Add missing close() calls to use of TableRowIterator, also add close() to ItemIterator (to close underlying TableRowIterator)

git-svn-id: http://scm.dspace.org/svn/repo/branches/dspace-1_5_x@3038 9c30dcfa-912a-0410-8fc2-9e0234be79fd

dspace-api/src/main/java/org/dspace/app/itemexport/ItemExport.java

@@ -259,9 +259,16 @@ public class ItemExport {
 
 			// it's a collection, so do a bunch of items
 			ItemIterator i = mycollection.getItems();
-
+            try
+            {
                 exportItem(c, i, destDirName, seqStart);
             }
+            finally
+            {
+                if (i != null)
+                    i.close();
+            }
+        }
 
 		c.complete();
 	}
@@ -623,6 +630,7 @@ public class ItemExport {
 				for (Collection collection : collections) {
 					// get all the items in each collection
 					ItemIterator iitems = collection.getItems();
+                    try {
                         while (iitems.hasNext()) {
                             Item item = iitems.next();
                             // get all the bundles in the item
@@ -637,11 +645,16 @@ public class ItemExport {
                             }
                             items.add(item.getID());
                         }
+                    } finally {
+                        if (iitems != null)
+                            iitems.close();
+                    }
                 }
 			} else if (dso.getType() == Constants.COLLECTION) {
 				Collection collection = (Collection) dso;
 				// get all the items in the collection
 				ItemIterator iitems = collection.getItems();
+                try {
                     while (iitems.hasNext()) {
                         Item item = iitems.next();
                         // get all thebundles in the item
@@ -656,6 +669,10 @@ public class ItemExport {
                         }
                         items.add(item.getID());
                     }
+                } finally {
+                    if (iitems != null)
+                        iitems.close();
+                }
             } else if (dso.getType() == Constants.ITEM) {
 				Item item = (Item) dso;
 				// get all the bundles in the item
@@ -699,12 +716,13 @@ public class ItemExport {
 			Thread go = new Thread() {
 				public void run() {
 					Context context;
+                    ItemIterator iitems = null;
                     try {
 						// create a new dspace context
 						context = new Context();
 						// ignore auths
 						context.setIgnoreAuthorization(true);
-						ItemIterator iitems = new ItemIterator(context, items);
+						iitems = new ItemIterator(context, items);
 
 						String fileName = assembleFileName("item", eperson, new Date());
 						String workDir = getExportWorkDirectory()
@@ -747,6 +765,9 @@ public class ItemExport {
 							// wont throw here
 						}
 						throw new RuntimeException(e1);
+					} finally {
+                        if (iitems != null)
+                            iitems.close();
                     }
 				}
 

dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterManager.java

@@ -420,11 +420,19 @@ public class MediaFilterManager
         {
             //otherwise, just find every item and process
             ItemIterator i = Item.findAll(c);
+            try
+            {
                 while (i.hasNext() && processed < max2Process)
                 {
                     applyFiltersItem(c, i.next());
                 }
             }
+            finally
+            {
+                if (i != null)
+                    i.close();
+            }
+        }
     }
     
     public static void applyFiltersCommunity(Context c, Community community)
@@ -453,11 +461,19 @@ public class MediaFilterManager
         if(!inSkipList(collection.getHandle()))
         {
             ItemIterator i = collection.getItems();
+            try
+            {
                 while (i.hasNext() && processed < max2Process)
                 {
                     applyFiltersItem(c, i.next());
                 }
             }
+            finally
+            {
+                if (i != null)
+                    i.close();
+            }
+        }
     }
        
     public static void applyFiltersItem(Context c, Item item) throws Exception

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

@@ -178,7 +178,8 @@ public class METSExport
         }
 
         ItemIterator items = null;
-
+        try
+        {
             if (line.hasOption('c'))
             {
                 String handle = getHandleArg(line.getOptionValue('c'));
@@ -213,6 +214,12 @@ public class METSExport
             {
                 writeAIP(context, items.next(), dest);
             }
+        }
+        finally
+        {
+            if (items != null)
+                items.close();
+        }
         
         context.abort();
         System.exit(0);

dspace-api/src/main/java/org/dspace/app/sitemap/GenerateSitemaps.java

@@ -234,6 +234,8 @@ public class GenerateSitemaps
         }
 
         ItemIterator allItems = Item.findAll(c);
+        try
+        {
             int itemCount = 0;
 
             while (allItems.hasNext())
@@ -268,6 +270,12 @@ public class GenerateSitemaps
                                 + comms.length + ",collections=" + colls.length
                                 + ",items=" + itemCount));
             }
+        }
+        finally
+        {
+            if (allItems != null)
+                allItems.close();
+        }
         
         c.abort();
     }

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

@@ -186,7 +186,8 @@ public class PolicySet
             Group group = Group.find(c, groupID);
 
             ItemIterator i = collection.getItems();
-
+            try
+            {
                 if (contentType == Constants.ITEM)
                 {
                     // build list of all items in a collection
@@ -294,5 +295,11 @@ public class PolicySet
                     }
                 }
             }
+            finally
+            {
+                if (i != null)
+                    i.close();
+            }
+        }
     }
 }

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

@@ -258,6 +258,8 @@ public class BrowseCreateDAOOracle implements BrowseCreateDAO
             // Find all existing mappings for this item
             TableRowIterator tri = DatabaseManager.queryTable(context, table, "SELECT * FROM " + table + " WHERE item_id=?", itemID);
             if (tri != null)
+            {
+                try
                 {
                     while (tri.hasNext())
                     {
@@ -282,6 +284,11 @@ public class BrowseCreateDAOOracle implements BrowseCreateDAO
                             DatabaseManager.delete(context, tr);
                     }
                 }
+                finally
+                {
+                    tri.close();
+                }
+            }
 
             // Any remaining mappings need to be added to the database
             for (int i = 0; i < distinctIDs.length; i++)
@@ -543,6 +550,7 @@ public class BrowseCreateDAOOracle implements BrowseCreateDAO
         }
         finally
         {
+            if (tri != null)
                 tri.close();
         }
     }
@@ -567,6 +575,8 @@ public class BrowseCreateDAOOracle implements BrowseCreateDAO
             // Find all existing mappings for this item
             TableRowIterator tri = DatabaseManager.queryTable(context, "Communities2Item", "SELECT * FROM Communities2Item WHERE item_id=?", itemID);
             if (tri != null)
+            {
+                try
                 {
                     while (tri.hasNext())
                     {
@@ -591,6 +601,11 @@ public class BrowseCreateDAOOracle implements BrowseCreateDAO
                             DatabaseManager.delete(context, tr);
                     }
                 }
+                finally
+                {
+                    tri.close();
+                }
+            }
 
             // Any remaining mappings need to be added to the database
             for (int i = 0; i < commID.length; i++)

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

@@ -255,6 +255,8 @@ public class BrowseCreateDAOPostgres implements BrowseCreateDAO
             // Find all existing mappings for this item
             TableRowIterator tri = DatabaseManager.queryTable(context, table, "SELECT * FROM " + table + " WHERE item_id=?", itemID);
             if (tri != null)
+            {
+                try
                 {
                     while (tri.hasNext())
                     {
@@ -279,6 +281,11 @@ public class BrowseCreateDAOPostgres implements BrowseCreateDAO
                             DatabaseManager.delete(context, tr);
                     }
                 }
+                finally
+                {
+                    tri.close();
+                }
+            }
 
             // Any remaining mappings need to be added to the database
             for (int i = 0; i < distinctIDs.length; i++)
@@ -568,6 +575,8 @@ public class BrowseCreateDAOPostgres implements BrowseCreateDAO
             // Find all existing mappings for this item
             TableRowIterator tri = DatabaseManager.queryTable(context, "Communities2Item", "SELECT * FROM Communities2Item WHERE item_id=?", itemID);
             if (tri != null)
+            {
+                try
                 {
                     while (tri.hasNext())
                     {
@@ -592,6 +601,11 @@ public class BrowseCreateDAOPostgres implements BrowseCreateDAO
                             DatabaseManager.delete(context, tr);
                     }
                 }
+                finally
+                {
+                    tri.close();
+                }
+            }
 
             // Any remaining mappings need to be added to the database
             for (int i = 0; i < commID.length; i++)

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

@@ -1092,6 +1092,11 @@ public class Collection extends DSpaceObject
         	log.error("caught exception: ", e);
         	throw new IOException(e.getMessage());
         }
+        finally
+        {
+            if (items != null)
+                items.close();
+        }
 
         // Delete bitstream logo
         setLogo(null);

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

@@ -1558,6 +1558,8 @@ public class Item extends DSpaceObject
             // looking for matches
             TableRowIterator tri = retrieveMetadata();
             if (tri != null)
+            {
+                try
                 {
                     while (tri.hasNext())
                     {
@@ -1626,6 +1628,11 @@ public class Item extends DSpaceObject
                         }
                     }
                 }
+                finally
+                {
+                    tri.close();
+                }
+            }
 
             // Add missing in-memory DC
             for (int dcIdx = 0; dcIdx < dublinCore.size(); dcIdx++)

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

@@ -270,4 +270,13 @@ public class ItemIterator
             return null;
         }
     }
+
+    /**
+     * Dispose of this Iterator, and it's underlying resources
+     */
+    public void close()
+    {
+        if (itemRows != null)
+            itemRows.close();
+    }
 }

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

@@ -314,7 +314,8 @@ public class EPerson extends DSpaceObject
 
         // Get all the epeople that match the query
 		TableRowIterator rows = DatabaseManager.query(context, dbquery, paramArr);
-		
+		try
+        {
             List epeopleRows = rows.toList();
             EPerson[] epeople = new EPerson[epeopleRows.size()];
 
@@ -338,6 +339,12 @@ public class EPerson extends DSpaceObject
 
             return epeople;
         }
+        finally
+        {
+            if (rows != null)
+                rows.close();
+        }
+    }
 
     /**
      * Returns the total number of epeople returned by a specific query, without the overhead 
@@ -428,6 +435,8 @@ public class EPerson extends DSpaceObject
         TableRowIterator rows = DatabaseManager.query(context,
                 "SELECT * FROM eperson ORDER BY "+s);
 
+        try
+        {
             List epeopleRows = rows.toList();
 
             EPerson[] epeople = new EPerson[epeopleRows.size()];
@@ -452,6 +461,12 @@ public class EPerson extends DSpaceObject
 
             return epeople;
         }
+        finally
+        {
+            if (rows != null)
+                rows.close();
+        }
+    }
 
     /**
      * Create a new eperson

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

@@ -776,6 +776,8 @@ public class Group extends DSpaceObject
         		context, "epersongroup",
                 "SELECT * FROM epersongroup ORDER BY "+s);
 
+        try
+        {
             List gRows = rows.toList();
 
             Group[] groups = new Group[gRows.size()];
@@ -800,6 +802,12 @@ public class Group extends DSpaceObject
 
             return groups;
         }
+        finally
+        {
+            if (rows != null)
+                rows.close();
+        }
+    }
     
     
     /**
@@ -897,6 +905,8 @@ public class Group extends DSpaceObject
         TableRowIterator rows =
 			DatabaseManager.query(context, dbquery, paramArr);
 
+        try
+        {
             List groupRows = rows.toList();
             Group[] groups = new Group[groupRows.size()];
 
@@ -919,6 +929,12 @@ public class Group extends DSpaceObject
             }
             return groups;
         }
+        finally
+        {
+            if (rows != null)
+                rows.close();
+        }
+	}
 
     /**
      * Returns the total number of groups returned by a specific query, without the overhead 

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

@@ -570,16 +570,23 @@ public class DSIndexer
      * @param force 
      */
     public static void updateIndex(Context context, boolean force) {
-
     		try
     		{
-    			
+                ItemIterator items = null;
-    			for(ItemIterator i = Item.findAll(context);i.hasNext();)
+                try
                 {
-    	            Item item = (Item) i.next();
+                    for(items = Item.findAll(context);items.hasNext();)
+                    {
+                        Item item = (Item) items.next();
                         indexContent(context,item,force);
                         item.decache();
                     }
+                }
+                finally
+                {
+                    if (items != null)
+                        items.close();
+                }
 
                 Collection[] collections = Collection.findAll(context);
     	        for (int i = 0; i < collections.length; i++)
@@ -603,7 +610,6 @@ public class DSIndexer
     		{
     			log.error(e.getMessage(), e);
     		}
-
     }
     
     /**

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

@@ -342,6 +342,8 @@ public class Harvest
                         "AND collection2item.collection_id=handle.resource_id AND collection2item.item_id = ? ",
                         Constants.COLLECTION, itemInfo.itemID);
 
+        try
+        {
             // Chuck 'em in the itemInfo object
             itemInfo.collectionHandles = new LinkedList();
 
@@ -350,8 +352,13 @@ public class Harvest
                 TableRow r = colRows.next();
                 itemInfo.collectionHandles.add(r.getStringColumn("handle"));
             }
+        }
+        finally
+        {
+            if (colRows != null)
                 colRows.close();
         }
+    }
 
     
     /**

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

@@ -162,6 +162,8 @@ public class DatabaseManager
         }
         
         PreparedStatement statement = context.getDBConnection().prepareStatement(query);
+        try
+        {
             loadParameters(statement,parameters);
 
             TableRowIterator retTRI = new TableRowIterator(statement.executeQuery(),
@@ -170,6 +172,14 @@ public class DatabaseManager
             retTRI.setStatement(statement);
             return retTRI;
         }
+        catch (SQLException sqle)
+        {
+            if (statement != null)
+                try { statement.close(); } catch (SQLException s) { }
+
+            throw sqle;
+        }
+    }
     
     /**
      * Return an iterator with the results of the query.
@@ -204,14 +214,23 @@ public class DatabaseManager
         }
 
         PreparedStatement statement = context.getDBConnection().prepareStatement(query);
+        try
+        {
             loadParameters(statement,parameters);
 
             TableRowIterator retTRI = new TableRowIterator(statement.executeQuery());
 
-        
             retTRI.setStatement(statement);
             return retTRI;
         }
+        catch (SQLException sqle)
+        {
+            if (statement != null)
+                try { statement.close(); } catch (SQLException s) { }
+
+            throw sqle;
+        }
+    }
     
     /**
      * Return an iterator with the results of executing statement. The table

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

@@ -197,13 +197,18 @@ public class TableRowIterator
     {
         List resultsList = new ArrayList();
 
+        try
+        {
             while (hasNext())
             {
                 resultsList.add(next());
             }
-
+        }
+        finally
+        {
             // Close the connection after converting it to a list.
             this.close();
+        }
         
         return resultsList;
     }

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

@@ -766,16 +766,23 @@ public class MyDSpaceServlet extends DSpaceServlet
             throws ServletException, IOException, SQLException,
             AuthorizeException
     {
+        // Turn the iterator into a list
+        List subList = new LinkedList();
         ItemIterator subs = Item.findBySubmitter(context, context
                 .getCurrentUser());
 
-        // Turn the iterator into a list
+        try
-        List subList = new LinkedList();
+        {
-
             while (subs.hasNext())
             {
                 subList.add(subs.next());
             }
+        }
+        finally
+        {
+            if (subs != null)
+                subs.close();
+        }
 
         Item[] items = new Item[subList.size()];
 

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

@@ -126,7 +126,8 @@ public class ItemMapServlet extends DSpaceServlet
     		
     		// get all items from that collection, add them to a hash
     		ItemIterator i = myCollection.getItems();
-    		
+    		try
+            {
                 // iterate through the items in this collection, and count how many
                 // are native, and how many are imports, and which collections they
                 // came from
@@ -168,6 +169,12 @@ public class ItemMapServlet extends DSpaceServlet
                     // store the item
                     myItems.put(myKey, myItem);
                 }
+            }
+            finally
+            {
+                if (i != null)
+                    i.close();
+            }
             
             // remove this collection's entry because we already have a native
     		// count
@@ -381,6 +388,8 @@ public class ItemMapServlet extends DSpaceServlet
     			// FIXME: oh god this is so annoying - what an API /Richard
     			// we need to deduplicate against existing items in this collection
     			ItemIterator itr = myCollection.getItems();
+                try
+                {
                     ArrayList idslist = new ArrayList();
                     while (itr.hasNext())
                     {
@@ -399,7 +408,12 @@ public class ItemMapServlet extends DSpaceServlet
                             }
                         }
                     }
-    			
+                }
+                finally
+                {
+                    if (itr != null)
+                        itr.close();
+                }
             }
     		catch (BrowseException e)
     		{
@@ -424,9 +438,10 @@ public class ItemMapServlet extends DSpaceServlet
     		
     		// now find all imported items from that collection
     		// seemingly inefficient, but database should have this query cached
-    		ItemIterator i = myCollection.getItems();
             Map items = new HashMap();
-    		
+    		ItemIterator i = myCollection.getItems();
+            try
+            {
                 while (i.hasNext())
                 {
                     Item myItem = i.next();
@@ -437,6 +452,12 @@ public class ItemMapServlet extends DSpaceServlet
                         items.put(myKey, myItem);
                     }
                 }
+            }
+            finally
+            {
+                if (i != null)
+                    i.close();
+            }
     		
             request.setAttribute("collection", myCollection);
     		request.setAttribute("browsetext", targetCollection

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/DAVCollection.java

@@ -160,12 +160,21 @@ class DAVCollection extends DAVDSpaceObject
     {
         Vector result = new Vector();
         ItemIterator ii = this.collection.getItems();
+        try
+        {
             while (ii.hasNext())
             {
                 Item item = ii.next();
                 result.add(new DAVItem(this.context, this.request, this.response,
                         makeChildPath(item), item));
             }
+        }
+        finally
+        {
+            if (ii != null)
+                ii.close();
+        }
+        
         return (DAVResource[]) result.toArray(new DAVResource[result.size()]);
     }
 

dspace-xmlui/dspace-xmlui-api/src/main/java/org/dspace/app/xmlui/aspect/administrative/mapper/BrowseItemForm.java

@@ -195,7 +195,8 @@ public class BrowseItemForm extends AbstractDSpaceTransformer {
 		
 		// get all items from that collection
         ItemIterator iterator = collection.getItems();
-        
+        try
+        {
             while (iterator.hasNext())
             {
                 Item item = iterator.next();
@@ -203,6 +204,12 @@ public class BrowseItemForm extends AbstractDSpaceTransformer {
                 if (! item.isOwningCollection(collection))
                     items.add(item);
             }
+        }
+        finally
+        {
+            if (iterator != null)
+                iterator.close();
+        }
         
         return items;
 	}

dspace-xmlui/dspace-xmlui-api/src/main/java/org/dspace/app/xmlui/aspect/administrative/mapper/MapperMain.java

@@ -157,6 +157,8 @@ public class MapperMain extends AbstractDSpaceTransformer {
 		// get all items from that collection
         ItemIterator iterator = collection.getItems();
 
+        try
+        {
             // iterate through the items in this collection, and count how many
             // are native, and how many are imports, and which collections they
             // came from
@@ -169,6 +171,12 @@ public class MapperMain extends AbstractDSpaceTransformer {
                 else
                     count_import++;
             }
+        }
+        finally
+        {
+            if (iterator != null)
+                iterator.close();
+        }
         
         int[] counts = new int[2];
         counts[0] = count_native;