VIVO 3828: Remove SDB in preparation to moving to new Jena.

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java

@@ -73,9 +73,9 @@ public int compare (DataProperty dp1, DataProperty dp2) {
     }
 
     public DataPropertyDaoJena(RDFService rdfService,
-                               DatasetWrapperFactory dwf,
+                               DatasetWrapper dw,
                                WebappDaoFactoryJena wadf) {
-        super(rdfService, dwf, wadf);
+        super(rdfService, dw, wadf);
     }
 
     public void deleteDataProperty(DataProperty dtp) {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyStatementDaoDB.java

@@ -0,0 +1,113 @@
+/* $This file is distributed under the terms of the license in LICENSE$ */
+
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntModelSpec;
+import org.apache.jena.query.Dataset;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QueryFactory;
+import org.apache.jena.rdf.model.Literal;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
+import org.apache.jena.shared.Lock;
+import org.apache.jena.vocabulary.RDF;
+
+import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
+import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+
+/**
+ * An extension of {@link DataPropertyStatementDaoJena} for databases, such as TDB.
+ */
+public class DataPropertyStatementDaoDB extends DataPropertyStatementDaoJena implements DataPropertyStatementDao {
+
+    /**
+     * Initialize the data property statement DAO.
+     *
+     * @param dw The data wrapper.
+     * @param wadf The web application DAO factory.
+     */
+    public DataPropertyStatementDaoDB(DatasetWrapper dw, WebappDaoFactoryDB wadf) {
+        super (dw, wadf);
+    }
+
+    /**
+     * Fill existing data property statements for an individual.
+     *
+     * @param entity The individual.
+     *
+     * @return A filled out individual.
+     */
+    public Individual fillExistingDataPropertyStatementsForIndividual(Individual entity) {
+        if (entity.getURI() == null) {
+            return entity;
+        }
+
+        String query =
+            "CONSTRUCT { \n" +
+            "   <" + entity.getURI() + "> ?p ?o . \n" +
+            "} WHERE { \n" +
+            "   <" + entity.getURI() + "> ?p ?o . \n" +
+            "   FILTER(isLiteral(?o)) \n" +
+            "}" ;
+        Model results = null;
+        Dataset dataset = getDataWrapper().getDataset();
+        QueryExecution qexec = null;
+
+        dataset.getLock().enterCriticalSection(Lock.READ);
+        try {
+            qexec = QueryExecutionFactory.create(QueryFactory.create(query), dataset);
+            results = qexec.execConstruct();
+        } finally {
+            if (qexec != null) qexec.close();
+            dataset.getLock().leaveCriticalSection();
+            getDataWrapper().close();
+        }
+
+        OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, results);
+        ontModel.enterCriticalSection(Lock.READ);
+        try {
+            Resource ind = ontModel.getResource(entity.getURI());
+            List<DataPropertyStatement> edList = new ArrayList<>();
+            StmtIterator stmtIt = ind.listProperties();
+
+            while (stmtIt.hasNext()) {
+                Statement st = stmtIt.next();
+                boolean addToList = st.getObject().isLiteral() &&
+                      (
+                          (
+                              RDF.value.equals(st.getPredicate())
+                              || VitroVocabulary.value.equals(st.getPredicate().getURI()))
+                              || MONIKER.equals(st.getPredicate())
+                              || !(NONUSER_NAMESPACES.contains(st.getPredicate().getNameSpace())
+                          )
+                      );
+
+                if (addToList) {
+                    DataPropertyStatement ed = new DataPropertyStatementImpl();
+                    Literal lit = (Literal)st.getObject();
+                    fillDataPropertyStatementWithJenaLiteral(ed,lit);
+                    ed.setDatapropURI(st.getPredicate().getURI());
+                    ed.setIndividualURI(ind.getURI());
+                    ed.setIndividual(entity);
+                    edList.add(ed);
+                }
+            }
+
+            entity.setDataPropertyStatements(edList);
+            return entity;
+        } finally {
+            ontModel.leaveCriticalSection();
+        }
+    }
+}

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

@@ -50,15 +50,22 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
 {
     private static final Log log = LogFactory.getLog(DataPropertyStatementDaoJena.class);
 
+    private DatasetWrapper dw;
 
-    private DatasetWrapperFactory dwf;
-
-    public DataPropertyStatementDaoJena(DatasetWrapperFactory dwf,
+    public DataPropertyStatementDaoJena(DatasetWrapper dw,
                                         WebappDaoFactoryJena wadf) {
         super(wadf);
-        this.dwf = dwf;
+        this.dw = dw;
     }
 
+    /**
+     * Get the data wrapper.
+     * 
+     * @return The data wrapper.
+     */
+    public DatasetWrapper getDataWrapper() {
+        return dw;
+    }
 
     public void deleteDataPropertyStatement( DataPropertyStatement dataPropertyStatement )
     {
@@ -366,13 +373,11 @@ public List<Literal> getDataPropertyValuesForIndividualByProperty(String subject
 
         // Run the SPARQL query to get the properties
         List<Literal> values = new ArrayList<Literal>();
-        DatasetWrapper w = dwf.getDatasetWrapper();
-        Dataset dataset = w.getDataset();
+        Dataset dataset = dw.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);
         QueryExecution qexec = null;
         try {
-            qexec = QueryExecutionFactory.create(
-                    queryString, dataset);
+            qexec = QueryExecutionFactory.create(queryString, dataset);
             ResultSet results = qexec.execSelect();
 
             while (results.hasNext()) {
@@ -388,7 +393,7 @@ public List<Literal> getDataPropertyValuesForIndividualByProperty(String subject
 
         } finally {
             dataset.getLock().leaveCriticalSection();
-            w.close();
+            dw.close();
             if (qexec != null) {
                 qexec.close();
             }
@@ -430,8 +435,7 @@ public List<Literal> getDataPropertyValuesForIndividualByProperty(
 
         // Run the SPARQL query to get the properties
         List<Literal> values = new ArrayList<Literal>();
-        DatasetWrapper w = dwf.getDatasetWrapper();
-        Dataset dataset = w.getDataset();
+        Dataset dataset = dw.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);
         QueryExecution qexec = null;
         try {
@@ -459,7 +463,7 @@ public List<Literal> getDataPropertyValuesForIndividualByProperty(
             return Collections.emptyList();
         } finally {
             dataset.getLock().leaveCriticalSection();
-            w.close();
+            dw.close();
             if (qexec != null) {
                 qexec.close();
             }
@@ -497,8 +501,7 @@ private Model constructModelForSelectQueries(String subjectUri,
             initialBindings.add(
                     "property", ResourceFactory.createResource(propertyUri));
 
-            DatasetWrapper w = dwf.getDatasetWrapper();
-            Dataset dataset = w.getDataset();
+            Dataset dataset = dw.getDataset();
             dataset.getLock().enterCriticalSection(Lock.READ);
             QueryExecution qe = null;
             try {
@@ -512,7 +515,7 @@ private Model constructModelForSelectQueries(String subjectUri,
                     qe.close();
                 }
                 dataset.getLock().leaveCriticalSection();
-                w.close();
+                dw.close();
             }
         }
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/DatasetMode.java

@@ -0,0 +1,22 @@
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+/**
+ * Modes for optimizing database queries.
+ */
+public enum DatasetMode {
+
+    /**
+     * Only perform assertions.
+     */
+    ASSERTIONS_ONLY,
+
+    /**
+     * Only perform inferences.
+     */
+    INFERENCES_ONLY,
+
+    /**
+     * Perform both assertions and inferences.
+     */
+    ASSERTIONS_AND_INFERENCES,
+}