NIHVIVO-215
This commit is contained in:
sjm222
parent
ae7b5b9835
commit
174ca4dbcb
2 changed files with 170 additions and 48 deletions
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@ -10,14 +10,12 @@ import java.util.HashMap;
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import java.util.HashSet;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.Iterator;
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import java.util.List;
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import java.util.List;
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import java.util.Set;
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import org.apache.commons.logging.Log;
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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 org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
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import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
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import com.hp.hpl.jena.ontology.DatatypeProperty;
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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.OntModel;
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import com.hp.hpl.jena.ontology.OntProperty;
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import com.hp.hpl.jena.ontology.OntProperty;
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import com.hp.hpl.jena.ontology.OntResource;
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import com.hp.hpl.jena.ontology.OntResource;
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@ -575,26 +573,12 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
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ontModel.enterCriticalSection(Lock.WRITE);
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ontModel.enterCriticalSection(Lock.WRITE);
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try {
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try {
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com.hp.hpl.jena.ontology.DatatypeProperty jDataprop = ontModel.getDatatypeProperty(dtp.getURI());
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com.hp.hpl.jena.ontology.DatatypeProperty jDataprop = ontModel.getDatatypeProperty(dtp.getURI());
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if (dtp.getPublicName() == null || dtp.getPublicName().length() == 0) {
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jDataprop.removeAll(RDFS.label);
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updateRDFSLabel(jDataprop, dtp.getPublicName());
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} else {
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jDataprop.setLabel(dtp.getPublicName(), (String) getDefaultLanguage());
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updatePropertyResourceURIValue(jDataprop, RDFS.domain,dtp.getDomainClassURI(),ontModel);
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}
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updatePropertyResourceURIValue(jDataprop, RDFS.range,dtp.getRangeDatatypeURI(),ontModel);
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Resource domainRes = null;
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if ( (dtp.getDomainClassURI() != null) && (dtp.getDomainClassURI().length()>0) ) {
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domainRes = ontModel.getResource(dtp.getDomainClassURI());
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}
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jDataprop.removeAll(RDFS.domain);
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if (domainRes != null) {
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jDataprop.setDomain(domainRes);
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}
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if (dtp.getRangeDatatypeURI() != null && !dtp.getRangeDatatypeURI().equals("")) {
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Resource rangeResource = ontModel.getResource(dtp.getRangeDatatypeURI());
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if (rangeResource != null)
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jDataprop.setRange(rangeResource);
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} else {
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jDataprop.removeAll(RDFS.range);
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}
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if (dtp.getFunctional()) {
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if (dtp.getFunctional()) {
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if (!ontModel.contains(jDataprop,RDF.type,OWL.FunctionalProperty)) {
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if (!ontModel.contains(jDataprop,RDF.type,OWL.FunctionalProperty)) {
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ontModel.add(jDataprop,RDF.type,OWL.FunctionalProperty);
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ontModel.add(jDataprop,RDF.type,OWL.FunctionalProperty);
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@ -604,37 +588,25 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
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ontModel.remove(jDataprop,RDF.type,OWL.FunctionalProperty);
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ontModel.remove(jDataprop,RDF.type,OWL.FunctionalProperty);
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}
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}
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}
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}
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updatePropertyStringValue(jDataprop, EXAMPLE, dtp.getExample(), ontModel);
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updatePropertyStringValue(jDataprop, EXAMPLE, dtp.getExample(), ontModel);
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updatePropertyStringValue(jDataprop, DESCRIPTION_ANNOT, dtp.getDescription(), ontModel);
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updatePropertyStringValue(jDataprop, DESCRIPTION_ANNOT, dtp.getDescription(), ontModel);
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updatePropertyStringValue(jDataprop, PUBLIC_DESCRIPTION_ANNOT, dtp.getPublicDescription(), ontModel);
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updatePropertyStringValue(jDataprop, PUBLIC_DESCRIPTION_ANNOT, dtp.getPublicDescription(), ontModel);
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updatePropertyNonNegativeIntValue(jDataprop, DISPLAY_RANK_ANNOT, dtp.getDisplayTier(), ontModel);
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updatePropertyNonNegativeIntValue(jDataprop, DISPLAY_RANK_ANNOT, dtp.getDisplayTier(), ontModel);
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updatePropertyNonNegativeIntValue(jDataprop, DISPLAY_LIMIT, dtp.getDisplayLimit(), ontModel);
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updatePropertyNonNegativeIntValue(jDataprop, DISPLAY_LIMIT, dtp.getDisplayLimit(), ontModel);
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//updatePropertyStringValue(jDataprop, HIDDEN_ANNOT, dtp.getHidden(), ontModel);
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jDataprop.removeAll(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT);
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if (dtp.getHiddenFromDisplayBelowRoleLevel() != null) {
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if (HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT != null && dtp.getHiddenFromDisplayBelowRoleLevel() != null) { // only need to add if present
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updatePropertyResourceURIValue(jDataprop,HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT,dtp.getHiddenFromDisplayBelowRoleLevel().getURI(),ontModel);
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jDataprop.addProperty(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT, ResourceFactory.createResource(dtp.getHiddenFromDisplayBelowRoleLevel().getURI()));
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}
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}
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jDataprop.removeAll(PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT);
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if (dtp.getProhibitedFromUpdateBelowRoleLevel() != null) {
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if (PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT != null && dtp.getProhibitedFromUpdateBelowRoleLevel() != null) { // only need to add if present
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updatePropertyResourceURIValue(jDataprop,PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT,dtp.getProhibitedFromUpdateBelowRoleLevel().getURI(),ontModel);
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jDataprop.addProperty(PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT, ResourceFactory.createResource(dtp.getProhibitedFromUpdateBelowRoleLevel().getURI()));
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}
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}
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/*
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if (dtp.getGroupURI() != null) {
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updatePropertyBooleanValue(jDataprop, PROPERTY_SELFEDITPROHIBITEDANNOT, dtp.isSelfEditProhibited(), ontModel, JenaBaseDao.KEEP_ONLY_IF_TRUE);
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updatePropertyResourceURIValue(jDataprop,PROPERTY_INPROPERTYGROUPANNOT,dtp.getGroupURI(),ontModel);
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updatePropertyBooleanValue(jDataprop, PROPERTY_CURATOREDITPROHIBITEDANNOT, dtp.isCuratorEditProhibited(), ontModel, JenaBaseDao.KEEP_ONLY_IF_TRUE);
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}
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*/
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try {
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jDataprop.removeAll(PROPERTY_INPROPERTYGROUPANNOT);
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if (dtp.getGroupURI() != null && dtp.getGroupURI().length()>0) {
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String badURIErrorStr = checkURI(dtp.getGroupURI());
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if (badURIErrorStr == null) {
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jDataprop.addProperty(PROPERTY_INPROPERTYGROUPANNOT, ontModel.getResource(dtp.getGroupURI()));
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} else {
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log.error(badURIErrorStr);
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}
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}
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} catch (Exception e) {
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log.error("error linking data property "+dtp.getURI()+" to property group");
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}
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updatePropertyStringValue(jDataprop,PROPERTY_CUSTOMENTRYFORMANNOT,dtp.getCustomEntryForm(),ontModel);
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updatePropertyStringValue(jDataprop,PROPERTY_CUSTOMENTRYFORMANNOT,dtp.getCustomEntryForm(),ontModel);
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} finally {
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} finally {
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ontModel.leaveCriticalSection();
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ontModel.leaveCriticalSection();
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@ -0,0 +1,150 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.dao.jena;
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import org.junit.Assert;
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import org.junit.Test;
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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.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.vocabulary.OWL;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDFS;
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import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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/**
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*
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*
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*/
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public class DataPropertyDaoJenaTest {
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@Test
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// Test that the DataPropertyDaoJena::updateDataProperty method will only update the jena model for
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// those properties in DataProperty that have a different value from what is already in the
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// jena model for that property.
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//
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// Specifically, updateDataProperty method should not remove a statement from the model and
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// then add the same statement back in. The reason for this is that in vitro the "immutable" properties
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// are stored in a sub-model and the user-editable properties are stored in a super-model and
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// all updates are performed against the super-model, so removing and then re-adding
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// the same statement may result in a change of state (if the statement was in the sub-model
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// it will migrate to the super-model) because of the way jena handles additions and
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// deletions with respect to super and sub models. This migration of statements may cause
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// undesirable behavior in the vitro application.
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public void minimalUpdates(){
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// 1. create two models and attach one as a sub-model of the other
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// 2. populate the sub-model with one statement for each of the 13 properties represented in DataProperty
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// 3. save the state of both the sub-model and the super-model
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// 4. populate a DataProperty object with the data in the (combined) model and call the updateDataProperty
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// (having made no changes to the DataProperty object)
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// 5. verify that both the sub-model and the super-model are unchanged
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String propertyURI = "http://vivoweb.org/ontology/core#addressCity";
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OntModel superModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); // this simulates the user-editable ontology in vivo
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OntModel subModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); // this simulates the core ontology in vivo
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superModel.addSubModel(subModel);
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String rdfsLabel = "this is the rdfs label";
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String lang = "en-US";
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// populate sub-model
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DatatypeProperty property1 = subModel.createDatatypeProperty(propertyURI);
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property1.setLabel(rdfsLabel,lang);
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property1.setPropertyValue(RDFS.domain, subModel.createResource("http://thisIsTheDomainClassURI"));
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property1.setPropertyValue(RDFS.range, subModel.createResource("http://thisIsTheRangeClassURI"));
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property1.addProperty(RDF.type, OWL.FunctionalProperty);
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.EXAMPLE_ANNOT), subModel.createTypedLiteral("this is the example"));
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.DESCRIPTION_ANNOT), subModel.createTypedLiteral("this is the description"));
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.PUBLIC_DESCRIPTION_ANNOT), subModel.createTypedLiteral("this is the public description"));
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.DISPLAY_RANK_ANNOT), subModel.createTypedLiteral(21));
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.DISPLAY_LIMIT), subModel.createTypedLiteral(5));
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT), subModel.createResource("http://vitro.mannlib.cornell.edu/ns/vitro/role#curator"));
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT), subModel.createResource("http://vitro.mannlib.cornell.edu/ns/vitro/role#selfEditor"));
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.PROPERTY_INPROPERTYGROUPANNOT), subModel.createResource("http://thisIsTheInPropertyGroupURI"));
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property1.setPropertyValue(subModel.createProperty(VitroVocabulary.PROPERTY_CUSTOMENTRYFORMANNOT), subModel.createResource("http://thisIsTheCustomFormEntryURI"));
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// Save copies of sub-model and super-model
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// uncommment the next two lines to debug failures
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//System.out.println("**Before updating data property:");
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//printModels(superModel, subModel);
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superModel.removeSubModel(subModel);
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OntModel origSubModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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origSubModel.add(subModel);
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OntModel origSuperModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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origSuperModel.add(superModel);
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superModel.addSubModel(subModel);
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// Populate the DataProperty with the data in the sub-model and then update the combined model
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// (from the unchanged object).
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WebappDaoFactoryJena wdfj = new WebappDaoFactoryJena(superModel);
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DataPropertyDaoJena dpdj = (DataPropertyDaoJena) wdfj.getDataPropertyDao();
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DataProperty dataProperty = dpdj.getDataPropertyByURI(propertyURI); // the DataProperty will be populated
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// with the information already in
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// the jena model.
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Assert.assertEquals(dataProperty.getPublicName(), property1.getLabel(lang));
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dpdj.updateDataProperty(dataProperty); // we haven't changed any values here, so
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// the models should be unchanged.
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// Verify that the sub-model and super-model are both unchanged
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// uncommment the next two lines to debug failures
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//System.out.println("\n**After updating data property:");
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//printModels(superModel,subModel);
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superModel.removeSubModel(subModel);
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//modtime affects the diff but we don't care about that difference
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wipeOutModTime(origSubModel);
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wipeOutModTime(origSuperModel);
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wipeOutModTime(subModel);
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wipeOutModTime(superModel);
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Assert.assertTrue(subModel.isIsomorphicWith(origSubModel));
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Assert.assertTrue(superModel.isIsomorphicWith(origSuperModel));
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}
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void printModels(OntModel superModel, OntModel subModel) {
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// Detach the submodel for printing to get an accurate
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// account of what is in each.
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superModel.removeSubModel(subModel);
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System.out.println("\nThe sub-model has " + subModel.size() + " statements:");
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System.out.println("---------------------------------------------------");
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subModel.writeAll(System.out,"N3",null);
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System.out.println("\nThe super-model has " + superModel.size() + " statements:");
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System.out.println("---------------------------------------------------");
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superModel.write(System.out,"N3",null);
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superModel.addSubModel(subModel);
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}
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void wipeOutModTime(Model model){
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model.removeAll(null, model.createProperty(VitroVocabulary.MODTIME), null);
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}
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}
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