NIHVIVO-1761 bugfix for backend property deletion

webapp/src/edu/cornell/mannlib/vedit/controller/OperationController.java

@@ -215,7 +215,10 @@ public class OperationController extends BaseEditController {
     	Object newObj = null;
     	if (epo.getOriginalBean() != null) { // we're updating or deleting an existing bean
             if (epo.getImplementationClass() != null) {
-                newObj = OperationUtils.cloneBean(epo.getOriginalBean(), epo.getImplementationClass());
+                newObj = OperationUtils.cloneBean(
+                        epo.getOriginalBean(), 
+                        epo.getImplementationClass(), 
+                        epo.getBeanClass());
             } else {
                 newObj = OperationUtils.cloneBean(epo.getOriginalBean());
             }

webapp/src/edu/cornell/mannlib/vedit/util/OperationUtils.java

@@ -67,7 +67,7 @@ public class OperationUtils{
      * @return
      */
     public static Object cloneBean (Object bean) {
-        return cloneBean(bean, bean.getClass());
+        return cloneBean(bean, bean.getClass(), bean.getClass());
     }
 
     /**
@@ -76,39 +76,61 @@ public class OperationUtils{
      * @param bean
      * @return
      */
-    public static Object cloneBean (Object bean, Class beanClass){
+    public static Object cloneBean (Object bean, Class beanClass, Class iface){
         Object newBean = null;
         try {
             newBean = beanClass.newInstance();
-            Method[] beanMeths = beanClass.getMethods();
+            Method[] beanMeths = iface.getMethods();
-            for (int i=0; i<beanMeths.length ; ++i){
+            for (int i=0; i<beanMeths.length ; ++i) {
-                String methName = beanMeths[i].getName();
+                Method beanMeth = beanMeths[i];
-                if (methName.indexOf("get")==0){
+                String methName = beanMeth.getName();
+                if (methName.startsWith("get") 
+                        && beanMeth.getParameterTypes().length == 0 ) {
                     String fieldName = methName.substring(3,methName.length());
-                    Class returnType = beanMeths[i].getReturnType();
+                    Class returnType = beanMeth.getReturnType();
                     try {
                         Class[] args = new Class[1];
                         args[0] = returnType;
-                        Method setterMethod = beanClass.getMethod("set"+fieldName,args);
+                        Method setterMethod = iface.getMethod("set"+fieldName,args);
                         try {
-                            Object fieldVal = beanMeths[i].invoke(bean,(Object[])null);
+                            Object fieldVal = beanMeth.invoke(bean,(Object[])null);
                             try {
                                 Object[] setArgs = new Object[1];
                                 setArgs[0] = fieldVal;
                                 setterMethod.invoke(newBean,setArgs);
                             } catch (IllegalAccessException iae) {
-                                log.error("edu.cornell.mannlib.vitro.edit.utils.OperationUtils encountered IllegalAccessException invoking "+setterMethod.getName());
+                                log.error(OperationUtils.class.getName() +
+                                        ".cloneBean() " +
+                                        " encountered IllegalAccessException " +
+                                        " invoking " + 
+                                        setterMethod.getName(), iae);
+                                throw new RuntimeException(iae);
                             } catch (InvocationTargetException ite) {
-                                log.error("edu.cornell.mannlib.vitro.edit.utils.OperationUtils encountered InvocationTargetException invoking "+setterMethod.getName());
+                                log.error(OperationUtils.class.getName() +
-                                log.error(ite.getTargetException().getClass().toString());
+                                        ".cloneBean() " +
+                                        " encountered InvocationTargetException" 
+                                        + " invoking " 
+                                        + setterMethod.getName(), ite);
+                                throw new RuntimeException(ite);
                             }
                         } catch (IllegalAccessException iae) {
-                            log.error(OperationUtils.class.getName()+" encountered IllegalAccessException invoking "+beanMeths[i].getName());
+                            log.error(OperationUtils.class.getName() + 
+                                    ".cloneBean() encountered " +
+                                    " IllegalAccessException invoking " + 
+                                    beanMeths[i].getName(), iae);
+                            throw new RuntimeException(iae);
                         } catch (InvocationTargetException ite) {
-                            log.error(OperationUtils.class.getName()+" encountered InvocationTargetException invoking "+beanMeths[i].getName());
+                            log.error(OperationUtils.class.getName() + 
-                            log.error(ite.getTargetException().getClass().toString());
+                                    ".cloneBean() encountered " +
-                        } catch (IllegalArgumentException iae) {
+                                    " InvocationTargetException invoking " + 
-                            // log.error(OperationUtils.class.getName()+" found that "+beanMeths[i].getName()+" requires one or more arguments. Skipping.");
+                                    beanMeths[i].getName(), ite);
+                            throw new RuntimeException(ite);
+                        } catch (IllegalArgumentException iae) {
+                            log.error(OperationUtils.class.getName() + 
+                                    ".cloneBean() encountered " +
+                                    " IllegalArgumentException invoking " + 
+                                    beanMeths[i].getName(), iae);
+                            throw new RuntimeException(iae);
                         }
                     } catch (NoSuchMethodException nsme){
                         // ignore this field because there is no setter method

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyStatementDaoJena.java

@@ -65,26 +65,40 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
         this.dwf = dwf;
     }
 
-    public void deleteDataPropertyStatement(DataPropertyStatement dataPropertyStmt) {
-    	deleteDataPropertyStatement(dataPropertyStmt, getOntModelSelector().getABoxModel());
-    }
 
-    public void deleteDataPropertyStatement( DataPropertyStatement dataPropertyStatement, OntModel ontModel )
+    public void deleteDataPropertyStatement( DataPropertyStatement dataPropertyStatement )
     {
-    	try {
+        OntModel ontModel = getOntModelSelector().getABoxModel();
-	    	ontModel.enterCriticalSection(Lock.WRITE);
+        try {
-	    	getOntModel().getBaseModel().notifyEvent(new IndividualUpdateEvent(getWebappDaoFactory().getUserURI(),true,dataPropertyStatement.getIndividualURI()));
+            ontModel.enterCriticalSection(Lock.WRITE);
-	        com.hp.hpl.jena.ontology.Individual ind = ontModel.getIndividual(dataPropertyStatement.getIndividualURI());
+            getOntModel().getBaseModel().notifyEvent(
-	        Property prop = ontModel.getProperty(dataPropertyStatement.getDatapropURI());
+                    new IndividualUpdateEvent(
-	        Literal l = jenaLiteralFromDataPropertyStatement(dataPropertyStatement, ontModel);
+                            getWebappDaoFactory().getUserURI(),
-	        if (ind != null && prop != null && l != null) {
+                            true,
-	            ontModel.getBaseModel().remove(ind, prop, l);
+                            dataPropertyStatement.getIndividualURI()));
-	        }
+            com.hp.hpl.jena.ontology.Individual ind = ontModel.getIndividual(
-    	} finally {
+                        dataPropertyStatement.getIndividualURI());
-    		getOntModel().getBaseModel().notifyEvent(new IndividualUpdateEvent(getWebappDaoFactory().getUserURI(),false,dataPropertyStatement.getIndividualURI()));
+            OntModel tboxModel = getOntModelSelector().getTBoxModel();
-    		ontModel.leaveCriticalSection();
+            tboxModel.enterCriticalSection(Lock.READ);
-    		
+            try {
-    	}
+                Property prop = tboxModel.getProperty(
+                        dataPropertyStatement.getDatapropURI());
+                Literal l = jenaLiteralFromDataPropertyStatement(
+                        dataPropertyStatement, ontModel);
+                if (ind != null && prop != null && l != null) {
+                    ontModel.getBaseModel().remove(ind, prop, l);
+                }
+            } finally {
+                tboxModel.leaveCriticalSection();
+            }
+        } finally {
+            getOntModel().getBaseModel().notifyEvent(
+                    new IndividualUpdateEvent(
+                            getWebappDaoFactory().getUserURI(),
+                            false,
+                            dataPropertyStatement.getIndividualURI()));
+            ontModel.leaveCriticalSection();       
+        }
     }
 
     public Individual fillExistingDataPropertyStatementsForIndividual( Individual entity/*, boolean allowAnyNameSpace*/)
@@ -143,19 +157,29 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
         deleteDataPropertyStatementsForIndividualByDataProperty(individualURI, dataPropertyURI, getOntModelSelector().getABoxModel());
     }
 
-    public void deleteDataPropertyStatementsForIndividualByDataProperty(String individualURI, String dataPropertyURI, OntModel ontModel) {
+    public void deleteDataPropertyStatementsForIndividualByDataProperty(
+            String individualURI, 
+            String dataPropertyURI, 
+            OntModel ontModel) {
+        
         ontModel.enterCriticalSection(Lock.WRITE);
-        getOntModel().getBaseModel().notifyEvent(new IndividualUpdateEvent(getWebappDaoFactory().getUserURI(),true,individualURI));
+        getOntModel().getBaseModel().notifyEvent(new IndividualUpdateEvent(
+                getWebappDaoFactory().getUserURI(),
+                true,
+                individualURI));
         try {
-            Resource indRes = ontModel.getResource(individualURI);
+            Resource indRes = ResourceFactory.createResource(individualURI);
-            DatatypeProperty datatypeProperty = ontModel.getDatatypeProperty(dataPropertyURI);
+            Property datatypeProperty = ResourceFactory.createProperty(
-            if (indRes != null && datatypeProperty != null) {
+                    dataPropertyURI);
-                ontModel.removeAll(indRes, datatypeProperty, (Literal)null);
+            ontModel.removeAll(indRes, datatypeProperty, (Literal)null);
-            }
         } finally {
-        	getOntModel().getBaseModel().notifyEvent(new IndividualUpdateEvent(getWebappDaoFactory().getUserURI(),false,individualURI));
+        	getOntModel().getBaseModel().notifyEvent(new IndividualUpdateEvent(
+        	        getWebappDaoFactory().getUserURI(),
+        	        false,
+        	        individualURI));
             ontModel.leaveCriticalSection();
         }
+        
     }
 
     public void deleteDataPropertyStatementsForIndividualByDataProperty(Individual individual, DataProperty dataProperty) {

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualSDB.java

@@ -24,6 +24,7 @@ import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.ontology.OntResource;
 import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
@@ -427,15 +428,14 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         if (sunrise != null) {
             return sunrise;
         } else {
-          
+            constructProperty(ind, VitroVocabulary.SUNRISE);
         	ind.getOntModel().enterCriticalSection(Lock.READ);
             try {
                 sunrise = webappDaoFactory.getJenaBaseDao()
                         .getPropertyDateTimeValue(
                                 ind,webappDaoFactory.getJenaBaseDao().SUNRISE);
                 return sunrise;
-            } finally {
+            } finally { 
-               
             	ind.getOntModel().leaveCriticalSection();
             }
         }
@@ -445,7 +445,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         if (sunset != null) {
             return sunset;
         } else {
-           
+            constructProperty(ind, VitroVocabulary.SUNSET);
         	ind.getOntModel().enterCriticalSection(Lock.READ);
             try {
                 sunset = webappDaoFactory.getJenaBaseDao()
@@ -463,7 +463,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         if (timekey != null) {
             return timekey;
         } else {
-            
+            constructProperty(ind, VitroVocabulary.TIMEKEY);
         	ind.getOntModel().enterCriticalSection(Lock.READ);
             try {
                 timekey = webappDaoFactory.getJenaBaseDao()
@@ -554,7 +554,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         if (this.blurb != null) {
             return blurb;
         } else {
-            
+            constructProperty(ind, VitroVocabulary.BLURB);
         	ind.getOntModel().enterCriticalSection(Lock.READ);
             try {
                 blurb = webappDaoFactory.getJenaBaseDao().getPropertyStringValue(ind,webappDaoFactory.getJenaBaseDao().BLURB);
@@ -570,7 +570,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         if (this.description != null) {
             return description;
         } else {
-           
+            constructProperty(ind, VitroVocabulary.DESCRIPTION);
         	ind.getOntModel().enterCriticalSection(Lock.READ);
             try {
                 description = webappDaoFactory.getJenaBaseDao()
@@ -584,6 +584,24 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         }
     }
 
+    private synchronized void constructProperty(OntResource ind, String propertyURI) {
+        DatasetWrapper w = getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+        dataset.getLock().enterCriticalSection(Lock.READ);
+        try {
+            String queryStr = "CONSTRUCT { ?ind <" + 
+                    propertyURI + "> ?value } \n" +
+                    "WHERE { GRAPH ?g {  ?ind <" +
+                    propertyURI + "> ?value } } \n";
+            Query query = QueryFactory.create(queryStr);
+            QueryExecution qe = QueryExecutionFactory.create(
+                    query, dataset);
+            qe.execConstruct(ind.getModel());
+        } finally {
+            dataset.getLock().leaveCriticalSection();
+            w.close();
+        }
+    }
 
     public Float getSearchBoost(){ 
         if( this._searchBoostJena != null ){

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaBaseDao.java

@@ -142,7 +142,6 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     protected void addPropertyStringValue(Resource res, Property dataprop, String value, Model model) {
         if (res != null && dataprop != null && value != null && value.length()>0) {
             model.add(res, dataprop, value, XSDDatatype.XSDstring);
-            System.out.println("JenaBaseDao" + value);
         }
     }
     

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyDaoJena.java

@@ -48,7 +48,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         "PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" +
         "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#>";
     
-    private DatasetWrapperFactory dwf;
+    protected DatasetWrapperFactory dwf;
     
     public PropertyDaoJena(DatasetWrapperFactory dwf, 
                            WebappDaoFactoryJena wadf) {
@@ -396,7 +396,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         subjectBinding.add("subject", 
                 ResourceFactory.createResource(subjectUri));
 
-        // Run the SPARQL query to get the properties        
+        // Run the SPARQL query to get the properties
         DatasetWrapper w = dwf.getDatasetWrapper();
         Dataset dataset = w.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/WebappDaoFactoryJena.java

@@ -118,6 +118,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         this.userURI = userURI;
         this.flag2ValueMap = base.flag2ValueMap;
         this.flag2ClassLabelMap = base.flag2ClassLabelMap;
+        this.dwf = base.dwf;
     }
 
     public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/WebappDaoFactorySDB.java

@@ -18,6 +18,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
 public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 	
@@ -62,6 +63,18 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
         super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
         this.dwf = new ReconnectingDatasetFactory(bds, storeDesc);
     }
+    
+    public WebappDaoFactorySDB(WebappDaoFactorySDB base, String userURI) {
+        super(base.ontModelSelector);
+        this.ontModelSelector = base.ontModelSelector;
+        this.defaultNamespace = base.defaultNamespace;
+        this.nonuserNamespaces = base.nonuserNamespaces;
+        this.preferredLanguages = base.preferredLanguages;
+        this.userURI = userURI;
+        this.flag2ValueMap = base.flag2ValueMap;
+        this.flag2ClassLabelMap = base.flag2ClassLabelMap;
+        this.dwf = base.dwf;
+    }
 	
 	@Override
     public IndividualDao getIndividualDao() {
@@ -95,6 +108,11 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 			return vClassDao = new VClassDaoSDB(dwf, this);
 	}
 	
+	public WebappDaoFactory getUserAwareDaoFactory(String userURI) {
+        // TODO: put the user-aware factories in a hashmap so we don't keep re-creating them
+        return new WebappDaoFactorySDB(this, userURI);
+    }
+	
 	private class ReconnectingDatasetFactory implements DatasetWrapperFactory {
 	    
 	    private BasicDataSource _bds;