Changeset 3857

Timestamp:

Oct 17, 2007, 12:41:17 PM (16 years ago)

Author:

Jari Häkkinen

Message:

Merged patch release 2.4.4 to the trunk. Delta 2.4.4 - 2.4.3

Location:

trunk

Files:

• bin/dynamicdb.bat (copied) (copied from tags/2.4.4/bin/dynamicdb.bat)
• bin/dynamicdb.sh (copied) (copied from tags/2.4.4/bin/dynamicdb.sh)
• doc/specifications/technical.html (modified) (1 diff)
• doc/src/docbook/admindoc/installation_upgrade.xml (modified) (4 diffs)
• src/clients/jobagent/net/sf/basedb/clients/jobagent/JobRunner.java (modified) (3 diffs)
• src/clients/jobagent/net/sf/basedb/clients/jobagent/executors/DummyJobExecutor.java (modified) (1 diff)
• src/clients/jobagent/net/sf/basedb/clients/jobagent/executors/ThreadJobExecutor.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (1 diff)
• src/core/net/sf/basedb/core/AnnotationRestriction.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/Application.java (modified) (6 diffs)
• src/core/net/sf/basedb/core/BasicItem.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/BioAssaySet.java (modified) (11 diffs)
• src/core/net/sf/basedb/core/DataQuery.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/DiskUsageStatistics.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Group.java (modified) (1 diff)
• src/core/net/sf/basedb/core/HibernateUtil.java (modified) (12 diffs)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/core/InternalJobQueue.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/InternalStorageController.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ItemKey.java (modified) (6 diffs)
• src/core/net/sf/basedb/core/ItemQuery.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Keyring.java (modified) (15 diffs)
• src/core/net/sf/basedb/core/PluginDefinition.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Project.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/ProjectKey.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawDataBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ReporterScoreQuery.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/SessionControl.java (modified) (11 diffs)
• src/core/net/sf/basedb/core/Trashcan.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Update.java (modified) (12 diffs)
• src/core/net/sf/basedb/core/User.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/VirtualColumn.java (modified) (13 diffs)
• src/core/net/sf/basedb/util/overview/ExperimentOverview.java (modified) (1 diff)
• src/install/net/sf/basedb/install/InitDB.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java (modified) (1 diff)
• www/include/menu.jsp (modified) (2 diffs)

trunk/doc/specifications/technical.html

@@ -163 +163 @@
     <li>
     Possible to add support for other import and export file formats, including
-    very cryptic ones (i.e. everyting else than tab-separated text files).
+    very cryptic ones (i.e. everything else than tab-separated text files).
     </li>
     <li>

trunk/doc/src/docbook/admindoc/installation_upgrade.xml

@@ -67 +67 @@
     <title>Upgrade instructions</title>
 
-    <important>
-      <title>Note to PostgreSQL users</title>
-      Upgrading BASE to versions earlier
-      than v2.2 is not be safe with an PostgreSQL database engine due
-      to a bug in Hibernate. The problem is reported to Hibernate
-      developers. There now exists a workaround for this problem. Read
-      more about the workaround on
-      the <ulink
-      url="http://base.thep.lu.se/wiki/UpgradePostgres">Upgrading a
-      Postgres database prior to BASE 2.2</ulink> page. This fix is
-      not needed for the release which this document is a part of.
+    <important id="dropindexes">
+      <title>Upgrading from BASE 2.4.3 or lower to 2.4.4 or higher</title>
+      <para>
+        Older releases of BASE 2 used to create indexes for many columns
+        in the dynamic database. The same columns are part of the primary
+        key for the tables so the indexes are not really needed. The 
+        result is very bad performance since the database engine sometimes 
+        get stuck in "index update" mode making the entire server
+        very slow. BASE 2.4.4 no longer creates the indexes. Indexes on
+        existing tables should be dropped to increase the performance.
+        Tests have shown a 50-90% decrease in execution time for some 
+        plug-ins
+        (<ulink url="http://base.thep.lu.se/ticket/294">http://base.thep.lu.se/ticket/294</ulink>). 
+      </para>
+      <para>
+        Removing the indexes is very simple. <emphasis>After the server
+        has been upgraded</emphasis> following the usual instructions below, issue the
+        the following commands:
+      </para>
+    
+      <programlisting>
+cd &lt;basedir&gt;/bin
+./dynamicdb.sh -v -dropindexes
+</programlisting>
+
+      <para>
+        Skip the <option>-dropindexes</option> option to do a dry
+        run without actually deleting the indexes.
+      </para>
     </important>
 
@@ -876 +894 @@
             properties are defined in
             <filename>/path/to/base/www/WEB-INF/classes/extended-properties.xml</filename>.
-            There is an administrator <ulink
+            There is an
+            administrator <ulink
             url="http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html">document
-              discussing extended properties</ulink> available.
+            discussing extended properties</ulink> available. If you
+            plan to perform a migration of a BASE 1.2 database you
+            should probably not remove any extended properties
+            columns (this is not tested so the outcome is currently
+            undefined). However, adding columns does not affect
+            migration.
           </para>
         </listitem>
@@ -1064 +1088 @@
       changes to the BASE 1.2 schema you need to patch the BASE 2
       schema as well as make proper changes to the migration program.
+      If there are added columns to the reporter table in your BASE
+      1.2 database you need to transfer the additional information
+      after migration (even if you modified the BASE
+      2 <filename>extended-properties.xml</filename> file).
     </para>
 
@@ -1166 +1194 @@
         <listitem>
           <para>
+            <emphasis>Optional, depends on your BASE 1.2 reporter
+            table.</emphasis> Additional columns (as compared with a
+            pristine database schema) in the reporter table in the
+            BASE 1.2 schema are not transferred during migration. You
+            have to perform the transfer manually after
+            migration. Simply export the reporter information from
+            BASE 1.2, and import the data into BASE 2. In BASE 1.2: i)
+            View the reporters, ii) Use `Get as tab-separated text` to
+            create a tab separated file (right click and save). In
+            BASE 2, to import the file follow the instructions in
+            <xref linkend="reporters.import"/>.
+          </para>
+        </listitem>
+
+        <listitem>
+          <para>
             Migration done! Happy BASEing.
           </para>

trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/JobRunner.java

@@ -26 +26 @@
 import java.util.Arrays;
 
+import net.sf.basedb.core.Application;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.ItemModifiedException;
@@ -119 +120 @@
       }
       
+      // To protect the session control from timeouts
+      Application.Pinger pinger = Application.newPinger(sc);
       try
       {
@@ -131 +134 @@
         dc.commit();
         throw t;
+      }
+      finally
+      {
+        if (pinger != null) pinger.stop();
       }
       

trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/executors/DummyJobExecutor.java

@@ -81 +81 @@
   public void init(Agent agent)
   {
-    wait = Values.getInt(agent.getProperty("agent.executor.wait"), -1);
+    wait = Values.getInt(agent.getProperty("agent.executor.dummy.wait"), -1);
   }
   

trunk/src/clients/jobagent/net/sf/basedb/clients/jobagent/executors/ThreadJobExecutor.java

@@ -147 +147 @@
     SessionControl sc = null;
     SessionControl impersonated = null;
+    Application.Pinger pinger = null;
     try
     {
@@ -169 +170 @@
       
       Thread.currentThread().setPriority(threadPriority);
+      pinger = Application.newPinger(sc);
       executor.executeJob(impersonated, null, job, settings, null);
     }
@@ -178 +180 @@
     finally
     {
+      if (pinger != null) pinger.stop();
       if (dc != null) dc.close();
       if (impersonated != null && impersonated.isLoggedIn()) impersonated.logout();

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -401 +401 @@
       
       // Current item
-      String itemId = request.getParameter("item_id");
+      String itemId = Values.getStringOrNull(request.getParameter("item_id"));
       cc.setId(Values.getInt(itemId, cc.getId()));
       

trunk/src/core/net/sf/basedb/core/AnnotationRestriction.java

@@ -105 +105 @@
     throws BaseException
   {
+    SessionControl sc = dc.getSessionControl();
     String valueTable = null;
     if (valueType == Type.INT)
@@ -168 +169 @@
     {
       if (debugSqlEnabled) logSql.debug("Executing annotation query: " + sql);
-      List<Object[]> twoIds = HibernateUtil.loadList(Object[].class, sqlQuery);
+      List<Object[]> twoIds = HibernateUtil.loadList(Object[].class, sqlQuery, sc);
       StringBuilder annotationSets = new StringBuilder("0");
       StringBuilder annotations = new StringBuilder("0");
@@ -192 +193 @@
         sqlQuery.addScalar("annotationset_id", org.hibernate.Hibernate.INTEGER);
         if (debugSqlEnabled) logSql.debug("Executing annotation query: " + sql);
-        List<Integer> ids = HibernateUtil.loadList(Integer.class, sqlQuery);
+        List<Integer> ids = HibernateUtil.loadList(Integer.class, sqlQuery, sc);
         annotationSets = new StringBuilder(annotationSetIds);
         for (Integer id : ids)
@@ -204 +205 @@
     {
       if (debugSqlEnabled) logSql.debug("Executing annotation query: " + sql);
-      List<Integer> ids = HibernateUtil.loadList(Integer.class, sqlQuery);
+      List<Integer> ids = HibernateUtil.loadList(Integer.class, sqlQuery, sc);
       StringBuilder annotationSets = new StringBuilder("0");
       for (Integer id : ids)

trunk/src/core/net/sf/basedb/core/Application.java

@@ -33 +33 @@
 import java.util.Calendar;
 import java.util.GregorianCalendar;
+import java.util.HashSet;
 import java.util.Map;
 import java.util.HashMap;
@@ -38 +39 @@
 import java.util.Iterator;
 import java.util.Random;
+import java.util.Set;
 import java.util.Timer;
 import java.util.TimerTask;
@@ -471 +473 @@
   
         // Adding a task that cleans the session control cache at regular intervale
-        long milliSeconds = 60*1000*sessionCacheTimeout;
+        long milliSeconds = 60 * 1000 * sessionCacheTimeout;
         getScheduler().schedule(new SessionControlCacheCleaner(), milliSeconds, milliSeconds, false);
         
         if (useInternalJobQueue == null) useInternalJobQueue = Config.getBoolean("jobqueue.internal.enabled");
+        log.info("jobqueue.internal.enabled = " + useInternalJobQueue);
         if (useInternalJobQueue)
         {
@@ -892 +895 @@
   private static void cleanSessionControlCache(boolean force)
   {
+    if (!force)
+    {
+      // Ping all sessioncontrols in the pingers set
+      for (Pinger p : pingers)
+      {
+        p.ping();
+      }
+    }
+    
     synchronized(sessionCache)
     {
       Iterator<SessionControl> i = sessionCache.values().iterator();
       long now = System.currentTimeMillis();
+      long timout = 60 * 1000 * sessionCacheTimeout;
       while (i.hasNext())
       {
         SessionControl sc = i.next();
-        if (force || ((now - sc.getLastAccess()) > 60*1000*sessionCacheTimeout))
+        if (force || ((now - sc.getLastAccess()) > timout))
         {
           log.info("cleanSessionControlCache: Remove[ID="+sc.getId()+"]");
@@ -906 +919 @@
             if (sc.isLoggedIn()) sc.logout();
           }
-          catch (BaseException ex)
+          catch (Throwable t)
           {
-            log.error("Exception during cleanSessionControlCache", ex);
+            log.error("Exception during cleanSessionControlCache", t);
           }
           finally
           {
+            sc.close();
             i.remove();
           }
@@ -1005 +1019 @@
   }
   
+  private static Set<Pinger> pingers = 
+    Collections.synchronizedSet(new HashSet<Pinger>());
+  
+  /**
+    Create a new <code>Pinger</code> object that is used
+    to keep a session control alive.
+    
+    @param sc The SessionControl that the pinger should protect
+    @return A pinger object
+    @since 2.4.5
+  */
+  public static Pinger newPinger(SessionControl sc)
+  {
+    Pinger p = new Pinger(sc);
+    pingers.add(p);
+    return p;
+  }
+  
+  private static void stopPinger(Pinger p)
+  {
+    pingers.remove(p);
+  }
+  
+  /**
+    A <code>Pinger</code> is an object that is used to protect another
+    object from timing out by automatically pinging it. This can for
+    example be used by a client to override the timeout for SessionControl
+    items.
+    
+    @since 2.4.5
+  */
+  public static class Pinger
+  {
+    private final SessionControl sc;
+    private Pinger(SessionControl sc)
+    {
+      this.sc = sc;
+    }
+    /**
+      Ping the SessionControl by updating the last access time:
+      {@link SessionControl#updateLastAccess()}
+    */
+    public void ping()
+    {
+      if (!sc.isClosed()) sc.updateLastAccess();
+    }
+    /**
+      Stop this pinger.
+    */
+    public void stop()
+    {
+      Application.stopPinger(this);
+    }
+  }
+  
 }

trunk/src/core/net/sf/basedb/core/BasicItem.java

@@ -251 +251 @@
     query.setInteger("toType", this.getType().getValue());
     Set<ItemProxy> using = new TreeSet<ItemProxy>();
-    for (Object[] u : HibernateUtil.loadList(Object[].class, query))
+    for (Object[] u : HibernateUtil.loadList(Object[].class, query, getSessionControl()))
     {
       using.add(new ItemProxy((Integer)u[0], Item.fromValue((Integer)u[1])));
@@ -268 +268 @@
   protected void addUsingItems(Set<ItemProxy> using, Item itemType, org.hibernate.Query query)
   {
-    for (Integer itemId : HibernateUtil.loadList(Integer.class, query))
+    for (Integer itemId : HibernateUtil.loadList(Integer.class, query, getSessionControl()))
     {
       using.add(new ItemProxy(itemId, itemType));
@@ -282 +282 @@
   protected void addUsingItems(Set<ItemProxy> using, org.hibernate.Query query)
   {
-    for (BasicData item : HibernateUtil.loadList(BasicData.class, query))
+    for (BasicData item : HibernateUtil.loadList(BasicData.class, query, getSessionControl()))
     {
       using.add(new ItemProxy(item.getId(), Item.fromDataClass(item.getClass())));

trunk/src/core/net/sf/basedb/core/BioAssaySet.java

@@ -635 +635 @@
     }
     
-    // Everyting is ok, create the new bioassay
+    // Everything is ok, create the new bioassay
     BioAssay ba = newBioAssay(parent.getDataCubeColumn(), Collections.singleton(parent));
     ba.setName(parent.getName());
@@ -1209 +1209 @@
   {
     DbControl dc = getDbControl();
+    SessionControl sc = dc.getSessionControl();
     
     // 1. Find all child bioassaysets recursively
@@ -1227 +1228 @@
     */
     query.setParameterList("basList", all);
-    List<DataCubeData> possibleCubes = HibernateUtil.loadList(DataCubeData.class, query);
+    List<DataCubeData> possibleCubes = HibernateUtil.loadList(DataCubeData.class, query, sc);
     
     // 2b. Among the found data cubes, find those that are also used by other bioassaysets
@@ -1242 +1243 @@
       query.setParameterList("basList", all);
       query.setParameterList("possibleCubes", possibleCubes);
-      possibleCubes.removeAll(HibernateUtil.loadList(DataCubeData.class, query));
+      possibleCubes.removeAll(HibernateUtil.loadList(DataCubeData.class, query, sc));
       
   
@@ -1279 +1280 @@
       query.setParameterList("deletedCubes", possibleCubes);
     }
-    List<DataCubeLayerData> possibleLayers = HibernateUtil.loadList(DataCubeLayerData.class, query);
+    List<DataCubeLayerData> possibleLayers = HibernateUtil.loadList(DataCubeLayerData.class, query, sc);
     
     if (possibleLayers.size() > 0)
@@ -1294 +1295 @@
       query.setParameterList("basList", all);
       query.setParameterList("possibleLayers", possibleLayers);
-      possibleLayers.removeAll(HibernateUtil.loadList(DataCubeLayerData.class, query));
+      possibleLayers.removeAll(HibernateUtil.loadList(DataCubeLayerData.class, query, sc));
       
       // 3c. Delete data from the remaining layers
@@ -1330 +1331 @@
       query.setParameterList("deletedCubes", possibleCubes);
     }
-    List<DataCubeFilterData> possibleFilters = HibernateUtil.loadList(DataCubeFilterData.class, query);
+    List<DataCubeFilterData> possibleFilters = HibernateUtil.loadList(DataCubeFilterData.class, query, sc);
     
     if (possibleFilters.size() > 0)
@@ -1345 +1346 @@
       query.setParameterList("basList", all);
       query.setParameterList("possibleFilters", possibleFilters);
-      possibleFilters.removeAll(HibernateUtil.loadList(DataCubeFilterData.class, query));
+      possibleFilters.removeAll(HibernateUtil.loadList(DataCubeFilterData.class, query, sc));
 
       // 4c. Delete data from the remaining layers
@@ -1381 +1382 @@
       query.setParameterList("deletedCubes", possibleCubes);
     }
-    List<DataCubeExtraValueData> possibleExtraValues = HibernateUtil.loadList(DataCubeExtraValueData.class, query);
+    List<DataCubeExtraValueData> possibleExtraValues = HibernateUtil.loadList(DataCubeExtraValueData.class, query, sc);
     
     if (possibleExtraValues.size() > 0)
@@ -1396 +1397 @@
       query.setParameterList("basList", all);
       query.setParameterList("possibleExtraValues", possibleExtraValues);
-      possibleExtraValues.removeAll(HibernateUtil.loadList(DataCubeExtraValueData.class, query));
+      possibleExtraValues.removeAll(HibernateUtil.loadList(DataCubeExtraValueData.class, query, sc));
       
       // 5c. Delete data from the remaining extra values
@@ -1430 +1431 @@
     }
     findChildren.setEntity("parent", parent);
-    List<BioAssaySetData> children = HibernateUtil.loadList(BioAssaySetData.class, findChildren);
+    List<BioAssaySetData> children = HibernateUtil.loadList(BioAssaySetData.class, findChildren, null);
     for (BioAssaySetData child : children)
     {

trunk/src/core/net/sf/basedb/core/DataQuery.java

@@ -82 +82 @@
     enableFilters(dc);
     long totalCount = -1;
+    SessionControl sc = dc.getSessionControl();
 
     // Load the total count if it is requested
@@ -90 +91 @@
     
     // Load the results
-    ScrollIterator<I> result = HibernateUtil.loadIterator(dataClass,  getMainHqlQuery(dc));
+    ScrollIterator<I> result = 
+      HibernateUtil.loadIterator(dataClass,  getMainHqlQuery(dc), sc);
     disableFilters(dc);
     return new DataResultIterator<I>(result, dc.getSessionControl(), 

trunk/src/core/net/sf/basedb/core/DiskUsageStatistics.java

@@ -237 +237 @@
     private void loadDiskUsage(org.hibernate.Query query)
     {
-      List<Object[]> du = HibernateUtil.loadList(Object[].class, query);
+      List<Object[]> du = HibernateUtil.loadList(Object[].class, query, null);
       for (Object[] row : du)
       {

trunk/src/core/net/sf/basedb/core/Group.java

@@ -147 +147 @@
       {
         query.setParameterList("groups", allGroups, org.hibernate.Hibernate.INTEGER);
-      } while (allGroups.addAll(HibernateUtil.loadList(Integer.class, query)));
+      } while (allGroups.addAll(HibernateUtil.loadList(Integer.class, query, null)));
     }
     return allGroups;

trunk/src/core/net/sf/basedb/core/HibernateUtil.java

@@ -46 +46 @@
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Iterator;
@@ -1449 +1450 @@
     @param clazz The list should contain objects of this class
     @param query The query to execute
+    @param sc A optional SessionControl that is automatically protected from
+      timeouts during the time the query is running
   */
   @SuppressWarnings({"unchecked"})
-  static <T> List<T> loadList(Class<T> clazz, Query query)
+  static <T> List<T> loadList(Class<T> clazz, Query query, SessionControl sc)
     throws BaseException
   {
     assert query != null : "query == null";
-    try
-    {
+    Application.Pinger pinger = null;
+    try
+    {
+      if (sc != null) pinger = Application.newPinger(sc);
       return (List<T>)query.list();
     }
@@ -1462 +1467 @@
     {
       throw new BaseException(ex);
+    }
+    finally
+    {
+      if (pinger != null) pinger.stop();
     }
   }
@@ -1469 +1478 @@
     @param clazz The iterator returns objects of this class
     @param query The query to execute
-  */
-  static <T> ScrollIterator<T> loadIterator(Class<T> clazz, Query query)
+    @param sc A optional SessionControl that is automatically protected from
+      timeouts during the time the query is running
+  */
+  static <T> ScrollIterator<T> loadIterator(Class<T> clazz, Query query, SessionControl sc)
     throws BaseException
   {
     assert query != null : "query == null";
-    try
-    {
+    Application.Pinger pinger = null;
+    try
+    {
+      if (sc != null) pinger = Application.newPinger(sc);
+      Thread.sleep(5000);
       ScrollableResults result = query.scroll(ScrollMode.FORWARD_ONLY);
       return new ScrollIterator<T>(clazz, result);
@@ -1482 +1496 @@
     {
       throw new BaseException(ex);
+    }
+    finally
+    {
+      if (pinger != null) pinger.stop();
     }
   }
@@ -1675 +1693 @@
   
   /**
+    Prints a lot of useful stuff about the dynamic database to standard output.
+    For each table the output includes information about columns, indexes,
+    primary keys and foreign keys as found in the current database.
+    
+    @param verbose If true, lots of information will be printed
+    @param silent If true, no information will be printed
+    @param dropIndexes If true, all indexes will be dropped
+  */
+  @SuppressWarnings("unchecked")
+  public static void dynamicDbIndexes(boolean verbose, boolean silent, boolean dropIndexes)
+  {
+    if (silent) verbose = false;
+    Session session = newSession();
+    Connection connection = HibernateUtil.getConnection(session);
+    DatabaseMetaData metaData = null;
+    List<Table> tables = new LinkedList<Table>();
+    
+    try
+    {
+      metaData = connection.getMetaData();
+      ResultSet result = metaData.getTables(Application.getDynamicCatalog(), 
+          Application.getDynamicSchema(), null, null);
+      
+      while (result.next())
+      {
+        String tableName = result.getString("TABLE_NAME");
+        String tableCatalog = result.getString("TABLE_CAT");
+        String tableSchema = result.getString("TABLE_SCHEM");
+        Table table = new Table();
+        table.setName(tableName);
+        table.setCatalog(tableCatalog);
+        table.setSchema(tableSchema);
+        tables.add(table);
+      }
+    }
+    catch (SQLException ex)
+    {
+      throw new BaseException(ex);
+    }
+    
+    for (Table table : tables)
+    {
+
+      if (!silent)
+      {
+        System.out.println("=================");
+        System.out.println("Table   : " + table.getName());
+      }
+      if (verbose)
+      {
+        System.out.println("Catalog : " + table.getCatalog());
+        System.out.println("Schema  : " + table.getSchema());
+      }
+
+      Map<Set<String>, String> indexedColumns = new HashMap<Set<String>, String>();
+      Map<Set<String>, String> uniqueColumns = new HashMap<Set<String>, String>();
+      
+      String pkName = null;
+      Set<String> fkNames = new HashSet<String>();
+
+      if (verbose)
+      {
+        System.out.println("Database information");
+        System.out.println("--------------------");
+      }
+      
+      TableInfo tiDb = null;
+      try
+      {
+        tiDb = new TableInfo(table, metaData);
+      }
+      catch (SQLException ex)
+      {
+        throw new BaseException(ex);
+      }
+
+      if (tiDb != null)
+      {
+        if (verbose)
+        {
+          // Write all columns
+          for (ColumnInfo ci : tiDb.getColumns())
+          {
+            System.out.println("  Column       : " + ci);
+          }
+          
+          // Write primary key
+          System.out.println("  Primary key  : " + tiDb.getPrimaryKey());
+        
+          // Write foreign keys
+          for (ForeignKeyInfo fk : tiDb.getForeignKeys())
+          {
+            System.out.println("  Foreign key  : " + fk);
+          }
+        }
+      
+        // Write indexes and unique constraints
+        for (IndexInfo ii : tiDb.getIndexes())
+        {
+          if (!silent)
+          {
+            if (ii.isUnique())
+            {
+              System.out.println("  Unique       : " + ii);
+            }
+            else
+            {
+              System.out.println("  Index        : " + ii);
+            }
+          }
+          
+          boolean safeToDrop = tiDb.safeToDrop(ii);
+
+          String dropSql = dbEngine.getDropIndexSql(
+            table.getCatalog(), table.getSchema(), table.getName(), 
+            ii.getName(), ii.isUnique());
+          boolean actionDrop = dropIndexes && safeToDrop;
+
+          if (!silent)
+          {
+            System.out.println("    Safe drop  : " + safeToDrop);
+            System.out.println("    DROP-SQL   : " + dropSql);
+            System.out.println("    Actions    : " + (actionDrop ? "DROP " : ""));
+          }
+          
+          if (actionDrop )
+          {
+            Statement st = null;
+            try
+            {
+              st = connection.createStatement();
+              if (actionDrop) 
+              {
+                log.info("Dropping index: + " + dropSql);
+                st.executeUpdate(dropSql);
+              }
+              connection.commit();
+              st.close();
+              st = null;
+            }
+            catch (SQLException ex)
+            {
+              log.error("Exception", ex);
+              throw new BaseException(ex);
+            }
+            finally
+            {
+              if (st != null)
+              {
+                try
+                {
+                  st.close();
+                }
+                catch (Throwable t)
+                {
+                  log.error("Exception", t);
+                }
+              }
+            }
+          }
+          
+        }
+      }
+      
+      if (!silent)
+      {
+        System.out.println("=================");
+        System.out.println("");
+      }
+    }
+  }
+  
+  
+  /**
     Prints a lot of useful stuff about the database to standard output.
     For each table the output includes information about columns, indexes,
@@ -1716 +1908 @@
         System.out.println("Schema  : " + table.getSchema());
       }
-
+  
       Map<Set<String>, String> indexedColumns = new HashMap<Set<String>, String>();
       Map<Set<String>, String> uniqueColumns = new HashMap<Set<String>, String>();
@@ -1722 +1914 @@
       String pkName = null;
       Set<String> fkNames = new HashSet<String>();
-
+  
       if (verbose)
       {
@@ -1738 +1930 @@
         throw new BaseException(ex);
       }
-
+  
       if (verbose && tiDb != null)
       {
@@ -1795 +1987 @@
         }
       }
-
+  
       // Write indexes and unique constraints
       for (IndexInfo ii : tiHib.getIndexes())
@@ -1814 +2006 @@
         boolean exists = dbName != null;
         boolean safeToDrop = exists && tiDb.safeToDrop(ii);
-
+  
         String dropSql = exists ? 
-          dbEngine.getDropIndexSql(null, null, table.getName(), dbName, ii.isUnique()) : "";
+          dbEngine.getDropIndexSql(table.getCatalog(), table.getSchema(), 
+            table.getName(), dbName, ii.isUnique()) : "";
         String createSql = 
-          dbEngine.getCreateIndexSql(null, null, table.getName(), table.getName() + "_" + ii.getName(), 
+          dbEngine.getCreateIndexSql(table.getCatalog(), table.getSchema(),
+            table.getName(), table.getName() + "_" + ii.getName(), 
           ii.getColumns(), ii.isUnique());
         boolean actionDrop = dropIndexes && exists && safeToDrop;
@@ -1882 +2076 @@
     }
   }
-  
+
 
 }

trunk/src/core/net/sf/basedb/core/Install.java

@@ -196 +196 @@
       if (progress != null) progress.display((int)(3*progress_factor), "--Creating roles...");
       RoleData roleAdmin = createRole(Role.ADMINISTRATOR, "Administrator", false, "Users with this role get full permission to BASE.");
-      RoleData roleSuper = createRole(Role.SUPERVISOR, "Supervisor", false, "Users with this role get full READ permission to everyting in BASE.");
+      RoleData roleSuper = createRole(Role.SUPERVISOR, "Supervisor", false, "Users with this role get full READ permission to everything in BASE.");
       RoleData rolePower = createRole(Role.POWER_USER, "Power user", false, "Users with this role may do some things that an ordinary user may not.");
       RoleData roleUser = createRole(Role.USER, "User", true, "This permissions in this role should be sufficient for most regular users.");

trunk/src/core/net/sf/basedb/core/InternalJobQueue.java

@@ -253 +253 @@
       query.setInteger("status", Job.Status.WAITING.getValue());
       query.setInteger("type", Job.Type.RUN_PLUGIN.getValue());
-      List<JobData> jobs = HibernateUtil.loadList(JobData.class, query);
+      List<JobData> jobs = HibernateUtil.loadList(JobData.class, query, null);
       
       log.info("Found " + jobs.size() + " jobs waiting for execution");
@@ -485 +485 @@
     */
     /**
-      Never reload since everyting is static.
+      Never reload since everything is static.
     */
     boolean getReload()

trunk/src/core/net/sf/basedb/core/InternalStorageController.java

@@ -339 +339 @@
     */
     /**
-      Never reload since everyting is static.
+      Never reload since everything is static.
     */
     boolean getReload()

trunk/src/core/net/sf/basedb/core/ItemKey.java

@@ -157 +157 @@
         WHERE NOT sd.itemKey IS NULL
       */
-      Set<Integer> used = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query));
+      Set<Integer> used = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query, null));
       if (used.size() == 0) used.add(0);
       query = HibernateUtil.getPredefinedQuery(session, "SELECT_UNUSED_ITEMKEYS");
@@ -165 +165 @@
       */
       query.setParameterList("used", used, org.hibernate.Hibernate.INTEGER);
-      List<ItemKeyData> unused = HibernateUtil.loadList(ItemKeyData.class, query);
+      List<ItemKeyData> unused = HibernateUtil.loadList(ItemKeyData.class, query, null);
       for (ItemKeyData ik : unused)
       {
@@ -363 +363 @@
       */
       query.setInteger("numPermissions", numPermissions);
-      List<Integer> candidates = HibernateUtil.loadList(Integer.class, query);
+      List<Integer> candidates = HibernateUtil.loadList(Integer.class, query, null);
       if (candidates.size() > 0 && numPermissions > 0 && userPermissions != null)
       {
@@ -385 +385 @@
         query.setParameterList("candidates", candidates, org.hibernate.Hibernate.INTEGER);
         query.setInteger("numPermissions", numPermissions);
-        candidates = HibernateUtil.loadList(Integer.class, query);
+        candidates = HibernateUtil.loadList(Integer.class, query, null);
       }
       
@@ -403 +403 @@
         query.setInteger("numPermissions", numPermissions);
         query.setParameterList("candidates", candidates, org.hibernate.Hibernate.INTEGER);
-        candidates = HibernateUtil.loadList(Integer.class, query);        
+        candidates = HibernateUtil.loadList(Integer.class, query, null);        
       }
 
@@ -428 +428 @@
         query.setParameterList("candidates", candidates, org.hibernate.Hibernate.INTEGER);
         query.setInteger("numPermissions", numPermissions);
-        candidates = HibernateUtil.loadList(Integer.class, query);
+        candidates = HibernateUtil.loadList(Integer.class, query, null);
       }
   

trunk/src/core/net/sf/basedb/core/ItemQuery.java

@@ -90 +90 @@
   {
     enableFilters(dc);
+    SessionControl sc = dc.getSessionControl();
     
-    List<? extends BasicData> result = HibernateUtil.loadList(dataClass, getMainHqlQuery(dc));
+    List<? extends BasicData> result = HibernateUtil.loadList(dataClass, getMainHqlQuery(dc), sc);
     long totalCount = result.size();
     
@@ -115 +116 @@
     enableFilters(dc);
     long totalCount = -1;
+    SessionControl sc = dc.getSessionControl();
     
     // Load the total count if it is requested
@@ -122 +124 @@
     }
 
-    ScrollIterator<? extends BasicData> result = HibernateUtil.loadIterator(dataClass, getMainHqlQuery(dc));
+    ScrollIterator<? extends BasicData> result = 
+      HibernateUtil.loadIterator(dataClass, getMainHqlQuery(dc), sc);
     disableFilters(dc);
     return new ItemResultIterator<I>(result, dc, itemClass, totalCount);

trunk/src/core/net/sf/basedb/core/Keyring.java

@@ -323 +323 @@
       */
       query.setInteger("userId", userId);
-      temp = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query));
+      temp = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query, null));
       roles = Collections.unmodifiableSet(temp);
     }
@@ -350 +350 @@
       */
       query.setInteger("userId", userId);
-      temp = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query));
+      temp = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query, null));
       
       query = HibernateUtil.getPredefinedQuery(session, "GET_QUOTA_GROUP_ID_FOR_USER");
@@ -375 +375 @@
         {
           query.setParameterList("groups", temp, org.hibernate.Hibernate.INTEGER);
-        } while (temp.addAll(HibernateUtil.loadList(Integer.class, query)));
+        } while (temp.addAll(HibernateUtil.loadList(Integer.class, query, null)));
         // repeat until no more new groups are found
       }
@@ -406 +406 @@
       */
       query.setInteger("userId", userId);
-      for (Integer i : HibernateUtil.loadList(Integer.class, query))
+      for (Integer i : HibernateUtil.loadList(Integer.class, query, null))
       {
         temp.put(i, ALL_ITEM);
@@ -419 +419 @@
       */
       query.setInteger("userId", userId);
-      for (UserProjects up : HibernateUtil.loadList(UserProjects.class, query))
+      for (UserProjects up : HibernateUtil.loadList(UserProjects.class, query, null))
       {
         Integer i = temp.get(up.getProjectId());
@@ -435 +435 @@
         */
         query.setParameterList("groups", groups, org.hibernate.Hibernate.INTEGER);
-        for (GroupProjects gp : HibernateUtil.loadList(GroupProjects.class, query))
+        for (GroupProjects gp : HibernateUtil.loadList(GroupProjects.class, query, null))
         {
           Integer i = temp.get(gp.getProjectId());
@@ -471 +471 @@
         */
         query.setParameterList("groups", groups, org.hibernate.Hibernate.INTEGER);
-        temp.addAll(HibernateUtil.loadList(Integer.class, query));
+        temp.addAll(HibernateUtil.loadList(Integer.class, query, null));
         
         // Get the users that have a quota group among the same groups
@@ -481 +481 @@
         */
         query.setParameterList("groups", groups, org.hibernate.Hibernate.INTEGER);
-        temp.addAll(HibernateUtil.loadList(Integer.class, query));
+        temp.addAll(HibernateUtil.loadList(Integer.class, query, null));
       }
       
@@ -498 +498 @@
         */
         query.setInteger("projectId", projectId);
-        temp.addAll(HibernateUtil.loadList(Integer.class, query));
+        temp.addAll(HibernateUtil.loadList(Integer.class, query, null));
         
         // Get groups that are direct members of the active project
@@ -509 +509 @@
         query.setInteger("projectId", projectId);
         // Load the direct groups and subgroups
-        Set<Integer> projectGroups = Group.getGroupsRecursive(session, HibernateUtil.loadList(Integer.class, query));
+        Set<Integer> projectGroups = Group.getGroupsRecursive(session, HibernateUtil.loadList(Integer.class, query, null));
 
         // Load users that are members of the project groups
@@ -541 +541 @@
       */
       query.setInteger("userId", userId);
-      List<KeyPermission> keys = HibernateUtil.loadList(KeyPermission.class, query);
+      List<KeyPermission> keys = HibernateUtil.loadList(KeyPermission.class, query, null);
 
       // Load keys shared to any of the groups where the user is a member
@@ -553 +553 @@
         */
         query.setParameterList("groups", groups, org.hibernate.Hibernate.INTEGER);
-        keys.addAll(HibernateUtil.loadList(KeyPermission.class, query));
+        keys.addAll(HibernateUtil.loadList(KeyPermission.class, query, null));
       }
 
@@ -612 +612 @@
       */
       query.setInteger("userId", userId);
-      List<RoleKeys> roleKeys = HibernateUtil.loadList(RoleKeys.class, query);
+      List<RoleKeys> roleKeys = HibernateUtil.loadList(RoleKeys.class, query, null);
       
       // Copy the permission from the list to the array
@@ -665 +665 @@
       */
       query.setInteger("pluginId", pluginId);
-      List<PluginKeys> keys = HibernateUtil.loadList(PluginKeys.class, query);
+      List<PluginKeys> keys = HibernateUtil.loadList(PluginKeys.class, query, null);
       
       // Copy the permissions from the list to the array
@@ -701 +701 @@
       */
       query.setInteger("projectId", projectId);
-      List<ProjectKeys> keys = HibernateUtil.loadList(ProjectKeys.class, query);
+      List<ProjectKeys> keys = HibernateUtil.loadList(ProjectKeys.class, query, null);
 
       // Copy the permissions from the List to the array

trunk/src/core/net/sf/basedb/core/PluginDefinition.java

@@ -317 +317 @@
     query.setParameterList("projectKeys", projectKeys, org.hibernate.Hibernate.INTEGER);
   
-    List<Object> pluginCount = HibernateUtil.loadList(Object.class, query);
+    List<Object> pluginCount = HibernateUtil.loadList(Object.class, query, dc.getSessionControl());
     Map<Plugin.MainType, Integer> result = new HashMap<Plugin.MainType, Integer>(5);
     for (Object cnt : pluginCount)
@@ -1125 +1125 @@
     org.hibernate.Query query = HibernateUtil.createQuery(
       getDbControl().getHibernateSession(), "SELECT pt FROM PluginTypeData pt");
-    List<PluginTypeData> types = HibernateUtil.loadList(PluginTypeData.class, query);
+    List<PluginTypeData> types = HibernateUtil.loadList(PluginTypeData.class, query, null);
 
     for (PluginTypeData pt : types)

trunk/src/core/net/sf/basedb/core/Project.java

@@ -393 +393 @@
       */
       query.setInteger("projectId", this.getId());
-      projectKeys = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query));
+      projectKeys = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query, sc));
       
       include.remove(Include.OTHERS);
@@ -458 +458 @@
       FROM net.sf.basedb.core.data.ShareableData item
     */
-    List<ShareableData> inProject = HibernateUtil.loadList(ShareableData.class, query);
+    List<ShareableData> inProject = HibernateUtil.loadList(ShareableData.class, query, sc);
     List<Shareable> items = new ArrayList<Shareable>(inProject.size());
 

trunk/src/core/net/sf/basedb/core/ProjectKey.java

@@ -142 +142 @@
         WHERE NOT sd.projectKey IS NULL
       */
-      Set<Integer> used = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query));
+      Set<Integer> used = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query, null));
       if (used.size() == 0) used.add(0);
       query = HibernateUtil.getPredefinedQuery(session, "SELECT_UNUSED_PROJECTKEYS");
@@ -150 +150 @@
       */
       query.setParameterList("used", used, org.hibernate.Hibernate.INTEGER);
-      List<ProjectKeyData> unused = HibernateUtil.loadList(ProjectKeyData.class, query);
+      List<ProjectKeyData> unused = HibernateUtil.loadList(ProjectKeyData.class, query, null);
       for (ProjectKeyData pk : unused)
       {
@@ -307 +307 @@
       */
       query.setInteger("numPermissions", numPermissions);
-      List<Integer> candidates = HibernateUtil.loadList(Integer.class, query);
+      List<Integer> candidates = HibernateUtil.loadList(Integer.class, query, null);
       if (candidates.size() > 0)
       {
@@ -330 +330 @@
         query.setParameterList("candidates", candidates, org.hibernate.Hibernate.INTEGER);
         query.setInteger("numPermissions", numPermissions);
-        candidates = HibernateUtil.loadList(Integer.class, query);
+        candidates = HibernateUtil.loadList(Integer.class, query, null);
       }
       if (candidates.size() == 0)

trunk/src/core/net/sf/basedb/core/RawBioAssay.java

@@ -1087 +1087 @@
       */
       query.setInteger("arrayDesign", design.getId());
-      ScrollIterator<FeatureData> si = HibernateUtil.loadIterator(FeatureData.class, query);
+      ScrollIterator<FeatureData> si = 
+        HibernateUtil.loadIterator(FeatureData.class, query, dc.getSessionControl());
       while (si.hasNext())
       {

trunk/src/core/net/sf/basedb/core/RawDataBatcher.java

@@ -192 +192 @@
       */
       query.setInteger("arrayDesign", arrayDesign.getId());
-      ScrollIterator<FeatureData> si = HibernateUtil.loadIterator(FeatureData.class, query);
+      ScrollIterator<FeatureData> si = 
+        HibernateUtil.loadIterator(FeatureData.class, query, dc.getSessionControl());
       while (si.hasNext())
       {

trunk/src/core/net/sf/basedb/core/ReporterScoreQuery.java

@@ -58 +58 @@
     enableFilters(dc);
     long totalCount = -1;
+    SessionControl sc = dc.getSessionControl();
     
     // Load the total count if it is requested
@@ -65 +66 @@
     }
 
-    ScrollIterator<ReporterListScoreData> result = HibernateUtil.loadIterator(ReporterListScoreData.class, getMainHqlQuery(dc));
+    ScrollIterator<ReporterListScoreData> result = 
+      HibernateUtil.loadIterator(ReporterListScoreData.class, getMainHqlQuery(dc), sc);
     disableFilters(dc);
     return new ReporterScoreResultIterator(result, dc, totalCount);

trunk/src/core/net/sf/basedb/core/SessionControl.java

@@ -112 +112 @@
   
   /**
+    If the session control has been closed it can no longer be used.
+  */
+  private boolean closed;
+  
+  /**
     Stores name and value from {@link ClientDefaultSettingData}.
   */
@@ -192 +197 @@
     Get the time this object last was accessed. Used by the cleanup timer
     in {@link Application#cleanSessionControlCache(boolean)}
-  */
-  long getLastAccess()
+    @since 2.4.5
+  */
+  public long getLastAccess()
   {
     return lastAccess;
@@ -204 +210 @@
   public void updateLastAccess()
   {
+    if (closed) throw new PermissionDeniedException("SessonControl is closed");
     lastAccess = System.currentTimeMillis();
   }
+  
+  /**
+    If this session control has been closed or not. A closed session
+    control can't be used.
+    @return TRUE if the session control is closed
+    @since 2.4.5
+  */
+  public boolean isClosed()
+  {
+    return closed;
+  }
+  
+  /**
+    Close this session control so it can't be used again.
+    @since 2.4.5
+  */
+  public void close()
+  {
+    if (isLoggedIn()) logout();
+    closed = true;
+  }
+  
   
   /**
@@ -693 +722 @@
   public boolean isLoggedIn()
   {
-    updateLastAccess();
     return loginInfo != null;
   }
@@ -1405 +1433 @@
       query.setInteger("itemType", item.getValue());
       query.setString("subContext", subContext);
-      for (Object ctx : HibernateUtil.loadList(Object.class, query))
+      for (Object ctx : HibernateUtil.loadList(Object.class, query, null))
       {
         Object[] o = (Object[])ctx;
@@ -1665 +1693 @@
     */
     query.setInteger("client", clientId);
-    return listToMap(HibernateUtil.loadList(ClientDefaultSettingData.class, query));
+    return listToMap(HibernateUtil.loadList(ClientDefaultSettingData.class, query, null));
   }
 
@@ -1680 +1708 @@
     */
     query.setInteger("user", userId);
-    return listToMap(HibernateUtil.loadList(UserDefaultSettingData.class, query));
+    return listToMap(HibernateUtil.loadList(UserDefaultSettingData.class, query, null));
   }
 
@@ -1696 +1724 @@
     query.setInteger("user", userId);
     query.setInteger("client", clientId);
-    return listToMap(HibernateUtil.loadList(UserClientSettingData.class, query));
+    return listToMap(HibernateUtil.loadList(UserClientSettingData.class, query, null));
   }
   
@@ -1716 +1744 @@
   {
     // Load the existing settings from the database
-    List<I> dbSettings = HibernateUtil.loadList(dataClass, query);
+    List<I> dbSettings = HibernateUtil.loadList(dataClass, query, null);
     // Iterator the existing settings and check what has happened to them
     for (SettingData s : dbSettings)
@@ -1786 +1814 @@
   protected void cleanUp()
   {
-    if (isLoggedIn()) logout();
+    if (!isClosed() && isLoggedIn()) logout();
   }
   
@@ -1799 +1827 @@
       cleanUp();
     }
-    catch (BaseException ex)
-    {
-      log.warn("Exception during SessionControl.finalize()", ex);
+    catch (Throwable t)
+    {
+      log.warn("Exception during SessionControl.finalize()", t);
     }
     super.finalize();
   }
-
+  
   /**
     Internal class to hold information about the logged in user.

trunk/src/core/net/sf/basedb/core/Trashcan.java

@@ -73 +73 @@
     {
       org.hibernate.Session session = dc.getHibernateSession();
+      SessionControl sc = dc.getSessionControl();
       org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, "GET_REMOVED_ITEMS");
       /*
@@ -82 +83 @@
       filter.setParameter("owner", dc.getSessionControl().getLoggedInUserId());
       
-      List<RemovableData> removed = HibernateUtil.loadList(RemovableData.class, query);
+      List<RemovableData> removed = HibernateUtil.loadList(RemovableData.class, query, sc);
       List<Removable> items = new ArrayList<Removable>(removed.size());
       

trunk/src/core/net/sf/basedb/core/Update.java

@@ -950 +950 @@
       // Delete all affymetrix formulas
       query = HibernateUtil.createQuery(session, "SELECT frm FROM FormulaData frm WHERE frm.rawDataType = 'affymetrix'");
-      List<FormulaData> affyFormulas = HibernateUtil.loadList(FormulaData.class, query);
+      List<FormulaData> affyFormulas = HibernateUtil.loadList(FormulaData.class, query, null);
       for (FormulaData affyFormula : affyFormulas)
       {
@@ -1189 +1189 @@
         FROM FileData f
       */
-      List<Integer> ids = HibernateUtil.loadList(Integer.class, query);
+      List<Integer> ids = HibernateUtil.loadList(Integer.class, query, null);
       if (ids.size() > 0)
       {
@@ -1204 +1204 @@
         FROM ExperimentData xp
       */
-      ids = HibernateUtil.loadList(Integer.class, query);
+      ids = HibernateUtil.loadList(Integer.class, query, null);
       if (ids.size() > 0)
       {
@@ -1219 +1219 @@
         FROM RawBioAssayData rba
       */
-      ids = HibernateUtil.loadList(Integer.class, query);
+      ids = HibernateUtil.loadList(Integer.class, query, null);
       if (ids.size() > 0)
       {
@@ -1268 +1268 @@
         WHERE dcd.id = :dataCube
       */
-      for (DataCubeData cubeData : HibernateUtil.loadList(DataCubeData.class, query))
+      for (DataCubeData cubeData : HibernateUtil.loadList(DataCubeData.class, query, null))
       {
         DataCube cube = dc.getItem(DataCube.class, cubeData);
@@ -1329 +1329 @@
           JOIN evt.sources src          
          */
-      List<Object[]> events = HibernateUtil.loadList(Object[].class, eventQuery);
-      events.addAll(HibernateUtil.loadList(Object[].class, sourcesQuery));
+      List<Object[]> events = HibernateUtil.loadList(Object[].class, eventQuery, null);
+      events.addAll(HibernateUtil.loadList(Object[].class, sourcesQuery, null));
       
       // Calculate the remaining quantity for each biomaterial
@@ -1410 +1410 @@
         WHERE f.lastUpdate IS NULL AND NOT f.internalName IS NULL
       */
-      List<FileData> files = HibernateUtil.loadList(FileData.class, query);
+      List<FileData> files = HibernateUtil.loadList(FileData.class, query, null);
       for (FileData fData : files)
       {
@@ -1453 +1453 @@
         "SELECT f FROM FileData f");
       
-      List<FileData> files = HibernateUtil.loadList(FileData.class, query);
+      List<FileData> files = HibernateUtil.loadList(FileData.class, query, null);
       for (FileData fData : files)
       {
@@ -1505 +1505 @@
         "SELECT t FROM TransformationData t");
       
-      List<TransformationData> transformations = HibernateUtil.loadList(TransformationData.class, query);
+      List<TransformationData> transformations = HibernateUtil.loadList(TransformationData.class, query, null);
       Map<JobData, Set<ExperimentData>> experiments = new HashMap<JobData, Set<ExperimentData>>(); 
       for (TransformationData transformation : transformations)
@@ -1579 +1579 @@
       query.setEntity("pluginDefinition", base1Executer);
       List<PluginConfigurationData> configurations = 
-        HibernateUtil.loadList(PluginConfigurationData.class, query);
+        HibernateUtil.loadList(PluginConfigurationData.class, query, null);
 
       // Delete AnyToAny for each configuration
@@ -1948 +1948 @@
             )
           */
-          List<PlateMappingData> mappings = HibernateUtil.loadList(PlateMappingData.class, pmQuery);
+          List<PlateMappingData> mappings = HibernateUtil.loadList(PlateMappingData.class, pmQuery, null);
           if (mappings != null && mappings.size() > 0)
           {
@@ -1967 +1967 @@
             {
               pQuery.setEntity("plateMapping", mapping);
-              List<PlateData> plates = HibernateUtil.loadList(PlateData.class, pQuery);
+              List<PlateData> plates = HibernateUtil.loadList(PlateData.class, pQuery, null);
               if (plates != null && plates.size() > 0)
               {

trunk/src/core/net/sf/basedb/core/User.java

@@ -146 +146 @@
       */
       query.setParameterList("groups", groupIds, org.hibernate.Hibernate.INTEGER);
-      userIds.addAll(HibernateUtil.loadList(Integer.class, query));
+      userIds.addAll(HibernateUtil.loadList(Integer.class, query, null));
       
       // Get the users that have a quota group among the same groups
@@ -156 +156 @@
       */
       query.setParameterList("groups", groupIds, org.hibernate.Hibernate.INTEGER);
-      userIds.addAll(HibernateUtil.loadList(Integer.class, query));
+      userIds.addAll(HibernateUtil.loadList(Integer.class, query, null));
     }
     return userIds;
@@ -174 +174 @@
       WHERE grp.default = true
     */
-    List<GroupData> defaultGroups = HibernateUtil.loadList(GroupData.class, query);
+    List<GroupData> defaultGroups = HibernateUtil.loadList(GroupData.class, query, null);
     for (GroupData group : defaultGroups)
     {
@@ -185 +185 @@
       WHERE rle.default = true
     */
-    List<RoleData> defaultRoles = HibernateUtil.loadList(RoleData.class, query);
+    List<RoleData> defaultRoles = HibernateUtil.loadList(RoleData.class, query, null);
     for (RoleData role : defaultRoles)
     {
@@ -1090 +1090 @@
     query.setEntity("user", this.getData());
 
-    List<OwnableData> ownedBy = HibernateUtil.loadList(OwnableData.class, query);
+    List<OwnableData> ownedBy = HibernateUtil.loadList(OwnableData.class, query, sc);
     List<Ownable> items = new ArrayList<Ownable>(ownedBy.size());
 

trunk/src/core/net/sf/basedb/core/VirtualColumn.java

@@ -68 +68 @@
   */
   public static final VirtualColumn CUBE = 
-    new VirtualColumn("cube", "cube", Hibernate.SHORT, 0, INDEXED, !NULLABLE, PRIMARY_KEY);
+    new VirtualColumn("cube", "cube", Hibernate.SHORT, 0, 
+      !INDEXED, !NULLABLE, PRIMARY_KEY);
     
   /**
@@ -75 +76 @@
   */
   public static final VirtualColumn LAYER = 
-    new VirtualColumn("layer", "layer", Hibernate.SHORT, 0, INDEXED, !NULLABLE, PRIMARY_KEY);
+    new VirtualColumn("layer", "layer", Hibernate.SHORT, 0, 
+      !INDEXED, !NULLABLE, PRIMARY_KEY);
 
   /**
@@ -82 +84 @@
   */
   public static final VirtualColumn COLUMN = 
-    new VirtualColumn("column", "column", Hibernate.SHORT, 0, INDEXED, !NULLABLE, PRIMARY_KEY);
+    new VirtualColumn("column", "column", Hibernate.SHORT, 0, 
+      !INDEXED, !NULLABLE, PRIMARY_KEY);
   
   /**
@@ -88 +91 @@
   */
   public static final VirtualColumn POSITION = 
-    new VirtualColumn("position", "position", Hibernate.INTEGER, 0, INDEXED, !NULLABLE, PRIMARY_KEY);
+    new VirtualColumn("position", "position", Hibernate.INTEGER, 0, 
+      !INDEXED, !NULLABLE, PRIMARY_KEY);
   
   /**
@@ -95 +99 @@
   */
   public static final VirtualColumn FILTER = 
-    new VirtualColumn("filter", "filter", Hibernate.SHORT, 0, INDEXED, !NULLABLE, PRIMARY_KEY);
+    new VirtualColumn("filter", "filter", Hibernate.SHORT, 0, 
+      !INDEXED, !NULLABLE, PRIMARY_KEY);
 
   /**
@@ -102 +107 @@
   */
   public static final VirtualColumn EXTRA = 
-    new VirtualColumn("extra", "extra", Hibernate.SHORT, 0, INDEXED, !NULLABLE, PRIMARY_KEY);
+    new VirtualColumn("extra", "extra", Hibernate.SHORT, 0, 
+      !INDEXED, !NULLABLE, PRIMARY_KEY);
 
   /**
@@ -110 +116 @@
   */
   public static final VirtualColumn REPORTER_ID =
-    new VirtualColumn("reporterId", "reporter_id", Hibernate.INTEGER, 0, INDEXED, NULLABLE, !PRIMARY_KEY);
+    new VirtualColumn("reporterId", "reporter_id", Hibernate.INTEGER, 0, 
+      !INDEXED, NULLABLE, !PRIMARY_KEY);
 
   /**
@@ -118 +125 @@
   */
   public static final VirtualColumn RAWDATA_ID =
-    new VirtualColumn("rawDataId", "rawdata_id", Hibernate.INTEGER, 0, INDEXED, !NULLABLE, PRIMARY_KEY);
+    new VirtualColumn("rawDataId", "rawdata_id", Hibernate.INTEGER, 0, 
+      !INDEXED, !NULLABLE, PRIMARY_KEY);
   
   /**
@@ -126 +134 @@
   */
   public static final VirtualColumn RAWBIOASSAY_ID =
-    new VirtualColumn("rawBioAssayId", "rawbioassay_id", Hibernate.INTEGER, 0, INDEXED, !NULLABLE, PRIMARY_KEY);
+    new VirtualColumn("rawBioAssayId", "rawbioassay_id", Hibernate.INTEGER, 0, 
+      !INDEXED, !NULLABLE, PRIMARY_KEY);
 
   /**
@@ -132 +141 @@
   */
   public static final VirtualColumn EXTRA_INT =
-    new VirtualColumn("extraInt", "value", Hibernate.INTEGER, 0, !INDEXED, NULLABLE, !PRIMARY_KEY);
+    new VirtualColumn("extraInt", "value", Hibernate.INTEGER, 0, 
+      !INDEXED, NULLABLE, !PRIMARY_KEY);
 
   /**
@@ -138 +148 @@
   */
   public static final VirtualColumn EXTRA_FLOAT =
-    new VirtualColumn("extraFloat", "value", Hibernate.FLOAT, 0, !INDEXED, NULLABLE, !PRIMARY_KEY);
+    new VirtualColumn("extraFloat", "value", Hibernate.FLOAT, 0, 
+      !INDEXED, NULLABLE, !PRIMARY_KEY);
 
   /**
@@ -144 +155 @@
   */
   public static final VirtualColumn EXTRA_STRING =
-    new VirtualColumn("extraString", "value", Hibernate.STRING, 255, !INDEXED, NULLABLE, !PRIMARY_KEY);
+    new VirtualColumn("extraString", "value", Hibernate.STRING, 255, 
+      !INDEXED, NULLABLE, !PRIMARY_KEY);
 
   /**
     A cache of virtual column objects for channels.
   */
-  private static final Map<Integer, VirtualColumn> channels = new HashMap<Integer, VirtualColumn>();
+  private static final Map<Integer, VirtualColumn> channels = 
+    new HashMap<Integer, VirtualColumn>();
   
   /**
     A cache of virtual column objects for extra value types.
   */
-  private static final Map<Type, VirtualColumn> extraValueColumns = new HashMap<Type, VirtualColumn>();
+  private static final Map<Type, VirtualColumn> extraValueColumns = 
+    new HashMap<Type, VirtualColumn>();
   
   // Initialise the cache
@@ -173 +187 @@
     if (ch == null)
     {
-      ch = new VirtualColumn("ch"+channel, "ch"+channel, Hibernate.FLOAT, 0, !INDEXED, NULLABLE, !PRIMARY_KEY);
+      ch = new VirtualColumn("ch"+channel, "ch"+channel, Hibernate.FLOAT, 0, 
+          !INDEXED, NULLABLE, !PRIMARY_KEY);
       synchronized (channels)
       {

trunk/src/core/net/sf/basedb/util/overview/ExperimentOverview.java

@@ -1500 +1500 @@
       {
         ProtocolType pt = protocol.getProtocolType();
-        if (!pt.getSystemId().equals(defaultProtocol.getType()))
+        String requiredId = defaultProtocol == null ? null : defaultProtocol.getType();
+        if (requiredId != null && !requiredId.equals(pt.getSystemId()))
         {
           failures.add(new Failure(Validator.INCORRECT_PROTOCOLTYPE, parentNode, null,

trunk/src/install/net/sf/basedb/install/InitDB.java

@@ -24 +24 @@
 */
 package net.sf.basedb.install;
+
+import java.util.Arrays;
+import java.util.List;
 
 import net.sf.basedb.core.Application;
@@ -94 +97 @@
         Application.stop();
       }
+      else if ("dynamicdb".equals(cmd))
+      {
+        List<String> opt = Arrays.asList(args);
+        boolean verbose = opt.contains("-v");
+        boolean drop = opt.contains("-dropindexes");
+        Application.start(false);
+        HibernateUtil.dynamicDbIndexes(verbose, false, drop);
+        Application.stop();
+      }
       else 
       {
         System.out.println("Unknown command: " + cmd);
-        System.out.println("Usage: InitDB cmd");
-        System.out.println("       cmd: install | update | info | updateindexes | dropindexes");
+        System.out.println("Usage: InitDB cmd <options>");
+        System.out.println("    cmd: install | update | info | updateindexes | dropindexes | dynamicdb");
+        System.out.println("options: ");
+        System.out.println("           -v : Verbose output (if cmd = updateindexes, dropindexs or dynamicdb)");
+        System.out.println(" -dropindexes : Drop indexes when cmd = dynamicdb");
       }
     }

trunk/src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java

@@ -96 +96 @@
     (
         "Packed file exporter",
-        "This plugin is used to packed one or more files/directories " +
+        "This plugin is used to pack one or more files/directories " +
         "into a single file. Items should be selected before starting the plug-in and " +
         "they must all be located in the same parent directory. " +

trunk/www/include/menu.jsp

@@ -106 +106 @@
         for (String recent : recentlyViewed)
         {
-          String[] tmp = recent.split("=");
-          Item itemType = Item.valueOf(tmp[0]);
-          int itemId = Values.getInt(tmp[1], 0);
-          if (itemId != 0)
+          try
           {
-            String shortName = "";
-            String fullName = "";
-            if (loadNames)
+            String[] tmp = recent.split("=");
+            Item itemType = Item.valueOf(tmp[0]);
+            int itemId = Values.getInt(tmp[1], 0);
+            if (itemId != 0)
             {
-              try
+              String shortName = "";
+              String fullName = "";
+              if (loadNames)
               {
-                BasicItem item = itemType.getById(dc, itemId);
-                fullName = ((Nameable)item).getName();
-                shortName = HTML.encodeTags(StringUtil.trimString(fullName, 35));
+                try
+                {
+                  BasicItem item = itemType.getById(dc, itemId);
+                  fullName = ((Nameable)item).getName();
+                  shortName = HTML.encodeTags(StringUtil.trimString(fullName, 35));
+                }
+                catch (Throwable t)
+                {
+                  continue;
+                }
               }
-              catch (Throwable t)
+              else
               {
-                continue;
+                fullName = itemType.toString() + "; id=" + itemId;
+                shortName = itemType + " (id=" + itemId + ")";
               }
+              numItems++;
+              %>
+              <m:menuitem
+                title="<%=numItems + ". " + shortName%>"
+                onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + itemId + ")"%>"
+                tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
+              />
+              <%
             }
-            else
-            {
-              fullName = itemType.toString() + "; id=" + itemId;
-              shortName = itemType + " (id=" + itemId + ")";
-            }
-            numItems++;
-            %>
-            <m:menuitem
-              title="<%=numItems + ". " + shortName%>"
-              onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + itemId + ")"%>"
-              tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
-            />
-            <%
           }
+          catch (Throwable t)
+          {}
         }
       }
@@ -162 +167 @@
         for (String recentItem : stickyItems.split(":"))
         {
-          Item itemType = Item.valueOf(recentItem);
-          ItemContext cc = sc.getCurrentContext(itemType);
-          if (cc.getId() != 0)
+          try
           {
-            String shortName = "";
-            String fullName = "";
-            if (loadNames)
+            Item itemType = Item.valueOf(recentItem);
+            ItemContext cc = sc.getCurrentContext(itemType);
+            if (cc.getId() != 0)
             {
-              try
+              String shortName = "";
+              String fullName = "";
+              if (loadNames)
               {
-                BasicItem item = itemType.getById(dc, cc.getId());
-                fullName = ((Nameable)item).getName();
-                shortName = ": " + HTML.encodeTags(StringUtil.trimString(fullName, 30));
+                try
+                {
+                  BasicItem item = itemType.getById(dc, cc.getId());
+                  fullName = ((Nameable)item).getName();
+                  shortName = ": " + HTML.encodeTags(StringUtil.trimString(fullName, 30));
+                }
+                catch (Throwable t)
+                {
+                  continue;
+                }
               }
-              catch (Throwable t)
+              else
               {
-                continue;
+                fullName = itemType.toString() + "; id=" + cc.getId();
+                shortName = " (id=" + cc.getId() + ")";
+              }
+              numItems++;
+              numSticky++;
+              %>
+              <m:menuitem
+                title="<%=itemType + shortName%>"
+                onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + cc.getId() + ")"%>"
+                tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
+              />
+              <%
+              if (itemType == Item.BIOASSAYSET)
+              {
+                // Add menu for Experiment explorer as well
+                %>
+                <m:menuitem
+                  title="<%="Experiment explorer"+HTML.encodeTags(shortName)%>"
+                  onclick="<%="location.href = '"+root+"views/experiments/explorer/view/index.jsp?ID=" + ID + "&bioassayset_id="+cc.getId()+"'"%>"
+                  tooltip="Go to experiment explorer"
+                />
+                <%
               }
             }
-            else
-            {
-              fullName = itemType.toString() + "; id=" + cc.getId();
-              shortName = " (id=" + cc.getId() + ")";
-            }
-            numItems++;
-            numSticky++;
-            %>
-            <m:menuitem
-              title="<%=itemType + shortName%>"
-              onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + cc.getId() + ")"%>"
-              tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
-            />
-            <%
-            if (itemType == Item.BIOASSAYSET)
-            {
-              // Add menu for Experiment explorer as well
-              %>
-              <m:menuitem
-                title="<%="Experiment explorer"+HTML.encodeTags(shortName)%>"
-                onclick="<%="location.href = '"+root+"views/experiments/explorer/view/index.jsp?ID=" + ID + "&bioassayset_id="+cc.getId()+"'"%>"
-                tooltip="Go to experiment explorer"
-              />
-              <%
-            }
           }
+          catch (Throwable t)
+          {}
         }
         if (numSticky == 0)