diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoJena.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoJena.java index 6d413d9d9..ebcfcf664 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoJena.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoJena.java @@ -50,7 +50,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement; import edu.cornell.mannlib.vitro.webapp.beans.Individual; import edu.cornell.mannlib.vitro.webapp.beans.Keyword; import edu.cornell.mannlib.vitro.webapp.beans.KeywordIndividualRelation; -import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement; import edu.cornell.mannlib.vitro.webapp.beans.VClass; import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao; import edu.cornell.mannlib.vitro.webapp.dao.InsertException; @@ -132,21 +131,21 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { } } - public List /*of Entity*/ getIndividualsByVClass(VClass vclass ) { + public List getIndividualsByVClass(VClass vclass ) { return getIndividualsByVClassURI(vclass.getURI(),-1,-1); } - public List /*of Entity*/ getIndividualsByVClassURI(String vclassURI) { + public List getIndividualsByVClassURI(String vclassURI) { return getIndividualsByVClassURI(vclassURI,-1,-1); } - public List getIndividualsByVClassURI(String vclassURI, int offset, int quantity ) { + public List getIndividualsByVClassURI(String vclassURI, int offset, int quantity ) { if (vclassURI==null) { return null; } - List ents = new ArrayList(); + List ents = new ArrayList(); Resource theClass = (vclassURI.indexOf(PSEUDO_BNODE_NS) == 0) ? getOntModel().createResource(new AnonId(vclassURI.split("#")[1])) @@ -187,7 +186,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { getOntModel().enterCriticalSection(Lock.READ); try { OntClass cls = getOntModel().getOntClass(vclassURI); - Iterator indIt = cls.listInstances(); + Iterator indIt = cls.listInstances(); while (indIt.hasNext()) { count++; } @@ -242,7 +241,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { if (ent.getName() != null) { ind.setLabel(ent.getName(), (String) getDefaultLanguage()); } - List vclasses = ent.getVClasses(false); + List vclasses = ent.getVClasses(false); if (vclasses != null) { for (Iterator typeIt = vclasses.iterator(); typeIt.hasNext(); ) { VClass vc = typeIt.next(); @@ -378,8 +377,8 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { ind.setLabel(ent.getName(), getDefaultLanguage()); } Set oldTypeURIsSet = new HashSet(); - for (Iterator typeIt = ind.listRDFTypes(true); typeIt.hasNext();) { - Resource t = (Resource) typeIt.next(); + for (Iterator typeIt = ind.listRDFTypes(true); typeIt.hasNext();) { + Resource t = typeIt.next(); if (t.getURI() != null) { oldTypeURIsSet.add(t.getURI()); } @@ -597,27 +596,27 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { entity.setVClass(getWebappDaoFactory().getVClassDao().getVClassByURI(entity.getVClassURI())); } - public List monikers( String typeURI ) { + public List monikers( String typeURI ) { getOntModel().enterCriticalSection(Lock.READ); try { HashSet monikers = new HashSet(); OntClass cls = getOntModel().getOntClass(typeURI); - Iterator inds = cls.listInstances(); + Iterator inds = cls.listInstances(); while (inds.hasNext()) { - com.hp.hpl.jena.ontology.Individual ind = (com.hp.hpl.jena.ontology.Individual) inds.next(); + OntResource ind = inds.next(); if (MONIKER != null) { - Iterator monikerIt = ind.listProperties(MONIKER); + Iterator monikerIt = ind.listProperties(MONIKER); while (monikerIt.hasNext()) { - Statement monikerStmt = (Statement) monikerIt.next(); + Statement monikerStmt = monikerIt.next(); monikers.add(((Literal)monikerStmt.getObject()).getString()); } } } List monikerList = new ArrayList(); if (monikers.size()>0) { - Iterator monikerIt = monikers.iterator(); + Iterator monikerIt = monikers.iterator(); while (monikerIt.hasNext()) { - monikerList.add((String)monikerIt.next()); + monikerList.add(monikerIt.next()); } Collections.sort(monikerList,new Comparator() { public int compare( String first, String second ) { @@ -640,10 +639,9 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { } } - @SuppressWarnings("unchecked") public List getKeywordsForIndividual(String entityURI) { KeywordDao kDao = getWebappDaoFactory().getKeywordDao(); - List keywords = new LinkedList(); + List keywords = new LinkedList(); List kirs = getWebappDaoFactory().getKeys2EntsDao().getKeywordIndividualRelationsByIndividualURI(entityURI); Iterator kirsIt = kirs.iterator(); while (kirsIt.hasNext()) { @@ -653,10 +651,9 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { return keywords; } - @SuppressWarnings("unchecked") public List getKeywordsForIndividualByMode(String entityURI, String modeStr) { KeywordDao kDao = getWebappDaoFactory().getKeywordDao(); - List keywords = new LinkedList(); + List keywords = new LinkedList(); List kirs = getWebappDaoFactory().getKeys2EntsDao().getKeywordIndividualRelationsByIndividualURI(entityURI); Iterator kirsIt = kirs.iterator(); while (kirsIt.hasNext()) { @@ -669,10 +666,9 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { return keywords; } - @SuppressWarnings("unchecked") public List getKeywordObjectsForIndividual(String entityURI) { KeywordDao kDao = getWebappDaoFactory().getKeywordDao(); - List keywords = new LinkedList(); + List keywords = new LinkedList(); List kirs = getWebappDaoFactory().getKeys2EntsDao().getKeywordIndividualRelationsByIndividualURI(entityURI); Iterator kirsIt = kirs.iterator(); while (kirsIt.hasNext()) { @@ -831,7 +827,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { getOntModel().leaveCriticalSection(); } - List rv = new ArrayList(individualsMap.size()); + List rv = new ArrayList(individualsMap.size()); rv.addAll(individualsMap.values()); return rv; } @@ -901,15 +897,15 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { return null; } - public Iterator getAllOfThisTypeIterator() { + public Iterator getAllOfThisTypeIterator() { final List list = new LinkedList(); getOntModel().enterCriticalSection(Lock.READ); try { - ClosableIterator allIndIt = getOntModel().listIndividuals(); + ClosableIterator allIndIt = getOntModel().listIndividuals(); try { while (allIndIt.hasNext()) { - com.hp.hpl.jena.ontology.Individual ind = (com.hp.hpl.jena.ontology.Individual) allIndIt.next(); + com.hp.hpl.jena.ontology.Individual ind = allIndIt.next(); //don't include anything that lacks a label, issue VIVO-119. if( getLabel(ind) == null ) @@ -917,10 +913,10 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { boolean userVisible = true; //Check for non-user visible types, maybe this should be an annotation? - ClosableIterator typeIt = ind.listRDFTypes(false); + ClosableIterator typeIt = ind.listRDFTypes(false); try { while (typeIt.hasNext()) { - Resource typeRes = (Resource) typeIt.next(); + Resource typeRes = typeIt.next(); String type = typeRes.getURI(); // brute forcing this until we implement a better strategy if (VitroVocabulary.PORTAL.equals(type) || @@ -958,12 +954,12 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { getOntModel().leaveCriticalSection(); } if (list.size() >0){ - return new Iterator(){ + return new Iterator(){ Iterator innerIt = list.iterator(); public boolean hasNext() { return innerIt.hasNext(); } - public Object next() { + public Individual next() { return new IndividualJena(innerIt.next(), (WebappDaoFactoryJena) getWebappDaoFactory()); } public void remove() { @@ -975,14 +971,14 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { return null; } - public Iterator getAllOfThisVClassIterator(String vClassURI) { + public Iterator getAllOfThisVClassIterator(String vClassURI) { getOntModel().enterCriticalSection(Lock.READ); try { - List ents = new LinkedList(); + List ents = new LinkedList(); OntClass cls = getOntModel().getOntClass(vClassURI); - Iterator indIt = cls.listInstances(); + Iterator indIt = cls.listInstances(); while (indIt.hasNext()) { - com.hp.hpl.jena.ontology.Individual ind = (com.hp.hpl.jena.ontology.Individual) indIt.next(); + OntResource ind = indIt.next(); ents.add(new IndividualJena(ind, (WebappDaoFactoryJena) getWebappDaoFactory())); } return ents.iterator(); @@ -991,8 +987,8 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { } } - public Iterator getUpdatedSinceIterator(long updatedSince){ - List ents = new ArrayList(); + public Iterator getUpdatedSinceIterator(long updatedSince){ + List ents = new ArrayList(); Date since = new DateTime(updatedSince).toDate(); String sinceStr = xsdDateTimeFormat.format(since); getOntModel().enterCriticalSection(Lock.READ); @@ -1018,10 +1014,10 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao { com.hp.hpl.jena.ontology.Individual ent = getOntModel().getIndividual(res.getURI()); if (ent != null) { boolean userVisible = false; - ClosableIterator typeIt = ent.listRDFTypes(true); + ClosableIterator typeIt = ent.listRDFTypes(true); try { while (typeIt.hasNext()) { - Resource typeRes = (Resource) typeIt.next(); + Resource typeRes = typeIt.next(); if (typeRes.getNameSpace() == null || (!NONUSER_NAMESPACES.contains(typeRes.getNameSpace()))) { userVisible = true; break;