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applying ABox update to all graphs

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brianjlowe 2013-09-12 10:37:24 -04:00
parent f7d03b6de8
commit d5c032f33e
4 changed files with 334 additions and 256 deletions
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383
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
View file

@ -14,6 +14,7 @@ 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.OntModelSpec;
import com.hp.hpl.jena.ontology.OntProperty; 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.Literal;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; 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.OWL;
import com.hp.hpl.jena.vocabulary.RDF; 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.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 * 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 final Log log = LogFactory.getLog(ABoxUpdater.class);
private OntModel oldTboxModel; private OntModel oldTboxModel;
private OntModel newTboxModel; private OntModel newTboxModel;
private OntModel aboxModel; private Dataset dataset;
private RDFService rdfService;
private OntModel newTBoxAnnotationsModel; private OntModel newTBoxAnnotationsModel;
private ChangeLogger logger; private ChangeLogger logger;
private ChangeRecord record; private ChangeRecord record;
@ -59,14 +63,15 @@ public class ABoxUpdater {
*/ */
public ABoxUpdater(OntModel oldTboxModel, public ABoxUpdater(OntModel oldTboxModel,
OntModel newTboxModel, OntModel newTboxModel,
OntModel aboxModel, RDFService rdfService,
OntModel newAnnotationsModel, OntModel newAnnotationsModel,
ChangeLogger logger, ChangeLogger logger,
ChangeRecord record) { ChangeRecord record) {
this.oldTboxModel = oldTboxModel; this.oldTboxModel = oldTboxModel;
this.newTboxModel = newTboxModel; this.newTboxModel = newTboxModel;
this.aboxModel = aboxModel; this.dataset = new RDFServiceDataset(rdfService);
this.rdfService = rdfService;
this.newTBoxAnnotationsModel = newAnnotationsModel; this.newTBoxAnnotationsModel = newAnnotationsModel;
this.logger = logger; this.logger = logger;
this.record = record; this.record = record;
@ -126,68 +131,75 @@ public class ABoxUpdater {
public void renameClass(AtomicOntologyChange change) throws IOException { 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 { 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 additions = ModelFactory.createDefaultModel();
Model retractions = ModelFactory.createDefaultModel(); Model retractions = ModelFactory.createDefaultModel();
//TODO - look for these in the models and log error if not found //TODO - look for these in the models and log error if not found
Resource oldClass = ResourceFactory.createResource(change.getSourceURI()); Resource oldClass = ResourceFactory.createResource(change.getSourceURI());
Resource newClass = ResourceFactory.createResource(change.getDestinationURI()); Resource newClass = ResourceFactory.createResource(change.getDestinationURI());
// Change class references in the subjects of statements // Change class references in the subjects of statements
// BJL 2010-04-09 : In future versions we need to keep track of // BJL 2010-04-09 : In future versions we need to keep track of
// the difference between true direct renamings and "use-insteads." // the difference between true direct renamings and "use-insteads."
// For now, the best behavior is to remove any remaining statements // For now, the best behavior is to remove any remaining statements
// where the old class is the subject, *unless* the statements // where the old class is the subject, *unless* the statements
// is part of the new annotations file (see comment below) or the // is part of the new annotations file (see comment below) or the
// predicate is vitro:autolinkedToTab. In the latter case, // predicate is vitro:autolinkedToTab. In the latter case,
// the autolinking annotation should be rewritten using the // the autolinking annotation should be rewritten using the
// new class name. // new class name.
StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null); StmtIterator iter = aboxModel.listStatements(oldClass, (Property) null, (RDFNode) null);
int removeCount = 0; int removeCount = 0;
while (iter.hasNext()) { while (iter.hasNext()) {
Statement oldStatement = iter.next(); Statement oldStatement = iter.next();
removeCount++; removeCount++;
retractions.add(oldStatement); retractions.add(oldStatement);
} }
//log summary of changes //log summary of changes
if (removeCount > 0) { if (removeCount > 0) {
logger.log("Removed " + removeCount + " subject reference" + ((removeCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class"); logger.log("Removed " + removeCount + " subject reference" + ((removeCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class");
} }
// Change class references in the objects of rdf:type statements // Change class references in the objects of rdf:type statements
iter = aboxModel.listStatements((Resource) null, RDF.type, oldClass); iter = aboxModel.listStatements((Resource) null, RDF.type, oldClass);
int renameCount = 0; int renameCount = 0;
while (iter.hasNext()) { while (iter.hasNext()) {
renameCount++; renameCount++;
Statement oldStatement = iter.next(); Statement oldStatement = iter.next();
Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), RDF.type, newClass); Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), RDF.type, newClass);
retractions.add(oldStatement); retractions.add(oldStatement);
additions.add(newStatement); additions.add(newStatement);
} }
//log summary of changes //log summary of changes
if (renameCount > 0) { if (renameCount > 0) {
logger.log("Retyped " + renameCount + " individual" + ((renameCount > 1) ? "s" : "") + " from type " + oldClass.getURI() + " to type " + newClass.getURI()); logger.log("Retyped " + renameCount + " individual" + ((renameCount > 1) ? "s" : "") + " from type " + oldClass.getURI() + " to type " + newClass.getURI());
} }
aboxModel.remove(retractions); aboxModel.remove(retractions);
record.recordRetractions(retractions); record.recordRetractions(retractions);
aboxModel.add(additions); aboxModel.add(additions);
record.recordAdditions(additions); record.recordAdditions(additions);
} finally {
aboxModel.leaveCriticalSection();
}
} finally {
aboxModel.leaveCriticalSection();
}
}
} }
/** /**
@ -233,16 +245,17 @@ public class ABoxUpdater {
if (!parentOfAddedClass.equals(OWL.Thing)) { if (!parentOfAddedClass.equals(OWL.Thing)) {
StmtIterator stmtIter = aboxModel.listStatements(null, RDF.type, parentOfAddedClass); Iterator<String> graphIt = dataset.listNames();
while(graphIt.hasNext()) {
String graph = graphIt.next();
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
continue;
}
Model aboxModel = dataset.getNamedModel(graph);
int count = stmtIter.toList().size(); StmtIterator stmtIter = aboxModel.listStatements(null, RDF.type, parentOfAddedClass);
if (count > 0) {
String indList = ""; int count = stmtIter.toList().size();
while (stmtIter.hasNext()) {
Statement stmt = stmtIter.next();
indList += "\n\t" + stmt.getSubject().getURI();
}
if (count > 0) { if (count > 0) {
//TODO - take out the detailed logging after our internal testing is completed. //TODO - take out the detailed logging after our internal testing is completed.
@ -250,7 +263,8 @@ public class ABoxUpdater {
" 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 " + ((count > 1) ? "these" : "this") + " individual" + ((count > 1) ? "s" : "") + " to see whether " + ((count > 1) ? "they" : "it") + " should be of type: " + 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 // Remove instances of the deleted class
aboxModel.enterCriticalSection(Lock.WRITE); Iterator<String> graphIt = dataset.listNames();
try { while(graphIt.hasNext()) {
int count = 0; String graph = graphIt.next();
int refCount = 0; if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass); 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()) { while (iter.hasNext()) {
count++; count++;
Statement typeStmt = iter.next(); Statement typeStmt = iter.next();
refCount = deleteIndividual(typeStmt.getSubject()); refCount = deleteIndividual(typeStmt.getSubject());
} }
if (count > 0) { if (count > 0) {
logger.log("Removed " + count + " individual" + (((count > 1) ? "s" : "") + " of type " + deletedClass.getURI()) + " (refs = " + refCount + ")"); logger.log("Removed " + count + " individual" + (((count > 1) ? "s" : "") + " of type " + deletedClass.getURI()) + " (refs = " + refCount + ")");
} }
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
} }
}
} }
protected int deleteIndividual(Resource individual) throws IOException { protected int deleteIndividual(Resource individual) throws IOException {
@ -358,29 +380,37 @@ public class ABoxUpdater {
Model retractions = ModelFactory.createDefaultModel(); Model retractions = ModelFactory.createDefaultModel();
int refCount = 0; int refCount = 0;
aboxModel.enterCriticalSection(Lock.WRITE); Iterator<String> graphIt = dataset.listNames();
try { while(graphIt.hasNext()) {
StmtIterator iter = aboxModel.listStatements(individual, (Property) null, (RDFNode) null); 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()) { while (iter.hasNext()) {
Statement subjstmt = iter.next(); Statement subjstmt = iter.next();
retractions.add(subjstmt); retractions.add(subjstmt);
} }
iter = aboxModel.listStatements((Resource) null, (Property) null, individual); iter = aboxModel.listStatements((Resource) null, (Property) null, individual);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement objstmt = iter.next(); Statement objstmt = iter.next();
retractions.add(objstmt); retractions.add(objstmt);
refCount++; refCount++;
} }
aboxModel.remove(retractions); aboxModel.remove(retractions);
record.recordRetractions(retractions); record.recordRetractions(retractions);
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
} }
}
return refCount; return refCount;
} }
@ -439,37 +469,45 @@ public class ABoxUpdater {
if (inverseOfAddedProperty != null) { if (inverseOfAddedProperty != null) {
Model additions = ModelFactory.createDefaultModel(); Model additions = ModelFactory.createDefaultModel();
aboxModel.enterCriticalSection(Lock.WRITE); 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 { try {
StmtIterator iter = aboxModel.listStatements((Resource) null, inverseOfAddedProperty, (RDFNode) null); StmtIterator iter = aboxModel.listStatements((Resource) null, inverseOfAddedProperty, (RDFNode) null);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (stmt.getObject().isResource()) { if (stmt.getObject().isResource()) {
Statement newStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), addedProperty, stmt.getSubject()); Statement newStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), addedProperty, stmt.getSubject());
additions.add(newStmt); additions.add(newStmt);
} else { } 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)); 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); aboxModel.add(additions);
record.recordAdditions(additions); record.recordAdditions(additions);
if (additions.size() > 0) { if (additions.size() > 0) {
logger.log("Added " + additions.size() + " statement" + logger.log("Added " + additions.size() + " statement" +
((additions.size() > 1) ? "s" : "") + ((additions.size() > 1) ? "s" : "") +
" with predicate " + addedProperty.getURI() + " with predicate " + addedProperty.getURI() +
" (as an inverse to existing " + inverseOfAddedProperty.getURI() + " (as an inverse to existing " + inverseOfAddedProperty.getURI() +
" statement" + ((additions.size() > 1) ? "s" : "") + ")"); " statement" + ((additions.size() > 1) ? "s" : "") + ")");
} }
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
} }
}
} }
} }
@ -507,27 +545,35 @@ public class ABoxUpdater {
} }
} }
Model deletePropModel = ModelFactory.createDefaultModel(); 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) { if (replacementProperty == null) {
aboxModel.enterCriticalSection(Lock.WRITE); aboxModel.enterCriticalSection(Lock.WRITE);
try { try {
deletePropModel.add(aboxModel.listStatements((Resource) null, deletedProperty, (RDFNode) null)); deletePropModel.add(aboxModel.listStatements((Resource) null, deletedProperty, (RDFNode) null));
aboxModel.remove(deletePropModel); aboxModel.remove(deletePropModel);
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
} }
record.recordRetractions(deletePropModel); record.recordRetractions(deletePropModel);
boolean plural = (deletePropModel.size() > 1); boolean plural = (deletePropModel.size() > 1);
if (deletePropModel.size() > 0) { if (deletePropModel.size() > 0) {
logger.log("Removed " + deletePropModel.size() + " statement" + (plural ? "s" : "") + " with predicate " + logger.log("Removed " + deletePropModel.size() + " statement" + (plural ? "s" : "") + " with predicate " +
propObj.getSourceURI()); propObj.getSourceURI());
} }
} else { } else {
AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes()); AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes());
renameProperty(chg); renameProperty(chg);
} }
}
} }
@ -548,35 +594,44 @@ public class ABoxUpdater {
return; return;
} }
Model renamePropAddModel = ModelFactory.createDefaultModel(); Iterator<String> graphIt = dataset.listNames();
Model renamePropRetractModel = ModelFactory.createDefaultModel(); while(graphIt.hasNext()) {
String graph = graphIt.next();
if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
continue;
}
Model aboxModel = dataset.getNamedModel(graph);
aboxModel.enterCriticalSection(Lock.WRITE); Model renamePropAddModel = ModelFactory.createDefaultModel();
try { Model renamePropRetractModel = ModelFactory.createDefaultModel();
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); aboxModel.enterCriticalSection(Lock.WRITE);
record.recordRetractions(renamePropRetractModel); 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();
}
if (renamePropRetractModel.size() > 0) { record.recordAdditions(renamePropAddModel);
logger.log("Changed " + renamePropRetractModel.size() + " statement" + record.recordRetractions(renamePropRetractModel);
((renamePropRetractModel.size() > 1) ? "s" : "") +
" with predicate " + propObj.getSourceURI() + " to use " + if (renamePropRetractModel.size() > 0) {
propObj.getDestinationURI() + " instead"); 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 { public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {

117
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
View file

@ -24,19 +24,16 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.query.Query; import com.hp.hpl.jena.query.Dataset;
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.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator; 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.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService; 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.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils; import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase; import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
@ -123,10 +120,10 @@ public class KnowledgeBaseUpdater {
updateABox(changes); updateABox(changes);
log.info("performing SPARQL CONSTRUCT additions"); log.info("performing SPARQL CONSTRUCT additions");
performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), readModel, writeModel, ADD); performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
log.info("performing SPARQL CONSTRUCT retractions"); 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) * @param add (add = true; retract = false)
*/ */
private void performSparqlConstructs(String sparqlConstructDir, private void performSparqlConstructs(String sparqlConstructDir,
OntModel readModel, OntModel writeModel, RDFService rdfService,
boolean add) throws IOException { boolean add) throws IOException {
Dataset dataset = new RDFServiceDataset(rdfService);
File sparqlConstructDirectory = new File(sparqlConstructDir); File sparqlConstructDirectory = new File(sparqlConstructDir);
log.info("Using SPARQL CONSTRUCT director " + sparqlConstructDirectory); log.info("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
if (!sparqlConstructDirectory.isDirectory()) { if (!sparqlConstructDirectory.isDirectory()) {
String logMsg = this.getClass().getName() + String logMsg = this.getClass().getName() +
"performSparqlConstructs() expected to find a directory " + "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 Collections.sort(sparqlFiles); // queries may depend on being run in a certain order
JenaIngestUtils jiu = new JenaIngestUtils(); JenaIngestUtils jiu = new JenaIngestUtils();
for (File sparqlFile : sparqlFiles) { for (File sparqlFile : sparqlFiles) {
Model anonModel = ModelFactory.createDefaultModel();
StringBuffer fileContents = new StringBuffer(); StringBuffer fileContents = new StringBuffer();
try { try {
BufferedReader reader = new BufferedReader(new FileReader(sparqlFile)); BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
@ -176,59 +173,68 @@ public class KnowledgeBaseUpdater {
log.info(logMsg); log.info(logMsg);
continue; continue;
} }
Model anonModel = ModelFactory.createDefaultModel();
try { try {
log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName()); log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
readModel.enterCriticalSection(Lock.READ); anonModel = RDFServiceUtils.parseModel(
try { rdfService.sparqlConstructQuery(fileContents.toString(),
QueryExecution qe = QueryExecutionFactory.create(q, readModel); RDFService.ModelSerializationFormat.NTRIPLE),
long numBefore = anonModel.size(); ModelSerializationFormat.NTRIPLE);
qe.execConstruct(anonModel);
long numAfter = anonModel.size(); long num = anonModel.size();
long num = numAfter - numBefore; if (num > 0) {
if (num > 0) { String logMsg = (add ? "Added " : "Removed ") + num +
String logMsg = (add ? "Added " : "Removed ") + num + " statement" + ((num > 1) ? "s" : "") +
" statement" + ((num > 1) ? "s" : "") + " using the SPARQL construct query from file " +
" using the SPARQL construct query from file " + sparqlFile.getParentFile().getName() +
sparqlFile.getParentFile().getName() + "/" + sparqlFile.getName();
"/" + sparqlFile.getName(); logger.log(logMsg);
logger.log(logMsg); log.info(logMsg);
log.info(logMsg);
}
qe.close();
} finally {
readModel.leaveCriticalSection();
} }
} catch (Exception e) { } catch (Exception e) {
logger.logError(this.getClass().getName() + logger.logError(this.getClass().getName() +
".performSparqlConstructs() unable to execute " + ".performSparqlConstructs() unable to execute " +
"query at " + sparqlFile + ". Error message is: " + e.getMessage()); "query at " + sparqlFile + ". Error message is: " + e.getMessage());
log.error(e,e); log.error(e,e);
} }
writeModel.enterCriticalSection(Lock.WRITE);
try { if(!add) {
if(!add) { StmtIterator sit = anonModel.listStatements();
writeModel.remove(anonModel); while (sit.hasNext()) {
record.recordRetractions(anonModel); Statement stmt = sit.nextStatement();
//log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs"); Iterator<String> graphIt = dataset.listNames();
} else { while(graphIt.hasNext()) {
Model additions = jiu.renameBNodes( String graph = graphIt.next();
anonModel, settings.getDefaultNamespace() + "n", writeModel); if(!isUpdatableABoxGraph(graph)) {
Model actualAdditions = ModelFactory.createDefaultModel(); continue;
StmtIterator stmtIt = additions.listStatements(); }
while (stmtIt.hasNext()) { Model writeModel = dataset.getNamedModel(graph);
Statement stmt = stmtIt.nextStatement(); if (writeModel.contains(stmt)) {
if (!writeModel.contains(stmt)) { writeModel.remove(stmt);
actualAdditions.add(stmt);
} }
} }
writeModel.add(actualAdditions);
//log.info("added " + actualAdditions.size() + " statements from SPARQL CONSTRUCTs");
record.recordAdditions(actualAdditions);
} }
} finally { record.recordRetractions(anonModel);
writeModel.leaveCriticalSection(); //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 oldTBoxModel = settings.getOldTBoxModel();
OntModel newTBoxModel = settings.getNewTBoxModel(); OntModel newTBoxModel = settings.getNewTBoxModel();
OntModel ABoxModel = settings.getAssertionOntModelSelector().getABoxModel(); RDFService rdfService = settings.getRDFService();
ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, ABoxModel,settings.getNewTBoxAnnotationsModel(), logger, record); ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, rdfService, settings.getNewTBoxAnnotationsModel(), logger, record);
aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges()); aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
aboxUpdater.processClassChanges(changes.getAtomicClassChanges()); aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
} }
@ -367,7 +373,9 @@ public class KnowledgeBaseUpdater {
} }
} }
public static boolean isUpdatableABoxGraph(String graphName) {
return (!graphName.contains("tbox") && !graphName.contains("filegraph"));
}
/** /**
* A class that allows to access two different ontology change lists, * A class that allows to access two different ontology change lists,
@ -434,5 +442,6 @@ public class KnowledgeBaseUpdater {
public List<AtomicOntologyChange> getAtomicPropertyChanges() { public List<AtomicOntologyChange> getAtomicPropertyChanges() {
return atomicPropertyChanges; return atomicPropertyChanges;
} }
} }
} }

10
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/UpdateSettings.java
View file

@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector; import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
public class UpdateSettings { public class UpdateSettings {
@ -37,6 +38,8 @@ public class UpdateSettings {
private OntModel newDisplayModelFromFile; private OntModel newDisplayModelFromFile;
private OntModel loadedAtStartupDisplayModel; private OntModel loadedAtStartupDisplayModel;
private OntModel oldDisplayModelVivoListViewConfig; private OntModel oldDisplayModelVivoListViewConfig;
private RDFService rdfService;
public String getDataDir() { public String getDataDir() {
return dataDir; return dataDir;
} }
@ -223,6 +226,13 @@ public class UpdateSettings {
return this.oldDisplayModelVivoListViewConfig; return this.oldDisplayModelVivoListViewConfig;
} }
public RDFService getRDFService() {
return this.rdfService;
}
public void setRDFService(RDFService rdfService) {
this.rdfService = rdfService;
}
} }

4
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -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.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater; import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
import edu.cornell.mannlib.vitro.webapp.ontology.update.UpdateSettings; 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; import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
/** /**
@ -95,6 +98,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel); settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "everytime").toString()); OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "everytime").toString());
settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel); settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
settings.setRDFService(RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService());
boolean tryMigrateDisplay = true; boolean tryMigrateDisplay = true;
try { try {