applying ABox update to all graphs
This commit is contained in:
brianjlowe
parent
f7d03b6de8
commit
d5c032f33e
4 changed files with 334 additions and 256 deletions
|
|
@ -14,6 +14,7 @@ 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.ontology.OntProperty;
|
||||
import com.hp.hpl.jena.query.Dataset;
|
||||
import com.hp.hpl.jena.rdf.model.Literal;
|
||||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
|
|
@ -27,7 +28,9 @@ import com.hp.hpl.jena.shared.Lock;
|
|||
import com.hp.hpl.jena.vocabulary.OWL;
|
||||
import com.hp.hpl.jena.vocabulary.RDF;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
|
||||
import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
||||
|
||||
/**
|
||||
* Performs knowledge base updates to the abox to align with a new ontology version
|
||||
|
|
@ -38,7 +41,8 @@ public class ABoxUpdater {
|
|||
private final Log log = LogFactory.getLog(ABoxUpdater.class);
|
||||
private OntModel oldTboxModel;
|
||||
private OntModel newTboxModel;
|
||||
private OntModel aboxModel;
|
||||
private Dataset dataset;
|
||||
private RDFService rdfService;
|
||||
private OntModel newTBoxAnnotationsModel;
|
||||
private ChangeLogger logger;
|
||||
private ChangeRecord record;
|
||||
|
|
@ -59,14 +63,15 @@ public class ABoxUpdater {
|
|||
*/
|
||||
public ABoxUpdater(OntModel oldTboxModel,
|
||||
OntModel newTboxModel,
|
||||
OntModel aboxModel,
|
||||
RDFService rdfService,
|
||||
OntModel newAnnotationsModel,
|
||||
ChangeLogger logger,
|
||||
ChangeRecord record) {
|
||||
|
||||
this.oldTboxModel = oldTboxModel;
|
||||
this.newTboxModel = newTboxModel;
|
||||
this.aboxModel = aboxModel;
|
||||
this.dataset = new RDFServiceDataset(rdfService);
|
||||
this.rdfService = rdfService;
|
||||
this.newTBoxAnnotationsModel = newAnnotationsModel;
|
||||
this.logger = logger;
|
||||
this.record = record;
|
||||
|
|
@ -126,68 +131,75 @@ public class ABoxUpdater {
|
|||
public void renameClass(AtomicOntologyChange change) throws IOException {
|
||||
|
||||
//logger.log("Processing a class rename from: " + change.getSourceURI() + " to " + change.getDestinationURI());
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
|
||||
try {
|
||||
|
||||
Model additions = ModelFactory.createDefaultModel();
|
||||
Model retractions = ModelFactory.createDefaultModel();
|
||||
|
||||
//TODO - look for these in the models and log error if not found
|
||||
Resource oldClass = ResourceFactory.createResource(change.getSourceURI());
|
||||
Resource newClass = ResourceFactory.createResource(change.getDestinationURI());
|
||||
|
||||
// Change class references in the subjects of statements
|
||||
|
||||
// BJL 2010-04-09 : In future versions we need to keep track of
|
||||
// the difference between true direct renamings and "use-insteads."
|
||||
// For now, the best behavior is to remove any remaining statements
|
||||
// where the old class is the subject, *unless* the statements
|
||||
// is part of the new annotations file (see comment below) or the
|
||||
// predicate is vitro:autolinkedToTab. In the latter case,
|
||||
// the autolinking annotation should be rewritten using the
|
||||
// new class name.
|
||||
|
||||
StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null);
|
||||
|
||||
int removeCount = 0;
|
||||
while (iter.hasNext()) {
|
||||
Statement oldStatement = iter.next();
|
||||
removeCount++;
|
||||
retractions.add(oldStatement);
|
||||
}
|
||||
|
||||
//log summary of changes
|
||||
if (removeCount > 0) {
|
||||
logger.log("Removed " + removeCount + " subject reference" + ((removeCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class");
|
||||
}
|
||||
|
||||
// Change class references in the objects of rdf:type statements
|
||||
iter = aboxModel.listStatements((Resource) null, RDF.type, oldClass);
|
||||
|
||||
int renameCount = 0;
|
||||
while (iter.hasNext()) {
|
||||
renameCount++;
|
||||
Statement oldStatement = iter.next();
|
||||
Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), RDF.type, newClass);
|
||||
retractions.add(oldStatement);
|
||||
additions.add(newStatement);
|
||||
}
|
||||
|
||||
//log summary of changes
|
||||
if (renameCount > 0) {
|
||||
logger.log("Retyped " + renameCount + " individual" + ((renameCount > 1) ? "s" : "") + " from type " + oldClass.getURI() + " to type " + newClass.getURI());
|
||||
}
|
||||
|
||||
aboxModel.remove(retractions);
|
||||
record.recordRetractions(retractions);
|
||||
aboxModel.add(additions);
|
||||
record.recordAdditions(additions);
|
||||
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
|
||||
Iterator<String> graphIt = dataset.listNames();
|
||||
while(graphIt.hasNext()) {
|
||||
String graph = graphIt.next();
|
||||
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
|
||||
continue;
|
||||
}
|
||||
Model aboxModel = dataset.getNamedModel(graph);
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
|
||||
Model additions = ModelFactory.createDefaultModel();
|
||||
Model retractions = ModelFactory.createDefaultModel();
|
||||
|
||||
//TODO - look for these in the models and log error if not found
|
||||
Resource oldClass = ResourceFactory.createResource(change.getSourceURI());
|
||||
Resource newClass = ResourceFactory.createResource(change.getDestinationURI());
|
||||
|
||||
// Change class references in the subjects of statements
|
||||
|
||||
// BJL 2010-04-09 : In future versions we need to keep track of
|
||||
// the difference between true direct renamings and "use-insteads."
|
||||
// For now, the best behavior is to remove any remaining statements
|
||||
// where the old class is the subject, *unless* the statements
|
||||
// is part of the new annotations file (see comment below) or the
|
||||
// predicate is vitro:autolinkedToTab. In the latter case,
|
||||
// the autolinking annotation should be rewritten using the
|
||||
// new class name.
|
||||
|
||||
StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null);
|
||||
|
||||
int removeCount = 0;
|
||||
while (iter.hasNext()) {
|
||||
Statement oldStatement = iter.next();
|
||||
removeCount++;
|
||||
retractions.add(oldStatement);
|
||||
}
|
||||
|
||||
//log summary of changes
|
||||
if (removeCount > 0) {
|
||||
logger.log("Removed " + removeCount + " subject reference" + ((removeCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class");
|
||||
}
|
||||
|
||||
// Change class references in the objects of rdf:type statements
|
||||
iter = aboxModel.listStatements((Resource) null, RDF.type, oldClass);
|
||||
|
||||
int renameCount = 0;
|
||||
while (iter.hasNext()) {
|
||||
renameCount++;
|
||||
Statement oldStatement = iter.next();
|
||||
Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), RDF.type, newClass);
|
||||
retractions.add(oldStatement);
|
||||
additions.add(newStatement);
|
||||
}
|
||||
|
||||
//log summary of changes
|
||||
if (renameCount > 0) {
|
||||
logger.log("Retyped " + renameCount + " individual" + ((renameCount > 1) ? "s" : "") + " from type " + oldClass.getURI() + " to type " + newClass.getURI());
|
||||
}
|
||||
|
||||
aboxModel.remove(retractions);
|
||||
record.recordRetractions(retractions);
|
||||
aboxModel.add(additions);
|
||||
record.recordAdditions(additions);
|
||||
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -233,24 +245,26 @@ public class ABoxUpdater {
|
|||
|
||||
if (!parentOfAddedClass.equals(OWL.Thing)) {
|
||||
|
||||
StmtIterator stmtIter = aboxModel.listStatements(null, RDF.type, parentOfAddedClass);
|
||||
|
||||
int count = stmtIter.toList().size();
|
||||
if (count > 0) {
|
||||
|
||||
String indList = "";
|
||||
while (stmtIter.hasNext()) {
|
||||
Statement stmt = stmtIter.next();
|
||||
indList += "\n\t" + stmt.getSubject().getURI();
|
||||
}
|
||||
|
||||
Iterator<String> graphIt = dataset.listNames();
|
||||
while(graphIt.hasNext()) {
|
||||
String graph = graphIt.next();
|
||||
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
|
||||
continue;
|
||||
}
|
||||
Model aboxModel = dataset.getNamedModel(graph);
|
||||
|
||||
StmtIterator stmtIter = aboxModel.listStatements(null, RDF.type, parentOfAddedClass);
|
||||
|
||||
int count = stmtIter.toList().size();
|
||||
|
||||
if (count > 0) {
|
||||
//TODO - take out the detailed logging after our internal testing is completed.
|
||||
logger.log("There " + ((count > 1) ? "are" : "is") + " " + count + " individual" + ((count > 1) ? "s" : "") + " in the model that " + ((count > 1) ? "are" : "is") + " of type " + parentOfAddedClass.getURI() + "," +
|
||||
" and a new subclass of that class has been added: " + addedClass.getURI() + ". " +
|
||||
"Please review " + ((count > 1) ? "these" : "this") + " individual" + ((count > 1) ? "s" : "") + " to see whether " + ((count > 1) ? "they" : "it") + " should be of type: " + addedClass.getURI() );
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -332,25 +346,33 @@ public class ABoxUpdater {
|
|||
}
|
||||
|
||||
// Remove instances of the deleted class
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
int count = 0;
|
||||
int refCount = 0;
|
||||
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
count++;
|
||||
Statement typeStmt = iter.next();
|
||||
refCount = deleteIndividual(typeStmt.getSubject());
|
||||
}
|
||||
|
||||
if (count > 0) {
|
||||
logger.log("Removed " + count + " individual" + (((count > 1) ? "s" : "") + " of type " + deletedClass.getURI()) + " (refs = " + refCount + ")");
|
||||
}
|
||||
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
Iterator<String> graphIt = dataset.listNames();
|
||||
while(graphIt.hasNext()) {
|
||||
String graph = graphIt.next();
|
||||
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
|
||||
continue;
|
||||
}
|
||||
Model aboxModel = dataset.getNamedModel(graph);
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
int count = 0;
|
||||
int refCount = 0;
|
||||
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
count++;
|
||||
Statement typeStmt = iter.next();
|
||||
refCount = deleteIndividual(typeStmt.getSubject());
|
||||
}
|
||||
|
||||
if (count > 0) {
|
||||
logger.log("Removed " + count + " individual" + (((count > 1) ? "s" : "") + " of type " + deletedClass.getURI()) + " (refs = " + refCount + ")");
|
||||
}
|
||||
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
protected int deleteIndividual(Resource individual) throws IOException {
|
||||
|
|
@ -358,29 +380,37 @@ public class ABoxUpdater {
|
|||
Model retractions = ModelFactory.createDefaultModel();
|
||||
int refCount = 0;
|
||||
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
StmtIterator iter = aboxModel.listStatements(individual, (Property) null, (RDFNode) null);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
Statement subjstmt = iter.next();
|
||||
retractions.add(subjstmt);
|
||||
}
|
||||
|
||||
iter = aboxModel.listStatements((Resource) null, (Property) null, individual);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
Statement objstmt = iter.next();
|
||||
retractions.add(objstmt);
|
||||
refCount++;
|
||||
}
|
||||
|
||||
aboxModel.remove(retractions);
|
||||
record.recordRetractions(retractions);
|
||||
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
Iterator<String> graphIt = dataset.listNames();
|
||||
while(graphIt.hasNext()) {
|
||||
String graph = graphIt.next();
|
||||
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
|
||||
continue;
|
||||
}
|
||||
Model aboxModel = dataset.getNamedModel(graph);
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
StmtIterator iter = aboxModel.listStatements(individual, (Property) null, (RDFNode) null);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
Statement subjstmt = iter.next();
|
||||
retractions.add(subjstmt);
|
||||
}
|
||||
|
||||
iter = aboxModel.listStatements((Resource) null, (Property) null, individual);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
Statement objstmt = iter.next();
|
||||
retractions.add(objstmt);
|
||||
refCount++;
|
||||
}
|
||||
|
||||
aboxModel.remove(retractions);
|
||||
record.recordRetractions(retractions);
|
||||
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
return refCount;
|
||||
}
|
||||
|
|
@ -439,37 +469,45 @@ public class ABoxUpdater {
|
|||
|
||||
if (inverseOfAddedProperty != null) {
|
||||
Model additions = ModelFactory.createDefaultModel();
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
|
||||
try {
|
||||
StmtIterator iter = aboxModel.listStatements((Resource) null, inverseOfAddedProperty, (RDFNode) null);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
|
||||
Statement stmt = iter.next();
|
||||
|
||||
if (stmt.getObject().isResource()) {
|
||||
Statement newStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), addedProperty, stmt.getSubject());
|
||||
additions.add(newStmt);
|
||||
} else {
|
||||
logger.log("WARNING: expected the object of this statement to be a Resource but it is not. No inverse has been asserted: " + stmtString(stmt));
|
||||
}
|
||||
}
|
||||
|
||||
aboxModel.add(additions);
|
||||
record.recordAdditions(additions);
|
||||
|
||||
if (additions.size() > 0) {
|
||||
logger.log("Added " + additions.size() + " statement" +
|
||||
((additions.size() > 1) ? "s" : "") +
|
||||
" with predicate " + addedProperty.getURI() +
|
||||
" (as an inverse to existing " + inverseOfAddedProperty.getURI() +
|
||||
" statement" + ((additions.size() > 1) ? "s" : "") + ")");
|
||||
}
|
||||
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
Iterator<String> graphIt = dataset.listNames();
|
||||
while(graphIt.hasNext()) {
|
||||
String graph = graphIt.next();
|
||||
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
|
||||
continue;
|
||||
}
|
||||
Model aboxModel = dataset.getNamedModel(graph);
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
|
||||
try {
|
||||
StmtIterator iter = aboxModel.listStatements((Resource) null, inverseOfAddedProperty, (RDFNode) null);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
|
||||
Statement stmt = iter.next();
|
||||
|
||||
if (stmt.getObject().isResource()) {
|
||||
Statement newStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), addedProperty, stmt.getSubject());
|
||||
additions.add(newStmt);
|
||||
} else {
|
||||
logger.log("WARNING: expected the object of this statement to be a Resource but it is not. No inverse has been asserted: " + stmtString(stmt));
|
||||
}
|
||||
}
|
||||
|
||||
aboxModel.add(additions);
|
||||
record.recordAdditions(additions);
|
||||
|
||||
if (additions.size() > 0) {
|
||||
logger.log("Added " + additions.size() + " statement" +
|
||||
((additions.size() > 1) ? "s" : "") +
|
||||
" with predicate " + addedProperty.getURI() +
|
||||
" (as an inverse to existing " + inverseOfAddedProperty.getURI() +
|
||||
" statement" + ((additions.size() > 1) ? "s" : "") + ")");
|
||||
}
|
||||
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -507,27 +545,35 @@ public class ABoxUpdater {
|
|||
}
|
||||
}
|
||||
|
||||
Model deletePropModel = ModelFactory.createDefaultModel();
|
||||
|
||||
if (replacementProperty == null) {
|
||||
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
deletePropModel.add(aboxModel.listStatements((Resource) null, deletedProperty, (RDFNode) null));
|
||||
aboxModel.remove(deletePropModel);
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
record.recordRetractions(deletePropModel);
|
||||
boolean plural = (deletePropModel.size() > 1);
|
||||
if (deletePropModel.size() > 0) {
|
||||
logger.log("Removed " + deletePropModel.size() + " statement" + (plural ? "s" : "") + " with predicate " +
|
||||
propObj.getSourceURI());
|
||||
}
|
||||
} else {
|
||||
AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes());
|
||||
renameProperty(chg);
|
||||
}
|
||||
Iterator<String> graphIt = dataset.listNames();
|
||||
while(graphIt.hasNext()) {
|
||||
String graph = graphIt.next();
|
||||
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
|
||||
continue;
|
||||
}
|
||||
Model aboxModel = dataset.getNamedModel(graph);
|
||||
Model deletePropModel = ModelFactory.createDefaultModel();
|
||||
|
||||
if (replacementProperty == null) {
|
||||
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
deletePropModel.add(aboxModel.listStatements((Resource) null, deletedProperty, (RDFNode) null));
|
||||
aboxModel.remove(deletePropModel);
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
record.recordRetractions(deletePropModel);
|
||||
boolean plural = (deletePropModel.size() > 1);
|
||||
if (deletePropModel.size() > 0) {
|
||||
logger.log("Removed " + deletePropModel.size() + " statement" + (plural ? "s" : "") + " with predicate " +
|
||||
propObj.getSourceURI());
|
||||
}
|
||||
} else {
|
||||
AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes());
|
||||
renameProperty(chg);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -548,35 +594,44 @@ public class ABoxUpdater {
|
|||
return;
|
||||
}
|
||||
|
||||
Model renamePropAddModel = ModelFactory.createDefaultModel();
|
||||
Model renamePropRetractModel = ModelFactory.createDefaultModel();
|
||||
Iterator<String> graphIt = dataset.listNames();
|
||||
while(graphIt.hasNext()) {
|
||||
String graph = graphIt.next();
|
||||
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
|
||||
continue;
|
||||
}
|
||||
Model aboxModel = dataset.getNamedModel(graph);
|
||||
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
renamePropRetractModel.add( aboxModel.listStatements(
|
||||
(Resource) null, oldProperty, (RDFNode) null));
|
||||
StmtIterator stmItr = renamePropRetractModel.listStatements();
|
||||
while(stmItr.hasNext()) {
|
||||
Statement tempStatement = stmItr.nextStatement();
|
||||
renamePropAddModel.add( tempStatement.getSubject(),
|
||||
newProperty,
|
||||
tempStatement.getObject() );
|
||||
}
|
||||
aboxModel.remove(renamePropRetractModel);
|
||||
aboxModel.add(renamePropAddModel);
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
record.recordAdditions(renamePropAddModel);
|
||||
record.recordRetractions(renamePropRetractModel);
|
||||
|
||||
if (renamePropRetractModel.size() > 0) {
|
||||
logger.log("Changed " + renamePropRetractModel.size() + " statement" +
|
||||
((renamePropRetractModel.size() > 1) ? "s" : "") +
|
||||
" with predicate " + propObj.getSourceURI() + " to use " +
|
||||
propObj.getDestinationURI() + " instead");
|
||||
}
|
||||
Model renamePropAddModel = ModelFactory.createDefaultModel();
|
||||
Model renamePropRetractModel = ModelFactory.createDefaultModel();
|
||||
|
||||
aboxModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
renamePropRetractModel.add( aboxModel.listStatements(
|
||||
(Resource) null, oldProperty, (RDFNode) null));
|
||||
StmtIterator stmItr = renamePropRetractModel.listStatements();
|
||||
while(stmItr.hasNext()) {
|
||||
Statement tempStatement = stmItr.nextStatement();
|
||||
renamePropAddModel.add( tempStatement.getSubject(),
|
||||
newProperty,
|
||||
tempStatement.getObject() );
|
||||
}
|
||||
aboxModel.remove(renamePropRetractModel);
|
||||
aboxModel.add(renamePropAddModel);
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
record.recordAdditions(renamePropAddModel);
|
||||
record.recordRetractions(renamePropRetractModel);
|
||||
|
||||
if (renamePropRetractModel.size() > 0) {
|
||||
logger.log("Changed " + renamePropRetractModel.size() + " statement" +
|
||||
((renamePropRetractModel.size() > 1) ? "s" : "") +
|
||||
" with predicate " + propObj.getSourceURI() + " to use " +
|
||||
propObj.getDestinationURI() + " instead");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {
|
||||
|
|
|
|||
|
|
@ -24,19 +24,16 @@ import org.apache.commons.logging.Log;
|
|||
import org.apache.commons.logging.LogFactory;
|
||||
|
||||
import com.hp.hpl.jena.ontology.OntModel;
|
||||
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.Syntax;
|
||||
import com.hp.hpl.jena.query.Dataset;
|
||||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
import com.hp.hpl.jena.rdf.model.Statement;
|
||||
import com.hp.hpl.jena.rdf.model.StmtIterator;
|
||||
import com.hp.hpl.jena.shared.Lock;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
|
||||
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
|
||||
|
|
@ -123,10 +120,10 @@ public class KnowledgeBaseUpdater {
|
|||
updateABox(changes);
|
||||
|
||||
log.info("performing SPARQL CONSTRUCT additions");
|
||||
performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), readModel, writeModel, ADD);
|
||||
performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
|
||||
|
||||
log.info("performing SPARQL CONSTRUCT retractions");
|
||||
performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), readModel, writeModel, RETRACT);
|
||||
performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), settings.getRDFService(), RETRACT);
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -144,10 +141,11 @@ public class KnowledgeBaseUpdater {
|
|||
* @param add (add = true; retract = false)
|
||||
*/
|
||||
private void performSparqlConstructs(String sparqlConstructDir,
|
||||
OntModel readModel, OntModel writeModel,
|
||||
RDFService rdfService,
|
||||
boolean add) throws IOException {
|
||||
Dataset dataset = new RDFServiceDataset(rdfService);
|
||||
File sparqlConstructDirectory = new File(sparqlConstructDir);
|
||||
log.info("Using SPARQL CONSTRUCT director " + sparqlConstructDirectory);
|
||||
log.info("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
|
||||
if (!sparqlConstructDirectory.isDirectory()) {
|
||||
String logMsg = this.getClass().getName() +
|
||||
"performSparqlConstructs() expected to find a directory " +
|
||||
|
|
@ -161,7 +159,6 @@ public class KnowledgeBaseUpdater {
|
|||
Collections.sort(sparqlFiles); // queries may depend on being run in a certain order
|
||||
JenaIngestUtils jiu = new JenaIngestUtils();
|
||||
for (File sparqlFile : sparqlFiles) {
|
||||
Model anonModel = ModelFactory.createDefaultModel();
|
||||
StringBuffer fileContents = new StringBuffer();
|
||||
try {
|
||||
BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
|
||||
|
|
@ -176,59 +173,68 @@ public class KnowledgeBaseUpdater {
|
|||
log.info(logMsg);
|
||||
continue;
|
||||
}
|
||||
Model anonModel = ModelFactory.createDefaultModel();
|
||||
try {
|
||||
log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
|
||||
Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
|
||||
readModel.enterCriticalSection(Lock.READ);
|
||||
try {
|
||||
QueryExecution qe = QueryExecutionFactory.create(q, readModel);
|
||||
long numBefore = anonModel.size();
|
||||
qe.execConstruct(anonModel);
|
||||
long numAfter = anonModel.size();
|
||||
long num = numAfter - numBefore;
|
||||
if (num > 0) {
|
||||
String logMsg = (add ? "Added " : "Removed ") + num +
|
||||
" statement" + ((num > 1) ? "s" : "") +
|
||||
" using the SPARQL construct query from file " +
|
||||
sparqlFile.getParentFile().getName() +
|
||||
"/" + sparqlFile.getName();
|
||||
logger.log(logMsg);
|
||||
log.info(logMsg);
|
||||
}
|
||||
qe.close();
|
||||
} finally {
|
||||
readModel.leaveCriticalSection();
|
||||
|
||||
anonModel = RDFServiceUtils.parseModel(
|
||||
rdfService.sparqlConstructQuery(fileContents.toString(),
|
||||
RDFService.ModelSerializationFormat.NTRIPLE),
|
||||
ModelSerializationFormat.NTRIPLE);
|
||||
|
||||
long num = anonModel.size();
|
||||
if (num > 0) {
|
||||
String logMsg = (add ? "Added " : "Removed ") + num +
|
||||
" statement" + ((num > 1) ? "s" : "") +
|
||||
" using the SPARQL construct query from file " +
|
||||
sparqlFile.getParentFile().getName() +
|
||||
"/" + sparqlFile.getName();
|
||||
logger.log(logMsg);
|
||||
log.info(logMsg);
|
||||
}
|
||||
|
||||
} catch (Exception e) {
|
||||
logger.logError(this.getClass().getName() +
|
||||
".performSparqlConstructs() unable to execute " +
|
||||
"query at " + sparqlFile + ". Error message is: " + e.getMessage());
|
||||
log.error(e,e);
|
||||
}
|
||||
writeModel.enterCriticalSection(Lock.WRITE);
|
||||
try {
|
||||
if(!add) {
|
||||
writeModel.remove(anonModel);
|
||||
record.recordRetractions(anonModel);
|
||||
//log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs");
|
||||
} else {
|
||||
Model additions = jiu.renameBNodes(
|
||||
anonModel, settings.getDefaultNamespace() + "n", writeModel);
|
||||
Model actualAdditions = ModelFactory.createDefaultModel();
|
||||
StmtIterator stmtIt = additions.listStatements();
|
||||
while (stmtIt.hasNext()) {
|
||||
Statement stmt = stmtIt.nextStatement();
|
||||
if (!writeModel.contains(stmt)) {
|
||||
actualAdditions.add(stmt);
|
||||
|
||||
if(!add) {
|
||||
StmtIterator sit = anonModel.listStatements();
|
||||
while (sit.hasNext()) {
|
||||
Statement stmt = sit.nextStatement();
|
||||
Iterator<String> graphIt = dataset.listNames();
|
||||
while(graphIt.hasNext()) {
|
||||
String graph = graphIt.next();
|
||||
if(!isUpdatableABoxGraph(graph)) {
|
||||
continue;
|
||||
}
|
||||
}
|
||||
writeModel.add(actualAdditions);
|
||||
//log.info("added " + actualAdditions.size() + " statements from SPARQL CONSTRUCTs");
|
||||
record.recordAdditions(actualAdditions);
|
||||
}
|
||||
} finally {
|
||||
writeModel.leaveCriticalSection();
|
||||
Model writeModel = dataset.getNamedModel(graph);
|
||||
if (writeModel.contains(stmt)) {
|
||||
writeModel.remove(stmt);
|
||||
}
|
||||
}
|
||||
}
|
||||
record.recordRetractions(anonModel);
|
||||
//log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs");
|
||||
} else {
|
||||
Model writeModel = dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL);
|
||||
Model additions = jiu.renameBNodes(
|
||||
anonModel, settings.getDefaultNamespace() + "n", writeModel);
|
||||
Model actualAdditions = ModelFactory.createDefaultModel();
|
||||
StmtIterator stmtIt = additions.listStatements();
|
||||
while (stmtIt.hasNext()) {
|
||||
Statement stmt = stmtIt.nextStatement();
|
||||
if (!writeModel.contains(stmt)) {
|
||||
actualAdditions.add(stmt);
|
||||
}
|
||||
}
|
||||
writeModel.add(actualAdditions);
|
||||
//log.info("added " + actualAdditions.size() + " statements from SPARQL CONSTRUCTs");
|
||||
record.recordAdditions(actualAdditions);
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -245,8 +251,8 @@ public class KnowledgeBaseUpdater {
|
|||
|
||||
OntModel oldTBoxModel = settings.getOldTBoxModel();
|
||||
OntModel newTBoxModel = settings.getNewTBoxModel();
|
||||
OntModel ABoxModel = settings.getAssertionOntModelSelector().getABoxModel();
|
||||
ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, ABoxModel,settings.getNewTBoxAnnotationsModel(), logger, record);
|
||||
RDFService rdfService = settings.getRDFService();
|
||||
ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, rdfService, settings.getNewTBoxAnnotationsModel(), logger, record);
|
||||
aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
|
||||
aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
|
||||
}
|
||||
|
|
@ -366,8 +372,10 @@ public class KnowledgeBaseUpdater {
|
|||
" update to new ontology version: ", e);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
public static boolean isUpdatableABoxGraph(String graphName) {
|
||||
return (!graphName.contains("tbox") && !graphName.contains("filegraph"));
|
||||
}
|
||||
|
||||
/**
|
||||
* A class that allows to access two different ontology change lists,
|
||||
|
|
@ -434,5 +442,6 @@ public class KnowledgeBaseUpdater {
|
|||
public List<AtomicOntologyChange> getAtomicPropertyChanges() {
|
||||
return atomicPropertyChanges;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
|
|||
import com.hp.hpl.jena.ontology.OntModel;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
||||
|
||||
public class UpdateSettings {
|
||||
|
||||
|
|
@ -37,6 +38,8 @@ public class UpdateSettings {
|
|||
private OntModel newDisplayModelFromFile;
|
||||
private OntModel loadedAtStartupDisplayModel;
|
||||
private OntModel oldDisplayModelVivoListViewConfig;
|
||||
private RDFService rdfService;
|
||||
|
||||
public String getDataDir() {
|
||||
return dataDir;
|
||||
}
|
||||
|
|
@ -223,6 +226,13 @@ public class UpdateSettings {
|
|||
return this.oldDisplayModelVivoListViewConfig;
|
||||
}
|
||||
|
||||
public RDFService getRDFService() {
|
||||
return this.rdfService;
|
||||
}
|
||||
|
||||
public void setRDFService(RDFService rdfService) {
|
||||
this.rdfService = rdfService;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -41,6 +41,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
|
|||
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
||||
import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
|
||||
import edu.cornell.mannlib.vitro.webapp.ontology.update.UpdateSettings;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
|
||||
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
|
||||
|
||||
/**
|
||||
|
|
@ -95,6 +98,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
|
|||
settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
|
||||
OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "everytime").toString());
|
||||
settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
|
||||
settings.setRDFService(RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService());
|
||||
|
||||
boolean tryMigrateDisplay = true;
|
||||
try {
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue