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NIHVIVO-3498 modified VClassDaoJena.getRootClasses() to not return null; processing imports closure on ontology upload

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This commit is contained in:
brianjlowe 2011-12-14 16:53:18 +00:00
parent 5880846144
commit 83b2ca3720
4 changed files with 57 additions and 76 deletions
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3
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/ClassHierarchyListingController.java
View file

@ -88,8 +88,7 @@ public class ClassHierarchyListingController extends BaseEditController {
roots = vcDao.getRootClasses(); roots = vcDao.getRootClasses();
} }
// DEBUGGING if (roots.isEmpty()) {
if (roots == null) {
roots = new LinkedList<VClass>(); roots = new LinkedList<VClass>();
roots.add(vrequest.getFullWebappDaoFactory().getVClassDao() roots.add(vrequest.getFullWebappDaoFactory().getVClassDao()
.getTopConcept()); .getTopConcept());

3
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java
View file

@ -151,6 +151,9 @@ public class RDFUploadController extends BaseEditController {
/* ********** Do the model changes *********** */ /* ********** Do the model changes *********** */
if( !directRead && uploadModel != null ){ if( !directRead && uploadModel != null ){
uploadModel.loadImports();
long tboxstmtCount = 0L; long tboxstmtCount = 0L;
long aboxstmtCount = 0L; long aboxstmtCount = 0L;

54
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtils.java
View file

@ -91,34 +91,32 @@ public class JenaModelUtils {
ontModel.enterCriticalSection(Lock.READ); ontModel.enterCriticalSection(Lock.READ);
try { try {
try { try {
List<VClass> rootClasses = myWebappDaoFactory.getVClassDao() List<VClass> rootClasses = myWebappDaoFactory.getVClassDao()
.getRootClasses(); .getRootClasses();
if(rootClasses != null) { for (Iterator<VClass> rootClassIt = rootClasses.iterator();
for (Iterator rootClassIt = rootClasses.iterator(); rootClassIt.hasNext(); ) { rootClassIt.hasNext(); ) {
VClass rootClass = (VClass) rootClassIt.next(); VClass rootClass = (VClass) rootClassIt.next();
Individual classGroup = modelForClassgroups.createIndividual(
Individual classGroup = modelForClassgroups.createIndividual( wadf.getDefaultNamespace() + "vitroClassGroup" +
wadf.getDefaultNamespace() + "vitroClassGroup" + rootClass.getLocalName(), classGroupClass);
rootClass.getLocalName(), classGroupClass); classGroup.setLabel(rootClass.getName(), null);
classGroup.setLabel(rootClass.getName(), null);
Resource rootClassRes = modelForClassgroupAnnotations.getResource(
Resource rootClassRes = modelForClassgroupAnnotations.getResource( rootClass.getURI());
rootClass.getURI()); modelForClassgroupAnnotations.add(
modelForClassgroupAnnotations.add( rootClassRes, inClassGroupProperty, classGroup);
rootClassRes, inClassGroupProperty, classGroup); for (Iterator<String> childIt = myWebappDaoFactory.getVClassDao()
for (Iterator<String> childIt = myWebappDaoFactory.getVClassDao() .getAllSubClassURIs(rootClass.getURI()).iterator();
.getAllSubClassURIs(rootClass.getURI()).iterator(); childIt.hasNext(); ) {
childIt.hasNext(); ) { String childURI = (String) childIt.next();
String childURI = (String) childIt.next(); Resource childClass = modelForClassgroupAnnotations
Resource childClass = modelForClassgroupAnnotations .getResource(childURI);
.getResource(childURI); if (!modelForClassgroupAnnotations.contains(
if (!modelForClassgroupAnnotations.contains( childClass, inClassGroupProperty, (RDFNode) null)) {
childClass, inClassGroupProperty, (RDFNode) null)) { childClass.addProperty(inClassGroupProperty, classGroup);
childClass.addProperty(inClassGroupProperty, classGroup); }
} }
} }
}
}
} catch (Exception e) { } catch (Exception e) {
String errMsg = "Unable to create class groups automatically " + String errMsg = "Unable to create class groups automatically " +
"based on class hierarchy"; "based on class hierarchy";

73
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
View file

@ -435,19 +435,19 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
} }
public List <VClass> getAllVclasses() { public List <VClass> getAllVclasses() {
List classes = new ArrayList(); List<VClass> classes = new ArrayList<VClass>();
getOntModel().enterCriticalSection(Lock.READ); getOntModel().enterCriticalSection(Lock.READ);
try { try {
ClosableIterator classIt = getOntModel().listClasses(); ClosableIterator<OntClass> classIt = getOntModel().listClasses();
try { try {
while (classIt.hasNext()) { while (classIt.hasNext()) {
try { try {
OntClass cls = (OntClass) classIt.next(); OntClass cls = classIt.next();
if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) { if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) {
classes.add(new VClassJena(cls,getWebappDaoFactory())); classes.add(new VClassJena(cls,getWebappDaoFactory()));
} }
} catch (ClassCastException cce) { } catch (ClassCastException cce) {
cce.printStackTrace(); log.error(cce, cce);
} }
} }
} finally { } finally {
@ -459,45 +459,27 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
Collections.sort(classes); Collections.sort(classes);
return classes; return classes;
} }
/*
private boolean sameLevelOrHigher( RoleLevel userLevel, RoleLevel resourceLevel ){
if( resourceLevel == null )
return true; //default to visible
if ( userLevel == null ) { //default to PUBLIC
userLevel = BaseResourceBean.RoleLevel.PUBLIC;
}
int comparison = userLevel.compareTo(resourceLevel);
if (log.isDebugEnabled()) {
if (comparison == 0) {
log.debug("user role "+userLevel.getShorthand()+" judged equal to current user role "+resourceLevel.getShorthand());
} else if (comparison > 0) {
log.debug("user role "+userLevel.getShorthand()+" judged greater than current user role "+resourceLevel.getShorthand());
} else if (comparison < 0) {
log.debug("user role "+userLevel.getShorthand()+" judged less than current user role "+resourceLevel.getShorthand());
}
}
return ( userLevel.compareTo(resourceLevel) >= 0 );
} */
private Iterator<OntClass> smarterListHierarchyRootClasses(OntModel ontModel) {
private Iterator smarterListHierarchyRootClasses(OntModel ontModel) {
return smarterListHierarchyRootClasses(ontModel, null); return smarterListHierarchyRootClasses(ontModel, null);
} }
/** /**
* The basic idea here is that we ignore anonymous superclasses for the purpose of determining whether something is a root class. * The basic idea here is that we ignore anonymous superclasses for the purpose
* We also avoid ClassCastExceptions deep in Jena-land by eschewing Jena's listSuperClasses() method. * of determining whether something is a root class.
* We also avoid ClassCastExceptions deep in Jena-land by eschewing Jena's
* listSuperClasses() method.
* @author bjl23 * @author bjl23
*/ */
private Iterator smarterListHierarchyRootClasses(OntModel ontModel, String ontologyURI) { private Iterator<OntClass> smarterListHierarchyRootClasses(OntModel ontModel, String ontologyURI) {
List rootClassList = new ArrayList(); List<OntClass> rootClassList = new ArrayList<OntClass>();
ClosableIterator ci = ontModel.listClasses(); ClosableIterator ci = ontModel.listClasses();
try { try {
for (ClosableIterator i = ci ; i.hasNext(); ) { for (ClosableIterator i = ci ; i.hasNext(); ) {
try { try {
OntClass ontClass = (OntClass) i.next(); OntClass ontClass = (OntClass) i.next();
boolean isRoot = true; boolean isRoot = true;
for (Iterator j = ontClass.listPropertyValues(RDFS.subClassOf); j.hasNext(); ) { for (Iterator<RDFNode> j = ontClass.listPropertyValues(RDFS.subClassOf); j.hasNext(); ) {
Resource res = (Resource) j.next(); Resource res = (Resource) j.next();
if (res.canAs(OntClass.class)) { if (res.canAs(OntClass.class)) {
OntClass superClass = (OntClass) res.as(OntClass.class); OntClass superClass = (OntClass) res.as(OntClass.class);
@ -507,7 +489,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
!superClass.equals(ontClass) && !superClass.equals(ontClass) &&
!( ontModel.contains(ontClass,OWL.equivalentClass,superClass) || !( ontModel.contains(ontClass,OWL.equivalentClass,superClass) ||
ontModel.contains(superClass,OWL.equivalentClass,ontClass) ) ) { ontModel.contains(superClass,OWL.equivalentClass,ontClass) ) ) {
if ( (superClass.getNameSpace() != null) && (!(NONUSER_NAMESPACES.contains(superClass.getNameSpace()))) ) { if ( (superClass.getNameSpace() != null)
&& (!(NONUSER_NAMESPACES.contains(
superClass.getNameSpace()))) ) {
isRoot=false; isRoot=false;
break; break;
} }
@ -532,28 +516,23 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
} }
private List <VClass> getRootClasses(String ontologyURI) { private List <VClass> getRootClasses(String ontologyURI) {
List rootClasses = new ArrayList(); List<VClass> rootClasses = new ArrayList<VClass>();
getOntModel().enterCriticalSection(Lock.READ); getOntModel().enterCriticalSection(Lock.READ);
try { try {
//ClosableIterator rootIt = getOntModel().listHierarchyRootClasses(); Iterator<OntClass> rootIt = smarterListHierarchyRootClasses(
Iterator rootIt = smarterListHierarchyRootClasses(getOntModel(),ontologyURI); getOntModel(), ontologyURI);
try { while (rootIt.hasNext()) {
while (rootIt.hasNext()) { OntClass cls = rootIt.next();
try { if (!cls.isAnon() && cls.getNameSpace() != null
OntClass cls = (OntClass) rootIt.next(); && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) {
if (!cls.isAnon() && cls.getNameSpace() != null && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) { rootClasses.add(new VClassJena(cls,getWebappDaoFactory()));
rootClasses.add(new VClassJena(cls,getWebappDaoFactory()));
}
} catch (ClassCastException e) {}
} }
} finally {
//rootIt.close();
} }
Collections.sort(rootClasses); Collections.sort(rootClasses);
} finally { } finally {
getOntModel().leaveCriticalSection(); getOntModel().leaveCriticalSection();
} }
return (rootClasses.size()>0) ? rootClasses : null; return rootClasses;
} }
@ -839,7 +818,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
group.add(vcw); group.add(vcw);
} }
} }
} catch (ClassCastException cce) {cce.printStackTrace();} } catch (ClassCastException cce) {
log.error(cce, cce);
}
} }
} finally { } finally {
annotIt.close(); annotIt.close();