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NIHVIVO-3481 fixed 'create classgroups automatically' option

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brianjlowe 2011-12-12 16:48:50 +00:00
parent 83c4e54a34
commit 549d489bac
2 changed files with 557 additions and 517 deletions
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62
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java
View file

@ -34,6 +34,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils; import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector; import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker; import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSpecialModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent; import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
@ -80,8 +81,8 @@ public class RDFUploadController extends BaseEditController {
String languageStr = request.getParameter("language"); String languageStr = request.getParameter("language");
boolean makeClassgroups = boolean makeClassgroups = ("true".equals(request.getParameter(
(request.getParameter("makeClassgroups") != null); "makeClassgroups")));
// add directly to the ABox model without reading first into // add directly to the ABox model without reading first into
// a temporary in-memory model // a temporary in-memory model
@ -154,32 +155,29 @@ public class RDFUploadController extends BaseEditController {
long aboxstmtCount = 0L; long aboxstmtCount = 0L;
JenaModelUtils xutil = new JenaModelUtils(); JenaModelUtils xutil = new JenaModelUtils();
OntModel tboxModel = getTBoxModel( OntModel tboxModel = getTBoxModel(
request.getSession(), getServletContext()); request.getSession(), getServletContext());
OntModel aboxModel = getABoxModel( OntModel aboxModel = getABoxModel(
request.getSession(), getServletContext()); request.getSession(), getServletContext());
OntModel tboxChangeModel=null; OntModel tboxChangeModel = null;
Model aboxChangeModel=null; Model aboxChangeModel = null;
OntModelSelector ontModelSelector = ModelContext.getOntModelSelector(
getServletContext());
if (tboxModel != null) { if (tboxModel != null) {
boolean AGGRESSIVE = true; boolean AGGRESSIVE = true;
tboxChangeModel = xutil.extractTBox(uploadModel, AGGRESSIVE); tboxChangeModel = xutil.extractTBox(uploadModel, AGGRESSIVE);
// aggressively seek all statements that are part of the TBox // aggressively seek all statements that are part of the TBox
tboxstmtCount = operateOnModel( tboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(),
request.getFullWebappDaoFactory(), tboxModel, tboxChangeModel, ontModelSelector,
tboxModel,tboxChangeModel, remove, makeClassgroups, loginBean.getUserURI());
remove,
makeClassgroups,
loginBean.getUserURI());
} }
if (aboxModel != null) { if (aboxModel != null) {
aboxChangeModel = uploadModel.remove(tboxChangeModel); aboxChangeModel = uploadModel.remove(tboxChangeModel);
aboxstmtCount = operateOnModel( aboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(),
request.getFullWebappDaoFactory(), aboxModel, aboxChangeModel, ontModelSelector,
aboxModel, remove, makeClassgroups, loginBean.getUserURI());
aboxChangeModel,
remove,
makeClassgroups,
loginBean.getUserURI());
} }
request.setAttribute("uploadDesc", uploadDesc + ". " + verb + " " + request.setAttribute("uploadDesc", uploadDesc + ". " + verb + " " +
(tboxstmtCount + aboxstmtCount) + " statements."); (tboxstmtCount + aboxstmtCount) + " statements.");
@ -239,11 +237,10 @@ public class RDFUploadController extends BaseEditController {
private long operateOnModel(WebappDaoFactory webappDaoFactory, private long operateOnModel(WebappDaoFactory webappDaoFactory,
OntModel mainModel, OntModel mainModel,
Model changesModel, Model changesModel,
OntModelSelector ontModelSelector,
boolean remove, boolean remove,
boolean makeClassgroups, boolean makeClassgroups,
String userURI) { String userURI) {
mainModel.enterCriticalSection(Lock.WRITE);
try {
EditEvent startEvent = null, endEvent = null; EditEvent startEvent = null, endEvent = null;
@ -255,18 +252,33 @@ public class RDFUploadController extends BaseEditController {
endEvent = new EditEvent(userURI, false); endEvent = new EditEvent(userURI, false);
} }
Model[] classgroupModel = null;
if (makeClassgroups) {
classgroupModel = JenaModelUtils.makeClassGroupsFromRootClasses(
webappDaoFactory, changesModel);
OntModel appMetadataModel = ontModelSelector
.getApplicationMetadataModel();
appMetadataModel.enterCriticalSection(Lock.WRITE);
try {
appMetadataModel.add(classgroupModel[0]);
} finally {
appMetadataModel.leaveCriticalSection();
}
}
mainModel.enterCriticalSection(Lock.WRITE);
try {
mainModel.getBaseModel().notifyEvent(startEvent); mainModel.getBaseModel().notifyEvent(startEvent);
try { try {
if (makeClassgroups) {
Model classgroupModel =
JenaModelUtils.makeClassGroupsFromRootClasses(
webappDaoFactory, changesModel, changesModel);
mainModel.add(classgroupModel);
}
if (remove) { if (remove) {
mainModel.remove(changesModel); mainModel.remove(changesModel);
} else { } else {
mainModel.add(changesModel); mainModel.add(changesModel);
if (classgroupModel != null) {
mainModel.add(classgroupModel[1]);
}
} }
} finally { } finally {
mainModel.getBaseModel().notifyEvent(endEvent); mainModel.getBaseModel().notifyEvent(endEvent);

80
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtils.java
View file

@ -11,7 +11,6 @@ import java.util.Set;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
import com.hp.hpl.jena.ontology.Individual; import com.hp.hpl.jena.ontology.Individual;
import com.hp.hpl.jena.ontology.OntClass; import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
@ -25,6 +24,7 @@ import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property; import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory; import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
@ -55,13 +55,26 @@ public class JenaModelUtils {
nonIndividualTypeURIs.add(RDF.Property.getURI()); nonIndividualTypeURIs.add(RDF.Property.getURI());
} }
public synchronized static void makeClassGroupsFromRootClasses(WebappDaoFactory wadf, Model ontModel) { /**
makeClassGroupsFromRootClasses(wadf, ontModel, ontModel); * Creates a set of vitro:ClassGroup resources for each root class in
} * an ontology. Also creates annotations to place each root class and all
* of its children in the appropriate groups. In the case of multiple
* inheritance, classgroup assignment will be arbitrary.
* @param wadf
* @param tboxModel containing ontology classes
* @return resultArray of OntModels, where resultArray[0] is the model containing
* the triples about the classgroups, and resultArray[1] is the model containing
* annotation triples assigning ontology classes to classgroups.
*/
public synchronized static OntModel[] makeClassGroupsFromRootClasses(
WebappDaoFactory wadf, Model tboxModel) {
public synchronized static OntModel makeClassGroupsFromRootClasses(WebappDaoFactory wadf, Model baseModel, Model vitroInternalsSubmodel) { OntModel ontModel = ModelFactory.createOntologyModel(
OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM,baseModel); OntModelSpec.OWL_DL_MEM, tboxModel);
OntModel modelForClassgroups = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM); OntModel modelForClassgroups = ModelFactory.createOntologyModel(
OntModelSpec.OWL_DL_MEM);
OntModel modelForClassgroupAnnotations = ModelFactory.createOntologyModel(
OntModelSpec.OWL_DL_MEM);
SimpleOntModelSelector oms = new SimpleOntModelSelector(); SimpleOntModelSelector oms = new SimpleOntModelSelector();
oms.setTBoxModel(ontModel); oms.setTBoxModel(ontModel);
oms.setApplicationMetadataModel(modelForClassgroups); oms.setApplicationMetadataModel(modelForClassgroups);
@ -69,38 +82,53 @@ public class JenaModelUtils {
config.setDefaultNamespace(wadf.getDefaultNamespace()); config.setDefaultNamespace(wadf.getDefaultNamespace());
WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena( WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena(
new SimpleOntModelSelector(ontModel), config, null); new SimpleOntModelSelector(ontModel), config, null);
OntModel tempModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
Resource classGroupClass = ResourceFactory.createResource(VitroVocabulary.CLASSGROUP); Resource classGroupClass = ResourceFactory.createResource(
Property inClassGroupProperty = ResourceFactory.createProperty(VitroVocabulary.IN_CLASSGROUP); VitroVocabulary.CLASSGROUP);
Property inClassGroupProperty = ResourceFactory.createProperty(
VitroVocabulary.IN_CLASSGROUP);
ontModel.enterCriticalSection(Lock.READ); ontModel.enterCriticalSection(Lock.READ);
try { try {
try { try {
for (Iterator rootClassIt = myWebappDaoFactory.getVClassDao().getRootClasses().iterator(); rootClassIt.hasNext(); ) { for (Iterator rootClassIt = myWebappDaoFactory.getVClassDao()
.getRootClasses().iterator(); rootClassIt.hasNext(); ) {
VClass rootClass = (VClass) rootClassIt.next(); VClass rootClass = (VClass) rootClassIt.next();
Individual classGroup = tempModel.createIndividual(wadf.getDefaultNamespace()+"vitroClassGroup"+rootClass.getLocalName(), classGroupClass);
classGroup.addProperty(tempModel.getProperty(VitroVocabulary.DISPLAY_RANK_ANNOT),"50",XSDDatatype.XSDint); Individual classGroup = modelForClassgroups.createIndividual(
classGroup.setLabel(rootClass.getName(),null); wadf.getDefaultNamespace() + "vitroClassGroup" +
OntClass rootClassOntClass = ontModel.getOntClass(rootClass.getURI()); rootClass.getLocalName(), classGroupClass);
tempModel.add(rootClassOntClass, inClassGroupProperty, classGroup); classGroup.setLabel(rootClass.getName(), null);
for (Iterator childIt = myWebappDaoFactory.getVClassDao().getAllSubClassURIs(rootClass.getURI()).iterator(); childIt.hasNext(); ) {
Resource rootClassRes = modelForClassgroupAnnotations.getResource(
rootClass.getURI());
modelForClassgroupAnnotations.add(
rootClassRes, inClassGroupProperty, classGroup);
for (Iterator<String> childIt = myWebappDaoFactory.getVClassDao()
.getAllSubClassURIs(rootClass.getURI()).iterator();
childIt.hasNext(); ) {
String childURI = (String) childIt.next(); String childURI = (String) childIt.next();
OntClass childClass = ontModel.getOntClass(childURI); Resource childClass = modelForClassgroupAnnotations
.getResource(childURI);
if (!modelForClassgroupAnnotations.contains(
childClass, inClassGroupProperty, (RDFNode) null)) {
childClass.addProperty(inClassGroupProperty, classGroup); childClass.addProperty(inClassGroupProperty, classGroup);
} }
} }
} catch (Exception e) {
log.error("Unable to create class groups automatically based on class hierarchy");
} }
vitroInternalsSubmodel.enterCriticalSection(Lock.WRITE); } catch (Exception e) {
try { String errMsg = "Unable to create class groups automatically " +
vitroInternalsSubmodel.add(tempModel); "based on class hierarchy";
} finally { log.error(errMsg, e);
vitroInternalsSubmodel.leaveCriticalSection(); throw new RuntimeException(errMsg, e);
} }
} finally { } finally {
ontModel.leaveCriticalSection(); ontModel.leaveCriticalSection();
} }
return modelForClassgroups; OntModel[] resultArray = new OntModel[2];
resultArray[0] = modelForClassgroups;
resultArray[1] = modelForClassgroupAnnotations;
return resultArray;
} }
private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM; private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;