Fix various problems with resources potentially not being freed, and other minor fixes suggested by FindBugs

git-svn-id: http://scm.dspace.org/svn/repo/branches/dspace-1_5_x@3036 9c30dcfa-912a-0410-8fc2-9e0234be79fd

dspace-api/src/main/java/org/dspace/app/mets/METSExport.java

@@ -242,9 +242,18 @@ public class METSExport
                 + File.separator + "config" + File.separator + "dc2mods.cfg";
 
         // Read it in
-        InputStream is = new FileInputStream(configFile);
+        InputStream is = null;
-        dcToMODS = new Properties();
+        try
-        dcToMODS.load(is);
+        {
+            is = new FileInputStream(configFile);
+            dcToMODS = new Properties();
+            dcToMODS.load(is);
+        }
+        finally
+        {
+            if (is != null)
+                try { is.close(); } catch (IOException ioe) { }
+        }
     }
 
     /**

dspace-api/src/main/java/org/dspace/app/statistics/ReportGenerator.java

@@ -562,30 +562,41 @@ public class ReportGenerator
     {
         FileReader fr = null;
         BufferedReader br = null;
-        
+
-        // read in the map file, printing a warning if none is found
+        try
-        String record = null;
-        try 
-        {  
-            fr = new FileReader(map);
-            br = new BufferedReader(fr);
-        } 
-        catch (IOException e) 
-        {  
-            System.err.println("Failed to read map file: log file actions will be displayed without translation");
-            return;
-        } 
-        
-        // loop through the map file and read in the values
-        while ((record = br.readLine()) != null) 
         {
-            Matcher matchReal = real.matcher(record);
+            // read in the map file, printing a warning if none is found
-            
+            String record = null;
-            // if the line is real then read it in
+            try
-            if (matchReal.matches())
             {
-                actionMap.put(matchReal.group(1).trim(), matchReal.group(2).trim());
+                fr = new FileReader(map);
+                br = new BufferedReader(fr);
             }
+            catch (IOException e)
+            {
+                System.err.println("Failed to read map file: log file actions will be displayed without translation");
+                return;
+            }
+
+            // loop through the map file and read in the values
+            while ((record = br.readLine()) != null)
+            {
+                Matcher matchReal = real.matcher(record);
+
+                // if the line is real then read it in
+                if (matchReal.matches())
+                {
+                    actionMap.put(matchReal.group(1).trim(), matchReal.group(2).trim());
+                }
+            }
+        }
+        finally
+        {
+            if (br != null)
+                try { br.close(); } catch (IOException ioe) { }
+
+            if (fr != null)
+                try { fr.close(); } catch (IOException ioe) { }
         }
     }
     

dspace-api/src/main/java/org/dspace/authenticate/X509Authentication.java

@@ -140,12 +140,13 @@ public class X509Authentication
         // First look for keystore full of trusted certs.
         if (keystorePath != null)
         {
+            FileInputStream fis = null;
             if (keystorePassword == null)
                 keystorePassword = "";
             try {
                 KeyStore ks = KeyStore.getInstance("JKS");
-                ks.load(new FileInputStream(keystorePath),
+                fis = new FileInputStream(keystorePath);
-                                     keystorePassword.toCharArray());
+                ks.load(fis, keystorePassword.toCharArray());
                 caCertKeyStore = ks;
             }
             catch (IOException e)
@@ -158,14 +159,22 @@ public class X509Authentication
                 log.error("X509Authentication: Failed to extract CA keystore, file="+
                             keystorePath+", error="+e.toString());
             }
+            finally
+            {
+                if (fis != null)
+                    try { fis.close(); } catch (IOException ioe) { }
+            }
         }
 
         // Second, try getting public key out of CA cert, if that's configured.
         if (caCertPath != null)
         {
+            InputStream is = null;
+            FileInputStream fis = null;
             try
             {
-                InputStream is = new BufferedInputStream(new FileInputStream(caCertPath));
+                fis = new FileInputStream(caCertPath);
+                is = new BufferedInputStream(fis);
                 X509Certificate cert = (X509Certificate) CertificateFactory
                                        .getInstance("X.509").generateCertificate(is);
                 if (cert != null)
@@ -181,6 +190,14 @@ public class X509Authentication
                 log.error("X509Authentication: Failed to extract CA cert, file="+
                             caCertPath+", error="+e.toString());
             }
+            finally
+            {
+                if (is != null)
+                    try { is.close(); } catch (IOException ioe) { }
+
+                if (fis != null)
+                    try { fis.close(); } catch (IOException ioe) { }
+            }
         }
     }
 

dspace-api/src/main/java/org/dspace/authorize/AuthorizeManager.java

@@ -424,24 +424,31 @@ public class AuthorizeManager
 
         List<ResourcePolicy> policies = new ArrayList();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // first check the cache (FIXME: is this right?)
-            ResourcePolicy cachepolicy = (ResourcePolicy) c.fromCache(
-                    ResourcePolicy.class, row.getIntColumn("policy_id"));
-
-            if (cachepolicy != null)
             {
-                policies.add(cachepolicy);
+                TableRow row = tri.next();
-            }
+
-            else
+                // first check the cache (FIXME: is this right?)
-            {
+                ResourcePolicy cachepolicy = (ResourcePolicy) c.fromCache(
-                policies.add(new ResourcePolicy(c, row));
+                        ResourcePolicy.class, row.getIntColumn("policy_id"));
+
+                if (cachepolicy != null)
+                {
+                    policies.add(cachepolicy);
+                }
+                else
+                {
+                    policies.add(new ResourcePolicy(c, row));
+                }
             }
         }
-        tri.close();
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
 
         return policies;
     }
@@ -463,24 +470,31 @@ public class AuthorizeManager
 
         List<ResourcePolicy> policies = new ArrayList<ResourcePolicy>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // first check the cache (FIXME: is this right?)
-            ResourcePolicy cachepolicy = (ResourcePolicy) c.fromCache(
-                    ResourcePolicy.class, row.getIntColumn("policy_id"));
-
-            if (cachepolicy != null)
             {
-                policies.add(cachepolicy);
+                TableRow row = tri.next();
-            }
+
-            else
+                // first check the cache (FIXME: is this right?)
-            {
+                ResourcePolicy cachepolicy = (ResourcePolicy) c.fromCache(
-                policies.add(new ResourcePolicy(c, row));
+                        ResourcePolicy.class, row.getIntColumn("policy_id"));
+
+                if (cachepolicy != null)
+                {
+                    policies.add(cachepolicy);
+                }
+                else
+                {
+                    policies.add(new ResourcePolicy(c, row));
+                }
             }
         }
-        tri.close();
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
 
         return policies;
     }
@@ -507,24 +521,31 @@ public class AuthorizeManager
 
         List<ResourcePolicy> policies = new ArrayList<ResourcePolicy>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // first check the cache (FIXME: is this right?)
-            ResourcePolicy cachepolicy = (ResourcePolicy) c.fromCache(
-                    ResourcePolicy.class, row.getIntColumn("policy_id"));
-
-            if (cachepolicy != null)
             {
-                policies.add(cachepolicy);
+                TableRow row = tri.next();
-            }
+
-            else
+                // first check the cache (FIXME: is this right?)
-            {
+                ResourcePolicy cachepolicy = (ResourcePolicy) c.fromCache(
-                policies.add(new ResourcePolicy(c, row));
+                        ResourcePolicy.class, row.getIntColumn("policy_id"));
+
+                if (cachepolicy != null)
+                {
+                    policies.add(cachepolicy);
+                }
+                else
+                {
+                    policies.add(new ResourcePolicy(c, row));
+                }
             }
         }
-        tri.close();
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
 
         return policies;
     }
@@ -697,37 +718,44 @@ public class AuthorizeManager
         TableRowIterator tri = DatabaseManager.queryTable(c, "resourcepolicy",
                 "SELECT * FROM resourcepolicy WHERE resource_type_id= ? "+
                 "AND resource_id= ? AND action_id= ? ",o.getType(),o.getID(),actionID);
-    	
+
         List<Group> groups = new ArrayList<Group>();
-
+        try
-        while (tri.hasNext())
         {
-            TableRow row = tri.next();
 
-            // first check the cache (FIXME: is this right?)
+            while (tri.hasNext())
-            ResourcePolicy cachepolicy = (ResourcePolicy) c.fromCache(
-                    ResourcePolicy.class, row.getIntColumn("policy_id"));
-
-            ResourcePolicy myPolicy = null;
-
-            if (cachepolicy != null)
             {
-                myPolicy = cachepolicy;
+                TableRow row = tri.next();
-            }
-            else
-            {
-                myPolicy = new ResourcePolicy(c, row);
-            }
 
-            // now do we have a group?
+                // first check the cache (FIXME: is this right?)
-            Group myGroup = myPolicy.getGroup();
+                ResourcePolicy cachepolicy = (ResourcePolicy) c.fromCache(
+                        ResourcePolicy.class, row.getIntColumn("policy_id"));
 
-            if (myGroup != null)
+                ResourcePolicy myPolicy = null;
-            {
+
-                groups.add(myGroup);
+                if (cachepolicy != null)
+                {
+                    myPolicy = cachepolicy;
+                }
+                else
+                {
+                    myPolicy = new ResourcePolicy(c, row);
+                }
+
+                // now do we have a group?
+                Group myGroup = myPolicy.getGroup();
+
+                if (myGroup != null)
+                {
+                    groups.add(myGroup);
+                }
             }
         }
-        tri.close();
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
 
         Group[] groupArray = new Group[groups.size()];
         groupArray = groups.toArray(groupArray);

dspace-api/src/main/java/org/dspace/browse/ItemCountDAOOracle.java

@@ -96,11 +96,12 @@ public class ItemCountDAOOracle implements ItemCountDAO
 	public void collectionCount(Collection collection, int count) 
 		throws ItemCountException
 	{
-		try
+        TableRowIterator tri = null;
+        try
 		{
 			// first find out if we have a record
 			Object[] sparams = { new Integer(collection.getID()) };
-			TableRowIterator tri = DatabaseManager.query(context, collectionSelect, sparams);
+			tri = DatabaseManager.query(context, collectionSelect, sparams);
 			
 			if (tri.hasNext())
 			{
@@ -112,15 +113,18 @@ public class ItemCountDAOOracle implements ItemCountDAO
 				Object[] params = { new Integer(collection.getID()), new Integer(count) };
 				DatabaseManager.updateQuery(context, collectionInsert, params);
 			}
-			
-			tri.close();
 		}
 		catch (SQLException e)
 		{
 			log.error("caught exception: ", e);
 			throw new ItemCountException(e);
 		}
-	}
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
+    }
 
 	/**
 	 * Store the count of the given community
@@ -132,11 +136,12 @@ public class ItemCountDAOOracle implements ItemCountDAO
 	public void communityCount(Community community, int count) 
 		throws ItemCountException
 	{
-		try
+        TableRowIterator tri = null;
+        try
 		{
 			// first find out if we have a record
 			Object[] sparams = { new Integer(community.getID()) };
-			TableRowIterator tri = DatabaseManager.query(context, communitySelect, sparams);
+			tri = DatabaseManager.query(context, communitySelect, sparams);
 			
 			if (tri.hasNext())
 			{
@@ -148,15 +153,18 @@ public class ItemCountDAOOracle implements ItemCountDAO
 				Object[] params = { new Integer(community.getID()), new Integer(count) };
 				DatabaseManager.updateQuery(context, communityInsert, params);
 			}
-			
-			tri.close();
 		}
 		catch (SQLException e)
 		{
 			log.error("caught exception: ", e);
 			throw new ItemCountException(e);
 		}
-	}
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
+    }
 
 	/**
 	 * Set the dspace context to use
@@ -268,10 +276,11 @@ public class ItemCountDAOOracle implements ItemCountDAO
 	private int getCollectionCount(Collection collection)
 		throws ItemCountException
 	{
-		try
+        TableRowIterator tri = null;
+        try
 		{
 			Object[] params = { new Integer(collection.getID()) };
-			TableRowIterator tri = DatabaseManager.query(context, collectionSelect, params);
+			tri = DatabaseManager.query(context, collectionSelect, params);
 			
 			if (!tri.hasNext())
 			{
@@ -284,9 +293,7 @@ public class ItemCountDAOOracle implements ItemCountDAO
 			{
 				throw new ItemCountException("More than one count row in the database");
 			}
-			
+
-			tri.close();
-			
 			return tr.getIntColumn("count");
 		}
 		catch (SQLException e)
@@ -294,7 +301,12 @@ public class ItemCountDAOOracle implements ItemCountDAO
 			log.error("caught exception: ", e);
 			throw new ItemCountException(e);
 		}
-	}
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
+    }
 	
 	/**
 	 * get the count for the given community
@@ -306,10 +318,11 @@ public class ItemCountDAOOracle implements ItemCountDAO
 	private int getCommunityCount(Community community)
 		throws ItemCountException
 	{
-		try
+        TableRowIterator tri = null;
+        try
 		{
 			Object[] params = { new Integer(community.getID()) };
-			TableRowIterator tri = DatabaseManager.query(context, communitySelect, params);
+			tri = DatabaseManager.query(context, communitySelect, params);
 			
 			if (!tri.hasNext())
 			{
@@ -322,9 +335,7 @@ public class ItemCountDAOOracle implements ItemCountDAO
 			{
 				throw new ItemCountException("More than one count row in the database");
 			}
-			
+
-			tri.close();
-			
 			return tr.getIntColumn("count");
 		}
 		catch (SQLException e)
@@ -332,5 +343,10 @@ public class ItemCountDAOOracle implements ItemCountDAO
 			log.error("caught exception: ", e);
 			throw new ItemCountException(e);
 		}
-	}
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
+    }
 }

dspace-api/src/main/java/org/dspace/browse/ItemCountDAOPostgres.java

@@ -96,11 +96,12 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 	public void collectionCount(Collection collection, int count) 
 		throws ItemCountException
 	{
-		try
+        TableRowIterator tri = null;
+        try
 		{
 			// first find out if we have a record
 			Object[] sparams = { new Integer(collection.getID()) };
-			TableRowIterator tri = DatabaseManager.query(context, collectionSelect, sparams);
+			tri = DatabaseManager.query(context, collectionSelect, sparams);
 			
 			if (tri.hasNext())
 			{
@@ -112,15 +113,18 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 				Object[] params = { new Integer(collection.getID()), new Integer(count) };
 				DatabaseManager.updateQuery(context, collectionInsert, params);
 			}
-			
-			tri.close();
 		}
 		catch (SQLException e)
 		{
 			log.error("caught exception: ", e);
 			throw new ItemCountException(e);
 		}
-	}
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
+    }
 
 	/**
 	 * Store the count of the given community
@@ -132,11 +136,12 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 	public void communityCount(Community community, int count) 
 		throws ItemCountException
 	{
-		try
+        TableRowIterator tri = null;
+        try
 		{
 			// first find out if we have a record
 			Object[] sparams = { new Integer(community.getID()) };
-			TableRowIterator tri = DatabaseManager.query(context, communitySelect, sparams);
+			tri = DatabaseManager.query(context, communitySelect, sparams);
 			
 			if (tri.hasNext())
 			{
@@ -148,15 +153,18 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 				Object[] params = { new Integer(community.getID()), new Integer(count) };
 				DatabaseManager.updateQuery(context, communityInsert, params);
 			}
-			
-			tri.close();
 		}
 		catch (SQLException e)
 		{
 			log.error("caught exception: ", e);
 			throw new ItemCountException(e);
 		}
-	}
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
+    }
 
 	/**
 	 * Set the dspace context to use
@@ -268,10 +276,11 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 	private int getCollectionCount(Collection collection)
 		throws ItemCountException
 	{
-		try
+        TableRowIterator tri = null;
+        try
 		{
 			Object[] params = { new Integer(collection.getID()) };
-			TableRowIterator tri = DatabaseManager.query(context, collectionSelect, params);
+			tri = DatabaseManager.query(context, collectionSelect, params);
 			
 			if (!tri.hasNext())
 			{
@@ -284,9 +293,7 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 			{
 				throw new ItemCountException("More than one count row in the database");
 			}
-			
+
-			tri.close();
-			
 			return tr.getIntColumn("count");
 		}
 		catch (SQLException e)
@@ -294,7 +301,12 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 			log.error("caught exception: ", e);
 			throw new ItemCountException(e);
 		}
-	}
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
+    }
 	
 	/**
 	 * get the count for the given community
@@ -306,10 +318,11 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 	private int getCommunityCount(Community community)
 		throws ItemCountException
 	{
-		try
+        TableRowIterator tri = null;
+        try
 		{
 			Object[] params = { new Integer(community.getID()) };
-			TableRowIterator tri = DatabaseManager.query(context, communitySelect, params);
+			tri = DatabaseManager.query(context, communitySelect, params);
 			
 			if (!tri.hasNext())
 			{
@@ -322,9 +335,7 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 			{
 				throw new ItemCountException("More than one count row in the database");
 			}
-			
+
-			tri.close();
-			
 			return tr.getIntColumn("count");
 		}
 		catch (SQLException e)
@@ -332,5 +343,10 @@ public class ItemCountDAOPostgres implements ItemCountDAO
 			log.error("caught exception: ", e);
 			throw new ItemCountException(e);
 		}
-	}
+        finally
+        {
+            if (tri != null)
+                tri.close();
+        }
+    }
 }

dspace-api/src/main/java/org/dspace/checker/HandleDispatcher.java

@@ -98,59 +98,62 @@ public class HandleDispatcher implements BitstreamDispatcher
      * @throws SQLException
      *             if database access fails.
      */
-    private void init()
+    private synchronized void init()
     {
-        Context context = null;
+        if (init == Boolean.FALSE)
-        int dsoType = -1;
-
-        int id = -1;
-        try
         {
-            context = new Context();
+            Context context = null;
-            DSpaceObject dso = HandleManager.resolveToObject(context, handle);
+            int dsoType = -1;
-            id = dso.getID();
-            dsoType = dso.getType();
-            context.abort();
 
-        }
+            int id = -1;
-        catch (SQLException e)
+            try
-        {
-            LOG.error("init error " + e.getMessage(), e);
-            throw new RuntimeException("init error" + e.getMessage(), e);
-
-        }
-        finally
-        {
-            // Abort the context if it's still valid
-            if ((context != null) && context.isValid())
             {
+                context = new Context();
+                DSpaceObject dso = HandleManager.resolveToObject(context, handle);
+                id = dso.getID();
+                dsoType = dso.getType();
                 context.abort();
+
             }
+            catch (SQLException e)
+            {
+                LOG.error("init error " + e.getMessage(), e);
+                throw new RuntimeException("init error" + e.getMessage(), e);
+
+            }
+            finally
+            {
+                // Abort the context if it's still valid
+                if ((context != null) && context.isValid())
+                {
+                    context.abort();
+                }
+            }
+
+            List ids = new ArrayList();
+
+            switch (dsoType)
+            {
+            case Constants.BITSTREAM:
+                ids.add(new Integer(id));
+                break;
+
+            case Constants.ITEM:
+                ids = bitstreamInfoDAO.getItemBitstreams(id);
+                break;
+
+            case Constants.COLLECTION:
+                ids = bitstreamInfoDAO.getCollectionBitstreams(id);
+                break;
+
+            case Constants.COMMUNITY:
+                ids = bitstreamInfoDAO.getCommunityBitstreams(id);
+                break;
+            }
+
+            delegate = new ListDispatcher(ids);
+            init = Boolean.TRUE;
         }
-
-        List ids = new ArrayList();
-
-        switch (dsoType)
-        {
-        case Constants.BITSTREAM:
-            ids.add(new Integer(id));
-            break;
-
-        case Constants.ITEM:
-            ids = bitstreamInfoDAO.getItemBitstreams(id);
-            break;
-
-        case Constants.COLLECTION:
-            ids = bitstreamInfoDAO.getCollectionBitstreams(id);
-            break;
-
-        case Constants.COMMUNITY:
-            ids = bitstreamInfoDAO.getCommunityBitstreams(id);
-            break;
-        }
-
-        delegate = new ListDispatcher(ids);
-        init = Boolean.TRUE;
     }
 
     /**
@@ -160,12 +163,9 @@ public class HandleDispatcher implements BitstreamDispatcher
      */
     public int next()
     {
-        synchronized (init)
+        if (init == Boolean.FALSE)
         {
-            if (init == Boolean.FALSE)
+            init();
-            {
-                init();
-            }
         }
 
         return delegate.next();

dspace-api/src/main/java/org/dspace/content/Bitstream.java

@@ -581,27 +581,32 @@ public class Bitstream extends DSpaceObject
 
         // Build a list of Bundle objects
         List<Bundle> bundles = new ArrayList<Bundle>();
-
+        try
-        while (tri.hasNext())
         {
-            TableRow r = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Bundle fromCache = (Bundle) bContext.fromCache(Bundle.class, r
-                    .getIntColumn("bundle_id"));
-
-            if (fromCache != null)
             {
-                bundles.add(fromCache);
+                TableRow r = tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Bundle fromCache = (Bundle) bContext.fromCache(Bundle.class, r
-                bundles.add(new Bundle(bContext, r));
+                        .getIntColumn("bundle_id"));
+
+                if (fromCache != null)
+                {
+                    bundles.add(fromCache);
+                }
+                else
+                {
+                    bundles.add(new Bundle(bContext, r));
+                }
             }
         }
-
+        finally
-        // close the TableRowIterator to free up resources
+        {
-        tri.close();
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         Bundle[] bundleArray = new Bundle[bundles.size()];
         bundleArray = (Bundle[]) bundles.toArray(bundleArray);

dspace-api/src/main/java/org/dspace/content/BitstreamFormat.java

@@ -114,12 +114,19 @@ public class BitstreamFormat
                 "SELECT * FROM fileextension WHERE bitstream_format_id= ? ",
                  getID());
 
-        while (tri.hasNext())
+        try
         {
-            extensions.add(tri.next().getStringColumn("extension"));
+            while (tri.hasNext())
+            {
+                extensions.add(tri.next().getStringColumn("extension"));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         // Cache ourselves
         context.cache(this, row.getIntColumn("bitstream_format_id"));
@@ -298,26 +305,33 @@ public class BitstreamFormat
         TableRowIterator tri = DatabaseManager.queryTable(context, "bitstreamformatregistry",
                         "SELECT * FROM bitstreamformatregistry ORDER BY bitstream_format_id");
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // From cache?
-            BitstreamFormat fromCache = (BitstreamFormat) context.fromCache(
-                    BitstreamFormat.class, row
-                            .getIntColumn("bitstream_format_id"));
-
-            if (fromCache != null)
             {
-                formats.add(fromCache);
+                TableRow row = tri.next();
-            }
+
-            else
+                // From cache?
-            {
+                BitstreamFormat fromCache = (BitstreamFormat) context.fromCache(
-                formats.add(new BitstreamFormat(context, row));
+                        BitstreamFormat.class, row
+                                .getIntColumn("bitstream_format_id"));
+
+                if (fromCache != null)
+                {
+                    formats.add(fromCache);
+                }
+                else
+                {
+                    formats.add(new BitstreamFormat(context, row));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         // Return the formats as an array
         BitstreamFormat[] formatArray = new BitstreamFormat[formats.size()];
@@ -349,26 +363,33 @@ public class BitstreamFormat
         TableRowIterator tri = DatabaseManager.queryTable(context,
                 "bitstreamformatregistry", myQuery);
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // From cache?
-            BitstreamFormat fromCache = (BitstreamFormat) context.fromCache(
-                    BitstreamFormat.class, row
-                            .getIntColumn("bitstream_format_id"));
-
-            if (fromCache != null)
             {
-                formats.add(fromCache);
+                TableRow row = tri.next();
-            }
+
-            else
+                // From cache?
-            {
+                BitstreamFormat fromCache = (BitstreamFormat) context.fromCache(
-                formats.add(new BitstreamFormat(context, row));
+                        BitstreamFormat.class, row
+                                .getIntColumn("bitstream_format_id"));
+
+                if (fromCache != null)
+                {
+                    formats.add(fromCache);
+                }
+                else
+                {
+                    formats.add(new BitstreamFormat(context, row));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         // Return the formats as an array
         BitstreamFormat[] formatArray = new BitstreamFormat[formats.size()];

dspace-api/src/main/java/org/dspace/content/Bundle.java

@@ -110,26 +110,33 @@ public class Bundle extends DSpaceObject
                         + "bundle2bitstream.bitstream_id=bitstream.bitstream_id AND "
                         + "bundle2bitstream.bundle_id= ? ",
                 bundleRow.getIntColumn("bundle_id"));
-        
+
-        while (tri.hasNext())
+        try
         {
-            TableRow r = (TableRow) tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Bitstream fromCache = (Bitstream) context.fromCache(
-                    Bitstream.class, r.getIntColumn("bitstream_id"));
-
-            if (fromCache != null)
             {
-                bitstreams.add(fromCache);
+                TableRow r = (TableRow) tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Bitstream fromCache = (Bitstream) context.fromCache(
-                bitstreams.add(new Bitstream(ourContext, r));
+                        Bitstream.class, r.getIntColumn("bitstream_id"));
+
+                if (fromCache != null)
+                {
+                    bitstreams.add(fromCache);
+                }
+                else
+                {
+                    bitstreams.add(new Bitstream(ourContext, r));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         // Cache ourselves
         context.cache(this, row.getIntColumn("bundle_id"));
@@ -331,26 +338,33 @@ public class Bundle extends DSpaceObject
                 "item2bundle.item_id=item.item_id AND " +
                 "item2bundle.bundle_id= ? ",
                 bundleRow.getIntColumn("bundle_id"));
-        
+
-        while (tri.hasNext())
+        try
         {
-            TableRow r = (TableRow) tri.next();
+            while (tri.hasNext())
-
-            // Used cached copy if there is one
-            Item fromCache = (Item) ourContext.fromCache(Item.class, r
-                    .getIntColumn("item_id"));
-
-            if (fromCache != null)
             {
-                items.add(fromCache);
+                TableRow r = (TableRow) tri.next();
-            }
+
-            else
+                // Used cached copy if there is one
-            {
+                Item fromCache = (Item) ourContext.fromCache(Item.class, r
-                items.add(new Item(ourContext, r));
+                        .getIntColumn("item_id"));
+
+                if (fromCache != null)
+                {
+                    items.add(fromCache);
+                }
+                else
+                {
+                    items.add(new Item(ourContext, r));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         Item[] itemArray = new Item[items.size()];
         itemArray = (Item[]) items.toArray(itemArray);
@@ -503,13 +517,20 @@ public class Bundle extends DSpaceObject
                 "SELECT * FROM bundle2bitstream WHERE bitstream_id= ? ",
                 b.getID());
 
-        if (!tri.hasNext())
+        try
         {
-            // The bitstream is an orphan, delete it
+            if (!tri.hasNext())
-            b.delete();
+            {
+                // The bitstream is an orphan, delete it
+                b.delete();
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
     }
 
     /**

dspace-api/src/main/java/org/dspace/content/Collection.java

@@ -289,25 +289,32 @@ public class Collection extends DSpaceObject
 
         List<Collection> collections = new ArrayList<Collection>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Collection fromCache = (Collection) context.fromCache(
-                    Collection.class, row.getIntColumn("collection_id"));
-
-            if (fromCache != null)
             {
-                collections.add(fromCache);
+                TableRow row = tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Collection fromCache = (Collection) context.fromCache(
-                collections.add(new Collection(context, row));
+                        Collection.class, row.getIntColumn("collection_id"));
+
+                if (fromCache != null)
+                {
+                    collections.add(fromCache);
+                }
+                else
+                {
+                    collections.add(new Collection(context, row));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         Collection[] collectionArray = new Collection[collections.size()];
         collectionArray = (Collection[]) collections.toArray(collectionArray);
@@ -924,24 +931,31 @@ public class Collection extends DSpaceObject
                 "SELECT * FROM collection2item WHERE item_id= ? ",
                 item.getID());
 
-        if (!tri.hasNext())
+        try
         {
-            //make the right to remove the item explicit because the implicit
+            if (!tri.hasNext())
-            // relation
+            {
-            //has been removed. This only has to concern the currentUser
+                //make the right to remove the item explicit because the implicit
-            // because
+                // relation
-            //he started the removal process and he will end it too.
+                //has been removed. This only has to concern the currentUser
-            //also add right to remove from the item to remove it's bundles.
+                // because
-            AuthorizeManager.addPolicy(ourContext, item, Constants.DELETE,
+                //he started the removal process and he will end it too.
-                    ourContext.getCurrentUser());
+                //also add right to remove from the item to remove it's bundles.
-            AuthorizeManager.addPolicy(ourContext, item, Constants.REMOVE,
+                AuthorizeManager.addPolicy(ourContext, item, Constants.DELETE,
-                    ourContext.getCurrentUser());
+                        ourContext.getCurrentUser());
+                AuthorizeManager.addPolicy(ourContext, item, Constants.REMOVE,
+                        ourContext.getCurrentUser());
 
-            // Orphan; delete it
+                // Orphan; delete it
-            item.delete();
+                item.delete();
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
     }
 
     /**
@@ -1181,31 +1195,38 @@ public class Collection extends DSpaceObject
         // Build a list of Community objects
         List<Community> communities = new ArrayList<Community>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Community owner = (Community) ourContext.fromCache(Community.class,
-                    row.getIntColumn("community_id"));
-
-            if (owner == null)
             {
-                owner = new Community(ourContext, row);
+                TableRow row = tri.next();
-            }
 
-            communities.add(owner);
+                // First check the cache
+                Community owner = (Community) ourContext.fromCache(Community.class,
+                        row.getIntColumn("community_id"));
 
-            // now add any parent communities
+                if (owner == null)
-            Community[] parents = owner.getAllParents();
+                {
+                    owner = new Community(ourContext, row);
+                }
 
-            for (int i = 0; i < parents.length; i++)
+                communities.add(owner);
-            {
+
-                communities.add(parents[i]);
+                // now add any parent communities
+                Community[] parents = owner.getAllParents();
+
+                for (int i = 0; i < parents.length; i++)
+                {
+                    communities.add(parents[i]);
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         Community[] communityArray = new Community[communities.size()];
         communityArray = (Community[]) communities.toArray(communityArray);
@@ -1316,20 +1337,39 @@ public class Collection extends DSpaceObject
      public int countItems()
         throws SQLException
      {
-        String query = "SELECT count(*) FROM collection2item, item WHERE "
+         int itemcount = 0;
-            + "collection2item.collection_id =  ? "
+         PreparedStatement statement = null;
-            + "AND collection2item.item_id = item.item_id "
+         ResultSet rs = null;
-            + "AND in_archive ='1' AND item.withdrawn='0' ";
 
-        PreparedStatement statement = ourContext.getDBConnection().prepareStatement(query);
+         try
-        statement.setInt(1,getID());
+         {
-        
+             String query = "SELECT count(*) FROM collection2item, item WHERE "
-        ResultSet rs = statement.executeQuery();
+                    + "collection2item.collection_id =  ? "
-        
+                    + "AND collection2item.item_id = item.item_id "
-        rs.next();
+                    + "AND in_archive ='1' AND item.withdrawn='0' ";
-        int itemcount = rs.getInt(1);
 
-        statement.close();
+            statement = ourContext.getDBConnection().prepareStatement(query);
+            statement.setInt(1,getID());
+
+            rs = statement.executeQuery();
+            if (rs != null)
+            {
+                rs.next();
+                itemcount = rs.getInt(1);
+            }
+         }
+         finally
+         {
+             if (rs != null)
+             {
+                 try { rs.close(); } catch (SQLException sqle) { }
+             }
+
+             if (statement != null)
+             {
+                 try { statement.close(); } catch (SQLException sqle) { }
+             }
+         }
 
         return itemcount;
      }

dspace-api/src/main/java/org/dspace/content/Community.java

@@ -237,25 +237,32 @@ public class Community extends DSpaceObject
 
         List<Community> communities = new ArrayList<Community>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Community fromCache = (Community) context.fromCache(
-                    Community.class, row.getIntColumn("community_id"));
-
-            if (fromCache != null)
             {
-                communities.add(fromCache);
+                TableRow row = tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Community fromCache = (Community) context.fromCache(
-                communities.add(new Community(context, row));
+                        Community.class, row.getIntColumn("community_id"));
+
+                if (fromCache != null)
+                {
+                    communities.add(fromCache);
+                }
+                else
+                {
+                    communities.add(new Community(context, row));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         Community[] communityArray = new Community[communities.size()];
         communityArray = (Community[]) communities.toArray(communityArray);
@@ -283,25 +290,32 @@ public class Community extends DSpaceObject
 
         List<Community> topCommunities = new ArrayList<Community>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Community fromCache = (Community) context.fromCache(
-                    Community.class, row.getIntColumn("community_id"));
-
-            if (fromCache != null)
             {
-                topCommunities.add(fromCache);
+                TableRow row = tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Community fromCache = (Community) context.fromCache(
-                topCommunities.add(new Community(context, row));
+                        Community.class, row.getIntColumn("community_id"));
+
+                if (fromCache != null)
+                {
+                    topCommunities.add(fromCache);
+                }
+                else
+                {
+                    topCommunities.add(new Community(context, row));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         Community[] communityArray = new Community[topCommunities.size()];
         communityArray = (Community[]) topCommunities.toArray(communityArray);
@@ -514,25 +528,32 @@ public class Community extends DSpaceObject
             getID());
 
         // Make Collection objects
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Collection fromCache = (Collection) ourContext.fromCache(
-                    Collection.class, row.getIntColumn("collection_id"));
-
-            if (fromCache != null)
             {
-                collections.add(fromCache);
+                TableRow row = tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Collection fromCache = (Collection) ourContext.fromCache(
-                collections.add(new Collection(ourContext, row));
+                        Collection.class, row.getIntColumn("collection_id"));
+
+                if (fromCache != null)
+                {
+                    collections.add(fromCache);
+                }
+                else
+                {
+                    collections.add(new Collection(ourContext, row));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         // Put them in an array
         Collection[] collectionArray = new Collection[collections.size()];
@@ -562,25 +583,32 @@ public class Community extends DSpaceObject
         
 
         // Make Community objects
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Community fromCache = (Community) ourContext.fromCache(
-                    Community.class, row.getIntColumn("community_id"));
-
-            if (fromCache != null)
             {
-                subcommunities.add(fromCache);
+                TableRow row = tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Community fromCache = (Community) ourContext.fromCache(
-                subcommunities.add(new Community(ourContext, row));
+                        Community.class, row.getIntColumn("community_id"));
+
+                if (fromCache != null)
+                {
+                    subcommunities.add(fromCache);
+                }
+                else
+                {
+                    subcommunities.add(new Community(ourContext, row));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         // Put them in an array
         Community[] communityArray = new Community[subcommunities.size()];
@@ -608,25 +636,32 @@ public class Community extends DSpaceObject
                 getID());
         
         // Make Community object
-        if (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            if (tri.hasNext())
-
-            // First check the cache
-            Community fromCache = (Community) ourContext.fromCache(
-                    Community.class, row.getIntColumn("community_id"));
-
-            if (fromCache != null)
             {
-                parentCommunity = fromCache;
+                TableRow row = tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Community fromCache = (Community) ourContext.fromCache(
-                parentCommunity = new Community(ourContext, row);
+                        Community.class, row.getIntColumn("community_id"));
+
+                if (fromCache != null)
+                {
+                    parentCommunity = fromCache;
+                }
+                else
+                {
+                    parentCommunity = new Community(ourContext, row);
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         return parentCommunity;
     }
@@ -693,22 +728,29 @@ public class Community extends DSpaceObject
                 "community2collection",
                 "SELECT * FROM community2collection WHERE " +
                 "community_id= ? AND collection_id= ? ",getID(),c.getID());
-        
+
-        if (!tri.hasNext())
+        try
         {
-            // No existing mapping, so add one
+            if (!tri.hasNext())
-            TableRow mappingRow = DatabaseManager.create(ourContext,
+            {
-                    "community2collection");
+                // No existing mapping, so add one
+                TableRow mappingRow = DatabaseManager.create(ourContext,
+                        "community2collection");
 
-            mappingRow.setColumn("community_id", getID());
+                mappingRow.setColumn("community_id", getID());
-            mappingRow.setColumn("collection_id", c.getID());
+                mappingRow.setColumn("collection_id", c.getID());
 
-            ourContext.addEvent(new Event(Event.ADD, Constants.COMMUNITY, getID(), Constants.COLLECTION, c.getID(), c.getHandle()));
+                ourContext.addEvent(new Event(Event.ADD, Constants.COMMUNITY, getID(), Constants.COLLECTION, c.getID(), c.getHandle()));
 
-            DatabaseManager.update(ourContext, mappingRow);
+                DatabaseManager.update(ourContext, mappingRow);
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
     }
 
     /**
@@ -748,22 +790,29 @@ public class Community extends DSpaceObject
                 "community2community",
                 "SELECT * FROM community2community WHERE parent_comm_id= ? "+
                 "AND child_comm_id= ? ",getID(), c.getID());
-        
+
-        if (!tri.hasNext())
+        try
         {
-            // No existing mapping, so add one
+            if (!tri.hasNext())
-            TableRow mappingRow = DatabaseManager.create(ourContext,
+            {
-                    "community2community");
+                // No existing mapping, so add one
+                TableRow mappingRow = DatabaseManager.create(ourContext,
+                        "community2community");
 
-            mappingRow.setColumn("parent_comm_id", getID());
+                mappingRow.setColumn("parent_comm_id", getID());
-            mappingRow.setColumn("child_comm_id", c.getID());
+                mappingRow.setColumn("child_comm_id", c.getID());
 
-            ourContext.addEvent(new Event(Event.ADD, Constants.COMMUNITY, getID(), Constants.COMMUNITY, c.getID(), c.getHandle()));
+                ourContext.addEvent(new Event(Event.ADD, Constants.COMMUNITY, getID(), Constants.COMMUNITY, c.getID(), c.getHandle()));
 
-            DatabaseManager.update(ourContext, mappingRow);
+                DatabaseManager.update(ourContext, mappingRow);
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
     }
 
     /**
@@ -793,25 +842,32 @@ public class Community extends DSpaceObject
                 "SELECT * FROM community2collection WHERE collection_id= ? ",
                 c.getID());
 
-        if (!tri.hasNext())
+        try
         {
-            //make the right to remove the collection explicit because the
+            if (!tri.hasNext())
-            // implicit relation
+            {
-            //has been removed. This only has to concern the currentUser
+                //make the right to remove the collection explicit because the
-            // because
+                // implicit relation
-            //he started the removal process and he will end it too.
+                //has been removed. This only has to concern the currentUser
-            //also add right to remove from the collection to remove it's
+                // because
-            // items.
+                //he started the removal process and he will end it too.
-            AuthorizeManager.addPolicy(ourContext, c, Constants.DELETE,
+                //also add right to remove from the collection to remove it's
-                    ourContext.getCurrentUser());
+                // items.
-            AuthorizeManager.addPolicy(ourContext, c, Constants.REMOVE,
+                AuthorizeManager.addPolicy(ourContext, c, Constants.DELETE,
-                    ourContext.getCurrentUser());
+                        ourContext.getCurrentUser());
+                AuthorizeManager.addPolicy(ourContext, c, Constants.REMOVE,
+                        ourContext.getCurrentUser());
 
-            // Orphan; delete it
+                // Orphan; delete it
-            c.delete();
+                c.delete();
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
     }
 
     /**
@@ -841,25 +897,32 @@ public class Community extends DSpaceObject
                 "SELECT * FROM community2community WHERE child_comm_id= ? ",
                 c.getID());
 
-        if (!tri.hasNext())
+        try
         {
-            //make the right to remove the sub explicit because the implicit
+            if (!tri.hasNext())
-            // relation
+            {
-            //has been removed. This only has to concern the currentUser
+                //make the right to remove the sub explicit because the implicit
-            // because
+                // relation
-            //he started the removal process and he will end it too.
+                //has been removed. This only has to concern the currentUser
-            //also add right to remove from the subcommunity to remove it's
+                // because
-            // children.
+                //he started the removal process and he will end it too.
-            AuthorizeManager.addPolicy(ourContext, c, Constants.DELETE,
+                //also add right to remove from the subcommunity to remove it's
-                    ourContext.getCurrentUser());
+                // children.
-            AuthorizeManager.addPolicy(ourContext, c, Constants.REMOVE,
+                AuthorizeManager.addPolicy(ourContext, c, Constants.DELETE,
-                    ourContext.getCurrentUser());
+                        ourContext.getCurrentUser());
+                AuthorizeManager.addPolicy(ourContext, c, Constants.REMOVE,
+                        ourContext.getCurrentUser());
 
-            // Orphan; delete it
+                // Orphan; delete it
-            c.delete();
+                c.delete();
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
     }
 
     /**

dspace-api/src/main/java/org/dspace/content/FormatIdentifier.java

@@ -105,17 +105,24 @@ public class FormatIdentifier
                 extension);
 
         BitstreamFormat retFormat = null;
-        if (tri.hasNext())
+        try
         {
-            // Return first match
+            if (tri.hasNext())
-            retFormat = new BitstreamFormat(context, tri.next());
+            {
+                // Return first match
+                retFormat = new BitstreamFormat(context, tri.next());
+            }
+            else
+            {
+                retFormat = null;
+            }
         }
-        else
+        finally
         {
-            retFormat = null;
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
         return retFormat;
     }
 }

dspace-api/src/main/java/org/dspace/content/Item.java

@@ -143,39 +143,46 @@ public class Item extends DSpaceObject
         // Get Dublin Core metadata
         TableRowIterator tri = retrieveMetadata();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow resultRow = tri.next();
+            while (tri.hasNext())
-
-            // Get the associated metadata field and schema information
-            int fieldID = resultRow.getIntColumn("metadata_field_id");
-            MetadataField field = MetadataField.find(context, fieldID);
-
-            if (field == null)
             {
-                log.error("Loading item - cannot found metadata field "
+                TableRow resultRow = tri.next();
-                        + fieldID);
+
+                // Get the associated metadata field and schema information
+                int fieldID = resultRow.getIntColumn("metadata_field_id");
+                MetadataField field = MetadataField.find(context, fieldID);
+
+                if (field == null)
+                {
+                    log.error("Loading item - cannot found metadata field "
+                            + fieldID);
+                }
+                else
+                {
+                    MetadataSchema schema = MetadataSchema.find(
+                            context, field.getSchemaID());
+
+                    // Make a DCValue object
+                    DCValue dcv = new DCValue();
+                        dcv.element = field.getElement();
+                        dcv.qualifier = field.getQualifier();
+                    dcv.value = resultRow.getStringColumn("text_value");
+                    dcv.language = resultRow.getStringColumn("text_lang");
+                        //dcv.namespace = schema.getNamespace();
+                        dcv.schema = schema.getName();
+
+                    // Add it to the list
+                    dublinCore.add(dcv);
+                }
             }
-            else
-            {
-                MetadataSchema schema = MetadataSchema.find(
-                        context, field.getSchemaID());
-
-            // Make a DCValue object
-            DCValue dcv = new DCValue();
-                dcv.element = field.getElement();
-                dcv.qualifier = field.getQualifier();
-            dcv.value = resultRow.getStringColumn("text_value");
-            dcv.language = resultRow.getStringColumn("text_lang");
-                //dcv.namespace = schema.getNamespace();
-                dcv.schema = schema.getName();
-
-            // Add it to the list
-            dublinCore.add(dcv);
         }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         // Get our Handle if any
         handle = HandleManager.findHandle(context, this);
@@ -918,25 +925,32 @@ public class Item extends DSpaceObject
                         "collection2item.item_id= ? ",
                         itemRow.getIntColumn("item_id"));
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Collection fromCache = (Collection) ourContext.fromCache(
-                    Collection.class, row.getIntColumn("collection_id"));
-
-            if (fromCache != null)
             {
-                collections.add(fromCache);
+                TableRow row = tri.next();
-            }
+
-            else
+                // First check the cache
-            {
+                Collection fromCache = (Collection) ourContext.fromCache(
-                collections.add(new Collection(ourContext, row));
+                        Collection.class, row.getIntColumn("collection_id"));
+
+                if (fromCache != null)
+                {
+                    collections.add(fromCache);
+                }
+                else
+                {
+                    collections.add(new Collection(ourContext, row));
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         Collection[] collectionArray = new Collection[collections.size()];
         collectionArray = (Collection[]) collections.toArray(collectionArray);
@@ -963,31 +977,38 @@ public class Item extends DSpaceObject
                         "AND community2item.item_id= ? ",
                         itemRow.getIntColumn("item_id"));
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // First check the cache
-            Community owner = (Community) ourContext.fromCache(Community.class,
-                    row.getIntColumn("community_id"));
-
-            if (owner == null)
             {
-                owner = new Community(ourContext, row);
+                TableRow row = tri.next();
-            }
 
-            communities.add(owner);
+                // First check the cache
+                Community owner = (Community) ourContext.fromCache(Community.class,
+                        row.getIntColumn("community_id"));
 
-            // now add any parent communities
+                if (owner == null)
-            Community[] parents = owner.getAllParents();
+                {
+                    owner = new Community(ourContext, row);
+                }
 
-            for (int i = 0; i < parents.length; i++)
+                communities.add(owner);
-            {
+
-                communities.add(parents[i]);
+                // now add any parent communities
+                Community[] parents = owner.getAllParents();
+
+                for (int i = 0; i < parents.length; i++)
+                {
+                    communities.add(parents[i]);
+                }
             }
         }
-        // close the TableRowIterator to free up resources
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         Community[] communityArray = new Community[communities.size()];
         communityArray = (Community[]) communities.toArray(communityArray);
@@ -1012,25 +1033,32 @@ public class Item extends DSpaceObject
     					"item2bundle.item_id= ? ",
                         itemRow.getIntColumn("item_id"));
 
-    		while (tri.hasNext())
+            try
-    		{
+            {
-    			TableRow r = tri.next();
+                while (tri.hasNext())
+                {
+                    TableRow r = tri.next();
 
-    			// First check the cache
+                    // First check the cache
-    			Bundle fromCache = (Bundle) ourContext.fromCache(Bundle.class,
+                    Bundle fromCache = (Bundle) ourContext.fromCache(Bundle.class,
-    										r.getIntColumn("bundle_id"));
+                                                r.getIntColumn("bundle_id"));
 
-    			if (fromCache != null)
+                    if (fromCache != null)
-    			{
+                    {
-    				bundles.add(fromCache);
+                        bundles.add(fromCache);
-    			}
+                    }
-    			else
+                    else
-    			{
+                    {
-    				bundles.add(new Bundle(ourContext, r));
+                        bundles.add(new Bundle(ourContext, r));
-    			}
+                    }
-    		}
+                }
-    		// close the TableRowIterator to free up resources
+            }
-    		tri.close();
+            finally
+            {
+                // close the TableRowIterator to free up resources
+                if (tri != null)
+                    tri.close();
+            }
     	}
         
         Bundle[] bundleArray = new Bundle[bundles.size()];
@@ -1184,25 +1212,32 @@ public class Item extends DSpaceObject
                 "SELECT * FROM item2bundle WHERE bundle_id= ? ",
                 b.getID());
 
-        if (!tri.hasNext())
+        try
         {
-            //make the right to remove the bundle explicit because the implicit
+            if (!tri.hasNext())
-            // relation
+            {
-            //has been removed. This only has to concern the currentUser
+                //make the right to remove the bundle explicit because the implicit
-            // because
+                // relation
-            //he started the removal process and he will end it too.
+                //has been removed. This only has to concern the currentUser
-            //also add right to remove from the bundle to remove it's
+                // because
-            // bitstreams.
+                //he started the removal process and he will end it too.
-            AuthorizeManager.addPolicy(ourContext, b, Constants.DELETE,
+                //also add right to remove from the bundle to remove it's
-                    ourContext.getCurrentUser());
+                // bitstreams.
-            AuthorizeManager.addPolicy(ourContext, b, Constants.REMOVE,
+                AuthorizeManager.addPolicy(ourContext, b, Constants.DELETE,
-                    ourContext.getCurrentUser());
+                        ourContext.getCurrentUser());
+                AuthorizeManager.addPolicy(ourContext, b, Constants.REMOVE,
+                        ourContext.getCurrentUser());
 
-            // The bundle is an orphan, delete it
+                // The bundle is an orphan, delete it
-            b.delete();
+                b.delete();
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
     }
 
     /**

dspace-api/src/main/java/org/dspace/content/MetadataField.java

@@ -320,15 +320,20 @@ public class MetadataField
                     schemaID, element, qualifier);
         }
         
-
         TableRow row = null;
-        if (tri.hasNext())
+        try
         {
-            row = tri.next();
+            if (tri.hasNext())
+            {
+                row = tri.next();
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         if (row == null)
         {
@@ -354,14 +359,21 @@ public class MetadataField
         // Get all the metadatafieldregistry rows
         TableRowIterator tri = DatabaseManager.queryTable(context, "MetadataFieldRegistry",
                                "SELECT mfr.* FROM MetadataFieldRegistry mfr, MetadataSchemaRegistry msr where mfr.metadata_schema_id= msr.metadata_schema_id ORDER BY msr.short_id,  mfr.element, mfr.qualifier");
- 
+
-        // Make into DC Type objects
+        try
-        while (tri.hasNext())
         {
-            fields.add(new MetadataField(tri.next()));
+            // Make into DC Type objects
+            while (tri.hasNext())
+            {
+                fields.add(new MetadataField(tri.next()));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         // Convert list into an array
         MetadataField[] typeArray = new MetadataField[fields.size()];
@@ -386,13 +398,20 @@ public class MetadataField
                 "SELECT * FROM MetadataFieldRegistry WHERE metadata_schema_id= ? " +
                 " ORDER BY element, qualifier", schemaID);
 
-        // Make into DC Type objects
+        try
-        while (tri.hasNext())
         {
-            fields.add(new MetadataField(tri.next()));
+            // Make into DC Type objects
+            while (tri.hasNext())
+            {
+                fields.add(new MetadataField(tri.next()));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         // Convert list into an array
         MetadataField[] typeArray = new MetadataField[fields.size()];
@@ -509,41 +528,60 @@ public class MetadataField
             String qualifier) throws IOException, SQLException,
             AuthorizeException
     {
-        Connection con = context.getDBConnection();
-        TableRow reg = DatabaseManager.row("MetadataFieldRegistry");
-        
-        String qualifierClause = "";
-
-        if (qualifier == null)
-        {
-            qualifierClause = "and qualifier is null";
-        }
-        else
-        {
-            qualifierClause = "and qualifier = ?";
-        }
-
-        String query = "SELECT COUNT(*) FROM " + reg.getTable()
-        	+ " WHERE metadata_schema_id= ? "
-        	+ " and metadata_field_id != ? "
-        	+ " and element= ? " + qualifierClause;
-
-        PreparedStatement statement = con.prepareStatement(query);
-        statement.setInt(1,schemaID);
-        statement.setInt(2,fieldID);
-        statement.setString(3,element);
-        
-        if (qualifier != null)
-        {
-            statement.setString(4,qualifier);
-        }
-        
-        ResultSet rs = statement.executeQuery();
-
         int count = 0;
-        if (rs.next())
+        Connection con = null;
+        PreparedStatement statement = null;
+        ResultSet rs = null;
+
+        try
         {
-            count = rs.getInt(1);
+            con = context.getDBConnection();
+            TableRow reg = DatabaseManager.row("MetadataFieldRegistry");
+
+            String qualifierClause = "";
+
+            if (qualifier == null)
+            {
+                qualifierClause = "and qualifier is null";
+            }
+            else
+            {
+                qualifierClause = "and qualifier = ?";
+            }
+
+            String query = "SELECT COUNT(*) FROM " + reg.getTable()
+                + " WHERE metadata_schema_id= ? "
+                + " and metadata_field_id != ? "
+                + " and element= ? " + qualifierClause;
+
+            statement = con.prepareStatement(query);
+            statement.setInt(1,schemaID);
+            statement.setInt(2,fieldID);
+            statement.setString(3,element);
+
+            if (qualifier != null)
+            {
+                statement.setString(4,qualifier);
+            }
+
+            rs = statement.executeQuery();
+
+            if (rs.next())
+            {
+                count = rs.getInt(1);
+            }
+        }
+        finally
+        {
+            if (rs != null)
+            {
+                try { rs.close(); } catch (SQLException sqle) { }
+            }
+
+            if (statement != null)
+            {
+                try { statement.close(); } catch (SQLException sqle) { }
+            }
         }
 
         return (count == 0);
@@ -604,21 +642,36 @@ public class MetadataField
     {
         if (id2field != null)
             return;
-        id2field = new HashMap();
-        log.info("Loading MetadataField elements into cache.");
 
-        // Grab rows from DB
+        synchronized (MetadataField.class)
-        TableRowIterator tri = DatabaseManager.queryTable(context,"MetadataFieldRegistry",
-                "SELECT * from MetadataFieldRegistry");
-
-        while (tri.hasNext())
         {
-            TableRow row = tri.next();
+            if (id2field == null)
-            int fieldID = row.getIntColumn("metadata_field_id");
+            {
-            id2field.put(new Integer(fieldID), new MetadataField(row));
+                HashMap new_id2field = new HashMap();
-        }
+                log.info("Loading MetadataField elements into cache.");
 
-        // close the TableRowIterator to free up resources
+                // Grab rows from DB
-        tri.close();
+                TableRowIterator tri = DatabaseManager.queryTable(context,"MetadataFieldRegistry",
+                        "SELECT * from MetadataFieldRegistry");
+
+                try
+                {
+                    while (tri.hasNext())
+                    {
+                        TableRow row = tri.next();
+                        int fieldID = row.getIntColumn("metadata_field_id");
+                        new_id2field.put(new Integer(fieldID), new MetadataField(row));
+                    }
+                }
+                finally
+                {
+                    // close the TableRowIterator to free up resources
+                    if (tri != null)
+                        tri.close();
+                }
+
+                id2field = new_id2field;
+            }
+        }
     }
 }

dspace-api/src/main/java/org/dspace/content/MetadataSchema.java

@@ -262,13 +262,19 @@ public class MetadataSchema
                 namespace);
 
         TableRow row = null;
-        if (tri.hasNext())
+        try
         {
-            row = tri.next();
+            if (tri.hasNext())
+            {
+                row = tri.next();
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         if (row == null)
         {
@@ -360,13 +366,20 @@ public class MetadataSchema
         TableRowIterator tri = DatabaseManager.queryTable(context, "MetadataSchemaRegistry",
                         "SELECT * FROM MetadataSchemaRegistry ORDER BY metadata_schema_id");
 
-        // Make into DC Type objects
+        try
-        while (tri.hasNext())
         {
-            schemas.add(new MetadataSchema(tri.next()));
+            // Make into DC Type objects
+            while (tri.hasNext())
+            {
+                schemas.add(new MetadataSchema(tri.next()));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         // Convert list into an array
         MetadataSchema[] typeArray = new MetadataSchema[schemas.size()];
@@ -385,22 +398,41 @@ public class MetadataSchema
     private boolean uniqueNamespace(Context context, String namespace)
             throws SQLException
     {
-        Connection con = context.getDBConnection();
-        TableRow reg = DatabaseManager.row("MetadataSchemaRegistry");
-        
-        String query = "SELECT COUNT(*) FROM " + reg.getTable() + " " +
-        		"WHERE metadata_schema_id != ? " + 
-        		"AND namespace= ? ";
-        PreparedStatement statement = con.prepareStatement(query);
-        statement.setInt(1,schemaID);
-        statement.setString(2,namespace);
-        
-        ResultSet rs = statement.executeQuery();
-
         int count = 0;
-        if (rs.next())
+        Connection con = context.getDBConnection();
+        PreparedStatement statement = null;
+        ResultSet rs = null;
+
+        try
         {
-            count = rs.getInt(1);
+            TableRow reg = DatabaseManager.row("MetadataSchemaRegistry");
+
+            String query = "SELECT COUNT(*) FROM " + reg.getTable() + " " +
+                    "WHERE metadata_schema_id != ? " +
+                    "AND namespace= ? ";
+
+            statement = con.prepareStatement(query);
+            statement.setInt(1,schemaID);
+            statement.setString(2,namespace);
+
+            rs = statement.executeQuery();
+
+            if (rs.next())
+            {
+                count = rs.getInt(1);
+            }
+        }
+        finally
+        {
+            if (rs != null)
+            {
+                try { rs.close(); } catch (SQLException sqle) { }
+            }
+
+            if (statement != null)
+            {
+                try { statement.close(); } catch (SQLException sqle) { }
+            }
         }
 
         return (count == 0);
@@ -417,23 +449,41 @@ public class MetadataSchema
     private boolean uniqueShortName(Context context, String name)
             throws SQLException
     {
-        Connection con = context.getDBConnection();
-        TableRow reg = DatabaseManager.row("MetadataSchemaRegistry");
-        
-        String query = "SELECT COUNT(*) FROM " + reg.getTable() + " " +
-        		"WHERE metadata_schema_id != ? " +
-                "AND short_id = ? ";
-        
-        PreparedStatement statement = con.prepareStatement(query);
-        statement.setInt(1,schemaID);
-        statement.setString(2,name);
-        
-        ResultSet rs = statement.executeQuery();
-
         int count = 0;
-        if (rs.next())
+        Connection con = context.getDBConnection();
+        PreparedStatement statement = null;
+        ResultSet rs = null;
+
+        try
         {
-            count = rs.getInt(1);
+            TableRow reg = DatabaseManager.row("MetadataSchemaRegistry");
+
+            String query = "SELECT COUNT(*) FROM " + reg.getTable() + " " +
+                    "WHERE metadata_schema_id != ? " +
+                    "AND short_id = ? ";
+
+            statement = con.prepareStatement(query);
+            statement.setInt(1,schemaID);
+            statement.setString(2,name);
+
+            rs = statement.executeQuery();
+
+            if (rs.next())
+            {
+                count = rs.getInt(1);
+            }
+        }
+        finally
+        {
+            if (rs != null)
+            {
+                try { rs.close(); } catch (SQLException sqle) { }
+            }
+
+            if (statement != null)
+            {
+                try { statement.close(); } catch (SQLException sqle) { }
+            }
         }
 
         return (count == 0);
@@ -501,21 +551,38 @@ public class MetadataSchema
         if (id2schema != null && name2schema != null)
             return;
 
-        log.info("Loading schema cache for fast finds");
+        synchronized (MetadataSchema.class)
-        id2schema = new HashMap();
-        name2schema = new HashMap();
-
-        TableRowIterator tri = DatabaseManager.queryTable(context,"MetadataSchemaRegistry",
-                "SELECT * from MetadataSchemaRegistry");
-        while (tri.hasNext())
         {
-            TableRow row = tri.next();
+            if (id2schema == null && name2schema == null)
+            {
+                log.info("Loading schema cache for fast finds");
+                HashMap new_id2schema = new HashMap();
+                HashMap new_name2schema = new HashMap();
 
-            MetadataSchema s = new MetadataSchema(row);
+                TableRowIterator tri = DatabaseManager.queryTable(context,"MetadataSchemaRegistry",
-            id2schema.put(new Integer(s.schemaID), s);
+                        "SELECT * from MetadataSchemaRegistry");
-            name2schema.put(s.name, s);
+
+                try
+                {
+                    while (tri.hasNext())
+                    {
+                        TableRow row = tri.next();
+
+                        MetadataSchema s = new MetadataSchema(row);
+                        new_id2schema.put(new Integer(s.schemaID), s);
+                        new_name2schema.put(s.name, s);
+                    }
+                }
+                finally
+                {
+                    // close the TableRowIterator to free up resources
+                    if (tri != null)
+                        tri.close();
+                }
+
+                id2schema = new_id2schema;
+                name2schema = new_name2schema;
+            }
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
     }
 }

dspace-api/src/main/java/org/dspace/content/MetadataValue.java

@@ -278,13 +278,19 @@ public class MetadataValue
                 valueId);
 
         TableRow row = null;
-        if (tri.hasNext())
+        try
         {
-            row = tri.next();
+            if (tri.hasNext())
+            {
+                row = tri.next();
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         if (row == null)
         {
@@ -316,14 +322,20 @@ public class MetadataValue
 
         TableRow row = null;
         java.util.Collection ret = new ArrayList();
-        while (tri.hasNext())
+        try
         {
-            row = tri.next();
+            while (tri.hasNext())
-            ret.add(new MetadataValue(row));
+            {
+                row = tri.next();
+                ret.add(new MetadataValue(row));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         return ret;
     }

dspace-api/src/main/java/org/dspace/content/SupervisedItem.java

@@ -121,16 +121,23 @@ public class SupervisedItem extends WorkspaceItem
         TableRowIterator tri = DatabaseManager.queryTable(context,
                                     "workspaceitem",
                                     query);
-        
+
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-            SupervisedItem si = new SupervisedItem(context, row);
+            {
-            
+                TableRow row = tri.next();
-            sItems.add(si);
+                SupervisedItem si = new SupervisedItem(context, row);
+
+                sItems.add(si);
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
         
         SupervisedItem[] siArray = new SupervisedItem[sItems.size()];
         siArray = (SupervisedItem[]) sItems.toArray(siArray);
@@ -159,16 +166,23 @@ public class SupervisedItem extends WorkspaceItem
                        "ORDER BY epersongroup.name";
         
         TableRowIterator tri = DatabaseManager.queryTable(c,"epersongroup",query, wi);
-        
+
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-            Group group = Group.find(c,row.getIntColumn("eperson_group_id"));
+            {
-            
+                TableRow row = tri.next();
-            groupList.add(group);
+                Group group = Group.find(c,row.getIntColumn("eperson_group_id"));
+
+                groupList.add(group);
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
         
         Group[] groupArray = new Group[groupList.size()];
         groupArray = (Group[]) groupList.toArray(groupArray);
@@ -201,17 +215,24 @@ public class SupervisedItem extends WorkspaceItem
         TableRowIterator tri = DatabaseManager.queryTable(ourContext,
                                     "epersongroup",
                                     query, this.getID());
-        
+
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-            Group group = Group.find(ourContext,
+            {
-                                row.getIntColumn("eperson_group_id"));
+                TableRow row = tri.next();
-            
+                Group group = Group.find(ourContext,
-            groupList.add(group);
+                                    row.getIntColumn("eperson_group_id"));
+
+                groupList.add(group);
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
         
         Group[] groupArray = new Group[groupList.size()];
         groupArray = (Group[]) groupList.toArray(groupArray);
@@ -244,15 +265,22 @@ public class SupervisedItem extends WorkspaceItem
         TableRowIterator tri = DatabaseManager.queryTable(context,
                                     "workspaceitem",
                                     query,ep.getID());
-        
+
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-            SupervisedItem si = new SupervisedItem(context, row);
+            {
-            sItems.add(si);
+                TableRow row = tri.next();
+                SupervisedItem si = new SupervisedItem(context, row);
+                sItems.add(si);
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
         
         SupervisedItem[] siArray = new SupervisedItem[sItems.size()];
         siArray = (SupervisedItem[]) sItems.toArray(siArray);

dspace-api/src/main/java/org/dspace/content/WorkspaceItem.java

@@ -312,23 +312,30 @@ public class WorkspaceItem implements InProgressSubmission
                 "ORDER BY workspaceitem.workspace_item_id", 
                 ep.getID());
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // Check the cache
-            WorkspaceItem wi = (WorkspaceItem) context.fromCache(
-                    WorkspaceItem.class, row.getIntColumn("workspace_item_id"));
-
-            if (wi == null)
             {
-                wi = new WorkspaceItem(context, row);
+                TableRow row = tri.next();
-            }
 
-            wsItems.add(wi);
+                // Check the cache
+                WorkspaceItem wi = (WorkspaceItem) context.fromCache(
+                        WorkspaceItem.class, row.getIntColumn("workspace_item_id"));
+
+                if (wi == null)
+                {
+                    wi = new WorkspaceItem(context, row);
+                }
+
+                wsItems.add(wi);
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         WorkspaceItem[] wsArray = new WorkspaceItem[wsItems.size()];
         wsArray = (WorkspaceItem[]) wsItems.toArray(wsArray);
@@ -356,24 +363,31 @@ public class WorkspaceItem implements InProgressSubmission
                 "workspaceitem.collection_id= ? ",
                 c.getID());
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // Check the cache
-            WorkspaceItem wi = (WorkspaceItem) context.fromCache(
-                    WorkspaceItem.class, row.getIntColumn("workspace_item_id"));
-
-            // not in cache? turn row into workspaceitem
-            if (wi == null)
             {
-                wi = new WorkspaceItem(context, row);
+                TableRow row = tri.next();
-            }
 
-            wsItems.add(wi);
+                // Check the cache
+                WorkspaceItem wi = (WorkspaceItem) context.fromCache(
+                        WorkspaceItem.class, row.getIntColumn("workspace_item_id"));
+
+                // not in cache? turn row into workspaceitem
+                if (wi == null)
+                {
+                    wi = new WorkspaceItem(context, row);
+                }
+
+                wsItems.add(wi);
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        // close the TableRowIterator to free up resources
-        tri.close();
 
         WorkspaceItem[] wsArray = new WorkspaceItem[wsItems.size()];
         wsArray = (WorkspaceItem[]) wsItems.toArray(wsArray);
@@ -397,24 +411,31 @@ public class WorkspaceItem implements InProgressSubmission
                                     "workspaceitem",
                                     query);
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-            
-            // Check the cache
-            WorkspaceItem wi = (WorkspaceItem) context.fromCache(
-                    WorkspaceItem.class, row.getIntColumn("workspace_item_id"));
-
-            // not in cache? turn row into workspaceitem
-            if (wi == null)
             {
-                wi = new WorkspaceItem(context, row);
+                TableRow row = tri.next();
+
+                // Check the cache
+                WorkspaceItem wi = (WorkspaceItem) context.fromCache(
+                        WorkspaceItem.class, row.getIntColumn("workspace_item_id"));
+
+                // not in cache? turn row into workspaceitem
+                if (wi == null)
+                {
+                    wi = new WorkspaceItem(context, row);
+                }
+
+                wsItems.add(wi);
             }
-            
-            wsItems.add(wi);
         }
-        
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
         
         WorkspaceItem[] wsArray = new WorkspaceItem[wsItems.size()];
         wsArray = (WorkspaceItem[]) wsItems.toArray(wsArray);

dspace-api/src/main/java/org/dspace/content/crosswalk/MODSDisseminationCrosswalk.java

@@ -260,9 +260,11 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin
                 File.separator + "config" + File.separator;
             File propsFile = new File(parent, propsFilename);
             Properties modsConfig = new Properties();
+            FileInputStream pfs = null;
             try
             {
-                modsConfig.load(new FileInputStream(propsFile));
+                pfs = new FileInputStream(propsFile);
+                modsConfig.load(pfs);
             }
             catch (IOException e)
             {
@@ -270,6 +272,12 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin
                 throw new CrosswalkInternalException("MODS crosswalk cannot "+
                     "open config file: "+e.toString());
             }
+            finally
+            {
+                if (pfs != null)
+                    try { pfs.close(); } catch (IOException ioe) { }
+            }
+
             modsMap = new HashMap();
             Enumeration pe = modsConfig.propertyNames();
             while (pe.hasMoreElements())

dspace-api/src/main/java/org/dspace/content/crosswalk/QDCCrosswalk.java

@@ -280,7 +280,17 @@ public class QDCCrosswalk extends SelfNamedPlugin
             File.separator + "config" + File.separator;
         File propsFile = new File(parent, propsFilename);
         Properties qdcProps = new Properties();
-        qdcProps.load(new FileInputStream(propsFile));
+        FileInputStream pfs = null;
+        try
+        {
+            pfs = new FileInputStream(propsFile);
+            qdcProps.load(pfs);
+        }
+        finally
+        {
+            if (pfs != null)
+                try { pfs.close(); } catch (IOException ioe) { }
+        }
 
         // grovel properties to initialize qdc->element and element->qdc maps.
         // evaluate the XML fragment with a wrapper including namespaces.

dspace-api/src/main/java/org/dspace/content/crosswalk/XHTMLHeadDisseminationCrosswalk.java

@@ -120,7 +120,16 @@ public class XHTMLHeadDisseminationCrosswalk extends SelfNamedPlugin implements
 
         // Read in configuration
         Properties crosswalkProps = new Properties();
-        crosswalkProps.load(new FileInputStream(config));
+        FileInputStream fis = new FileInputStream(config);
+        try
+        {
+            crosswalkProps.load(fis);
+        }
+        finally
+        {
+            if (fis != null)
+                try { fis.close(); } catch (IOException ioe) { }
+        }
 
         Enumeration e = crosswalkProps.keys();
         while (e.hasMoreElements())

dspace-api/src/main/java/org/dspace/core/ConfigurationManager.java

@@ -177,9 +177,12 @@ public class ConfigurationManager
     {
     // Load in default license
 
+        FileReader fr = null;
+        BufferedReader br = null;
         try
         {
-            BufferedReader br = new BufferedReader(new FileReader(licenseFile));
+            fr = new FileReader(licenseFile);
+            br = new BufferedReader(fr);
             String lineIn;
             license = "";
             while ((lineIn = br.readLine()) != null)
@@ -195,6 +198,15 @@ public class ConfigurationManager
            // configuration we can't do anything
             System.exit(1);
         }
+        finally
+        {
+            if (br != null)
+                try { br.close(); } catch (IOException ioe) { }
+
+            if (fr != null)
+                try { fr.close(); } catch (IOException ioe) { }
+        }
+
         return license;
     }
      
@@ -480,7 +492,8 @@ public class ConfigurationManager
     protected static File getConfigurationFile()
     {
         // in case it hasn't been done yet.
-        loadConfig(null);
+        if (loadedFile == null)
+            loadConfig(null);
 
         return loadedFile;
     }
@@ -494,7 +507,7 @@ public class ConfigurationManager
      *            The <code>dspace.cfg</code> configuration file to use, or
      *            <code>null</code> to try default locations
      */
-    public static void loadConfig(String configFile)
+    public static synchronized void loadConfig(String configFile)
     {
         
         if (properties != null)
@@ -505,6 +518,7 @@ public class ConfigurationManager
 
         URL url = null;
         
+        InputStream is = null;
         try
         {
             String configProperty = null;
@@ -556,7 +570,8 @@ public class ConfigurationManager
             else
             {
                 properties = new Properties();
-                properties.load(url.openStream());
+                is = url.openStream();
+                properties.load(is);
 
                 // walk values, interpolating any embedded references.
                 for (Enumeration pe = properties.propertyNames(); pe.hasMoreElements(); )
@@ -577,16 +592,25 @@ public class ConfigurationManager
             // configuration we can't do anything
             throw new RuntimeException("Cannot load configuration: " + url, e);
         }
-        
+        finally
+        {
+            if (is != null)
+                try { is.close(); } catch (IOException ioe) { }
+        }
+
         // Load in default license
         File licenseFile = new File(getProperty("dspace.dir") + File.separator
                 + "config" + File.separator + "default.license");
+
+        FileInputStream  fir = null;
+        InputStreamReader ir = null;
+        BufferedReader br = null;
         try
         {
             
-            FileInputStream fir = new FileInputStream(licenseFile);
+            fir = new FileInputStream(licenseFile);
-            InputStreamReader ir = new InputStreamReader(fir, "UTF-8");
+            ir = new InputStreamReader(fir, "UTF-8");
-            BufferedReader br = new BufferedReader(ir);
+            br = new BufferedReader(ir);
             String lineIn;
             license = "";
 
@@ -605,7 +629,18 @@ public class ConfigurationManager
             // FIXME: Maybe something more graceful here, but with the
             // configuration we can't do anything
             throw new RuntimeException("Cannot load license: " + licenseFile.toString(),e);
-        }   
+        }
+        finally
+        {
+            if (br != null)
+                try { br.close(); } catch (IOException ioe) { }
+
+            if (ir != null)
+                try { ir.close(); } catch (IOException ioe) { }
+
+            if (fir != null)
+                try { fir.close(); } catch (IOException ioe) { }
+        }
 
         
         

dspace-api/src/main/java/org/dspace/core/LogManager.java

@@ -84,9 +84,8 @@ public class LogManager
             contextExtraInfo = "no_context";
         }
 
-        String result = new String(email + ":" + contextExtraInfo + ":"
+        StringBuilder result = new StringBuilder();
-                + action + ":" + extrainfo);
+        result.append(email).append(":").append(contextExtraInfo).append(":").append(action).append(":").append(extrainfo);
-
+        return result.toString();
-        return result;
     }
 }

dspace-api/src/main/java/org/dspace/core/PluginManager.java

@@ -564,6 +564,9 @@ public class PluginManager
     public static void checkConfiguration()
         throws IOException
     {
+        FileReader fr = null;
+        BufferedReader cr = null;
+
         /*  XXX TODO:  (maybe) test that implementation class is really a
          *  subclass or impl of the plugin "interface"
          */
@@ -574,51 +577,63 @@ public class PluginManager
         Map namedKey = new HashMap();
         Map selfnamedKey = new HashMap();
         Map reusableKey = new HashMap();
+        HashMap keyMap = new HashMap();
 
         // 1. First pass -- grovel the actual config file to check for
         //    duplicate keys, since Properties class hides them from us.
         //    Also build lists of each type of key, check for misspellings.
         File config = ConfigurationManager.getConfigurationFile();
-        BufferedReader cr = new BufferedReader(new FileReader(config));
+        try
-        String line = null;
-        boolean continued = false;
-        HashMap keyMap = new HashMap();
-        Pattern keyPattern = Pattern.compile("([^\\s\\=\\:]+)");
-        while ((line = cr.readLine()) != null)
         {
-            line = line.trim();
+            fr = new FileReader(config);
-            if (line.startsWith("!") || line.startsWith("#"))
+            cr = new BufferedReader(fr);
-                continued = false;
+            String line = null;
-            else
+            boolean continued = false;
+            Pattern keyPattern = Pattern.compile("([^\\s\\=\\:]+)");
+            while ((line = cr.readLine()) != null)
             {
-                if (!continued && line.startsWith("plugin."))
+                line = line.trim();
+                if (line.startsWith("!") || line.startsWith("#"))
+                    continued = false;
+                else
                 {
-                    Matcher km = keyPattern.matcher(line);
+                    if (!continued && line.startsWith("plugin."))
-                    if (km.find())
                     {
-                        String key = line.substring(0, km.end(1));
+                        Matcher km = keyPattern.matcher(line);
-                        if (keyMap.containsKey(key))
+                        if (km.find())
-                            log.error("Duplicate key \""+key+"\" in DSpace configuration file="+config.toString());
+                        {
-                        else
+                            String key = line.substring(0, km.end(1));
-                            keyMap.put(key, key);
+                            if (keyMap.containsKey(key))
+                                log.error("Duplicate key \""+key+"\" in DSpace configuration file="+config.toString());
+                            else
+                                keyMap.put(key, key);
 
-                        if (key.startsWith(SINGLE_PREFIX))
+                            if (key.startsWith(SINGLE_PREFIX))
-                            singleKey.put(key.substring(SINGLE_PREFIX.length()), key);
+                                singleKey.put(key.substring(SINGLE_PREFIX.length()), key);
-                        else if (key.startsWith(SEQUENCE_PREFIX))
+                            else if (key.startsWith(SEQUENCE_PREFIX))
-                            sequenceKey.put(key.substring(SEQUENCE_PREFIX.length()), key);
+                                sequenceKey.put(key.substring(SEQUENCE_PREFIX.length()), key);
-                        else if (key.startsWith(NAMED_PREFIX))
+                            else if (key.startsWith(NAMED_PREFIX))
-                            namedKey.put(key.substring(NAMED_PREFIX.length()), key);
+                                namedKey.put(key.substring(NAMED_PREFIX.length()), key);
-                        else if (key.startsWith(SELFNAMED_PREFIX))
+                            else if (key.startsWith(SELFNAMED_PREFIX))
-                            selfnamedKey.put(key.substring(SELFNAMED_PREFIX.length()), key);
+                                selfnamedKey.put(key.substring(SELFNAMED_PREFIX.length()), key);
-                        else if (key.startsWith(REUSABLE_PREFIX))
+                            else if (key.startsWith(REUSABLE_PREFIX))
-                            reusableKey.put(key.substring(REUSABLE_PREFIX.length()), key);
+                                reusableKey.put(key.substring(REUSABLE_PREFIX.length()), key);
-                        else
+                            else
-                            log.error("Key with unknown prefix \""+key+"\" in DSpace configuration file="+config.toString());
+                                log.error("Key with unknown prefix \""+key+"\" in DSpace configuration file="+config.toString());
+                        }
                     }
+                    continued = line.length() > 0 && line.charAt(line.length()-1) == '\\';
                 }
-                continued = line.length() > 0 && line.charAt(line.length()-1) == '\\';
             }
         }
+        finally
+        {
+            if (cr != null)
+                try { cr.close(); } catch (IOException ioe) { }
+
+            if (fr != null)
+                try { fr.close(); } catch (IOException ioe) { }
+        }
 
         // 1.1 Sanity check, make sure keyMap == set of keys from Configuration
         Enumeration pne = ConfigurationManager.propertyNames();

dspace-api/src/main/java/org/dspace/eperson/EPerson.java

@@ -908,36 +908,57 @@ public class EPerson extends DSpaceObject
                 "SELECT * from item where submitter_id= ? ",
                 getID());
 
-        if (tri.hasNext())
+        try
         {
-            tableList.add("item");
+            if (tri.hasNext())
+            {
+                tableList.add("item");
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
 
-        tri.close();
-        
         // check for eperson in workflowitem table
         tri = DatabaseManager.query(myContext,
                 "SELECT * from workflowitem where owner= ? ",
                 getID());
 
-        if (tri.hasNext())
+        try
         {
-            tableList.add("workflowitem");
+            if (tri.hasNext())
+            {
+                tableList.add("workflowitem");
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
 
-        tri.close();
-        
         // check for eperson in tasklistitem table
         tri = DatabaseManager.query(myContext,
                 "SELECT * from tasklistitem where eperson_id= ? ",
                 getID());
 
-        if (tri.hasNext())
+        try
         {
-            tableList.add("tasklistitem");
+            if (tri.hasNext())
+            {
+                tableList.add("tasklistitem");
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-
-        tri.close();
         
         // the list of tables can be used to construct an error message
         // explaining to the user why the eperson cannot be deleted.

dspace-api/src/main/java/org/dspace/eperson/Group.java

@@ -141,26 +141,33 @@ public class Group extends DSpaceObject
                                 "epersongroup2eperson.eperson_group_id= ?",
                                 myRow.getIntColumn("eperson_group_id"));
 
-                while (tri.hasNext())
+                try
                 {
-                    TableRow r = (TableRow) tri.next();
+                    while (tri.hasNext())
-
-                    // First check the cache
-                    EPerson fromCache = (EPerson) myContext.fromCache(
-                            EPerson.class, r.getIntColumn("eperson_id"));
-
-                    if (fromCache != null)
                     {
-                        epeople.add(fromCache);
+                        TableRow r = (TableRow) tri.next();
-                    }
+
-                    else
+                        // First check the cache
-                    {
+                        EPerson fromCache = (EPerson) myContext.fromCache(
-                        epeople.add(new EPerson(myContext, r));
+                                EPerson.class, r.getIntColumn("eperson_id"));
+
+                        if (fromCache != null)
+                        {
+                            epeople.add(fromCache);
+                        }
+                        else
+                        {
+                            epeople.add(new EPerson(myContext, r));
+                        }
                     }
                 }
+                finally
+                {
+                    // close the TableRowIterator to free up resources
+                    if (tri != null)
+                        tri.close();
+                }
 
-                tri.close();
-                
                 // now get Group objects
                 tri = DatabaseManager.queryTable(myContext,"epersongroup",
                                 "SELECT epersongroup.* FROM epersongroup, group2group WHERE " +
@@ -168,25 +175,32 @@ public class Group extends DSpaceObject
                                 "group2group.parent_id= ? ",
                                 myRow.getIntColumn("eperson_group_id"));
 
-                while (tri.hasNext())
+                try
                 {
-                    TableRow r = (TableRow) tri.next();
+                    while (tri.hasNext())
-
-                    // First check the cache
-                    Group fromCache = (Group) myContext.fromCache(Group.class,
-                            r.getIntColumn("eperson_group_id"));
-
-                    if (fromCache != null)
                     {
-                        groups.add(fromCache);
+                        TableRow r = (TableRow) tri.next();
-                    }
+
-                    else
+                        // First check the cache
-                    {
+                        Group fromCache = (Group) myContext.fromCache(Group.class,
-                        groups.add(new Group(myContext, r));
+                                r.getIntColumn("eperson_group_id"));
+
+                        if (fromCache != null)
+                        {
+                            groups.add(fromCache);
+                        }
+                        else
+                        {
+                            groups.add(new Group(myContext, r));
+                        }
                     }
                 }
-                
+                finally
-                tri.close();
+                {
+                    // close the TableRowIterator to free up resources
+                    if (tri != null)
+                        tri.close();
+                }
 
             }
             catch (Exception e)
@@ -449,16 +463,23 @@ public class Group extends DSpaceObject
 
         Set<Integer> groupIDs = new HashSet<Integer>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
+            {
+                TableRow row = tri.next();
 
-            int childID = row.getIntColumn("eperson_group_id");
+                int childID = row.getIntColumn("eperson_group_id");
 
-            groupIDs.add(new Integer(childID));
+                groupIDs.add(new Integer(childID));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
 
         // Also need to get all "Special Groups" user is a member of!
         // Otherwise, you're ignoring the user's membership to these groups!
@@ -501,16 +522,23 @@ public class Group extends DSpaceObject
                 "SELECT * FROM group2groupcache WHERE " + groupQuery,
                 parameters);
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
+            {
+                TableRow row = tri.next();
 
-            int parentID = row.getIntColumn("parent_id");
+                int parentID = row.getIntColumn("parent_id");
 
-            groupIDs.add(new Integer(parentID));
+                groupIDs.add(new Integer(parentID));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
 
         return groupIDs;
     }
@@ -570,16 +598,23 @@ public class Group extends DSpaceObject
         
         Set<Integer> groupIDs = new HashSet<Integer>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
+            {
+                TableRow row = tri.next();
 
-            int childID = row.getIntColumn("child_id");
+                int childID = row.getIntColumn("child_id");
 
-            groupIDs.add(new Integer(childID));
+                groupIDs.add(new Integer(childID));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
 
         // now we have all the groups (including this one)
         // it is time to find all the EPeople who belong to those groups
@@ -612,16 +647,23 @@ public class Group extends DSpaceObject
                 "SELECT * FROM epersongroup2eperson WHERE " + epersonQuery,
                 parameters);
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
+            {
+                TableRow row = tri.next();
 
-            int epersonID = row.getIntColumn("eperson_id");
+                int epersonID = row.getIntColumn("eperson_id");
-   
+
-            epeopleIDs.add(new Integer(epersonID));
+                epeopleIDs.add(new Integer(epersonID));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
 
         return epeopleIDs;
     }
@@ -1135,32 +1177,39 @@ public class Group extends DSpaceObject
 
         Map<Integer,Set<Integer>> parents = new HashMap<Integer,Set<Integer>>();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = (TableRow) tri.next();
+            while (tri.hasNext())
-
-            Integer parentID = new Integer(row.getIntColumn("parent_id"));
-            Integer childID = new Integer(row.getIntColumn("child_id"));
-
-            // if parent doesn't have an entry, create one
-            if (!parents.containsKey(parentID))
             {
-                Set<Integer> children = new HashSet<Integer>();
+                TableRow row = (TableRow) tri.next();
 
-                // add child id to the list
+                Integer parentID = new Integer(row.getIntColumn("parent_id"));
-                children.add(childID);
+                Integer childID = new Integer(row.getIntColumn("child_id"));
-                parents.put(parentID, children);
+
-            }
+                // if parent doesn't have an entry, create one
-            else
+                if (!parents.containsKey(parentID))
-            {
+                {
-                // parent has an entry, now add the child to the parent's record
+                    Set<Integer> children = new HashSet<Integer>();
-                // of children
+
-                Set<Integer> children =  parents.get(parentID);
+                    // add child id to the list
-                children.add(childID);
+                    children.add(childID);
+                    parents.put(parentID, children);
+                }
+                else
+                {
+                    // parent has an entry, now add the child to the parent's record
+                    // of children
+                    Set<Integer> children =  parents.get(parentID);
+                    children.add(childID);
+                }
             }
         }
-        
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         // now parents is a hash of all of the IDs of groups that are parents
         // and each hash entry is a hash of all of the IDs of children of those

dspace-api/src/main/java/org/dspace/eperson/Subscribe.java

@@ -112,20 +112,27 @@ public class Subscribe
                     " AND collection_id= ? ", 
                     eperson.getID(),collection.getID());
 
-            if (!r.hasNext())
+            try
             {
-                // Not subscribed, so add them
+                if (!r.hasNext())
-                TableRow row = DatabaseManager.create(context, "subscription");
+                {
-                row.setColumn("eperson_id", eperson.getID());
+                    // Not subscribed, so add them
-                row.setColumn("collection_id", collection.getID());
+                    TableRow row = DatabaseManager.create(context, "subscription");
-                DatabaseManager.update(context, row);
+                    row.setColumn("eperson_id", eperson.getID());
+                    row.setColumn("collection_id", collection.getID());
+                    DatabaseManager.update(context, row);
 
-                log.info(LogManager.getHeader(context, "subscribe",
+                    log.info(LogManager.getHeader(context, "subscribe",
-                        "eperson_id=" + eperson.getID() + ",collection_id="
+                            "eperson_id=" + eperson.getID() + ",collection_id="
-                                + collection.getID()));
+                                    + collection.getID()));
+                }
+            }
+            finally
+            {
+                // close the TableRowIterator to free up resources
+                if (r != null)
+                    r.close();
             }
-            
-            r.close();
         }
         else
         {
@@ -198,15 +205,22 @@ public class Subscribe
 
         List collections = new ArrayList();
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
+            {
+                TableRow row = tri.next();
 
-            collections.add(Collection.find(context, row
+                collections.add(Collection.find(context, row
-                    .getIntColumn("collection_id")));
+                        .getIntColumn("collection_id")));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
         }
-
-        tri.close();
         
         Collection[] collArray = new Collection[collections.size()];
 
@@ -231,11 +245,17 @@ public class Subscribe
                 "SELECT * FROM subscription WHERE eperson_id= ? " +
                 "AND collection_id= ? ", 
                 eperson.getID(),collection.getID());
-    	
+
-    	boolean result = tri.hasNext();
+        try
-    	tri.close();
+        {
-    	
+            return tri.hasNext();
-    	return result;
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
     }
 
     /**
@@ -265,42 +285,49 @@ public class Subscribe
         EPerson currentEPerson = null;
         List collections = null; // List of Collections
 
-        // Go through the list collating subscriptions for each e-person
+        try
-        while (tri.hasNext())
         {
-            TableRow row = tri.next();
+            // Go through the list collating subscriptions for each e-person
-
+            while (tri.hasNext())
-            // Does this row relate to the same e-person as the last?
-            if ((currentEPerson == null)
-                    || (row.getIntColumn("eperson_id") != currentEPerson
-                            .getID()))
             {
-                // New e-person. Send mail for previous e-person
+                TableRow row = tri.next();
-                if (currentEPerson != null)
-                {
 
-                    try
+                // Does this row relate to the same e-person as the last?
+                if ((currentEPerson == null)
+                        || (row.getIntColumn("eperson_id") != currentEPerson
+                                .getID()))
+                {
+                    // New e-person. Send mail for previous e-person
+                    if (currentEPerson != null)
                     {
-                        sendEmail(context, currentEPerson, collections, test);
+
-                    }
+                        try
-                    catch (MessagingException me)
+                        {
-                    {
+                            sendEmail(context, currentEPerson, collections, test);
-                        log.error("Failed to send subscription to eperson_id="
+                        }
-                                + currentEPerson.getID());
+                        catch (MessagingException me)
-                        log.error(me);
+                        {
+                            log.error("Failed to send subscription to eperson_id="
+                                    + currentEPerson.getID());
+                            log.error(me);
+                        }
                     }
+
+                    currentEPerson = EPerson.find(context, row
+                            .getIntColumn("eperson_id"));
+                    collections = new ArrayList();
                 }
 
-                currentEPerson = EPerson.find(context, row
+                collections.add(Collection.find(context, row
-                        .getIntColumn("eperson_id"));
+                        .getIntColumn("collection_id")));
-                collections = new ArrayList();
             }
-
-            collections.add(Collection.find(context, row
-                    .getIntColumn("collection_id")));
         }
-        
+        finally
-        tri.close();
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
         
         // Process the last person
         if (currentEPerson != null)

dspace-api/src/main/java/org/dspace/eperson/Supervisor.java

@@ -108,10 +108,17 @@ public class Supervisor {
         TableRowIterator tri = DatabaseManager.queryTable(context, 
                                     "epersongroup2workspaceitem", 
                                     query,groupID,wsItemID);
-        
+
-        boolean result = tri.hasNext();
+        try
-        tri.close();
+        {
-        return result;
+            return tri.hasNext();
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
     }
     
     /**

dspace-api/src/main/java/org/dspace/handle/HandleManager.java

@@ -327,13 +327,20 @@ public class HandleManager
         TableRowIterator iterator = DatabaseManager.queryTable(context, null, sql, prefix+"%");
         List results = new ArrayList();
 
-        while (iterator.hasNext())
+        try
         {
-            TableRow row = (TableRow) iterator.next();
+            while (iterator.hasNext())
-            results.add(row.getStringColumn("handle"));
+            {
+                TableRow row = (TableRow) iterator.next();
+                results.add(row.getStringColumn("handle"));
+            }
+        }
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (iterator != null)
+                iterator.close();
         }
-        
-        iterator.close();
 
         return results;
     }

dspace-api/src/main/java/org/dspace/search/Harvest.java

@@ -228,43 +228,51 @@ public class Harvest
         List infoObjects = new LinkedList();
         int index = 0;
 
-        // Process results of query into HarvestedItemInfo objects
+        try
-        while (tri.hasNext())
         {
-            TableRow row = tri.next();
+            // Process results of query into HarvestedItemInfo objects
-
+            while (tri.hasNext())
-            /*
-             * This conditional ensures that we only process items within any
-             * constraints specified by 'offset' and 'limit' parameters.
-             */
-            if ((index >= offset)
-                    && ((limit == 0) || (index < (offset + limit))))
             {
-                HarvestedItemInfo itemInfo = new HarvestedItemInfo();
+                TableRow row = tri.next();
-                
-                itemInfo.context = context;
-                itemInfo.handle = row.getStringColumn("handle");
-                itemInfo.itemID = row.getIntColumn("resource_id");
-                itemInfo.datestamp = row.getDateColumn("last_modified");
-                itemInfo.withdrawn = row.getBooleanColumn("withdrawn");
 
-                if (collections)
+                /*
+                 * This conditional ensures that we only process items within any
+                 * constraints specified by 'offset' and 'limit' parameters.
+                 */
+                if ((index >= offset)
+                        && ((limit == 0) || (index < (offset + limit))))
                 {
-                    fillCollections(context, itemInfo);
+                    HarvestedItemInfo itemInfo = new HarvestedItemInfo();
+
+                    itemInfo.context = context;
+                    itemInfo.handle = row.getStringColumn("handle");
+                    itemInfo.itemID = row.getIntColumn("resource_id");
+                    itemInfo.datestamp = row.getDateColumn("last_modified");
+                    itemInfo.withdrawn = row.getBooleanColumn("withdrawn");
+
+                    if (collections)
+                    {
+                        fillCollections(context, itemInfo);
+                    }
+
+                    if (items)
+                    {
+                        // Get the item
+                        itemInfo.item = Item.find(context, itemInfo.itemID);
+                    }
+
+                    infoObjects.add(itemInfo);
                 }
 
-                if (items)
+                index++;
-                {
-                    // Get the item
-                    itemInfo.item = Item.find(context, itemInfo.itemID);
-                }
-
-                infoObjects.add(itemInfo);
             }
-
-            index++;
         }
-        tri.close();
+        finally
+        {
+            // close the TableRowIterator to free up resources
+            if (tri != null)
+                tri.close();
+        }
 
         return infoObjects;
     }

dspace-api/src/main/java/org/dspace/sort/OrderFormat.java

@@ -107,24 +107,24 @@ public class OrderFormat
         	{
         		return delegate.makeSortString(value, language);
         	}
-    	}
+
-    	
+            // No delegates found, so apply defaults
-      	// No delegates found, so apply defaults
+            if (type.equalsIgnoreCase(OrderFormat.AUTHOR) && authorDelegate != null)
-    	if (type.equalsIgnoreCase(OrderFormat.AUTHOR) && authorDelegate != null)
+            {
-    	{
+              return authorDelegate.makeSortString(value, language);
-    		return authorDelegate.makeSortString(value, language);
+            }
+
+            if (type.equalsIgnoreCase(OrderFormat.TITLE) && titleDelegate != null)
+            {
+              return titleDelegate.makeSortString(value, language);
+            }
+
+            if (type.equalsIgnoreCase(OrderFormat.TEXT) && textDelegate != null)
+            {
+              return textDelegate.makeSortString(value, language);
+            }
     	}
 
-    	if (type.equalsIgnoreCase(OrderFormat.TITLE) && titleDelegate != null)
-    	{
-    		return titleDelegate.makeSortString(value, language);
-    	}
-
-    	if (type.equalsIgnoreCase(OrderFormat.TEXT) && textDelegate != null)
-    	{
-    		return textDelegate.makeSortString(value, language);
-    	}
-    	
     	return value;
     }
 

dspace-api/src/main/java/org/dspace/sort/SortOption.java

@@ -304,16 +304,21 @@ public class SortOption
     {
         if (SortOption.sortOptionsMap != null)
             return SortOption.sortOptionsMap;
-        
+
-        SortOption.sortOptionsMap = new HashMap<Integer, SortOption>();
+        synchronized (SortOption.class)
-        synchronized (SortOption.sortOptionsMap)
         {
-            for (SortOption so : SortOption.getSortOptions())
+            if (SortOption.sortOptionsMap == null)
             {
-                SortOption.sortOptionsMap.put(new Integer(so.getNumber()), so);
+                Map<Integer, SortOption> newSortOptionsMap = new HashMap<Integer, SortOption>();
+                for (SortOption so : SortOption.getSortOptions())
+                {
+                    newSortOptionsMap.put(new Integer(so.getNumber()), so);
+                }
+
+                SortOption.sortOptionsMap = newSortOptionsMap;
             }
         }
-        
+
     	return SortOption.sortOptionsMap;
     }
 
@@ -327,17 +332,22 @@ public class SortOption
         if (SortOption.sortOptionsSet != null)
             return SortOption.sortOptionsSet;
         
-        SortOption.sortOptionsSet = new HashSet<SortOption>();
+        synchronized (SortOption.class)
-        synchronized (SortOption.sortOptionsSet)
         {
-            int idx = 1;
+            if (SortOption.sortOptionsSet == null)
-            String option;
-
-            while ( ((option = ConfigurationManager.getProperty("webui.itemlist.sort-option." + idx))) != null)
             {
-                SortOption so = new SortOption(idx, option);
+                Set<SortOption> newSortOptionsSet = new HashSet<SortOption>();
-                SortOption.sortOptionsSet.add(so);
+                int idx = 1;
-                idx++;
+                String option;
+
+                while ( ((option = ConfigurationManager.getProperty("webui.itemlist.sort-option." + idx))) != null)
+                {
+                    SortOption so = new SortOption(idx, option);
+                    newSortOptionsSet.add(so);
+                    idx++;
+                }
+
+                SortOption.sortOptionsSet = newSortOptionsSet;
             }
         }
 

dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageManager.java

@@ -352,9 +352,13 @@ public class BitstreamStorageManager
 
         bitstream.setColumn("size_bytes", file.length());
 
-        bitstream.setColumn("checksum", Utils.toHex(dis.getMessageDigest()
+        if (dis != null)
-                .digest()));
+        {
-        bitstream.setColumn("checksum_algorithm", "MD5");
+            bitstream.setColumn("checksum", Utils.toHex(dis.getMessageDigest()
+                    .digest()));
+            bitstream.setColumn("checksum_algorithm", "MD5");
+        }
+        
         bitstream.setColumn("deleted", false);
         DatabaseManager.update(context, bitstream);
 

dspace-api/src/main/java/org/dspace/storage/rdbms/DatabaseManager.java

@@ -276,10 +276,19 @@ public class DatabaseManager
     public static TableRow querySingle(Context context, String query,
             Object... parameters) throws SQLException
     {
-        TableRowIterator iterator = query(context, query, parameters);
+        TableRow retRow = null;
+        TableRowIterator iterator = null;
+        try
+        {
+            iterator = query(context, query, parameters);
+            retRow = (!iterator.hasNext()) ? null : iterator.next();
+        }
+        finally
+        {
+            if (iterator != null)
+                iterator.close();
+        }
 
-        TableRow retRow = (!iterator.hasNext()) ? null : iterator.next();
-        iterator.close();
         return (retRow);
     }
     
@@ -304,10 +313,18 @@ public class DatabaseManager
     public static TableRow querySingleTable(Context context, String table,
             String query, Object... parameters) throws SQLException
     {
+        TableRow retRow = null;
         TableRowIterator iterator = queryTable(context, canonicalize(table), query, parameters);
 
-        TableRow retRow = (!iterator.hasNext()) ? null : iterator.next();
+        try
-        iterator.close();
+        {
+            retRow = (!iterator.hasNext()) ? null : iterator.next();
+        }
+        finally
+        {
+            if (iterator != null)
+                iterator.close();
+        }
         return (retRow);
     }
     
@@ -564,26 +581,44 @@ public class DatabaseManager
     public static void insert(Context context, TableRow row)
             throws SQLException
     {
+        int newID = -1;
         String table = canonicalize(row.getTable());
+        Statement statement = null;
+        ResultSet rs = null;
 
-        // Get an ID (primary key) for this row by using the "getnextid"
+        try
-        // SQL function in Postgres, or directly with sequences in Oracle
-        String myQuery = "SELECT getnextid('" + table + "') AS result";
-
-        if ("oracle".equals(ConfigurationManager.getProperty("db.name")))
         {
-            myQuery = "SELECT " + table + "_seq" + ".nextval FROM dual";
+            // Get an ID (primary key) for this row by using the "getnextid"
+            // SQL function in Postgres, or directly with sequences in Oracle
+            String myQuery = "SELECT getnextid('" + table + "') AS result";
+
+            if ("oracle".equals(ConfigurationManager.getProperty("db.name")))
+            {
+                myQuery = "SELECT " + table + "_seq" + ".nextval FROM dual";
+            }
+
+            statement = context.getDBConnection().createStatement();
+            rs = statement.executeQuery(myQuery);
+
+            rs.next();
+
+            newID = rs.getInt(1);
+        }
+        finally
+        {
+            if (rs != null)
+            {
+                try { rs.close(); } catch (SQLException sqle) { }
+            }
+
+            if (statement != null)
+            {
+                try { statement.close(); } catch (SQLException sqle) { }
+            }
         }
 
-        Statement statement = context.getDBConnection().createStatement();
+        if (newID < 0)
-        ResultSet rs = statement.executeQuery(myQuery);
+            throw new SQLException("Unable to retrieve sequence ID");
-
-        rs.next();
-
-        int newID = rs.getInt(1);
-        rs.close();
-
-        statement.close();
 
         // Set the ID in the table row object
         row.setColumn(getPrimaryKeyColumn(table), newID);
@@ -1354,7 +1389,9 @@ public class DatabaseManager
     private static Map retrieveColumnInfo(String table) throws SQLException
     {
         Connection connection = null;
-
+        ResultSet pkcolumns = null;
+        ResultSet columns = null;
+        
         try
         {
             String schema = ConfigurationManager.getProperty("db.schema");
@@ -1367,13 +1404,13 @@ public class DatabaseManager
             String tname = (table.length() >= max) ? table
                     .substring(0, max - 1) : table;
 
-            ResultSet pkcolumns = metadata.getPrimaryKeys(null, schema, tname);
+            pkcolumns = metadata.getPrimaryKeys(null, schema, tname);
             Set pks = new HashSet();
 
             while (pkcolumns.next())
                 pks.add(pkcolumns.getString(4));
 
-            ResultSet columns = metadata.getColumns(null, schema, tname, null);
+            columns = metadata.getColumns(null, schema, tname, null);
 
             while (columns.next())
             {
@@ -1394,9 +1431,19 @@ public class DatabaseManager
         }
         finally
         {
+            if (pkcolumns != null)
+            {
+                try { pkcolumns.close(); } catch (SQLException sqle) { }
+            }
+
+            if (columns != null)
+            {
+                try { columns.close(); } catch (SQLException sqle) { }
+            }
+
             if (connection != null)
             {
-                connection.close();
+                try { connection.close(); } catch (SQLException sqle) { }
             }
         }
     }

dspace-api/src/main/java/org/dspace/storage/rdbms/TableRowIterator.java

@@ -108,7 +108,7 @@ public class TableRowIterator
     /**
      * Finalize -- this method is called when this object is GC-ed.
      */
-    public void finalize()
+    protected void finalize()
     {
         close();
     }

dspace-api/src/main/java/org/dspace/workflow/WorkflowItem.java

@@ -171,15 +171,21 @@ public class WorkflowItem implements InProgressSubmission
         TableRowIterator tri = DatabaseManager.queryTable(c, "workflowitem",
                 "SELECT * FROM workflowitem");
 
-        // make a list of workflow items
+        try
-        while (tri.hasNext())
         {
-            TableRow row = tri.next();
+            // make a list of workflow items
-            WorkflowItem wi = new WorkflowItem(c, row);
+            while (tri.hasNext())
-            wfItems.add(wi);
+            {
+                TableRow row = tri.next();
+                WorkflowItem wi = new WorkflowItem(c, row);
+                wfItems.add(wi);
+            }
+        }
+        finally
+        {
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
 
         WorkflowItem[] wfArray = new WorkflowItem[wfItems.size()];
         wfArray = (WorkflowItem[]) wfItems.toArray(wfArray);
@@ -211,23 +217,29 @@ public class WorkflowItem implements InProgressSubmission
                 "ORDER BY workflowitem.workflow_id",
                 ep.getID());
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // Check the cache
-            WorkflowItem wi = (WorkflowItem) context.fromCache(
-                    WorkflowItem.class, row.getIntColumn("workflow_id"));
-
-            if (wi == null)
             {
-                wi = new WorkflowItem(context, row);
+                TableRow row = tri.next();
-            }
 
-            wfItems.add(wi);
+                // Check the cache
+                WorkflowItem wi = (WorkflowItem) context.fromCache(
+                        WorkflowItem.class, row.getIntColumn("workflow_id"));
+
+                if (wi == null)
+                {
+                    wi = new WorkflowItem(context, row);
+                }
+
+                wfItems.add(wi);
+            }
+        }
+        finally
+        {
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
 
         WorkflowItem[] wfArray = new WorkflowItem[wfItems.size()];
         wfArray = (WorkflowItem[]) wfItems.toArray(wfArray);
@@ -255,24 +267,30 @@ public class WorkflowItem implements InProgressSubmission
                 "workflowitem.collection_id= ? ",
                 c.getID());
 
-        while (tri.hasNext())
+        try
         {
-            TableRow row = tri.next();
+            while (tri.hasNext())
-
-            // Check the cache
-            WorkflowItem wi = (WorkflowItem) context.fromCache(
-                    WorkflowItem.class, row.getIntColumn("workflow_id"));
-
-            // not in cache? turn row into workflowitem
-            if (wi == null)
             {
-                wi = new WorkflowItem(context, row);
+                TableRow row = tri.next();
-            }
 
-            wsItems.add(wi);
+                // Check the cache
+                WorkflowItem wi = (WorkflowItem) context.fromCache(
+                        WorkflowItem.class, row.getIntColumn("workflow_id"));
+
+                // not in cache? turn row into workflowitem
+                if (wi == null)
+                {
+                    wi = new WorkflowItem(context, row);
+                }
+
+                wsItems.add(wi);
+            }
+        }
+        finally
+        {
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
 
         WorkflowItem[] wsArray = new WorkflowItem[wsItems.size()];
         wsArray = (WorkflowItem[]) wsItems.toArray(wsArray);

dspace-api/src/main/java/org/dspace/workflow/WorkflowManager.java

@@ -237,12 +237,18 @@ public class WorkflowManager
         TableRowIterator tri = DatabaseManager.queryTable(c, 
         		"workflowitem", myquery,e.getID());
 
-        while (tri.hasNext())
+        try
         {
-            mylist.add(new WorkflowItem(c, tri.next()));
+            while (tri.hasNext())
+            {
+                mylist.add(new WorkflowItem(c, tri.next()));
+            }
+        }
+        finally
+        {
+            if (tri != null)
+                tri.close();
         }
-        
-        tri.close();
 
         return mylist;
     }
@@ -265,12 +271,18 @@ public class WorkflowManager
         TableRowIterator tri = DatabaseManager
                 .queryTable(c, "workflowitem", myquery, e.getID());
 
-        while (tri.hasNext())
+        try
         {
-            mylist.add(new WorkflowItem(c, tri.next()));
+            while (tri.hasNext())
+            {
+                mylist.add(new WorkflowItem(c, tri.next()));
+            }
+        }
+        finally
+        {
+            if (tri != null)
+                tri.close();
         }
-
-        tri.close();
         
         return mylist;
     }

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/servlet/FeedServlet.java

@@ -190,7 +190,7 @@ public class FeedServlet extends DSpaceServlet
         
         //as long as this is not a site wide feed, 
         //attempt to retrieve the Collection or Community object
-        if(!handle.equals(SITE_FEED_KEY))
+        if(handle != null && !handle.equals(SITE_FEED_KEY))
         { 	
         	// Determine if handle is a valid reference
         	dso = HandleManager.resolveToObject(context, handle);
@@ -371,7 +371,7 @@ public class FeedServlet extends DSpaceServlet
     					: HandleManager.getCanonicalForm(dso.getHandle()); 
     			
     			// put in container-level data
-    			channel.setDescription(description.replaceAll("\\p{Cntrl}", ""));
+    			channel.setDescription(description == null ? "" : description.replaceAll("\\p{Cntrl}", ""));
     			channel.setLink(objectUrl);
     			//build channel title by passing in type and title
     			String channelTitle = MessageFormat.format(labels.getString(clazz + ".feed.title"),

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/servlet/StatisticsServlet.java

@@ -122,6 +122,7 @@ public class StatisticsServlet extends org.dspace.app.webui.servlet.DSpaceServle
         HttpServletRequest request, HttpServletResponse response)
         throws ServletException, IOException, SQLException, AuthorizeException
     {
+        StringBuffer report = new StringBuffer();
         String date = (String) request.getParameter("date");
         request.setAttribute("date", date);
         
@@ -135,123 +136,135 @@ public class StatisticsServlet extends org.dspace.app.webui.servlet.DSpaceServle
         FileInputStream fir = null;
         InputStreamReader ir = null;
         BufferedReader br = null;
-        
+
-        List monthsList = new ArrayList();
+        try
-        
-        Pattern monthly = Pattern.compile("report-([0-9][0-9][0-9][0-9]-[0-9]+)\\.html");
-        Pattern general = Pattern.compile("report-general-([0-9]+-[0-9]+-[0-9]+)\\.html");
-        
-        // FIXME: this whole thing is horribly inflexible and needs serious
-        // work; but as a basic proof of concept will suffice
-        
-        // if no date is passed then we want to get the most recent general
-        // report
-        if (date == null)
         {
-            request.setAttribute("general", new Boolean(true));
+            List monthsList = new ArrayList();
-            
+
-            SimpleDateFormat sdf = new SimpleDateFormat("yyyy'-'M'-'dd");
+            Pattern monthly = Pattern.compile("report-([0-9][0-9][0-9][0-9]-[0-9]+)\\.html");
-            Date mostRecentDate = null;
+            Pattern general = Pattern.compile("report-general-([0-9]+-[0-9]+-[0-9]+)\\.html");
-            
+
+            // FIXME: this whole thing is horribly inflexible and needs serious
+            // work; but as a basic proof of concept will suffice
+
+            // if no date is passed then we want to get the most recent general
+            // report
+            if (date == null)
+            {
+                request.setAttribute("general", new Boolean(true));
+
+                SimpleDateFormat sdf = new SimpleDateFormat("yyyy'-'M'-'dd");
+                Date mostRecentDate = null;
+
+                for (int i = 0; i < reports.length; i++)
+                {
+                    Matcher matchGeneral = general.matcher(reports[i].getName());
+                    if (matchGeneral.matches())
+                    {
+                        Date parsedDate = null;
+
+                        try
+                        {
+                             parsedDate = sdf.parse(matchGeneral.group(1).trim());
+                        }
+                        catch (ParseException e)
+                        {
+                            // FIXME: currently no error handling
+                        }
+
+                        if (mostRecentDate == null)
+                        {
+                            mostRecentDate = parsedDate;
+                            reportFile = reports[i];
+                        }
+
+                        if (parsedDate != null && parsedDate.compareTo(mostRecentDate) > 0)
+                        {
+                            mostRecentDate = parsedDate;
+                            reportFile = reports[i];
+                        }
+                    }
+                }
+            }
+
+            // if a date is passed then we want to get the file for that month
+            if (date != null)
+            {
+                String desiredReport = "report-" + date + ".html";
+
+                for (int i = 0; i < reports.length; i++)
+                {
+                    if (reports[i].getName().equals(desiredReport))
+                    {
+                        reportFile = reports[i];
+                    }
+                }
+            }
+
+            if (reportFile == null)
+            {
+                JSPManager.showJSP(request, response, "statistics/no-report.jsp");
+            }
+
+            // finally, build the list of report dates
+            SimpleDateFormat sdf = new SimpleDateFormat("yyyy'-'M");
             for (int i = 0; i < reports.length; i++)
             {
-                Matcher matchGeneral = general.matcher(reports[i].getName());
+                Matcher matchReport = monthly.matcher(reports[i].getName());
-                if (matchGeneral.matches())
+                if (matchReport.matches())
                 {
                     Date parsedDate = null;
 
-                    try 
+                    try
                     {
-                         parsedDate = sdf.parse(matchGeneral.group(1).trim());
+                         parsedDate = sdf.parse(matchReport.group(1).trim());
                     }
                     catch (ParseException e)
                     {
                         // FIXME: currently no error handling
                     }
-                    
+
-                    if (mostRecentDate == null)
+                    monthsList.add(parsedDate);
-                    {
-                        mostRecentDate = parsedDate;
-                        reportFile = reports[i];
-                    }
-                    
-                    if (parsedDate.compareTo(mostRecentDate) > 0)
-                    {
-                        mostRecentDate = parsedDate;
-                        reportFile = reports[i];
-                    }
                 }
             }
-        }
+
-        
+            Date[] months = new Date[monthsList.size()];
-        // if a date is passed then we want to get the file for that month
+            months = (Date[]) monthsList.toArray(months);
-        if (date != null)
+
-        {
+            Arrays.sort(months);
-            String desiredReport = "report-" + date + ".html";
+
-        
+            request.setAttribute("months", months);
-            for (int i = 0; i < reports.length; i++)
+
+            try
             {
-                if (reports[i].getName().equals(desiredReport))
+                fir = new FileInputStream(reportFile.getPath());
-                {
+                ir = new InputStreamReader(fir, "UTF-8");
-                    reportFile = reports[i];
+                br = new BufferedReader(ir);
-                }
             }
-        }
+            catch (IOException e)
-        
-        if (reportFile == null)
-        {
-            JSPManager.showJSP(request, response, "statistics/no-report.jsp");
-        }
-        
-        // finally, build the list of report dates
-        SimpleDateFormat sdf = new SimpleDateFormat("yyyy'-'M");
-        for (int i = 0; i < reports.length; i++)
-        {
-            Matcher matchReport = monthly.matcher(reports[i].getName());
-            if (matchReport.matches())
             {
-                Date parsedDate = null;
+                // FIXME: no error handing yet
-                
+                throw new RuntimeException(e.getMessage(),e);
-                try 
+            }
-                {
+
-                     parsedDate = sdf.parse(matchReport.group(1).trim());
+            // FIXME: there's got to be a better way of doing this
-                }
+            String line = null;
-                catch (ParseException e)
+            while ((line = br.readLine()) != null)
-                {
+            {
-                    // FIXME: currently no error handling
+                report.append(line);
-                }
-                
-                monthsList.add(parsedDate);
             }
         }
-        
+        finally
-        Date[] months = new Date[monthsList.size()];
-        months = (Date[]) monthsList.toArray(months);
-        
-        Arrays.sort(months);
-        
-        request.setAttribute("months", months);
-        
-        try 
-        {  
-        	fir = new FileInputStream(reportFile.getPath());
-            ir = new InputStreamReader(fir, "UTF-8");
-            br = new BufferedReader(ir);
-        } 
-        catch (IOException e) 
         {
-            // FIXME: no error handing yet
+            if (br != null)
-            throw new RuntimeException(e.getMessage(),e);
+                try { br.close(); } catch (IOException ioe) { }
-        } 
+
-        
+            if (ir != null)
-        // FIXME: there's got to be a better way of doing this
+                try { ir.close(); } catch (IOException ioe) { }
-        StringBuffer report = new StringBuffer();
+
-        String line = null;
+            if (fir != null)
-        while ((line = br.readLine()) != null)
+                try { fir.close(); } catch (IOException ioe) { }
-        {
-            report.append(line);
         }
-        
         // set the report to be displayed
         request.setAttribute("report", report.toString());
         

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/servlet/SuggestServlet.java

@@ -93,7 +93,7 @@ public class SuggestServlet extends DSpaceServlet
             if (item != null)
             {   
                 DCValue[] titleDC = item.getDC("title", null, Item.ANY);
-                if (titleDC != null || titleDC.length > 0)
+                if (titleDC != null && titleDC.length > 0)
                 {
                     title = titleDC[0].value;
                 }

dspace-oai/dspace-oai-api/src/main/java/org/dspace/app/oai/DIDLCrosswalk.java

@@ -231,8 +231,21 @@ public class DIDLCrosswalk extends Crosswalk
                                     byte[] buffer = new byte[intSize];
                                     
                                     Context contextl= new Context();
-                                    BufferedInputStream bis=new BufferedInputStream(BitstreamStorageManager.retrieve(contextl,bitstreams[k].getID()));
+                                    InputStream is = BitstreamStorageManager.retrieve(contextl,bitstreams[k].getID());
-                                    int size=bis.read(buffer);
+                                    BufferedInputStream bis = new BufferedInputStream(is);
+                                    try
+                                    {
+                                        int size=bis.read(buffer);
+                                    }
+                                    finally
+                                    {
+                                        if (bis != null)
+                                            try { bis.close(); } catch (IOException ioe) { }
+
+                                        if (is != null)
+                                            try { is.close(); } catch (IOException ioe) { }
+                                    }
+
                                     contextl.complete();
                                     
                                     String encoding = new String(Base64.encodeBase64(buffer), "ASCII");