NIHVIVO-3481 fixed 'create classgroups automatically' option
This commit is contained in:
brianjlowe
parent
83c4e54a34
commit
549d489bac
2 changed files with 557 additions and 517 deletions
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@ -34,6 +34,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
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import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
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@ -80,8 +81,8 @@ public class RDFUploadController extends BaseEditController {
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String languageStr = request.getParameter("language");
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boolean makeClassgroups =
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(request.getParameter("makeClassgroups") != null);
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boolean makeClassgroups = ("true".equals(request.getParameter(
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"makeClassgroups")));
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// add directly to the ABox model without reading first into
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// a temporary in-memory model
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@ -154,32 +155,29 @@ public class RDFUploadController extends BaseEditController {
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long aboxstmtCount = 0L;
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JenaModelUtils xutil = new JenaModelUtils();
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OntModel tboxModel = getTBoxModel(
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request.getSession(), getServletContext());
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OntModel aboxModel = getABoxModel(
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request.getSession(), getServletContext());
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OntModel tboxChangeModel=null;
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Model aboxChangeModel=null;
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OntModel tboxChangeModel = null;
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Model aboxChangeModel = null;
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OntModelSelector ontModelSelector = ModelContext.getOntModelSelector(
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getServletContext());
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if (tboxModel != null) {
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boolean AGGRESSIVE = true;
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tboxChangeModel = xutil.extractTBox(uploadModel, AGGRESSIVE);
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// aggressively seek all statements that are part of the TBox
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tboxstmtCount = operateOnModel(
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request.getFullWebappDaoFactory(),
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tboxModel,tboxChangeModel,
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remove,
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makeClassgroups,
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loginBean.getUserURI());
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tboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(),
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tboxModel, tboxChangeModel, ontModelSelector,
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remove, makeClassgroups, loginBean.getUserURI());
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}
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if (aboxModel != null) {
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aboxChangeModel = uploadModel.remove(tboxChangeModel);
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aboxstmtCount = operateOnModel(
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request.getFullWebappDaoFactory(),
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aboxModel,
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aboxChangeModel,
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remove,
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makeClassgroups,
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loginBean.getUserURI());
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aboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(),
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aboxModel, aboxChangeModel, ontModelSelector,
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remove, makeClassgroups, loginBean.getUserURI());
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}
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request.setAttribute("uploadDesc", uploadDesc + ". " + verb + " " +
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(tboxstmtCount + aboxstmtCount) + " statements.");
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@ -239,11 +237,10 @@ public class RDFUploadController extends BaseEditController {
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private long operateOnModel(WebappDaoFactory webappDaoFactory,
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OntModel mainModel,
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Model changesModel,
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OntModelSelector ontModelSelector,
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boolean remove,
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boolean makeClassgroups,
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String userURI) {
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mainModel.enterCriticalSection(Lock.WRITE);
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try {
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EditEvent startEvent = null, endEvent = null;
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@ -255,18 +252,33 @@ public class RDFUploadController extends BaseEditController {
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endEvent = new EditEvent(userURI, false);
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}
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Model[] classgroupModel = null;
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if (makeClassgroups) {
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classgroupModel = JenaModelUtils.makeClassGroupsFromRootClasses(
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webappDaoFactory, changesModel);
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OntModel appMetadataModel = ontModelSelector
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.getApplicationMetadataModel();
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appMetadataModel.enterCriticalSection(Lock.WRITE);
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try {
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appMetadataModel.add(classgroupModel[0]);
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} finally {
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appMetadataModel.leaveCriticalSection();
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}
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}
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mainModel.enterCriticalSection(Lock.WRITE);
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try {
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mainModel.getBaseModel().notifyEvent(startEvent);
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try {
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if (makeClassgroups) {
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Model classgroupModel =
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JenaModelUtils.makeClassGroupsFromRootClasses(
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webappDaoFactory, changesModel, changesModel);
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mainModel.add(classgroupModel);
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}
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if (remove) {
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mainModel.remove(changesModel);
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} else {
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mainModel.add(changesModel);
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if (classgroupModel != null) {
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mainModel.add(classgroupModel[1]);
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}
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}
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} finally {
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mainModel.getBaseModel().notifyEvent(endEvent);
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@ -11,7 +11,6 @@ import java.util.Set;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
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import com.hp.hpl.jena.ontology.Individual;
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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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@ -25,6 +24,7 @@ import com.hp.hpl.jena.query.QueryFactory;
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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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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.shared.Lock;
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@ -55,13 +55,26 @@ public class JenaModelUtils {
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nonIndividualTypeURIs.add(RDF.Property.getURI());
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}
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public synchronized static void makeClassGroupsFromRootClasses(WebappDaoFactory wadf, Model ontModel) {
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makeClassGroupsFromRootClasses(wadf, ontModel, ontModel);
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}
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/**
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* Creates a set of vitro:ClassGroup resources for each root class in
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* an ontology. Also creates annotations to place each root class and all
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* of its children in the appropriate groups. In the case of multiple
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* inheritance, classgroup assignment will be arbitrary.
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* @param wadf
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* @param tboxModel containing ontology classes
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* @return resultArray of OntModels, where resultArray[0] is the model containing
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* the triples about the classgroups, and resultArray[1] is the model containing
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* annotation triples assigning ontology classes to classgroups.
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*/
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public synchronized static OntModel[] makeClassGroupsFromRootClasses(
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WebappDaoFactory wadf, Model tboxModel) {
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public synchronized static OntModel makeClassGroupsFromRootClasses(WebappDaoFactory wadf, Model baseModel, Model vitroInternalsSubmodel) {
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OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM,baseModel);
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OntModel modelForClassgroups = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
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OntModel ontModel = ModelFactory.createOntologyModel(
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OntModelSpec.OWL_DL_MEM, tboxModel);
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OntModel modelForClassgroups = ModelFactory.createOntologyModel(
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OntModelSpec.OWL_DL_MEM);
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OntModel modelForClassgroupAnnotations = ModelFactory.createOntologyModel(
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OntModelSpec.OWL_DL_MEM);
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SimpleOntModelSelector oms = new SimpleOntModelSelector();
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oms.setTBoxModel(ontModel);
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oms.setApplicationMetadataModel(modelForClassgroups);
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@ -69,38 +82,53 @@ public class JenaModelUtils {
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config.setDefaultNamespace(wadf.getDefaultNamespace());
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WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena(
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new SimpleOntModelSelector(ontModel), config, null);
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OntModel tempModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
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Resource classGroupClass = ResourceFactory.createResource(VitroVocabulary.CLASSGROUP);
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Property inClassGroupProperty = ResourceFactory.createProperty(VitroVocabulary.IN_CLASSGROUP);
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Resource classGroupClass = ResourceFactory.createResource(
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VitroVocabulary.CLASSGROUP);
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Property inClassGroupProperty = ResourceFactory.createProperty(
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VitroVocabulary.IN_CLASSGROUP);
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ontModel.enterCriticalSection(Lock.READ);
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try {
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try {
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for (Iterator rootClassIt = myWebappDaoFactory.getVClassDao().getRootClasses().iterator(); rootClassIt.hasNext(); ) {
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for (Iterator rootClassIt = myWebappDaoFactory.getVClassDao()
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.getRootClasses().iterator(); rootClassIt.hasNext(); ) {
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VClass rootClass = (VClass) rootClassIt.next();
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Individual classGroup = tempModel.createIndividual(wadf.getDefaultNamespace()+"vitroClassGroup"+rootClass.getLocalName(), classGroupClass);
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classGroup.addProperty(tempModel.getProperty(VitroVocabulary.DISPLAY_RANK_ANNOT),"50",XSDDatatype.XSDint);
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classGroup.setLabel(rootClass.getName(),null);
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OntClass rootClassOntClass = ontModel.getOntClass(rootClass.getURI());
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tempModel.add(rootClassOntClass, inClassGroupProperty, classGroup);
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for (Iterator childIt = myWebappDaoFactory.getVClassDao().getAllSubClassURIs(rootClass.getURI()).iterator(); childIt.hasNext(); ) {
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Individual classGroup = modelForClassgroups.createIndividual(
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wadf.getDefaultNamespace() + "vitroClassGroup" +
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rootClass.getLocalName(), classGroupClass);
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classGroup.setLabel(rootClass.getName(), null);
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Resource rootClassRes = modelForClassgroupAnnotations.getResource(
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rootClass.getURI());
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modelForClassgroupAnnotations.add(
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rootClassRes, inClassGroupProperty, classGroup);
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for (Iterator<String> childIt = myWebappDaoFactory.getVClassDao()
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.getAllSubClassURIs(rootClass.getURI()).iterator();
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childIt.hasNext(); ) {
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String childURI = (String) childIt.next();
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OntClass childClass = ontModel.getOntClass(childURI);
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Resource childClass = modelForClassgroupAnnotations
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.getResource(childURI);
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if (!modelForClassgroupAnnotations.contains(
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childClass, inClassGroupProperty, (RDFNode) null)) {
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childClass.addProperty(inClassGroupProperty, classGroup);
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}
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}
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} catch (Exception e) {
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log.error("Unable to create class groups automatically based on class hierarchy");
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}
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vitroInternalsSubmodel.enterCriticalSection(Lock.WRITE);
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try {
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vitroInternalsSubmodel.add(tempModel);
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} finally {
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vitroInternalsSubmodel.leaveCriticalSection();
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} catch (Exception e) {
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String errMsg = "Unable to create class groups automatically " +
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"based on class hierarchy";
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log.error(errMsg, e);
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throw new RuntimeException(errMsg, e);
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}
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} finally {
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ontModel.leaveCriticalSection();
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}
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return modelForClassgroups;
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OntModel[] resultArray = new OntModel[2];
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resultArray[0] = modelForClassgroups;
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resultArray[1] = modelForClassgroupAnnotations;
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return resultArray;
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}
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private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
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