Changeset 6684

Timestamp:

Jan 14, 2015, 2:29:04 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

Merge changes between 3.4-beta-1 to 3.4.0 to the trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• build.xml (modified) (1 diff)
• doc/src/docbook/admin/installation.xml (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/extensions/skin/FixedSkinActionFactory.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/Page.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/AnyToAny.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/DbControl.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/HibernateUtil.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/ItemContext.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PropertyFilter.java (modified) (9 diffs)
• src/core/net/sf/basedb/core/RawDataTypes.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/ServiceSessionControl.java (modified) (6 diffs)
• src/core/net/sf/basedb/core/data/ExtractData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/dbengine/MySQLEngine.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/dbengine/PostgresDbEngine.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/dbengine/TableInfo.java (modified) (8 diffs)
• src/core/net/sf/basedb/core/hibernate/DbIndexWork.java (copied) (copied from tags/3.4.0/src/core/net/sf/basedb/core/hibernate/DbIndexWork.java)
• src/core/net/sf/basedb/core/hibernate/SchemaGenerator.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/signal/AbstractSignalReceiver.java (modified) (9 diffs)
• src/core/net/sf/basedb/util/timer/ThreadTimerTask.java (modified) (1 diff)
• src/test/TestAnyToAny.java (modified) (4 diffs)
• src/test/TestJarClassLoader.java (modified) (2 diffs)
• www/WEB-INF/base.tld (modified) (1 diff)
• www/admin/annotationtypes/edit_annotationtype.jsp (modified) (2 diffs)
• www/admin/extensions/tree.jsp (modified) (9 diffs)
• www/admin/roles/edit_role.jsp (modified) (1 diff)
• www/common/annotations/inherit.js (modified) (7 diffs)
• www/common/columns/configure.js (modified) (1 diff)
• www/common/overview/failures.js (modified) (1 diff)
• www/common/overview/failures.jsp (modified) (1 diff)
• www/common/overview/options.jsp (modified) (1 diff)
• www/common/plugin/parse_file.jsp (modified) (1 diff)
• www/filemanager/select_file.jsp (modified) (1 diff)
• www/include/scripts/main-2.js (modified) (2 diffs)
• www/info/about.jsp (modified) (3 diffs)
• www/lims/arrayslides/create_wizard.jsp (modified) (2 diffs)
• www/views/experiments/index.jsp (modified) (1 diff)
• www/views/jobs/view_job.jsp (modified) (1 diff)
• www/views/physicalbioassays/list_bioassays.jsp (modified) (1 diff)

trunk/build.xml

@@ -486 +486 @@
       <fileset dir="${core.src}" includes="**/*.hbm.xml" />
     </copy>
+    <copy todir="${build}/hbm"
+      description="Copy our data class files so xdoclet doesn't parse other code">
+      <fileset dir="${core.src}" includes="net/sf/basedb/core/data/**/*" />
+    </copy>
+    
     <hibernatedoclet
       destdir="${core.build}"
       excludedtags="@version,@author,@todo"
       mergedir="${core.build}"
-      verbose="${xdoclet.verbose}">
-      <fileset dir="${core.src}">
+      verbose="true"
+      >
+      <fileset dir="${build}/hbm">
         <include name="net/sf/basedb/core/data/**/*.java"/>
       </fileset>
-      <hibernate version="2.0"/>
+      <hibernate version="2.0" />
     </hibernatedoclet>
     

trunk/doc/src/docbook/admin/installation.xml

@@ -565 +565 @@
 
           <para>
-            The second command is important for PostgreSQL users since
-            the Hibernate database initialisation utility is not able
-            to create all required indexes. BASE will work without the
-            indexes but performance is impaired. Running the script as
-            a MySQL user does not have a negative impact.
+            The second command is important since
+            the Hibernate database initialisation utility is not always 
+            able to create all required indexes. In some cases, Hibernate
+            will also create a new index, even if one already exists. 
+            The command ensures that missing indexes are created and
+            that duplicates are removed. BASE will work without the
+            indexes but performance is impaired.
           </para>
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/skin/FixedSkinActionFactory.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web.extensions.skin;
 
+import java.util.Iterator;
+
 import net.sf.basedb.clients.web.extensions.AbstractJspActionFactory;
+import net.sf.basedb.clients.web.extensions.DynamicActionAttribute;
+import net.sf.basedb.clients.web.extensions.DynamicActionAttributes;
 import net.sf.basedb.clients.web.extensions.ExtensionsControl;
 import net.sf.basedb.util.extensions.InvokationContext;
@@ -103 +107 @@
   
   static class MySkinAction
-    implements SkinAction
+    implements SkinAction, DynamicActionAttributes
   {
     private final FixedSkinActionFactory factory;
@@ -136 +140 @@
     }
 
+    @Override
+    public Iterator<DynamicActionAttribute> getDynamicActionAttributes()
+    {
+      return factory.getDynamicActionAttributes();
+    }
     
   }

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Page.java

@@ -174 +174 @@
 
   /**
+    Set to TRUE to not use skin on the page.
+    @since 3.4
+  */
+  private boolean noSkin = false;
+  
+  /**
     The <!doctype xxx> setting.
   */
@@ -253 +259 @@
     return title;
   }
-
+  
+  /**
+    Set to TRUE to disable skins.
+    @since 3.4
+  */
+  public void setNoskin(boolean noSkin)
+  {
+    this.noSkin = noSkin;
+  }
+
+  public boolean getNoSkin()
+  {
+    return noSkin;
+  }
+  
   public void setType(String type)
   {
@@ -335 +355 @@
   public JspContext getSkinContext()
   {
-    return skinContext;
+    return noSkin ? null : skinContext;
   }
   
@@ -345 +365 @@
   public List<SkinAction> getSkinActions()
   {
-    return skinActions;
+    return noSkin ? null : skinActions;
   }
   
@@ -369 +389 @@
     if (type != PAGE_TYPE_INCLUDE)
     {
-      // Load skin extensions: net.sf.basedb.clients.web.global-skin
-      skinContext = ExtensionsControl.createContext(sc, pageContext);
-      skinContext.setAttribute("page-type", getTypeCode());
-      ExtensionsInvoker<SkinAction> invoker = (ExtensionsInvoker<SkinAction>)ExtensionsControl.useExtensions(skinContext, "net.sf.basedb.clients.web.global-skin");
-      ActionIterator<SkinAction> it = invoker.iterate();
-      skinActions = new ArrayList<SkinAction>();
-      ImageRemapper remapper = ImageRemapperUtil.getNewImageRemapperIfNeeded(pageContext.getServletContext());
-      while (it.hasNext())
+      if (!noSkin)
       {
-        SkinAction skin = it.next();
-        if (remapper != null) skin.remapImages(remapper);
-        skinActions.add(skin);
-        if (favicon == null)
+        // Load skin extensions: net.sf.basedb.clients.web.global-skin
+        skinContext = ExtensionsControl.createContext(sc, pageContext);
+        skinContext.setAttribute("page-type", getTypeCode());
+        ExtensionsInvoker<SkinAction> invoker = (ExtensionsInvoker<SkinAction>)ExtensionsControl.useExtensions(skinContext, "net.sf.basedb.clients.web.global-skin");
+        ActionIterator<SkinAction> it = invoker.iterate();
+        skinActions = new ArrayList<SkinAction>();
+        ImageRemapper remapper = ImageRemapperUtil.getNewImageRemapperIfNeeded(pageContext.getServletContext());
+        while (it.hasNext())
         {
-          String skinIcon = skin.getFavicon();
-          if (skinIcon != null) favicon = skinIcon;
+          SkinAction skin = it.next();
+          if (remapper != null) skin.remapImages(remapper);
+          skinActions.add(skin);
+          if (favicon == null)
+          {
+            String skinIcon = skin.getFavicon();
+            if (skinIcon != null) favicon = skinIcon;
+          }
         }
+        if (remapper != null) ImageRemapperUtil.setCurrentMapper(remapper);
       }
-      if (remapper != null) ImageRemapperUtil.setCurrentMapper(remapper);
       
       StringBuilder sb = new StringBuilder();

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

@@ -28 +28 @@
 import org.hibernate.mapping.Table;
 
-import net.sf.basedb.core.Transactional.Action;
 import net.sf.basedb.core.data.AnyToAnyData;
 import net.sf.basedb.core.hibernate.TypeWrapper;
@@ -52 +51 @@
 public class AnyToAny
   extends BasicItem<AnyToAnyData>
-  implements Nameable
+  implements Nameable, Transactional
 {
 
@@ -480 +479 @@
   {
     super.onBeforeCommit(action);
-    if (action == Action.CREATE)
+    if (action == Action.CREATE || action == Action.UPDATE && (getToId() == 0 || getFromId() == 0))
     {
       // In case either the to or from items are also new items

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

@@ -41 +41 @@
 import net.sf.basedb.util.extensions.manager.ExtensionsManager;
 
+import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
@@ -49 +50 @@
 import java.util.HashMap;
 import java.util.LinkedHashMap;
+import java.util.Set;
 import java.lang.reflect.Constructor;
 
@@ -146 +148 @@
   
   /**
+    Holds random strings that must be unique within a transaction. 
+  */
+  private Set<String> uniqueRandoms;
+  
+  /**
     Create a new object.
   */
@@ -169 +176 @@
     itemCache = new IdentityHashMap<BasicData, BasicItem>();
     commitQueue = new LinkedHashMap<BasicItem,Transactional.Action>();
+    uniqueRandoms = new HashSet<String>();
     isClosed = false;
     isConnected = true;
@@ -376 +384 @@
     commitQueue.clear();
     itemCache.clear();
+    uniqueRandoms.clear();
     if (batchers != null) batchers.clear();
     if (saveIfQueue != null) saveIfQueue.clear();
@@ -383 +392 @@
     transactionalActions = null;
     itemCache = null;
+    uniqueRandoms = null;
     batchers = null;
     isClosed = true;
@@ -1211 +1221 @@
 
   /**
+    Generate a random string value that is unique for the given transaction.
+    @since 3.4
+  */
+  public String uniqueRandom()
+  {
+    String random = null;
+    while (true)
+    {
+      random = Application.generateRandomId(4);
+      if (uniqueRandoms.add(random)) break;
+    }
+    return random;
+  }
+  
+  /**
     Add a <code>Batcher</code> to the batcher queue.
     @param batcher The <code>Batcher</code> to add

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

@@ -40 +40 @@
 import net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo;
 import net.sf.basedb.core.dbengine.TableInfo.IndexInfo;
+import net.sf.basedb.core.hibernate.DbIndexWork;
 import net.sf.basedb.core.hibernate.EntityQueryWrapper;
 import net.sf.basedb.core.hibernate.ExecuteUpdateWork;
@@ -640 +641 @@
     }
     
-    if (mode.requireEmptyDatabase())
-    {
-      if (!isEmptyDatabase())
-      {
-        throw new BaseException("Database already has tables.");
-      }
+    boolean emptyDatabase = isEmptyDatabase();
+    if (mode.requireEmptyDatabase() && !emptyDatabase)
+    {
+      throw new BaseException("Database already has tables.");
+    }
+    else if (!mode.requireEmptyDatabase() && emptyDatabase)
+    {
+      throw new BaseException("Database is empty");
     }
 
@@ -700 +703 @@
                 {
                   isEmpty = false;
-                  log.error("Table '"+t.getName()+"' already exists; install aborted");
+                  log.debug("Table '"+t.getName()+"' already exists");
+                }
+                else
+                {
+                  log.debug("Table '"+t.getName()+"' doesn't exists");
                 }
                 tables.close();
@@ -1252 +1259 @@
     try
     {
-      session.close();
+      if (session.isOpen()) session.close();
     }
     catch(HibernateException ex)
@@ -2204 +2211 @@
     final boolean dropIndexes, final boolean updateIndexes)
   {
-    final boolean isVerbose = verbose && !silent;
     Session session = newSession();
-    
-    try
-    {
-      HibernateUtil.doWork(session, 
-        new Work()
-        {
-          @Override
-          public void execute(Connection connection) 
-            throws SQLException
-          {
-            Iterator<Table> tables = (Iterator<Table>)cfg.getTableMappings();
-            DatabaseMetaData metaData = connection.getMetaData();
-            while (tables.hasNext())
-            {
-              Table table = tables.next();
-              if (!silent)
-              {
-                System.out.println("=================");
-                System.out.println("Table   : " + table.getName());
-              }
-              if (isVerbose)
-              {
-                System.out.println("Catalog : " + table.getCatalog());
-                System.out.println("Schema  : " + table.getSchema());
-              }
-          
-              if (isVerbose)
-              {
-                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 (isVerbose && tiDb != null)
-              {
-                // 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 (ii.isUnique())
-                  {
-                    System.out.println("  Unique       : " + ii);
-                  }
-                  else
-                  {
-                    System.out.println("  Index        : " + ii);
-                  }
-                }
-              }
-              
-              if (isVerbose)
-              {
-                System.out.println("Hibernate information");
-                System.out.println("---------------------");
-              }
-              
-              TableInfo tiHib = new TableInfo(table, dialect);
-              if (isVerbose)
-              {
-                // Write all columns
-                for (ColumnInfo ci : tiHib.getColumns())
-                {
-                  System.out.println("  Column       : " + ci);
-                }
-                
-                // Write primary key
-                System.out.println("  Primary key  : " + tiHib.getPrimaryKey());
-              }
-              
-              // Write foreign keys
-              for (ForeignKeyInfo fk : tiHib.getForeignKeys())
-              {
-                if (!silent) 
-                {
-                  System.out.println("  Foreign key  : " + fk);
-                }
-                
-                // Check that an index for the foreign key exists
-                String indexName = tiDb.findIndexName(fk.getName(), fk.getFkColumns());
-                boolean indexExists = indexName != null;
-                String createSql = 
-                  dbEngine.getCreateIndexSql(table.getCatalog(), table.getSchema(),
-                    table.getName(), fk.getName(), fk.getFkColumns(), false);
-                boolean actionCreate = updateIndexes && !indexExists;
-                
-                if (!silent)
-                {
-                  System.out.println("    Indexed    : " + indexExists + (indexExists ? "(" + indexName + ")" : ""));
-                  System.out.println("    INDEX-SQL  : " + createSql);
-                  System.out.println("    Actions    : " + (actionCreate ? "CREATE INDEX" : ""));
-                }
-                if (actionCreate)
-                {
-                  Statement st = null;
-                  try
-                  {
-                    st = connection.createStatement();
-                    if (actionCreate) 
-                    {
-                      log.info("Creating foreign key index: + " + createSql);
-                      st.executeUpdate(createSql);
-                    }
-                    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);
-                      }
-                    }
-                  }
-                }
-              }
-          
-              // Write indexes and unique constraints
-              for (IndexInfo ii : tiHib.getIndexes())
-              {
-                if (!silent)
-                {
-                  if (ii.isUnique())
-                  {
-                    System.out.println("  Unique       : " + ii);
-                  }
-                  else
-                  {
-                    System.out.println("  Index        : " + ii);
-                  }
-                }
-                  
-                String dbName = tiDb.findIndexName(ii.getName(), ii.getColumns());
-                boolean exists = dbName != null;
-                boolean safeToDrop = exists && tiDb.safeToDrop(ii);
-          
-                String dropSql = exists ? 
-                  dbEngine.getDropIndexSql(table.getCatalog(), table.getSchema(), 
-                    table.getName(), dbName, ii.isUnique()) : "";
-                String createSql = 
-                  dbEngine.getCreateIndexSql(table.getCatalog(), table.getSchema(),
-                    table.getName(), table.getName() + "_" + ii.getName(), 
-                  ii.getColumns(), ii.isUnique());
-                boolean actionDrop = dropIndexes && exists && safeToDrop;
-                boolean actionCreate = updateIndexes && (actionDrop || !exists);
-                
-                if (!silent)
-                {
-                  System.out.println("    Exists     : " + exists + (exists ? "(" + dbName + ")" : ""));
-                  System.out.println("    Safe drop  : " + safeToDrop);
-                  System.out.println("    DROP-SQL   : " + dropSql);
-                  System.out.println("    CREATE-SQL : " + createSql);
-                  System.out.println("    Actions    : " + (actionDrop ? "DROP " : "") + 
-                    (actionCreate ? "CREATE" : ""));
-                }
-                if (actionDrop || actionCreate)
-                {
-                  Statement st = null;
-                  try
-                  {
-                    st = connection.createStatement();
-                    if (actionDrop) 
-                    {
-                      log.info("Dropping index: + " + dropSql);
-                      st.executeUpdate(dropSql);
-                    }
-                    if (actionCreate) 
-                    {
-                      log.info("Creating index: + " + createSql);
-                      st.executeUpdate(createSql);
-                    }
-                    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("");
-              }
-            }
-            
-          }
-        
-        }
-      );
+    try
+    {
+      HibernateUtil.doWork(session, new DbIndexWork(cfg, dialect, dbEngine, verbose, silent, dropIndexes, updateIndexes));
     }
     catch (SQLException ex)
-    {
-      
-    }
-    
+    {}
   }
 

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

@@ -1720 +1720 @@
       // propertyDef is JEP expression
       Expression e = Jep.formulaToExpression(propertyDef.substring(1), ch, rawCh, raw, rep, mrep);
-      s = Selects.expression(e, "jep" + System.identityHashCode(e));
+      s = Selects.expression(e, "jep" + dc.uniqueRandom());
     }
     else

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

@@ -515 +515 @@
             if (obj != null)
             {
-              String parameterName = "p" + System.identityHashCode(obj);
+              String parameterName = "p" + dc.uniqueRandom();
               Type theValueType = obj instanceof Double ? Type.DOUBLE : getValueType();
               if (theValueType == Type.TIMESTAMP) theValueType = Type.DATE;
@@ -526 +526 @@
         else
         {
-          String parameterName = "p" + System.identityHashCode(this);
+          String parameterName = "p" + dc.uniqueRandom();
           Expression parameter = null;
           if (getValue() != null)
@@ -605 +605 @@
     else
     {
-      String parameterName = "p" + System.identityHashCode(this);
+      String parameterName = "p" + dc.uniqueRandom();
       Expression parameter = null;
       if (getValue() != null && !operator.isListOperator())
@@ -632 +632 @@
             if (obj != null)
             {
-              parameterName = "p" + System.identityHashCode(obj);
+              parameterName = "p" + dc.uniqueRandom();
               Type theValueType = obj instanceof Double ? Type.DOUBLE : getValueType();
               Expression e = Expressions.parameter(parameterName, obj, theValueType);
@@ -674 +674 @@
         String entityCollection = m.group(1);
         String collectionFilter = m.group(2);
+        boolean rewriteNullFilter = false;
+        if (collectionFilter.startsWith("%"))
+        {
+          collectionFilter = collectionFilter.substring(1);
+          rewriteNullFilter = true;
+        }
         
         /*
@@ -732 +738 @@
         }
         
+        boolean notContains = subfilterOperator != operator;
+        Operator actualOperator = subfilterOperator;
+        String actualValue = getValue();
+        if (rewriteNullFilter && actualValue == null && subfilterOperator == Operator.EQ)
+        {
+          // =ANY(... WHERE <property> IS NULL) is rewritten as
+          // <>ALL(... WHERE <property> LIKE '%') 
+          actualOperator = Operator.LIKE;
+          actualValue = "%";
+          notContains = !notContains;
+        }
+        
         // Restrict the subquery
         PropertyFilter pp = new PropertyFilter("$" + thisAlias + "." + collectionFilter, 
-            subfilterOperator, getValue(), getValueType());
+            actualOperator, actualValue, getValueType());
         subquery.restrict(pp.getRestriction(dc, query));
         
         // Create the main restriction
-        if (subfilterOperator != operator)
+        if (notContains)
         {
           // "not contains": root-entity <> ALL(subquery)
@@ -807 +825 @@
             if (obj != null)
             {
-              parameterName = "p" + System.identityHashCode(obj);
+              parameterName = "p" + dc.uniqueRandom();
               Type theValueType = obj instanceof Double ? Type.DOUBLE : getValueType();
               if (theValueType == Type.TIMESTAMP) theValueType = Type.DATE;
@@ -859 +877 @@
       propertyExpression = ItemContext.getDynamicExpression(dc, property);
     }
-    String parameterName = "p" + System.identityHashCode(this);
+    String parameterName = "p" + dc.uniqueRandom();
     
     String value = getValue();
@@ -900 +918 @@
           if (obj != null)
           {
-            parameterName = "p" + System.identityHashCode(obj);
+            parameterName = "p" + dc.uniqueRandom();
             e = Expressions.parameter(parameterName, obj);
           }

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

@@ -161 +161 @@
   {
     List<String> files = Application.getRawDataTypeFiles();
+    Set<String> usedNames = new HashSet<String>();
     try
     {
@@ -166 +167 @@
       {
         Document dom = XmlUtil2.getValidatedXml(RawDataTypes.class.getResource(xmlFile), dtdFile);
-        loadRawDataTypes(dom, xmlFile);
+        loadRawDataTypes(usedNames, dom, xmlFile);
         log.info("Loaded raw data types from file: " + xmlFile);
       }
@@ -334 +335 @@
     {@link #rawDataTypes} map.
   */
-  private static void loadRawDataTypes(Document dom, String xmlFile)
+  private static void loadRawDataTypes(Set<String> usedNames, Document dom, String xmlFile)
   {
     List<Element> rawDataTypeTags = dom.getRootElement().getChildren("raw-data-type");
     DbEngine engine = HibernateUtil.getDbEngine();
-    Set<String> usedNames = new HashSet<String>();
     for (Element el : rawDataTypeTags)
     {

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

@@ -31 +31 @@
 import net.sf.basedb.core.data.UserData;
 import net.sf.basedb.core.dbengine.DbEngine;
+import net.sf.basedb.core.hibernate.DbIndexWork;
 import net.sf.basedb.core.hibernate.GetCurrentCatalogWork;
 import net.sf.basedb.core.hibernate.SchemaExistsWork;
@@ -44 +45 @@
 import org.hibernate.boot.registry.StandardServiceRegistryBuilder;
 import org.hibernate.cfg.Configuration;
+import org.hibernate.dialect.Dialect;
 import org.hibernate.service.ServiceRegistry;
 
@@ -138 +140 @@
       // but MySQL don't have schemas so actual catalog is a combined of both
       DbEngine dbEngine = HibernateUtil.getDbEngine();
+      Dialect dialect = HibernateUtil.getDialect();
       String actualCatalog = dbEngine.getCatalogName(catalog, schema);
       String actualSchema = dbEngine.getSchemaName(catalog, schema);
 
-      if (log.isDebugEnabled()) log.debug("Actual catalog/schema: " + actualCatalog + "/" + actualSchema);
-      
+      if (log.isDebugEnabled()) log.debug("Actual catalog/schema: " + actualCatalog + "/" + actualSchema);    
       if (actualCatalog != null)
       {
@@ -188 +190 @@
       if (mode != null)
       {
+        // Generates tables and most other things
         SchemaGenerator schemaGenerator = 
-          new SchemaGenerator(cfg, HibernateUtil.getDialect(), dbEngine, mode, null);
+          new SchemaGenerator(cfg, dialect, dbEngine, mode, null);
         session.doWork(schemaGenerator);
+        // Generates missing indexes
+        DbIndexWork indexGenerator = new DbIndexWork(cfg, dialect, dbEngine, false, true, false, true);
+        session.doWork(indexGenerator);
+        // Update schema version in BASE
         if (config.getAppId() != null)
         {
@@ -196 +203 @@
         }
         HibernateUtil.commit(tx);
+        tx = null;
       }
       
@@ -228 +236 @@
   /**
     Create a new Hibernate session for the given session factory that
-    is piggy-backed on the given DbControl transaction.
+    is piggy-backed on the given DbControl transaction. 
+    
+    Note that the life-cycle of the returned session is managed by the
+    DbControl. There is no need to flush or close the session since this
+    is done automatically and may cause exceptions if done when not needed.
     
     @param A session builder (eg. SessionFactory.withOptions())

trunk/src/core/net/sf/basedb/core/data/ExtractData.java

@@ -75 +75 @@
   }
   
+  private Set<DerivedBioAssayData> derivedBioAssays;
+  /**
+    This is the inverse end. 
+    @see DerivedBioAssayData#getExtract()
+    @since 3.4
+    @hibernate.set lazy="true" inverse="true"
+    @hibernate.collection-key column="`extract_id`"
+    @hibernate.collection-one-to-many class="net.sf.basedb.core.data.DerivedBioAssayData"
+  */
+  Set<DerivedBioAssayData> getDerivedBioAssays()
+  {
+    return derivedBioAssays;
+  }
+  void setDerivedBioAssays(Set<DerivedBioAssayData> derivedBioAssays)
+  {
+    this.derivedBioAssays = derivedBioAssays;
+  }
+
 }

trunk/src/core/net/sf/basedb/core/dbengine/MySQLEngine.java

@@ -27 +27 @@
 import java.util.regex.Pattern;
 
+import net.sf.basedb.core.hibernate.SchemaGenerator;
+
+import org.hibernate.dialect.Dialect;
 import org.hibernate.mapping.PersistentClass;
 
@@ -211 +214 @@
 
   /**
+    Fix "alter table ... drop constraint ..." statements that are generated
+    incorrectly by Hibernate.
+    @since 3.4
+  */
+  @Override
+  public String inspectSchemaGenerationSQL(String sql, Dialect dialect,
+      SchemaGenerator.Mode mode)
+  {
+    sql = super.inspectSchemaGenerationSQL(sql, dialect, mode);
+    if (sql != null && sql.startsWith("alter table") && sql.contains("drop constraint"))
+    {
+      sql = sql.replace("drop constraint", "drop index");
+    }
+    return sql;
+  }
+
+  
+  /**
     Return true.
   */

trunk/src/core/net/sf/basedb/core/dbengine/PostgresDbEngine.java

@@ -77 +77 @@
     Generate <code>ALTER TABLE &lt;schema&gt;.&lt;table&gt; ADD CONSTRAINT &lt;name&gt;
     UNIQUE (&lt;columns&gt)</code> for a unique index, 
-    <code>CREATE INDEX &lt;schema&gt;.&lt;name&gt; ON &lt;schema&gt;.&lt;table&gt; (&lt;columns&gt;)</code>
+    <code>CREATE INDEX &lt;name&gt; ON &lt;schema&gt;.&lt;table&gt; (&lt;columns&gt;)</code>
     for other indexes.
     The catalog parameter is not supported.
@@ -98 +98 @@
     {
       sql.append("CREATE INDEX ");
-      if (schema != null) sql.append(getQuotedName(schema)).append(".");
       sql.append(getQuotedName(name)).append(" ON ");
       if (schema != null) sql.append(getQuotedName(schema)).append(".");

trunk/src/core/net/sf/basedb/core/dbengine/TableInfo.java

@@ -28 +28 @@
 import java.sql.Statement;
 import java.sql.Types;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -115 +116 @@
   }
   
+  
   /**
     Create table info by reading JDBC metadata from the current database
@@ -123 +125 @@
   */
   public TableInfo(Table table, DatabaseMetaData metaData)
+      throws SQLException
+  {
+    this(table, metaData, null, null);
+  }
+
+  /**
+    Create table info by reading JDBC metadata from the current database
+    
+    @param table The Hibernate table object
+    @param metaData The JDBC metadata connected to the current database
+    @param defaultCatalog Catalog to use if the table doesn't specify a catalog
+    @param defaultSchema Schema to use if the table doesn't specify a catalog
+    @throws SQLException If there is an error
+    @since 3.4
+  */
+  public TableInfo(Table table, DatabaseMetaData metaData, String defaultCatalog, String defaultSchema)
     throws SQLException
   {
     this(table);
     
-    ResultSet tables = metaData.getTables(table.getCatalog(), table.getSchema(), table.getName(), null);
+    String catalog = table.getCatalog();
+    if (catalog == null) catalog = defaultCatalog;
+    String schema = table.getSchema();
+    if (schema == null) schema = defaultSchema;
+    
+    ResultSet tables = metaData.getTables(catalog, schema, table.getName(), null);
     existsInDb = tables.next();
     tables.close();
-    
     if (!existsInDb) return;
     
     // Load column information
-    ResultSet sqlColumns = metaData.getColumns(table.getCatalog(), table.getSchema(), table.getName(), "%"); 
+    ResultSet sqlColumns = metaData.getColumns(catalog, schema, table.getName(), "%"); 
     while (sqlColumns.next())
     {
@@ -147 +169 @@
     
     // Load primary key information
-    ResultSet sqlPK = metaData.getPrimaryKeys(table.getCatalog(), table.getSchema(), table.getName());
+    ResultSet sqlPK = metaData.getPrimaryKeys(catalog, schema, table.getName());
     Set<String> pkColumns = new LinkedHashSet<String>();
     String pkName = null;
@@ -162 +184 @@
     
     // Load foreign keys
-    ResultSet sqlFK = metaData.getImportedKeys(table.getCatalog(), table.getSchema(), table.getName());
+    ResultSet sqlFK = metaData.getImportedKeys(catalog, schema, table.getName());
     Map<String, ForeignKeyInfo> fkInfo = new HashMap<String, ForeignKeyInfo>();
     while (sqlFK.next())
@@ -184 +206 @@
     
     // Load indexes
-    ResultSet sqlIndexes = metaData.getIndexInfo(table.getCatalog(), table.getSchema(), table.getName(), false, true);
+    ResultSet sqlIndexes = metaData.getIndexInfo(catalog, schema, table.getName(), false, true);
     Map<String, IndexInfo> indexInfo = new HashMap<String, IndexInfo>();
     while (sqlIndexes.next())
@@ -191 +213 @@
       String column = makeSafe(sqlIndexes.getString("COLUMN_NAME"));
       boolean isUnique = !sqlIndexes.getBoolean("NON_UNIQUE");
-      
       IndexInfo ii = indexInfo.get(indexName);
       if (ii == null)
@@ -441 +462 @@
     }
     return null;
+  }
+  
+  /**
+    Find all indexes with the given set of columns. Used for
+    getting rid of duplicates.
+    @param columns A set containing the column names that should be present in 
+      the index
+    @return A list with the index information or an empty list of no index is found
+    @since 3.4
+  */
+  public List<IndexInfo> findAll(Set<String> columns)
+  {
+    List<IndexInfo> all = new ArrayList<IndexInfo>();
+    for (IndexInfo iiInfo : indexes)
+    {
+      if (columns.equals(iiInfo.getColumns())) all.add(iiInfo);
+    }
+    return all;
   }
 

trunk/src/core/net/sf/basedb/core/hibernate/SchemaGenerator.java

@@ -120 +120 @@
       int numDone = 0;
       int interval = Math.max(1, numStatements / 30);
+      
       for (SchemaUpdateScript script : allSql)
       {
@@ -131 +132 @@
           }
           log.debug("Executing: " + actualSql);
-          stmt.executeUpdate(actualSql);
-          //System.out.println(actualSql);
+          try
+          {
+            stmt.executeUpdate(actualSql);
+          }
+          catch (SQLException | RuntimeException ex)
+          {
+            if (script.isQuiet())
+            {
+              log.info("Ignoring quiet SQL: "+ actualSql, ex);
+            }
+            else
+            {
+              throw ex;
+            }
+          }
           if (progress != null)
           {
@@ -153 +167 @@
       }
     }
-    catch (SQLException ex)
+    catch (SQLException | RuntimeException ex)
     {
       log.error("Schema update failed", ex);

trunk/src/core/net/sf/basedb/core/signal/AbstractSignalReceiver.java

@@ -28 +28 @@
 import java.util.HashMap;
 import java.util.Map;
+import java.util.WeakHashMap;
+
+import net.sf.basedb.core.Application;
 
 /**
@@ -76 +79 @@
   */
   private Map<String, SignalHandler> handlers;
+  private Map<SignalHandler, String> handlerIds;
   private String receiverId;
   private Thread notifyThread;
@@ -98 +102 @@
   {
     handlers = Collections.synchronizedMap(new HashMap<String, SignalHandler>());
+    handlerIds = new WeakHashMap<SignalHandler, String>();
     this.receiverId = receiverId;
     logger.info("Initializing signal receiver: id=" + receiverId);
@@ -165 +170 @@
   {
     if (notifyThread != null) throw new SignalException("Signal receiver is shutting down.");
+    String localId = getLocalSignalHandlerId(handler);
     String globalId = getGlobalSignalId(handler);
-    String localId = getLocalSignalHandlerId(handler);
     if (handlers != null) 
     {
-      if (handlers.containsKey(localId))
-      {
-        throw new SignalException("A handler with ID '" + localId + "' is already registered: "
-          + handlers.get(localId));
-      }
-      handlers.put(localId, handler);
+      synchronized (handlers)
+      {
+        if (handlers.containsKey(localId))
+        {
+          throw new SignalException("A handler with ID '" + localId + "' is already registered: "
+            + handlers.get(localId));
+        }
+        handlers.put(localId, handler);
+      }
     }
 
@@ -180 +188 @@
       "; global id=" + globalId + "; local id=" + localId);
     logger.debug("Current number of registered signal handlers: " + 
-      (handlers == null ? 0 : handlers.size()));
+      (handlers == null ? "0/0" : handlers.size()+"/"+handlerIds.size()));
     return globalId;
   }
@@ -196 +204 @@
     if (handlers != null) 
     {
-      handlers.remove(localId);
+      synchronized (handlers)
+      {
+        handlers.remove(localId);
+        handlerIds.remove(handler);
+      }
       // If called from the close() method() this is waiting for
       if (notifyThread != null && handlers.size() == 0)
@@ -205 +217 @@
     }
     logger.debug("Current number of registered signal handlers: " + 
-      (handlers == null ? 0 : handlers.size()));
+      (handlers == null ? "0/0" : handlers.size()+"/"+handlerIds.size()));
   }
   
@@ -274 +286 @@
   /**
     Get the local signal handler id of the given signal handler.
-    This implementation simply return the system hashcode for the
-    handler. The returned ID must be unique among the registered
-    signal handlers.
+    This implementation generates a unique ID for the handler.
     @param handler The handler to get the id for
     @return The local handler id
@@ -282 +292 @@
   protected String getLocalSignalHandlerId(SignalHandler handler)
   {
-    return String.valueOf(System.identityHashCode(handler));
+    if (handlerIds == null) return String.valueOf(System.identityHashCode(handler));
+    String id = handlerIds.get(handler);
+    if (id == null)
+    {
+      synchronized (handlers) 
+      {
+        while (true)
+        {
+          id = Application.generateRandomId(4);
+          if (!handlers.containsKey(id)) break;
+        }
+        handlerIds.put(handler, id);
+      }
+    }
+    return id;
   }
   

trunk/src/core/net/sf/basedb/util/timer/ThreadTimerTask.java

@@ -85 +85 @@
           public void run()
           {
-            task.run();
-            isExecuting = false;
+            try
+            {
+              task.run();
+            }
+            finally
+            {
+              isExecuting = false;
+            }
           }
         }

trunk/src/test/TestAnyToAny.java

@@ -71 +71 @@
     test_exists(sampleId, "third", false);
 
+    // Test relinking to a new item in a single transaction
+    int sampleId2 = test_relink(id);
+    
     // Standard test: Delete
     if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
@@ -82 +85 @@
     
     TestSample.test_delete(sampleId);
+    TestSample.test_delete(sampleId2);
     TestFile.test_delete(fileId1);
     TestFile.test_delete(fileId2);
@@ -121 +125 @@
   }
 
+  static int test_relink(int id)
+  {
+    if (id == 0) return 0;
+    int sampleId = 0;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Sample s = Sample.getNew(dc);
+      dc.saveItem(s);
+
+      AnyToAny a = AnyToAny.getById(dc, id);
+      a.setTo(s);
+      a.setDescription("Relinked "+new Date());
+      dc.commit();
+      
+      sampleId = s.getId();
+      dc = TestUtil.getDbControl();
+      dc.reattachItem(a, false);
+      write_item(0, a);
+      if (a.getToId() != sampleId)
+      {
+        throw new BaseException("Relink failed: " + a.getToId() + " != " + sampleId);
+      }
+      write("--Relink any-to-any OK");
+    }
+    catch (Throwable ex)
+    {
+      write("--Relink any-to-any FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+    return sampleId;    
+  }
+  
   static void test_load(int id)
   {
@@ -185 +228 @@
   {
     if (!TestUtil.getSilent()) System.out.println(i+":\t"+a.getId()+"\t"+a.getName()+"\t"+
-      a.getDescription()+"\t"+a.getFrom()+"\t"+a.getTo());
+      a.getDescription()+"\t"+a.getFromType()+"["+a.getFromId()+"]\t"+a.getToType()+"["+a.getToId()+"]");
   }
   static void write(String message)

trunk/src/test/TestJarClassLoader.java

@@ -43 +43 @@
     write("++Testing Jar class loader");
     
-    test_load("JarPlugin.jar", "JarPlugin", false, true);
+    test_load("JarPlugin.jar", "JarPlugin", false, true, false);
     test_resource("JarPlugin.jar", "META-INF/MANIFEST.MF", false, true);
     
     // Test parent delegation
-    test_load("JarPlugin.jar", "affymetrix.calvin.exception.CalvinException", false, true);
+    test_load("JarPlugin.jar", "affymetrix.calvin.exception.CalvinException", false, true, false);
     test_resource("JarPlugin.jar", "org/hibernate/hibernate-configuration-3.0.dtd", false, false);
-    test_load("JarPlugin.jar", "affymetrix.calvin.exception.CalvinException", true, false);
+    test_load("JarPlugin.jar", "affymetrix.calvin.exception.CalvinException", true, false, true);
     test_resource("JarPlugin.jar", "org/hibernate/hibernate-configuration-3.0.dtd", true, false);
     
@@ -57 +57 @@
 
   static void test_load(String jarPath, String className, 
-      boolean delegateFirst, boolean expectLoadedByJarClassLoader)
+      boolean delegateFirst, boolean expectLoadedByJarClassLoader, boolean useNewInstance)
   {
     try
     {
-      JarClassLoader cl = (JarClassLoader)JarClassLoader.getInstance(jarPath);
+      JarClassLoader cl = useNewInstance ? 
+        (JarClassLoader)JarClassLoader.newInstance(jarPath) : 
+        (JarClassLoader)JarClassLoader.getInstance(jarPath);
       cl.setDelegateFirst(delegateFirst);
       Class c = cl.loadClass(className);

trunk/www/WEB-INF/base.tld

@@ -62 +62 @@
       <rtexprvalue>true</rtexprvalue>
     </attribute>
+    <attribute>
+      <name>noskin</name>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
   </tag>
 

trunk/www/admin/annotationtypes/edit_annotationtype.jsp

@@ -861 +861 @@
                 data-initial-items="[<%=HTML.encodeTags(jsonUsableUnits.toJSONString()) %>]"
                 data-remove-to="allUnits"
-                size="10" multiple style="width: 100%;"
+                size="10" multiple style="width: calc(100% - 10px);"
                 title="If no unit is selected, all units can be used"
               >
@@ -886 +886 @@
             </td>
             <td style="width: 50%;">
-              <select name="allUnits" id="allUnits" size="10" multiple style="width: 100%;">
+              <select name="allUnits" id="allUnits" size="10" multiple style="width: calc(100% - 10px);">
               </select>
             </td>

trunk/www/admin/extensions/tree.jsp

@@ -49 +49 @@
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 <%!
-JSONObject newJoustExtensionPoint(JSONObject jsonParent, ExtensionsControl ec, ExtensionPoint ep, ExtensionsFile ef)
+JSONObject newJoustExtensionPoint(DbControl dc, JSONObject jsonParent, ExtensionsControl ec, ExtensionPoint ep, ExtensionsFile ef)
 {
   String id = ep.getId();
@@ -59 +59 @@
     icon = "ExtensionPointError";
   }
-  JSONObject json = newJoustEntry(jsonParent, icon, HTML.encodeTags(name), id);
+  JSONObject json = newJoustEntry(dc, jsonParent, icon, HTML.encodeTags(name), id);
   json.put("type", "extension-point");
   return json;
 }
 
-JSONObject newJoustExtension(JSONObject jsonParent, ExtensionsControl ec, Extension ext, ExtensionsFile ef, boolean inGroup, boolean showFile)
+JSONObject newJoustExtension(DbControl dc, JSONObject jsonParent, ExtensionsControl ec, Extension ext, ExtensionsFile ef, boolean inGroup, boolean showFile)
 {
   String id = ext.getId();
@@ -88 +88 @@
   }
   
-  JSONObject json = newJoustEntry(jsonParent, icon, name, id);
+  JSONObject json = newJoustEntry(dc, jsonParent, icon, name, id);
   json.put("type", "extension");
   return json;
 }
 
-JSONObject newJoustFile(JSONObject jsonParent, ExtensionsFile ef, ExtensionsControl ec)
+JSONObject newJoustFile(DbControl dc, JSONObject jsonParent, ExtensionsFile ef, ExtensionsControl ec)
 {
   String efName = ef.getName();
@@ -107 +107 @@
   if (ef.checkModified()) icon += "Modified";
   
-  JSONObject json = newJoustEntry(jsonParent, icon, HTML.encodeTags(efName), efName);
+  JSONObject json = newJoustEntry(dc, jsonParent, icon, HTML.encodeTags(efName), efName);
   json.put("id", efName);
   json.put("type", "file");
@@ -114 +114 @@
 }
 
-JSONObject newJoustExtensionGroup(JSONObject jsonParent, ExtensionsControl ec, Extension ext, String groupId)
+JSONObject newJoustExtensionGroup(DbControl dc, JSONObject jsonParent, ExtensionsControl ec, Extension ext, String groupId)
 {
   String id = ext.getId();
@@ -120 +120 @@
   String name = about == null || about.getName() == null ? id : about.getName();
   String icon = "Folder";
-  JSONObject json = newJoustEntry(jsonParent, icon, HTML.encodeTags(name), groupId);
+  JSONObject json = newJoustEntry(dc, jsonParent, icon, HTML.encodeTags(name), groupId);
   json.put("type", "group");
   return json;
 }
 
-JSONObject newJoustPlugin(JSONObject jsonParent, ExtensionsControl ex, PluginInfo info, ExtensionsFile ef)
+JSONObject newJoustPlugin(DbControl dc, JSONObject jsonParent, ExtensionsControl ex, PluginInfo info, ExtensionsFile ef)
 {
   String id = info.getClassName();
@@ -140 +140 @@
   }
   
-  JSONObject json = newJoustEntry(jsonParent, icon, name, id);
+  JSONObject json = newJoustEntry(dc, jsonParent, icon, name, id);
   json.put("type", "plugin");
   json.put("className", info.getClassName());
@@ -146 +146 @@
 }
 
-JSONObject newJoustEntry(JSONObject jsonParent, String icon, String text, String id)
+JSONObject newJoustEntry(DbControl dc, JSONObject jsonParent, String icon, String text, String id)
 {
   JSONObject jsonJoust = new JSONObject();
   jsonJoust.put("icon", icon);
   jsonJoust.put("text", text);
-  jsonJoust.put("id", "joust-"+System.identityHashCode(jsonJoust));
+  jsonJoust.put("id", "joust-"+dc.uniqueRandom());
   jsonJoust.put("externalId", id);
   if (jsonParent != null)
@@ -172 +172 @@
 DbControl dc = null;
 
-// Build the Joust menu tree
-JSONArray jsonJoust = new JSONArray();
-
-// Two ROOT items:
-JSONObject jsonByExtPoint = newJoustEntry(null, "Root", "By extension point", "root.by-extension-point");
-jsonByExtPoint.put("isOpen", 1);
-JSONObject jsonByFile = newJoustEntry(null, "Root", "By file", "root.by-file");
-jsonByFile.put("isOpen", 1);
-
-// Group some extension points inside sub-folders
-JSONObject jsonToolbars = newJoustEntry(jsonByExtPoint, "Folder", "Toolbars", "by-extension-point.toolbars");
-JSONObject jsonEditDialogs = newJoustEntry(jsonByExtPoint, "Folder", "Edit dialogs", "by-extension-point.edit-dialogs");
-JSONObject jsonListColumns = newJoustEntry(jsonByExtPoint, "Folder", "List columns", "by-extension-point.list-columns");
-
-jsonJoust.add(jsonByExtPoint);
-jsonJoust.add(jsonByFile);
-
-ExtensionsControl ec = ExtensionsControl.get(dc);
-List<ExtensionPoint<?>> extensionPoints = ec.getExtensionPoints();
-Collections.sort(extensionPoints, Registry.EXTENSIONPOINT_COMPARATOR);
-for (ExtensionPoint ep : extensionPoints)
-{
-  String id = ep.getId();
-  JSONObject jsonParent = jsonByExtPoint;
-  if (id.startsWith("net.sf.basedb.clients.web.toolbar.")) jsonParent = jsonToolbars;
-  if (id.startsWith("net.sf.basedb.clients.web.tabcontrol.edit.")) jsonParent = jsonEditDialogs;
-  if (id.startsWith("net.sf.basedb.clients.web.onsave.")) jsonParent = jsonEditDialogs;
-  if (id.startsWith("net.sf.basedb.clients.web.listcolumn.")) jsonParent = jsonListColumns;
-  
-  JSONObject jsonEp = newJoustExtensionPoint(jsonParent, ec, ep, ec.getFileByObjectKey(new ExtensionPointKey(ep)));
-
-  List<Extension<?>> extensions = ec.getExtensions(ep.getId());
-  Collections.sort(extensions, Registry.EXTENSION_COMPARATOR);
-  for (Extension ext : extensions)
-  {
-    newJoustExtension(jsonEp, ec, ext, ec.getFileByObjectKey(new ExtensionKey(ext)), false, true);
-  }
-}
-
-for (ExtensionsFile ef : ec.getFiles())
-{
-  if (!ef.isInstalled()) continue;
-  
-  JSONObject jsonFile = newJoustFile(jsonByFile, ef, ec);
-
-  List<ExtensionPoint> eps = ef.getObjectsOfClass(ExtensionPoint.class);
-  Collections.sort(eps, Registry.EXTENSIONPOINT_COMPARATOR);
-  for (ExtensionPoint ep : eps)
-  {
-    newJoustExtensionPoint(jsonFile, ec, ep, ef);
-  }
-  
-  List<Extension> exts = ef.getObjectsOfClass(Extension.class);
-  Collections.sort(exts, Registry.EXTENSION_COMPARATOR);
-  String currentGroupId = null;
-  JSONObject jsonGroup = null;
-  
-  for (Extension ext : exts)
-  {
-    int groupIndex = ext.getId().indexOf(":");
-    // ID:s containing ':' should be grouped
-    if (groupIndex > 0)
-    {
-      String groupId = ext.getId().substring(0, groupIndex);
-      if (!groupId.equals(currentGroupId))
+try
+{
+  dc = sc.newDbControl();
+  // Build the Joust menu tree
+  JSONArray jsonJoust = new JSONArray();
+  
+  // Two ROOT items:
+  JSONObject jsonByExtPoint = newJoustEntry(dc, null, "Root", "By extension point", "root.by-extension-point");
+  jsonByExtPoint.put("isOpen", 1);
+  JSONObject jsonByFile = newJoustEntry(dc, null, "Root", "By file", "root.by-file");
+  jsonByFile.put("isOpen", 1);
+  
+  // Group some extension points inside sub-folders
+  JSONObject jsonToolbars = newJoustEntry(dc, jsonByExtPoint, "Folder", "Toolbars", "by-extension-point.toolbars");
+  JSONObject jsonEditDialogs = newJoustEntry(dc, jsonByExtPoint, "Folder", "Edit dialogs", "by-extension-point.edit-dialogs");
+  JSONObject jsonListColumns = newJoustEntry(dc, jsonByExtPoint, "Folder", "List columns", "by-extension-point.list-columns");
+  
+  jsonJoust.add(jsonByExtPoint);
+  jsonJoust.add(jsonByFile);
+  
+  ExtensionsControl ec = ExtensionsControl.get(dc);
+  List<ExtensionPoint<?>> extensionPoints = ec.getExtensionPoints();
+  Collections.sort(extensionPoints, Registry.EXTENSIONPOINT_COMPARATOR);
+  for (ExtensionPoint ep : extensionPoints)
+  {
+    String id = ep.getId();
+    JSONObject jsonParent = jsonByExtPoint;
+    if (id.startsWith("net.sf.basedb.clients.web.toolbar.")) jsonParent = jsonToolbars;
+    if (id.startsWith("net.sf.basedb.clients.web.tabcontrol.edit.")) jsonParent = jsonEditDialogs;
+    if (id.startsWith("net.sf.basedb.clients.web.onsave.")) jsonParent = jsonEditDialogs;
+    if (id.startsWith("net.sf.basedb.clients.web.listcolumn.")) jsonParent = jsonListColumns;
+    
+    JSONObject jsonEp = newJoustExtensionPoint(dc, jsonParent, ec, ep, ec.getFileByObjectKey(new ExtensionPointKey(ep)));
+  
+    List<Extension<?>> extensions = ec.getExtensions(ep.getId());
+    Collections.sort(extensions, Registry.EXTENSION_COMPARATOR);
+    for (Extension ext : extensions)
+    {
+      newJoustExtension(dc, jsonEp, ec, ext, ec.getFileByObjectKey(new ExtensionKey(ext)), false, true);
+    }
+  }
+  
+  for (ExtensionsFile ef : ec.getFiles())
+  {
+    if (!ef.isInstalled()) continue;
+    
+    JSONObject jsonFile = newJoustFile(dc, jsonByFile, ef, ec);
+  
+    List<ExtensionPoint> eps = ef.getObjectsOfClass(ExtensionPoint.class);
+    Collections.sort(eps, Registry.EXTENSIONPOINT_COMPARATOR);
+    for (ExtensionPoint ep : eps)
+    {
+      newJoustExtensionPoint(dc, jsonFile, ec, ep, ef);
+    }
+    
+    List<Extension> exts = ef.getObjectsOfClass(Extension.class);
+    Collections.sort(exts, Registry.EXTENSION_COMPARATOR);
+    String currentGroupId = null;
+    JSONObject jsonGroup = null;
+    
+    for (Extension ext : exts)
+    {
+      int groupIndex = ext.getId().indexOf(":");
+      // ID:s containing ':' should be grouped
+      if (groupIndex > 0)
       {
-        currentGroupId = groupId;
-        jsonGroup = newJoustExtensionGroup(jsonFile, ec, ext, currentGroupId);
+        String groupId = ext.getId().substring(0, groupIndex);
+        if (!groupId.equals(currentGroupId))
+        {
+          currentGroupId = groupId;
+          jsonGroup = newJoustExtensionGroup(dc, jsonFile, ec, ext, currentGroupId);
+        }
       }
-    }
-    else
-    {
-      currentGroupId = null;
-      jsonGroup = null;
-    }
-    newJoustExtension(jsonGroup != null ? jsonGroup : jsonFile, ec, ext, ef, jsonGroup != null, false);
-  }
-  List<PluginInfo> plugins = ef.getObjectsOfClass(PluginInfo.class);
-  Collections.sort(plugins, PluginInfo.NAME_COMPARATOR);
-  for (PluginInfo info : plugins)
-  {
-    newJoustPlugin(jsonFile, ec, info, ef);
-  }
-}
-
-
-try
-{
-  dc = sc.newDbControl();
+      else
+      {
+        currentGroupId = null;
+        jsonGroup = null;
+      }
+      newJoustExtension(dc, jsonGroup != null ? jsonGroup : jsonFile, ec, ext, ef, jsonGroup != null, false);
+    }
+    List<PluginInfo> plugins = ef.getObjectsOfClass(PluginInfo.class);
+    Collections.sort(plugins, PluginInfo.NAME_COMPARATOR);
+    for (PluginInfo info : plugins)
+    {
+      newJoustPlugin(dc, jsonFile, ec, info, ef);
+    }
+  }
   %>
   <base:page title="" type="iframe">

trunk/www/admin/roles/edit_role.jsp

@@ -199 +199 @@
             ><label for="act_as_another_user">Act as another user</label><br>
           <input type="checkbox" name="select_jobagent" id="select_jobagent"
-            <%=PermissionUtil.getPermissionCode(EnumSet.of(Permission.SELECT_JOBAGENT))%>
+            value="<%=PermissionUtil.getPermissionCode(EnumSet.of(Permission.SELECT_JOBAGENT))%>"
             <%=hasSelectJobagent ? "checked" : ""%>
             ><label for="select_jobagent">Select job agent for jobs</label><br>

trunk/www/common/annotations/inherit.js

@@ -48 +48 @@
   inherit.onSelect = function(event)
   {
+    var frm = document.forms['annotations'];
     var menuItem = event.target.item;
     if (menuItem.type == 'annotation')
@@ -53 +54 @@
       Doc.element('annotationType').innerHTML = menuItem.annotationType;
       Doc.element('annotationValues').innerHTML = menuItem.values;
+      menuItem.modified = menuItem.inherited != frm[menuItem.id].checked;
     }
     else if (menuItem.type == 'annotation-set')
@@ -58 +60 @@
       if (menuItem.children)
       {
-        var frm = document.forms['annotations'];
         var checked = frm[menuItem.id].checked;
         // If the annotation-set is checked all child items should
@@ -67 +68 @@
         {
           var child = menuItem.children[childNo];
-          frm[child.id].checked = checked || child.inherited;
+          frm[child.id].checked = checked || (child.inherited != child.modified);
           frm[child.id].disabled = checked;
         }
@@ -73 +74 @@
     }
     
-    inherit.saveInheritedAnnotationsToForm();
   }
   
@@ -86 +86 @@
     
     var aFrm = document.forms['annotations'];
-    var menuElements = tree.getElementsByClassName('menuitem');
+    var menuElements = tree.getElementsByClassName('joustitem');
     for (var menuNo = 0; menuNo < menuElements.length; menuNo++)
     {
@@ -120 +120 @@
       }
     }
-    
     if (frm.addedAnnotations)
     {

trunk/www/common/columns/configure.js

@@ -122 +122 @@
   {
     var option = new Option(column.title, column.id);
+    option.title = column.title;
     if (column.alwaysShow)
     {

trunk/www/common/overview/failures.js

@@ -43 +43 @@
     else
     {
-      var failureId = Data.get(target, 'failure-id');
       var nodeId = Data.get(target, 'node-id');
       window.parent.frames['tree'].Tree.selectNode(nodeId);

trunk/www/common/overview/failures.jsp

@@ -157 +157 @@
           {
             index++;
-            String failureId = "F" + System.identityHashCode(failure);
             Node node = failure.getNode();
             BasicItem item = node.getItem();
             %>
-            <tr id="<%=failureId%>" class="failure highlight auto-init" data-auto-init="failure"
-              data-failure-id="<%=failureId%>" data-node-id="<%=node.getId()%>"
+            <tr class="failure highlight auto-init" data-auto-init="failure"
+              data-node-id="<%=node.getId()%>"
               <%
               if (item != null)

trunk/www/common/overview/options.jsp

@@ -82 +82 @@
     width: 17em;
     max-width: 17em;
+  }
+  
+  .special select
+  {
+    min-width: 14em;
   }
   

trunk/www/common/plugin/parse_file.jsp

@@ -446 +446 @@
       </div>
       
-      <div class="absolutefull topborder" style="top: 2em;">
-
-        <table class="fullform input100 special larger">
-        <tbody class="sectionheader">
-          <tr>
-            <th class="rightborder">Property</th>
-            <th class="rightborder">Mapping expression</th>
-            <th>File columns</th>
-          </tr>
-        </tbody>
-        <%
-        for (String name : mappingParameters)
-        {
-          %>
-          <tr class="highlight">
-            <th><%=HTML.encodeTags(request.getParameter("mapping." + name + ".label"))%></th>
-            <td>
-              <table style="width: 100%;">
-              <tr>
-                <td>
-                <input type="text" class="text auto-init" data-auto-init="column-mapping"
-                  name="mapping.<%=name%>.expression"
-                  maxlength="80" 
-                  value="<%=HTML.encodeTags(request.getParameter("mapping." + name + ".expression"))%>">
-                </td>
-              <td style="width: 22px;">
-                <base:icon image="cancel.png" subclass="auto-init" id="<%="clear."+name %>"
-                  data-auto-init="column-mapping-clear" data-mapping="<%=name%>"
-                  tooltip="Clear this expression"/>
-              </td>
-              </tr>
-              </table>
-            </td>
-            <td style="width: 15em;">
-              <select name="list.<%=name%>" class="auto-init" 
-                data-auto-init="column-mapping-preset" data-mapping="<%=name%>">
-              <option value="">
-              <%=mappings%>
-              </select>
-            </td>
-          </tr>
-          <%
-        }
-        %>
-        <tr class="dynamic">
-          <th></th>
-          <td></td>
-          <td></td>
-        </tr>
-        </table>
+      <div class="absolutefull input100" style="top: 2em;">
+
+        <tbl:table id="col-mappings">
+          <tbl:columndef 
+            id="property"
+            title="Property"
+          />
+          <tbl:columndef 
+            id="expression"
+            title="Mapping expression"
+          />
+          <tbl:columndef 
+            id="columns"
+            title="File columns"
+          />
+          <tbl:data>
+            <tbl:headers>
+              <tbl:headerrow>
+                <tbl:columnheaders />
+              </tbl:headerrow>
+            </tbl:headers>            
+            <tbl:rows>
+            <%
+            for (String name : mappingParameters)
+            {
+              %>
+              <tbl:row>
+                <tbl:cell column="property"><%=HTML.encodeTags(request.getParameter("mapping." + name + ".label"))%></tbl:cell>
+                <tbl:cell column="expression">
+                
+                    <table style="width: 100%;">
+                    <tr>
+                      <td>
+                      <input type="text" class="text auto-init" data-auto-init="column-mapping"
+                        name="mapping.<%=name%>.expression"
+                        maxlength="80" 
+                        value="<%=HTML.encodeTags(request.getParameter("mapping." + name + ".expression"))%>">
+                      </td>
+                    <td style="width: 22px;">
+                      <base:icon image="cancel.png" subclass="auto-init" id="<%="clear."+name %>"
+                        data-auto-init="column-mapping-clear" data-mapping="<%=name%>"
+                        tooltip="Clear this expression"/>
+                    </td>
+                    </tr>
+                    </table>
+                </tbl:cell>
+                
+                <tbl:cell column="columns">
+                  <select name="list.<%=name%>" class="auto-init"
+                    data-auto-init="column-mapping-preset" data-mapping="<%=name%>">
+                  <option value="">
+                  <%=mappings%>
+                  </select>
+                </tbl:cell>
+              
+              </tbl:row>
+              <%
+            }
+            %>
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
       </div>
     </form>

trunk/www/filemanager/select_file.jsp

@@ -42 +42 @@
 
 <base:body>
-  <h1><%=requestTitle == null ? title : requestTitle%></h1>
+  <h1 style="border-bottom-width: 0;"><%=requestTitle == null ? title : requestTitle%></h1>
   <div class="content bottomborder">
     <div id="page-data" class="datacontainer"

trunk/www/include/scripts/main-2.js

@@ -2410 +2410 @@
   {
     list = Doc.element(list);
-    if (list.style.width) 
-    {
-      forms.checkOptionText(list.style.width, option);
+    if (option.hasAttribute('text') && !option.hasAttribute('title'))
+    {
+      option.title = option.text;
     }
     if (index < 0 || index >= list.length)
@@ -2425 +2425 @@
   }
   
-  /**
-    Check the length text attribute of a selection list option against
-    the width of the selection list. If the text is longer than what
-    can be displayed in the list, the text is automatically shortened
-    and ... is appended. The full text is made available as a popup
-    tooltip. If the text ends with a part inside brackets, [],
-    that part is preserved, chopping is done on the text preceeding it.
-    @param listWidth Width og the list including unit (em or px is supported)
-    @param option The option that is beeing added to the list
-  */
-  forms.checkOptionText = function(listWidth, option)
-  {
-    var width = listWidth.match(/(\d+)(em|px)/);
-    if (width == null) return;
-    var maxLength;
-    if (width[2] == 'em')
-    {
-      maxLength = 1.2 * width[1] + 0.01 * width[1] * width[1];
-    }
-    else
-    {
-      maxLength = 0.1 * width[1];
-    }
-    var hellip = String.fromCharCode(8230);
-    if (option.text && option.text.length > maxLength)
-    {
-      var text = option.text;
-      option.title = text;
-      var parts = text.match(/(.*)\[(.*)\]/);
-      if (parts != null)
-      {
-        maxLength = maxLength - parts[2].length - 3;
-        if (maxLength < 4) maxLength = 4;
-        text = parts[1].substring(0, maxLength) + hellip + ' [' + parts[2] + ']';
-      }
-      else
-      {
-        text = text.substring(0, maxLength) + hellip;
-      }
-      option.text = text;
-    }
-  }
-
   /**
     Switch place of two options in a list

trunk/www/info/about.jsp

@@ -38 +38 @@
   import="java.sql.Driver"
   import="java.util.Properties"
+  import="java.util.List"
+  import="java.lang.management.ManagementFactory"
+  import="java.lang.management.MemoryPoolMXBean"
+  import="java.lang.management.MemoryType"
+  import="java.lang.management.MemoryUsage"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -63 +68 @@
 final Properties properties = System.getProperties();
 final Runtime runtime = Runtime.getRuntime();
-
+List<MemoryPoolMXBean> beans = ManagementFactory.getMemoryPoolMXBeans();
 %>
 <base:page type="popup" title="About">
-<base:head scripts="tabcontrol-2.js,~info.js" styles="tabcontrol.css" />
+<base:head scripts="tabcontrol-2.js,~info.js" styles="tabcontrol.css">
+<style>
+#memoryTable th, #memoryTable td
+{
+  text-align: right;
+  padding-left: 1em;
+  padding-right: 1.5em;
+}
+
+.memory-warning
+{
+  color: #C80000;
+  font-weight: bold;
+  background-image: url('../images/warning_small.png');
+  background-repeat: no-repeat;
+  background-position: 100% 50%;
+}
+</style>
+</base:head>
 <base:body data-read-only="1">
   <h1>BASE - BioArray Software Environment</h1>
@@ -135 +158 @@
       </td>
   </tr>
-  <tr>
+  <tr class="dynamic">
     <th>Memory</th>
-    <td class="info">Total: <%=Values.formatBytes(runtime.totalMemory())%><br>
-      Free: <%=Values.formatBytes(runtime.freeMemory()) %><br>
-      Max: <%=Values.formatBytes(runtime.maxMemory()) %></td>
-  </tr>
-  <tr class="dynamic">
-    <th></th>
-    <td></td>
+    <td class="info">
+      
+      <table id="memoryTable" style="xwidth:100%;">
+      <tr style="border-bottom-width: 1px;">
+        <th></th>
+        <th>Used</th>
+        <th>Max</th>
+        <th></th>
+      </tr>
+      <%
+      for (MemoryType mtype : MemoryType.values())
+      {
+        long sumUsed = 0;
+        long sumMax = 0;
+        for (MemoryPoolMXBean mbean : beans) 
+        {
+          if (mbean.getType() == mtype)
+          {
+            MemoryUsage usage = mbean.getUsage();
+            sumUsed += usage.getUsed();
+            sumMax += usage.getMax();
+            long percent = 100*usage.getUsed() / usage.getMax();
+            %>
+            <tr>
+            <td><%=mbean.getName() %></td>
+            <td><%=Values.formatBytes(usage.getUsed()) %></td>
+            <td><%=Values.formatBytes(usage.getMax()) %></td>
+            <td class="<%=percent > 75 ? "memory-warning" : "" %>"><%=percent %>%</td>
+            </tr>
+          <%
+          }
+        }
+        %>
+        <tr style="border-bottom-width: 1px; font-weight: bold;">
+          <td>Sum <%=mtype.toString() %></td>
+          <td><%=Values.formatBytes(sumUsed) %></td>
+          <td><%=Values.formatBytes(sumMax) %></td>
+          <td><%=100*sumUsed / sumMax %>%</td>
+        </tr>
+        <%
+      }
+      %>
+      
+      </table>
   </tr>
   </table>

trunk/www/lims/arrayslides/create_wizard.jsp

@@ -192 +192 @@
           <tbody class="sectionheader">
           <tr>
-            <th>&nbsp;</th>
-            <th>Name: 
+            <th style="border-top-width: 0;">&nbsp;</th>
+            <th style="border-top-width: 0;">Name: 
               <base:icon 
                 id="pasteMultipleName"
@@ -207 +207 @@
               />
             </th>
-            <th>Barcode:
+            <th style="border-top-width: 0;">Barcode:
               <base:icon 
                 id="pasteMultipleBarcode"

trunk/www/views/experiments/index.jsp

@@ -453 +453 @@
     cloneJob.setParameterValue("cloneSource", "Clone source", null, 
       new StringParameterType(), request.getParameter("cloneSource"));
+    cloneJob.setScheduled(null, null);
     dc.saveItem(cloneJob);
     dc.commit();

trunk/www/views/jobs/view_job.jsp

@@ -303 +303 @@
               %>
               <td style="padding-left: 10px;"><base:button 
-                subclass="link auto-init"
+                subclass="auto-init"
                 data-auto-init="view-file"
                 data-file-id="<%=logFile.getId()%>"

trunk/www/views/physicalbioassays/list_bioassays.jsp

@@ -235 +235 @@
         id="derivedBioAssays"
         title="Derived bioassays"
-        property="&rootDerivedBioAssays(name)"
+        property="&rootDerivedBioAssays(%name)"
         datatype="string"
         filterable="true"