Removing 1.4 (and before) specific migration logic (External Concepts, display model, recomputing mostSpecificType on startup)
This commit is contained in:
stellamit
parent
24f5562626
commit
fe044c759a
6 changed files with 4 additions and 345 deletions
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@ -563,179 +563,6 @@ public class ABoxUpdater {
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propObj.getDestinationURI() + " instead");
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propObj.getDestinationURI() + " instead");
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}
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}
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}
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}
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protected void migrateExternalConcepts() throws IOException {
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Property hasResearchArea = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#hasResearchArea");
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Property researchAreaOf = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#researchAreaOf");
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Property hasSubjectArea = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#hasSubjectArea");
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Property subjectAreaFor = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#subjectAreaFor");
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Property sourceVocabularyReference = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#sourceVocabularyReference");
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Property webpage = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#webpage");
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Property linkURI = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#linkURI");
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Property linkAnchorText = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#linkAnchorText");
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HashSet<Resource> resourcesToDelete = new HashSet<Resource>();
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HashSet<Resource> resourcesToDetype = new HashSet<Resource>();
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Model additions = ModelFactory.createDefaultModel();
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Model retractions = ModelFactory.createDefaultModel();
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int subjectRefCount = 0;
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int researchRefCount = 0;
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int webpageCount = 0;
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int typeCount = 0;
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int count = 0;
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aboxModel.enterCriticalSection(Lock.WRITE);
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try {
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StmtIterator iter = aboxModel.listStatements((Resource) null, sourceVocabularyReference, (RDFNode) null);
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while (iter.hasNext()) {
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Statement stmt = iter.next();
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Resource subjectAreaResource = stmt.getSubject();
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if (!stmt.getObject().isResource()) continue;
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Resource vocabularySourceReferenceResource = stmt.getObject().asResource();
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Resource externalConceptResource = null;
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Resource webpageResource = null;
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if (subjectAreaResource.hasProperty(webpage)) {
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Statement webpageStmt = subjectAreaResource.getProperty(webpage);
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RDFNode webpageObject = webpageStmt.getObject();
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if (!webpageObject.isResource()) continue;
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webpageResource = webpageObject.asResource();
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if (!webpageResource.hasProperty(linkURI)) continue;
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Statement linkURIStmt = webpageResource.asResource().getProperty(linkURI);
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RDFNode linkURIObject = linkURIStmt.getObject();
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if (!linkURIObject.isLiteral()) continue;
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externalConceptResource = ResourceFactory.createResource(linkURIObject.asLiteral().getString());
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if (externalConceptResource == null) continue;
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resourcesToDelete.add(webpageResource.asResource());
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resourcesToDetype.add(vocabularySourceReferenceResource);
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additions.add(externalConceptResource,RDFS.isDefinedBy,vocabularySourceReferenceResource);
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additions.add(externalConceptResource, RDF.type, OWL_THING);
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Statement conceptLabelStmt = subjectAreaResource.getProperty(RDFS.label);
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if (conceptLabelStmt == null) {
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conceptLabelStmt = webpageResource.asResource().getProperty(RDFS.label);
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}
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if (conceptLabelStmt != null) {
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additions.add(externalConceptResource, RDFS.label, conceptLabelStmt.getObject().asLiteral());
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}
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} else {
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continue;
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}
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subjectRefCount += migrateConceptReferences(externalConceptResource, subjectAreaResource, hasSubjectArea, subjectAreaFor, additions);
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researchRefCount += migrateConceptReferences(externalConceptResource, subjectAreaResource, hasResearchArea, researchAreaOf, additions);
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migrateRelatedConcepts(externalConceptResource, subjectAreaResource, additions);
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resourcesToDelete.add(subjectAreaResource);
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if (webpageResource != null) {
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resourcesToDelete.add(webpageResource);
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webpageCount++;
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}
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count++;
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}
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Iterator<Resource> vsrIter = resourcesToDetype.iterator();
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while (vsrIter.hasNext()) {
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Resource resource = vsrIter.next();
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StmtIterator typeiter = resource.listProperties(RDF.type);
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while (typeiter.hasNext()) {
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Statement typeStatement = typeiter.next();
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if (!typeStatement.getObject().equals(OWL_THING)) {
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retractions.add(typeStatement);
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}
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}
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additions.add(resource, RDF.type, OWL_THING);
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typeCount++;
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}
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aboxModel.add(additions);
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aboxModel.remove(retractions);
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} finally {
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aboxModel.leaveCriticalSection();
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}
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record.recordAdditions(additions);
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record.recordRetractions(retractions);
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Iterator<Resource> iter = resourcesToDelete.iterator();
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while (iter.hasNext()) {
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Resource ind = iter.next();
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deleteIndividual(ind);
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}
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if (count > 0) {
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; logger.log("migrated " + count + " external concept" + ((count == 1) ? "" : "s") + ", which involved deleting " +
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count + " vivo:SubjectArea individual" + ((count == 1) ? "" : "s") + " and " +
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webpageCount + " vivo:URLLink individual" + ((webpageCount == 1) ? "" : "s") +
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", and changing the type for " + typeCount + " vivo:VocabularySourceReference individual" + ((typeCount == 1) ? "" : "s") + " to owl:Thing");
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}
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if (subjectRefCount > 0) {
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logger.log("migrated " + subjectRefCount + " " + hasSubjectArea.getLocalName() + " external concept reference" + ((subjectRefCount == 1) ? "" : "s"));
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}
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if (researchRefCount > 0) {
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logger.log("migrated " + researchRefCount + " " + hasResearchArea.getLocalName() + " external concept reference" + ((researchRefCount == 1) ? "" : "s"));
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}
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return;
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}
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protected int migrateConceptReferences(Resource externalConceptResource, Resource subjectArea, Property hasConcept, Property conceptOf, Model additions) throws IOException {
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int count = 0;
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aboxModel.enterCriticalSection(Lock.WRITE);
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try {
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StmtIterator iter = aboxModel.listStatements((Resource) null, hasConcept, subjectArea);
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while (iter.hasNext()) {
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Statement stmt = iter.next();
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Resource agent = stmt.getSubject();
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if (!additions.contains(agent, hasConcept, externalConceptResource)) {
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additions.add(agent, hasConcept, externalConceptResource);
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count++;
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}
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if (!additions.contains(externalConceptResource, conceptOf, agent)) {
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additions.add(externalConceptResource, conceptOf, agent);
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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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return count;
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}
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protected void migrateRelatedConcepts(Resource externalConceptResource, Resource subjectAreaResource, Model additions) throws IOException {
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Property related = ResourceFactory.createProperty("http://www.w3.org/2004/02/skos/core#related");
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aboxModel.enterCriticalSection(Lock.WRITE);
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try {
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StmtIterator iter = subjectAreaResource.listProperties(related);
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while (iter.hasNext()) {
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Statement stmt = iter.next();
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if (!stmt.getObject().isResource()) continue;
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Resource relatedConcept = stmt.getObject().asResource();
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if (!additions.contains(externalConceptResource, related, relatedConcept)) {
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additions.add(externalConceptResource, related, relatedConcept);
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}
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if (!additions.contains(relatedConcept, related, externalConceptResource)) {
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additions.add(relatedConcept, related, externalConceptResource);
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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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}
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public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {
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public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {
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logChange(oldStatement,false);
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logChange(oldStatement,false);
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@ -236,7 +236,6 @@ public class KnowledgeBaseUpdater {
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OntModel newTBoxModel = settings.getNewTBoxModel();
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OntModel newTBoxModel = settings.getNewTBoxModel();
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OntModel ABoxModel = settings.getAssertionOntModelSelector().getABoxModel();
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OntModel ABoxModel = settings.getAssertionOntModelSelector().getABoxModel();
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ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, ABoxModel,settings.getNewTBoxAnnotationsModel(), logger, record);
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ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, ABoxModel,settings.getNewTBoxAnnotationsModel(), logger, record);
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aboxUpdater.migrateExternalConcepts();
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aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
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aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
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aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
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aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
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}
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}
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@ -912,66 +912,6 @@ public class SimpleReasoner extends StatementListener {
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log.info("ABox inference model updated");
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log.info("ABox inference model updated");
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}
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}
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public synchronized void computeMostSpecificType() {
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recomputing = true;
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try {
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doComputeMostSpecificType();
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} finally {
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recomputing = false;
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}
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}
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/*
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* Special for version 1.4
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*/
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public synchronized void doComputeMostSpecificType() {
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log.info("Computing mostSpecificType annotations.");
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HashSet<String> unknownTypes = new HashSet<String>();
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try {
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String queryString = "select distinct ?subject where {?subject <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2004/02/skos/core#Concept>}";
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ArrayList<String> individuals = this.getIndividualURIs(queryString);
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int numStmts = 0;
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for (String individualURI : individuals ) {
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Resource individual = ResourceFactory.createResource(individualURI);
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try {
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setMostSpecificTypes(individual, inferenceModel, unknownTypes);
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} catch (NullPointerException npe) {
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log.error("a NullPointerException was received while computing mostSpecificType annotations. Halting inference computation.");
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return;
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} catch (JenaException je) {
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if (je.getMessage().equals("Statement models must no be null")) {
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log.error("Exception while computing mostSpecificType annotations.: " + je.getMessage() + ". Halting inference computation.");
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return;
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}
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log.error("Exception while computing mostSpecificType annotations.: " + je.getMessage());
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} catch (Exception e) {
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log.error("Exception while computing mostSpecificType annotations", e);
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}
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numStmts++;
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if ((numStmts % 10000) == 0) {
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log.info("Still computing mostSpecificType annotations...");
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}
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if (stopRequested) {
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log.info("a stopRequested signal was received during computeMostSpecificType. Halting Processing.");
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return;
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}
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}
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} catch (Exception e) {
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log.error("Exception while computing mostSpecificType annotations", e);
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return;
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}
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log.info("Finished computing mostSpecificType annotations");
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}
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public synchronized boolean isABoxReasoningAsynchronous() {
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public synchronized boolean isABoxReasoningAsynchronous() {
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if (batchMode1 || batchMode2) {
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if (batchMode1 || batchMode2) {
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return true;
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return true;
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@ -129,11 +129,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
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new Thread(new ABoxRecomputer(simpleReasoner),"ABoxRecomputer").start();
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new Thread(new ABoxRecomputer(simpleReasoner),"ABoxRecomputer").start();
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}
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}
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} else if ( isMSTComputeRequired(sce.getServletContext()) ) {
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}
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log.info("mostSpecificType computation required. It will be done in a separate thread.");
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waitForTBoxReasoning(pelletListener);
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new Thread(new MostSpecificTypeRecomputer(simpleReasoner),"MostSpecificTypeComputer").start();
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}
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SimpleReasonerTBoxListener simpleReasonerTBoxListener = new SimpleReasonerTBoxListener(simpleReasoner);
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SimpleReasonerTBoxListener simpleReasonerTBoxListener = new SimpleReasonerTBoxListener(simpleReasoner);
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sce.getServletContext().setAttribute(SimpleReasonerTBoxListener.class.getName(),simpleReasonerTBoxListener);
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sce.getServletContext().setAttribute(SimpleReasonerTBoxListener.class.getName(),simpleReasonerTBoxListener);
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@ -231,20 +227,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
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simpleReasoner.recompute();
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simpleReasoner.recompute();
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}
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}
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}
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}
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private class MostSpecificTypeRecomputer implements Runnable {
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private SimpleReasoner simpleReasoner;
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public MostSpecificTypeRecomputer(SimpleReasoner simpleReasoner) {
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this.simpleReasoner = simpleReasoner;
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}
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public void run() {
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simpleReasoner.computeMostSpecificType();
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}
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}
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/**
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/**
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* Read the names of the plugin classes classes.
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* Read the names of the plugin classes classes.
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*
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*
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@ -109,10 +109,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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try {
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try {
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if (ontologyUpdater.updateRequired()) {
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if (ontologyUpdater.updateRequired()) {
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ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
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ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
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log.info("Migrating data model");
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doMigrateDisplayModel(ctx);
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log.info("Display model migrated");
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ontologyUpdater.update();
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}
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}
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} catch (IOException ioe) {
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} catch (IOException ioe) {
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String errMsg = "IOException updating knowledge base " +
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String errMsg = "IOException updating knowledge base " +
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@ -136,56 +132,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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if (!(o instanceof OntModel)) {
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if (!(o instanceof OntModel)) {
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return;
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return;
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}
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}
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OntModel displayModel = (OntModel) o;
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OntModel displayModel = (OntModel) o;
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migrateDisplayModel(displayModel);
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}
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}
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public static void migrateDisplayModel(Model displayModel) {
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Resource browseDataGetterClass = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.BrowseDataGetter");
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Resource pageDataGetterClass = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.ClassGroupPageData");
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Resource internalDataGetterClass = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.InternalClassesDataGetter");
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Resource individualsDataGetterClass = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.IndividualsForClassesDataGetter");
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Resource homeDataGetter = ResourceFactory.createResource(DisplayVocabulary.DISPLAY_NS + "homeDataGetter");
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Property dataGetterProperty = displayModel.getProperty(DisplayVocabulary.HAS_DATA_GETTER);
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Resource homePage = displayModel.getResource(DisplayVocabulary.HOME_PAGE_URI);
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Resource classGroupPage = displayModel.getResource(DisplayVocabulary.CLASSGROUP_PAGE_TYPE);
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Resource internalClassesPage = displayModel.getResource(DisplayVocabulary.CLASSINDIVIDUALS_INTERNAL_TYPE);
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Resource individualsPage = displayModel.getResource(DisplayVocabulary.CLASSINDIVIDUALS_PAGE_TYPE);
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displayModel.add(homePage, dataGetterProperty, homeDataGetter);
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displayModel.add(homeDataGetter, RDF.type, browseDataGetterClass);
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Model additions = ModelFactory.createDefaultModel();
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Model retractions = ModelFactory.createDefaultModel();
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StmtIterator iter = displayModel.listStatements((Resource) null, RDF.type, internalClassesPage);
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while (iter.hasNext()) {
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Statement stmt = iter.next();
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retractions.add(stmt);
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additions.add(stmt.getSubject(), RDF.type, internalDataGetterClass);
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}
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iter = displayModel.listStatements((Resource) null, RDF.type, classGroupPage);
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while (iter.hasNext()) {
|
|
||||||
Statement stmt = iter.next();
|
|
||||||
retractions.add(stmt);
|
|
||||||
additions.add(stmt.getSubject(), RDF.type, pageDataGetterClass);
|
|
||||||
}
|
|
||||||
|
|
||||||
iter = displayModel.listStatements((Resource) null, RDF.type, individualsPage);
|
|
||||||
while (iter.hasNext()) {
|
|
||||||
Statement stmt = iter.next();
|
|
||||||
retractions.add(stmt);
|
|
||||||
additions.add(stmt.getSubject(), RDF.type, individualsDataGetterClass);
|
|
||||||
}
|
|
||||||
|
|
||||||
displayModel.remove(retractions);
|
|
||||||
displayModel.add(additions);
|
|
||||||
}
|
|
||||||
|
|
||||||
private OntModel loadModelFromDirectory(String directoryPath) {
|
private OntModel loadModelFromDirectory(String directoryPath) {
|
||||||
|
|
||||||
OntModel om = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
OntModel om = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||||
|
|
|
||||||
|
|
@ -12,48 +12,9 @@ import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||||
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
|
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
|
||||||
|
|
||||||
public class UpdateKnowledgeBaseTest extends AbstractTestClass {
|
public class UpdateKnowledgeBaseTest extends AbstractTestClass {
|
||||||
|
|
||||||
//@org.junit.Test
|
|
||||||
public void testMigrateDisplayModel12() {
|
|
||||||
|
|
||||||
String version12DisplayModel = "\n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#PrimaryLuceneIndex> " +
|
|
||||||
" a <http://www.w3.org/2002/07/owl#Thing> . \n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Organizations> \n" +
|
|
||||||
" a <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#ClassGroupPage> , \n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Page> ; \n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#forClassGroup> \n " +
|
|
||||||
" <http://vivoweb.org/ontology#vitroClassGrouporganizations> ; \n " +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#title> \n" +
|
|
||||||
" \"Organizations\" ; \n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#urlMapping> \n " +
|
|
||||||
" \"/organizations\" . ";
|
|
||||||
|
|
||||||
String version13DisplayModel = "\n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#SearchIndex> " +
|
|
||||||
" a <http://www.w3.org/2002/07/owl#Thing> . \n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Organizations> \n" +
|
|
||||||
" a <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Page> ; \n " +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#hasDataGetter> \n " +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#OrganizationsDataGetter1> ; " +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#title> \n " +
|
|
||||||
" \"Organizations\" ; \n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#urlMapping> \n" +
|
|
||||||
" \"/organizations\" . \n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#OrganizationsDataGetter1> \n" +
|
|
||||||
" a <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#ClassGroupPage> ; \n" +
|
|
||||||
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#forClassGroup> \n" +
|
|
||||||
" <http://vivoweb.org/ontology#vitroClassGrouporganizations> .";
|
|
||||||
|
|
||||||
Model preMigrate = ModelFactory.createDefaultModel().read(new StringReader(version12DisplayModel), null, "N3");
|
|
||||||
Model postMigrate = ModelFactory.createDefaultModel().read(new StringReader(version13DisplayModel), null, "N3");
|
|
||||||
UpdateKnowledgeBase.migrateDisplayModel(preMigrate);
|
|
||||||
Assert.assertTrue(preMigrate.isIsomorphicWith(postMigrate));
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
@org.junit.Test
|
@org.junit.Test
|
||||||
public void testMigrateDisplayModel13() {
|
public void testMigrateDisplayModel14() {
|
||||||
|
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
|
|
|
||||||
Loading…
Add table
Reference in a new issue