Keep the close commands previously removed when replacing dataset wrapper with dataset.

The previous code is only closing the connection when the SDB has a connection.
This makes no sense for TDB and unless TDB is requiring a functioning SDB then this is a no-op command.

This seems wrong.
I removed the close entirely in the previous commit based on this observation.
However, I suspect that the SDB connection might still be being made even when using TDB.
Put the close back.
It also makes more sense to me to properly close things.

Author: kaladay

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

@@ -386,6 +386,7 @@ public List<Literal> getDataPropertyValuesForIndividualByProperty(String subject
 
         } finally {
             dataset.getLock().leaveCriticalSection();
+            dataset.close();
             if (qexec != null) {
                 qexec.close();
             }
@@ -454,6 +455,7 @@ public List<Literal> getDataPropertyValuesForIndividualByProperty(
             return Collections.emptyList();
         } finally {
             dataset.getLock().leaveCriticalSection();
+            dataset.close();
             if (qexec != null) {
                 qexec.close();
             }
@@ -504,6 +506,7 @@ private Model constructModelForSelectQueries(String subjectUri,
                     qe.close();
                 }
                 dataset.getLock().leaveCriticalSection();
+                dataset.close();
             }
         }
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java

@@ -397,28 +397,36 @@ private Model parseModel(ModelChange modelChange) {
     private InputStream getRDFResultStream(String query, boolean construct,
             ModelSerializationFormat resultFormat) throws RDFServiceException {
         Dataset d = getDataset();
-        Query q = createQuery(query);
-        QueryExecution qe = createQueryExecution(query, q, d);
-        ByteArrayOutputStream serializedModel = new ByteArrayOutputStream();
         try {
-            // TODO pipe this
-            Model m = construct ? qe.execConstruct() : qe.execDescribe();
-            m.write(serializedModel, getSerializationFormatString(resultFormat));
-            InputStream result = new ByteArrayInputStream(serializedModel.toByteArray());
-            return result;
+            Query q = createQuery(query);
+            QueryExecution qe = createQueryExecution(query, q, d);
+            ByteArrayOutputStream serializedModel = new ByteArrayOutputStream();
+            try {
+                // TODO pipe this
+                Model m = construct ? qe.execConstruct() : qe.execDescribe();
+                m.write(serializedModel, getSerializationFormatString(resultFormat));
+                InputStream result = new ByteArrayInputStream(serializedModel.toByteArray());
+                return result;
+            } finally {
+                qe.close();
+            }
         } finally {
-            qe.close();
+            d.close();
         }
     }
 
     private void getRDFModel(String query, boolean construct, Model model) throws RDFServiceException {
         Dataset d = getDataset();
-        Query q = createQuery(query);
-        QueryExecution qe = createQueryExecution(query, q, d);
         try {
-            Model m = construct ? qe.execConstruct(model) : qe.execDescribe(model);
+            Query q = createQuery(query);
+            QueryExecution qe = createQueryExecution(query, q, d);
+            try {
+                Model m = construct ? qe.execConstruct(model) : qe.execDescribe(model);
+            } finally {
+                qe.close();
+            }
         } finally {
-            qe.close();
+            d.close();
         }
     }
 
@@ -449,56 +457,68 @@ public InputStream sparqlDescribeQuery(String query,
     public InputStream sparqlSelectQuery(String query, ResultFormat resultFormat)
             throws RDFServiceException {
         Dataset d = getDataset();
-        Query q = createQuery(query);
-        QueryExecution qe = createQueryExecution(query, q, d);
         try {
-            ResultSet resultSet = qe.execSelect();
-            ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
-            switch (resultFormat) {
-               case CSV:
-                  ResultSetFormatter.outputAsCSV(outputStream,resultSet);
-                  break;
-               case TEXT:
-                  ResultSetFormatter.out(outputStream,resultSet);
-                  break;
-               case JSON:
-                  ResultSetFormatter.outputAsJSON(outputStream, resultSet);
-                  break;
-               case XML:
-                  ResultSetFormatter.outputAsXML(outputStream, resultSet);
-                  break;
-               default:
-                  throw new RDFServiceException("unrecognized result format");
+            Query q = createQuery(query);
+            QueryExecution qe = createQueryExecution(query, q, d);
+            try {
+                ResultSet resultSet = qe.execSelect();
+                ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+                switch (resultFormat) {
+                   case CSV:
+                      ResultSetFormatter.outputAsCSV(outputStream,resultSet);
+                      break;
+                   case TEXT:
+                      ResultSetFormatter.out(outputStream,resultSet);
+                      break;
+                   case JSON:
+                      ResultSetFormatter.outputAsJSON(outputStream, resultSet);
+                      break;
+                   case XML:
+                      ResultSetFormatter.outputAsXML(outputStream, resultSet);
+                      break;
+                   default:
+                      throw new RDFServiceException("unrecognized result format");
+                }
+                InputStream result = new ByteArrayInputStream(outputStream.toByteArray());
+                return result;
+            } finally {
+                qe.close();
             }
-            InputStream result = new ByteArrayInputStream(outputStream.toByteArray());
-            return result;
         } finally {
-            qe.close();
+            d.close();
         }
     }
 
     @Override
     public void sparqlSelectQuery(String query, ResultSetConsumer consumer)
             throws RDFServiceException {
         Dataset d = getDataset();
-        Query q = createQuery(query);
-        QueryExecution qe = createQueryExecution(query, q, d);
         try {
-            consumer.processResultSet(qe.execSelect());
+            Query q = createQuery(query);
+            QueryExecution qe = createQueryExecution(query, q, d);
+            try {
+                consumer.processResultSet(qe.execSelect());
+            } finally {
+                qe.close();
+            }
         } finally {
-            qe.close();
+            d.close();
         }
     }
 
      @Override
     public boolean sparqlAskQuery(String query) throws RDFServiceException {
         Dataset d = getDataset();
-        Query q = createQuery(query);
-        QueryExecution qe = createQueryExecution(query, q, d);
         try {
-            return qe.execAsk();
+            Query q = createQuery(query);
+            QueryExecution qe = createQueryExecution(query, q, d);
+            try {
+                return qe.execAsk();
+            } finally {
+                qe.close();
+            }
         } finally {
-            qe.close();
+            d.close();
         }
     }
 
@@ -507,15 +527,16 @@ public List<String> getGraphURIs() throws RDFServiceException {
         if (rebuildGraphURICache) {
             synchronized (RDFServiceJena.class) {
                 if (rebuildGraphURICache) {
+                    Dataset d = getDataset();
                     try {
-                        Dataset d = getDataset();
                         Iterator<String> nameIt = d.listNames();
                         graphURIs.clear();
                         while (nameIt.hasNext()) {
                             graphURIs.add(nameIt.next());
                         }
                         return graphURIs;
                     } finally {
+                        d.close();
                         rebuildGraphURICache = false;
                     }
                 }
@@ -546,19 +567,23 @@ public void serializeGraph(String graphURI, OutputStream outputStream)
 
 	private void serialize(OutputStream outputStream, String query) throws RDFServiceException {
         Dataset d = getDataset();
-        Query q = createQuery(query);
-        QueryExecution qe = createQueryExecution(query, q, d);
         try {
-            ResultSet resultSet = qe.execSelect();
-            if (resultSet.getResultVars().contains("g")) {
-                Iterator<Quad> quads = new ResultSetQuadsIterator(resultSet);
-                RDFDataMgr.writeQuads(outputStream, quads);
-            } else {
-                Iterator<Triple> triples = new ResultSetTriplesIterator(resultSet);
-                RDFDataMgr.writeTriples(outputStream, triples);
+            Query q = createQuery(query);
+            QueryExecution qe = createQueryExecution(query, q, d);
+            try {
+                ResultSet resultSet = qe.execSelect();
+                if (resultSet.getResultVars().contains("g")) {
+                    Iterator<Quad> quads = new ResultSetQuadsIterator(resultSet);
+                    RDFDataMgr.writeQuads(outputStream, quads);
+                } else {
+                    Iterator<Triple> triples = new ResultSetTriplesIterator(resultSet);
+                    RDFDataMgr.writeTriples(outputStream, triples);
+                }
+            } finally {
+                qe.close();
             }
         } finally {
-            qe.close();
+            d.close();
         }
 	}
 
@@ -612,6 +637,8 @@ public long countTriples(RDFNode subject, RDFNode predicate, RDFNode object) thr
                 Literal literal = soln.getLiteral("count");
                 return literal.getLong();
             }
+        } finally {
+            d.close();
         }
 
         return 0;
@@ -637,8 +664,12 @@ public Model getTriples(RDFNode subject, RDFNode predicate, RDFNode object, long
         Model triples = ModelFactory.createDefaultModel();
 
         Dataset d = getDataset();
-        try (QueryExecution qexec = QueryExecutionFactory.create(query, d, map)) {
-            qexec.execConstruct(triples);
+        try {
+            try (QueryExecution qexec = QueryExecutionFactory.create(query, d, map)) {
+                qexec.execConstruct(triples);
+            }
+        } finally {
+            d.close();
         }
 
         return triples;