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incremental development for nihvivo-3206

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This commit is contained in:
stellamit 2011-10-26 20:31:48 +00:00
parent b0b2fb98e1
commit d1b745863c
4 changed files with 53 additions and 32 deletions
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25
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
View file

@ -95,7 +95,7 @@ public class ABoxUpdater {
break; break;
case DELETE: case DELETE:
if ("Delete".equals(change.getNotes())) { if ("Delete".equals(change.getNotes())) {
deleteClass(change); deleteIndividualsOfType(change);
} else { } else {
renameClassToParent(change); renameClassToParent(change);
} }
@ -325,13 +325,13 @@ public class ABoxUpdater {
/** /**
* *
* Remove all instances of and references to a class in the abox of the knowledge base. * Remove all instances of the given class from the abox of the knowledge base.
* *
* @param change - an AtomicOntologyChange object representing a class * @param change - an AtomicOntologyChange object representing a class
* delete operation. * delete operation.
* *
*/ */
public void deleteClass(AtomicOntologyChange change) throws IOException { public void deleteIndividualsOfType(AtomicOntologyChange change) throws IOException {
//logger.log("Processing a class deletion of class " + change.getSourceURI()); //logger.log("Processing a class deletion of class " + change.getSourceURI());
@ -348,17 +348,32 @@ public class ABoxUpdater {
aboxModel.enterCriticalSection(Lock.WRITE); aboxModel.enterCriticalSection(Lock.WRITE);
try { try {
int count = 0; int count = 0;
int refCount = 0;
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass); 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();
retractions.add(typeStmt);
StmtIterator iter2 = aboxModel.listStatements(typeStmt.getSubject(), (Property) null, (RDFNode) null);
while (iter2.hasNext()) {
Statement subjstmt = iter2.next();
retractions.add(subjstmt);
}
StmtIterator iter3 = aboxModel.listStatements((Resource) null, (Property) null, typeStmt.getSubject());
while (iter3.hasNext()) {
Statement objstmt = iter3.next();
retractions.add(objstmt);
refCount++;
}
} }
//log summary of changes //log summary of changes
if (count > 0) { if (count > 0) {
logger.log("Removed " + count + " " + deletedClass.getURI() + " type assertion" + ((count > 1) ? "s" : "")); logger.log("Removed " + count + " individual " + ((count > 1) ? "s" : "" + " of type " + deletedClass.getURI()) + " (refs = " + refCount + ")");
} }
aboxModel.remove(retractions); aboxModel.remove(retractions);

52
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
View file

@ -32,11 +32,8 @@ import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils; import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
/** /**
* Performs knowledge base updates if necessary to align with a * Performs knowledge base updates necessary to align with a
* new ontology version. * new ontology version.
*
* @author bjl23
*
*/ */
public class KnowledgeBaseUpdater { public class KnowledgeBaseUpdater {
@ -90,9 +87,9 @@ public class KnowledgeBaseUpdater {
private void performUpdate() throws IOException { private void performUpdate() throws IOException {
log.info("\tperforming SPARQL construct additions (abox)"); log.info("\tperforming SPARQL construct additions (abox)");
performSparqlConstructAdditions(settings.getSparqlConstructAdditionsDir(), settings.getAssertionOntModelSelector().getABoxModel()); performSparqlConstructAdditions(settings.getSparqlConstructAdditionsDir(), settings.getUnionOntModelSelector().getABoxModel() , settings.getAssertionOntModelSelector().getABoxModel());
log.info("\tperforming SPARQL construct deletions (inferences)"); log.info("\tperforming SPARQL construct deletions (inferences)");
performSparqlConstructRetractions(settings.getSparqlConstructDeletionsDir(), settings.getInferenceOntModelSelector().getABoxModel()); performSparqlConstructRetractions(settings.getSparqlConstructDeletionsDir(), settings.getUnionOntModelSelector().getABoxModel() , settings.getAssertionOntModelSelector().getABoxModel());
List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges(); List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
@ -107,51 +104,50 @@ public class KnowledgeBaseUpdater {
updateABox(changes); updateABox(changes);
} }
private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel aboxModel) throws IOException { private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
Model anonModel = performSparqlConstructs(sparqlConstructDir, aboxModel, true); Model anonModel = performSparqlConstructs(sparqlConstructDir, readModel, true);
if (anonModel == null) { if (anonModel == null) {
return; return;
} }
aboxModel.enterCriticalSection(Lock.WRITE); writeModel.enterCriticalSection(Lock.WRITE);
try { try {
JenaIngestUtils jiu = new JenaIngestUtils(); JenaIngestUtils jiu = new JenaIngestUtils();
Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", aboxModel); Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", writeModel);
Model actualAdditions = ModelFactory.createDefaultModel(); Model actualAdditions = ModelFactory.createDefaultModel();
StmtIterator stmtIt = additions.listStatements(); StmtIterator stmtIt = additions.listStatements();
while (stmtIt.hasNext()) { while (stmtIt.hasNext()) {
Statement stmt = stmtIt.nextStatement(); Statement stmt = stmtIt.nextStatement();
if (!aboxModel.contains(stmt)) { if (!writeModel.contains(stmt)) {
actualAdditions.add(stmt); actualAdditions.add(stmt);
} }
} }
aboxModel.add(actualAdditions); writeModel.add(actualAdditions);
record.recordAdditions(actualAdditions); record.recordAdditions(actualAdditions);
} finally { } finally {
aboxModel.leaveCriticalSection(); writeModel.leaveCriticalSection();
}
} }
} private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel model) throws IOException { Model retractions = performSparqlConstructs(sparqlConstructDir, readModel, false);
Model retractions = performSparqlConstructs(sparqlConstructDir, model, false);
if (retractions == null) { if (retractions == null) {
return; return;
} }
model.enterCriticalSection(Lock.WRITE); writeModel.enterCriticalSection(Lock.WRITE);
try { try {
model.remove(retractions); writeModel.remove(retractions);
record.recordRetractions(retractions); record.recordRetractions(retractions);
} finally { } finally {
model.leaveCriticalSection(); writeModel.leaveCriticalSection();
} }
} }
@ -165,7 +161,8 @@ public class KnowledgeBaseUpdater {
* @param aboxModel * @param aboxModel
*/ */
private Model performSparqlConstructs(String sparqlConstructDir, private Model performSparqlConstructs(String sparqlConstructDir,
OntModel aboxModel, boolean add) throws IOException { OntModel readModel,
boolean add) throws IOException {
Model anonModel = ModelFactory.createDefaultModel(); Model anonModel = ModelFactory.createDefaultModel();
File sparqlConstructDirectory = new File(sparqlConstructDir); File sparqlConstructDirectory = new File(sparqlConstructDir);
@ -182,32 +179,33 @@ public class KnowledgeBaseUpdater {
for (int i = 0; i < sparqlFiles.length; i ++) { for (int i = 0; i < sparqlFiles.length; i ++) {
File sparqlFile = sparqlFiles[i]; File sparqlFile = sparqlFiles[i];
try { try {
BufferedReader reader = BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
new BufferedReader(new FileReader(sparqlFile));
StringBuffer fileContents = new StringBuffer(); StringBuffer fileContents = new StringBuffer();
String ln; String ln;
while ( (ln = reader.readLine()) != null) { while ( (ln = reader.readLine()) != null) {
fileContents.append(ln).append('\n'); fileContents.append(ln).append('\n');
} }
try { try {
log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFiles[i].getName()); log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFiles[i].getName());
Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ); Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
aboxModel.enterCriticalSection(Lock.WRITE); readModel.enterCriticalSection(Lock.READ);
try { try {
QueryExecution qe = QueryExecutionFactory.create(q, aboxModel); QueryExecution qe = QueryExecutionFactory.create(q, readModel);
long numBefore = anonModel.size(); long numBefore = anonModel.size();
qe.execConstruct(anonModel); qe.execConstruct(anonModel);
long numAfter = anonModel.size(); long numAfter = anonModel.size();
long num = numAfter - numBefore; long num = numAfter - numBefore;
if (num > 0) { if (num > 0) {
logger.log((add ? "Added " : "Removed ") + num + (add ? "" : " inferred") + logger.log((add ? "Added " : "Removed ") + num +
" statement" + ((num > 1) ? "s" : "") + " statement" + ((num > 1) ? "s" : "") +
" using the SPARQL construct query from file " + sparqlFiles[i].getName()); " using the SPARQL construct query from file " + sparqlFiles[i].getName());
} }
qe.close(); qe.close();
} finally { } finally {
aboxModel.leaveCriticalSection(); readModel.leaveCriticalSection();
} }
} catch (Exception e) { } catch (Exception e) {
logger.logError(this.getClass().getName() + logger.logError(this.getClass().getName() +

7
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/UpdateSettings.java
View file

@ -23,6 +23,7 @@ public class UpdateSettings {
private String defaultNamespace; private String defaultNamespace;
private OntModelSelector assertionOntModelSelector; private OntModelSelector assertionOntModelSelector;
private OntModelSelector inferenceOntModelSelector; private OntModelSelector inferenceOntModelSelector;
private OntModelSelector unionOntModelSelector;
private OntModel oldTBoxModel; private OntModel oldTBoxModel;
private OntModel newTBoxModel; private OntModel newTBoxModel;
private OntModel oldTBoxAnnotationsModel; private OntModel oldTBoxAnnotationsModel;
@ -82,6 +83,9 @@ public class UpdateSettings {
public OntModelSelector getInferenceOntModelSelector() { public OntModelSelector getInferenceOntModelSelector() {
return inferenceOntModelSelector; return inferenceOntModelSelector;
} }
public OntModelSelector getUnionOntModelSelector() {
return unionOntModelSelector;
}
public String getLogFile() { public String getLogFile() {
return logFile; return logFile;
} }
@ -118,6 +122,9 @@ public class UpdateSettings {
public void setInferenceOntModelSelector(OntModelSelector ontModelSelector) { public void setInferenceOntModelSelector(OntModelSelector ontModelSelector) {
this.inferenceOntModelSelector = ontModelSelector; this.inferenceOntModelSelector = ontModelSelector;
} }
public void setUnionOntModelSelector(OntModelSelector ontModelSelector) {
this.unionOntModelSelector = ontModelSelector;
}
public OntModel getOldTBoxModel() { public OntModel getOldTBoxModel() {
return oldTBoxModel; return oldTBoxModel;
} }

1
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -90,6 +90,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
settings.setDefaultNamespace(wadf.getDefaultNamespace()); settings.setDefaultNamespace(wadf.getDefaultNamespace());
settings.setAssertionOntModelSelector(ModelContext.getBaseOntModelSelector(ctx)); settings.setAssertionOntModelSelector(ModelContext.getBaseOntModelSelector(ctx));
settings.setInferenceOntModelSelector(ModelContext.getInferenceOntModelSelector(ctx)); settings.setInferenceOntModelSelector(ModelContext.getInferenceOntModelSelector(ctx));
settings.setUnionOntModelSelector(ModelContext.getUnionOntModelSelector(ctx));
try { try {
OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR)); OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));