improving logging in the update code; refactored some class names; added an additional sparql construct to delete data
This commit is contained in:
sjm222
parent
eb7a3933e4
commit
99e1668862
11 changed files with 92 additions and 75 deletions
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@ -7,7 +7,6 @@ import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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import com.hp.hpl.jena.ontology.DatatypeProperty;
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import com.hp.hpl.jena.ontology.OntClass;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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@ -38,8 +37,8 @@ public class ABoxUpdater {
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private OntModel newTboxModel;
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private OntModel aboxModel;
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private OntModel newTBoxAnnotationsModel;
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private OntologyChangeLogger logger;
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private OntologyChangeRecord record;
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private ChangeLogger logger;
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private ChangeRecord record;
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private OntClass OWL_THING = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createClass(OWL.Thing.getURI());
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/**
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@ -59,8 +58,8 @@ public class ABoxUpdater {
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OntModel newTboxModel,
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OntModel aboxModel,
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OntModel newAnnotationsModel,
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OntologyChangeLogger logger,
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OntologyChangeRecord record) {
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ChangeLogger logger,
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ChangeRecord record) {
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this.oldTboxModel = oldTboxModel;
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this.newTboxModel = newTboxModel;
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@ -177,10 +176,12 @@ public class ABoxUpdater {
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//log summary of changes
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if (renameCount > 0) {
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logger.log("Changed " + renameCount + " subject reference" + ((renameCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class to be " + newClass.getURI());
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//logger.log("Changed " + renameCount + " subject reference" + ((renameCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class to be " + newClass.getURI());
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logger.log(renameCount + " subject reference" + ((renameCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class " + ((renameCount > 1) ? "were" : "was") +" changed to " + newClass.getURI());
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}
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if (removeCount > 0) {
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logger.log("Removed " + removeCount + " remaining subject reference" + ((removeCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class");
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//logger.log("Removed " + removeCount + " remaining subject reference" + ((removeCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class");
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logger.log(removeCount + " remaining subject reference" + ((removeCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class " + ((removeCount > 1) ? "were" : "was") + "removed." );
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}
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// Change class references in the objects of rdf:type statements
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@ -193,14 +194,12 @@ public class ABoxUpdater {
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Statement newStatement = ResourceFactory.createStatement(oldStatement.getSubject(), oldStatement.getPredicate(), newClass);
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retractions.add(oldStatement);
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additions.add(newStatement);
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//TODO - worried about logging changes before the changes have actually been made
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// in the model
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//logChanges(oldStatement, newStatement);
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}
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//log summary of changes
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if (renameCount > 0) {
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logger.log("Changed " + renameCount + " object reference" + ((renameCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class to be " + newClass.getURI());
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logger.log(renameCount + " object reference" + ((renameCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class " + ((renameCount > 1) ? "were" : "was") + " changed to " + newClass.getURI());
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//logger.log("Changed " + renameCount + " object reference" + ((renameCount > 1) ? "s" : "") + " to the " + oldClass.getURI() + " class to be " + newClass.getURI());
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}
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aboxModel.remove(retractions);
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@ -4,7 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
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import java.io.IOException;
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public interface OntologyChangeLogger {
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public interface ChangeLogger {
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public void log(String logMessage) throws IOException;
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@ -4,7 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
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import com.hp.hpl.jena.rdf.model.Model;
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public interface OntologyChangeRecord {
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public interface ChangeRecord {
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public void recordAdditions(Model incrementalAdditions);
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@ -35,8 +35,8 @@ import com.hp.hpl.jena.shared.Lock;
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public class DateTimeMigration {
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private OntModel aboxModel;
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private OntologyChangeLogger logger;
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private OntologyChangeRecord record;
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private ChangeLogger logger;
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private ChangeRecord record;
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private static final String dateTimeURI = "http://vivoweb.org/ontology/core#dateTime";
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private static final String dateTimePrecisionURI = "http://vivoweb.org/ontology/core#dateTimePrecision";
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@ -68,7 +68,7 @@ public class DateTimeMigration {
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* @param record - for writing to the additions model
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* and the retractions model.
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*/
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public DateTimeMigration(OntModel aboxModel,OntologyChangeLogger logger, OntologyChangeRecord record) {
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public DateTimeMigration(OntModel aboxModel,ChangeLogger logger, ChangeRecord record) {
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this.aboxModel = aboxModel;
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this.logger = logger;
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@ -216,7 +216,7 @@ public class DateTimeMigration {
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if (additions.size() > 0) {
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logger.log(additions.size() + " date/time literal" +
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((additions.size() > 1) ? "s" : "") + ((additions.size() > 1) ? " were " : " was ") +
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"updated to the 1.2 representation.");
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"updated to the xsd:dateTime representation.");
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}
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} finally {
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aboxModel.leaveCriticalSection();
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@ -34,18 +34,18 @@ import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
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* @author bjl23
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*
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*/
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public class OntologyUpdater {
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public class KnowledgeBaseUpdater {
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//private final Log log = LogFactory.getLog(OntologyUpdater.class);
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private OntologyUpdateSettings settings;
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private OntologyChangeLogger logger;
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private OntologyChangeRecord record;
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private UpdateSettings settings;
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private ChangeLogger logger;
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private ChangeRecord record;
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public OntologyUpdater(OntologyUpdateSettings settings) {
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public KnowledgeBaseUpdater(UpdateSettings settings) {
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this.settings = settings;
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this.logger = null;
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this.record = new SimpleOntologyChangeRecord(settings.getAddedDataFile(), settings.getRemovedDataFile());
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this.record = new SimpleChangeRecord(settings.getAddedDataFile(), settings.getRemovedDataFile());
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}
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public boolean update() throws IOException {
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@ -56,7 +56,7 @@ public class OntologyUpdater {
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if (updateRequired) {
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if (this.logger == null) {
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this.logger = new SimpleOntologyChangeLogger(settings.getLogFile(), settings.getErrorLogFile());
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this.logger = new SimpleChangeLogger(settings.getLogFile(), settings.getErrorLogFile());
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}
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try {
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@ -101,7 +101,7 @@ public class OntologyUpdater {
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private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel aboxModel) throws IOException {
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Model anonModel = performSparqlConstructs(sparqlConstructDir, aboxModel);
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Model anonModel = performSparqlConstructs(sparqlConstructDir, aboxModel, true);
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if (anonModel == null) {
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return;
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@ -110,24 +110,28 @@ public class OntologyUpdater {
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aboxModel.enterCriticalSection(Lock.WRITE);
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try {
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JenaIngestUtils jiu = new JenaIngestUtils();
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Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n",
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aboxModel);
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Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", aboxModel);
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Model actualAdditions = ModelFactory.createDefaultModel();
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StmtIterator stmtIt = additions.listStatements();
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while (stmtIt.hasNext()) {
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Statement stmt = stmtIt.nextStatement();
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if (!aboxModel.contains(stmt)) {
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actualAdditions.add(stmt);
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}
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}
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aboxModel.add(actualAdditions);
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record.recordAdditions(actualAdditions);
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/*
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if (actualAdditions.size() > 0) {
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logger.log("Constructed " + actualAdditions.size() + " new " +
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"statement"
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+ ((actualAdditions.size() > 1) ? "s" : "") +
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" using SPARQL CONSTRUCT queries.");
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" using SPARQL construct queries.");
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}
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record.recordAdditions(actualAdditions);
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*/
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} finally {
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aboxModel.leaveCriticalSection();
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}
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@ -136,7 +140,7 @@ public class OntologyUpdater {
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private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel aboxModel) throws IOException {
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Model retractions = performSparqlConstructs(sparqlConstructDir, aboxModel);
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Model retractions = performSparqlConstructs(sparqlConstructDir, aboxModel, false);
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if (retractions == null) {
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return;
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@ -153,12 +157,13 @@ public class OntologyUpdater {
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}
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}
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aboxModel.remove(actualRetractions);
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if (actualRetractions.size() > 0) {
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logger.log("Removed " + actualRetractions.size() + " statement"
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+ ((actualRetractions.size() > 1) ? "s" : "") +
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" using SPARQL CONSTRUCT queries.");
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}
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record.recordRetractions(actualRetractions);
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/*
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if (actualRetractions.size() > 0) {
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logger.log("Removed " + actualRetractions.size() + " statement" + ((actualRetractions.size() > 1) ? "s" : "") + " using SPARQL CONSTRUCT queries.");
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}
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*/
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} finally {
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aboxModel.leaveCriticalSection();
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}
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@ -174,7 +179,7 @@ public class OntologyUpdater {
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* @param aboxModel
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*/
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private Model performSparqlConstructs(String sparqlConstructDir,
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OntModel aboxModel) throws IOException {
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OntModel aboxModel, boolean add) throws IOException {
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Model anonModel = ModelFactory.createDefaultModel();
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File sparqlConstructDirectory = new File(sparqlConstructDir);
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@ -186,6 +191,7 @@ public class OntologyUpdater {
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" SPARQL CONSTRUCTS.");
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return null;
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}
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File[] sparqlFiles = sparqlConstructDirectory.listFiles();
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for (int i = 0; i < sparqlFiles.length; i ++) {
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File sparqlFile = sparqlFiles[i];
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@ -198,13 +204,21 @@ public class OntologyUpdater {
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fileContents.append(ln).append('\n');
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}
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try {
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Query q = QueryFactory.create(fileContents.toString(),
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Syntax.syntaxARQ);
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Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
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aboxModel.enterCriticalSection(Lock.WRITE);
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try {
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QueryExecution qe = QueryExecutionFactory.create(q,
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aboxModel);
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QueryExecution qe = QueryExecutionFactory.create(q, aboxModel);
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long numBefore = anonModel.size();
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qe.execConstruct(anonModel);
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long numAfter = anonModel.size();
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long num = numAfter - numBefore;
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if (num > 0) {
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logger.log((add ? "Added " : "Removed ") + num +
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" statement" + ((num > 1) ? "s" : "") +
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" using the SPARQL construct query from file " + sparqlFiles[i].getName());
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}
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} finally {
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aboxModel.leaveCriticalSection();
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}
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@ -214,9 +228,8 @@ public class OntologyUpdater {
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"query at " + sparqlFile + ". Error message is: " + e.getMessage());
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}
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} catch (FileNotFoundException fnfe) {
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logger.logError(this.getClass().getName() +
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".performSparqlConstructs() could not find " +
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" SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.");
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logger.log("WARNING: performSparqlConstructs() could not find " +
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" SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.");
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}
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}
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@ -252,8 +265,8 @@ public class OntologyUpdater {
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settings.getNewTBoxAnnotationsModel(),
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settings.getOntModelSelector().getABoxModel(), logger, record);
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tboxUpdater.updateVitroPropertyDefaultValues();
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tboxUpdater.updateVitroAnnotationsModel();
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tboxUpdater.updateDefaultAnnotationValues();
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tboxUpdater.updateAnnotationModel();
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}
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/**
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@ -23,9 +23,9 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
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public class OntologyChangeParser {
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private OntologyChangeLogger logger;
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private ChangeLogger logger;
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public OntologyChangeParser(OntologyChangeLogger logger) {
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public OntologyChangeParser(ChangeLogger logger) {
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this.logger = logger;
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}
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@ -8,14 +8,14 @@ import java.io.FileWriter;
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import java.io.IOException;
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import java.io.Writer;
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public class SimpleOntologyChangeLogger implements OntologyChangeLogger {
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public class SimpleChangeLogger implements ChangeLogger {
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private Writer logWriter;
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private Writer errorWriter;
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private boolean errorsWritten = false;
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public SimpleOntologyChangeLogger( String logPath,
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public SimpleChangeLogger( String logPath,
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String errorPath ) {
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File logFile = new File(logPath);
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File errorFile = new File(errorPath);
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@ -36,7 +36,8 @@ public class SimpleOntologyChangeLogger implements OntologyChangeLogger {
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className = className.substring(className.lastIndexOf('.') + 1 );
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String methodName = ((StackTraceElement)elements[1]).getMethodName();
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logWriter.write(className + "." + methodName + ": " + logMessage + "\n\n");
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logWriter.write(className + ": " + logMessage + "\n\n");
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//logWriter.write(className + "." + methodName + ": " + logMessage + "\n\n");
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logWriter.flush();
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}
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@ -14,10 +14,10 @@ import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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public class SimpleOntologyChangeRecord implements OntologyChangeRecord {
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public class SimpleChangeRecord implements ChangeRecord {
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private final static Log log =
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LogFactory.getLog(SimpleOntologyChangeRecord.class);
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LogFactory.getLog(SimpleChangeRecord.class);
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private final static String RDF_SYNTAX = "N3";
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@ -26,7 +26,7 @@ public class SimpleOntologyChangeRecord implements OntologyChangeRecord {
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private File additionsFile;
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private File retractionsFile;
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public SimpleOntologyChangeRecord(
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public SimpleChangeRecord(
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String additionsFile, String retractionsFile) {
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this.additionsFile = new File(additionsFile);
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try {
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@ -5,7 +5,6 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
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import java.io.IOException;
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import java.util.List;
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import com.hp.hpl.jena.ontology.DatatypeProperty;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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import com.hp.hpl.jena.rdf.model.Literal;
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@ -32,8 +31,8 @@ public class TBoxUpdater {
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private OntModel oldTboxAnnotationsModel;
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private OntModel newTboxAnnotationsModel;
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private OntModel siteModel;
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private OntologyChangeLogger logger;
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private OntologyChangeRecord record;
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private ChangeLogger logger;
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private ChangeRecord record;
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private boolean detailLogs = false;
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private static final String classGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#ClassGroup";
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@ -57,8 +56,8 @@ public class TBoxUpdater {
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public TBoxUpdater(OntModel oldTboxAnnotationsModel,
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OntModel newTboxAnnotationsModel,
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OntModel siteModel,
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OntologyChangeLogger logger,
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OntologyChangeRecord record) {
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ChangeLogger logger,
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ChangeRecord record) {
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this.oldTboxAnnotationsModel = oldTboxAnnotationsModel;
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this.newTboxAnnotationsModel = newTboxAnnotationsModel;
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@ -92,7 +91,7 @@ public class TBoxUpdater {
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* Note: as specified, this method for now assumes that no new vitro annotation
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* properties have been introduced. This should be updated for future versions.
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*/
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public void updateVitroPropertyDefaultValues() throws IOException {
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public void updateDefaultAnnotationValues() throws IOException {
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siteModel.enterCriticalSection(Lock.WRITE);
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@ -296,9 +295,9 @@ public class TBoxUpdater {
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// log the additions - summary
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if (newAnnotationSettingsToAdd.size() > 0) {
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boolean plural = (newAnnotationSettingsToAdd.size() > 1);
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logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property setting" + (plural ? "s" : "") + " to the knowledge base. This includes " +
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logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property setting" + (plural ? "s" : "") + " to the knowledge base. This includes only " +
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"existing annotation properties applied to existing classes where they weren't applied before, or existing " +
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"properties applied to new classes. No new annotation properties have been introduced.");
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"properties applied to new classes.");
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}
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} finally {
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@ -319,7 +318,7 @@ public class TBoxUpdater {
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* knowledge base.
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*
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*/
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public void updateVitroAnnotationsModel() throws IOException {
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public void updateAnnotationModel() throws IOException {
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// for each ClassGroup in the old vitro annotations model: if it is not in
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// the new vitro annotations model and the site has no classes asserted to
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@ -335,22 +334,20 @@ public void updateVitroAnnotationsModel() throws IOException {
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StmtIterator iter = oldTboxAnnotationsModel.listStatements((Resource) null, RDF.type, classGroupClass);
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int count = 0;
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while (iter.hasNext()) {
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Statement stmt = iter.next();
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|
||||
if (!newTboxAnnotationsModel.contains(stmt) && !usesGroup(siteModel, stmt.getSubject())) {
|
||||
count++;
|
||||
retractions.add(siteModel.listStatements(stmt.getSubject(),(Property) null,(RDFNode)null));
|
||||
logger.log("Removed the " + stmt.getSubject().getURI() + " ClassGroup from the annotations model.");
|
||||
}
|
||||
}
|
||||
|
||||
if (retractions.size() > 0) {
|
||||
siteModel.remove(retractions);
|
||||
record.recordRetractions(retractions);
|
||||
|
||||
logger.log("Removed " + count + " Class Group" + (count > 1 ? "s" : "") + " from the annotations model.");
|
||||
}
|
||||
}
|
||||
|
||||
} finally {
|
||||
siteModel.leaveCriticalSection();
|
||||
}
|
||||
|
|
@ -364,12 +361,19 @@ public void updateVitroAnnotationsModel() throws IOException {
|
|||
|
||||
public boolean usesGroup(Model model, Resource theClassGroup) throws IOException {
|
||||
|
||||
//logger.log("called for " + theClassGroup.getLocalName() );
|
||||
|
||||
model.enterCriticalSection(Lock.READ);
|
||||
|
||||
try {
|
||||
return (model.contains((Resource) null, inClassGroupProp, theClassGroup) ? true : false);
|
||||
StmtIterator iter = model.listStatements((Resource) null, inClassGroupProp, theClassGroup);
|
||||
while (iter.hasNext()) {
|
||||
logger.log("statement: " + ABoxUpdater.stmtString(iter.next()));
|
||||
}
|
||||
|
||||
return (model.contains((Resource) null, inClassGroupProp, theClassGroup) ? true : false);
|
||||
} finally {
|
||||
model.leaveCriticalSection();
|
||||
model.leaveCriticalSection();
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ import com.hp.hpl.jena.ontology.OntModel;
|
|||
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
|
||||
|
||||
public class OntologyUpdateSettings {
|
||||
public class UpdateSettings {
|
||||
|
||||
private String dataDir;
|
||||
private String sparqlConstructAdditionsDir;
|
||||
|
|
@ -27,8 +27,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
|
|||
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.jena.SimpleOntModelSelector;
|
||||
import edu.cornell.mannlib.vitro.webapp.ontology.update.OntologyUpdateSettings;
|
||||
import edu.cornell.mannlib.vitro.webapp.ontology.update.OntologyUpdater;
|
||||
import edu.cornell.mannlib.vitro.webapp.ontology.update.UpdateSettings;
|
||||
import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.lucene.LuceneSetup;
|
||||
|
||||
/**
|
||||
|
|
@ -71,7 +71,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
|
|||
(OntModel) sce.getServletContext().getAttribute(
|
||||
JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME));
|
||||
|
||||
OntologyUpdateSettings settings = new OntologyUpdateSettings();
|
||||
UpdateSettings settings = new UpdateSettings();
|
||||
settings.setAskQueryFile(ctx.getRealPath(ASK_QUERY_FILE));
|
||||
settings.setDataDir(ctx.getRealPath(DATA_DIR));
|
||||
settings.setSparqlConstructAdditionsDir(ctx.getRealPath(SPARQL_CONSTRUCT_ADDITIONS_DIR));
|
||||
|
|
@ -99,7 +99,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
|
|||
|
||||
try {
|
||||
|
||||
OntologyUpdater ontologyUpdater = new OntologyUpdater(settings);
|
||||
KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
|
||||
|
||||
try {
|
||||
if (ontologyUpdater.updateRequired()) {
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue