new version of the ontology AND if
// the site hasn't overidden the previous default in their knowledge base.
StmtIterator iter = oldTboxModel.listStatements();
int stmtCount = 0;
@ -120,7 +135,10 @@ public class TBoxUpdater {
if (!siteObject.equals(oldObject)) {
try {
siteModel.removeAll(subject, predicate, null);
StmtIterator it = siteModel.listStatements(subject, predicate, (RDFNode)null);
while (it.hasNext()) {
retractions.add(it.next());
}
} catch (Exception e) {
logger.logError("Error removing statement for subject = " + subject.getURI() +
"and property = " + predicate.getURI() +
@ -128,7 +146,7 @@ public class TBoxUpdater {
}
try {
siteModel.add(subject, predicate, newObject);
additions.add(subject, predicate, newObject);
logger.log("Changed the value of property " + predicate.getURI() +
" of class = " + subject.getURI() +
@ -143,6 +161,51 @@ public class TBoxUpdater {
}
}
}
}
}
}
siteModel.add(additions);
record.recordAdditions(additions);
siteModel.remove(retractions);
record.recordRetractions(retractions);
// log summary of changes
StmtIterator addedIter = additions.listStatements();
logger.log("Updated the default vitro annotation value for " +
addedIter.toList().size() + " statments in the knowledge base.");
StmtIterator removedIter = retractions.listStatements();
int numRemoved = removedIter.toList().size() - addedIter.toList().size();
logger.log("Removed " + numRemoved +
" superfluous vitro annotation property settings from the knowledge base.");
// Copy annotation property settings that were introduced in the new ontology
// into the site model.
//
Model newAnnotationSettings = newTboxModel.difference(oldTboxModel);
siteModel.add(newAnnotationSettings);
record.recordAdditions(newAnnotationSettings);
// log the additions
iter = newAnnotationSettings.listStatements();
//summary
logger.log("Added " + iter.toList().size() + " new annotation property settings to the knowledge base. This includes " +
"exsiting annotation properties applied to exsiting classes where they weren't applied before, or existing " +
"properties applied to new classes. No new annotation properties have been introduced.");
//details
while (iter.hasNext()) {
Statement statement = iter.next();
logger.log( "added Statement: subject = " + statement.getSubject().getURI() +
" property = " + statement.getPredicate().getURI() +
" object = " + (statement.getObject().isLiteral() ? ((Resource)statement.getObject()).getURI()
: ((Literal)statement.getObject()).getLexicalForm()));
}
} finally {
siteModel.leaveCriticalSection();
}
}
}