Changeset 6576

Timestamp:

Oct 22, 2014, 6:41:55 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 3.3.2 to the trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• credits.txt (modified) (2 diffs)
• doc/src/docbook/developer/documentation.xml (modified) (1 diff)
• doc/src/docbook/developer/migrate_2_3.xml (modified) (1 diff)
• doc/src/docbook/developer/plugins.xml (modified) (1 diff)
• doc/src/docbook/overview/resources.xml (modified) (1 diff)
• doc/src/docbook/user/webclient.xml (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/extensions/WebClientRegisterExtensionsProcessor.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/menu/FixedMenuItemFactory.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/menu/MenuItemBean.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/menu/PermissionMenuItemFactory.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/tabcontrol/FixedTabFactory.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/tabcontrol/IncludeContentTabFactory.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/tabcontrol/TabBean.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/ButtonBean.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/FixedButtonFactory.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/Body.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/Button.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/CalendarButton.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/DeprecationLogger.java (copied) (copied from tags/3.3.2/src/clients/web/net/sf/basedb/clients/web/taglib/DeprecationLogger.java)
• src/clients/web/net/sf/basedb/clients/web/taglib/Head.java (modified) (6 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/Icon.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/Select.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/StylableTag.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/extensions/Scripts.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/extensions/Stylesheets.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/menu/Menuitem.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/tab/Tab.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/tab/TabControl.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Button.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/DbControl.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Job.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Project.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/query/CaseExpression.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/query/Hql.java (modified) (10 diffs)
• src/core/net/sf/basedb/core/query/WhenStatement.java (modified) (5 diffs)
• src/core/net/sf/basedb/util/extensions/manager/processor/PluginInstallationProcessor.java (modified) (5 diffs)
• src/plugins/core/net/sf/basedb/plugins/RawDataFlatFileImporter.java (modified) (1 diff)
• src/test/TestFile.java (modified) (2 diffs)
• src/test/TestFileServer.java (modified) (1 diff)
• src/test/TestItemImporter.java (modified) (2 diffs)
• src/test/data/base.onk.lu.se.crt (copied) (copied from tags/3.3.2/src/test/data/base.onk.lu.se.crt)
• src/test/data/base2.thep.lu.se.crt (deleted)
• src/test/data/test.batchimport.files.txt (modified) (1 diff)
• src/test/data/test.download.base-2.17.2.md5 (deleted)
• src/test/data/test.download.baselogo.png (copied) (copied from tags/3.3.2/src/test/data/test.download.baselogo.png)
• www/ajax.jsp (copied) (copied from tags/3.3.2/www/ajax.jsp)
• www/biomaterials/extracts/extracts.js (modified) (1 diff)
• www/biomaterials/samples/samples.js (modified) (1 diff)
• www/common/import/select_file.jsp (modified) (3 diffs)
• www/common/plugin/configure.jsp (modified) (2 diffs)
• www/common/share/share.js (modified) (4 diffs)
• www/filemanager/files/files.js (modified) (2 diffs)
• www/filemanager/select_file.js (modified) (4 diffs)
• www/footnote.js (modified) (2 diffs)
• www/footnote.jsp (modified) (4 diffs)
• www/include/menu.jsp (modified) (1 diff)
• www/include/scripts/main-2.js (modified) (12 diffs)
• www/include/scripts/main.js (modified) (25 diffs)
• www/include/scripts/popup.js (modified) (2 diffs)
• www/include/scripts/table.js (modified) (5 diffs)
• www/login.js (modified) (1 diff)
• www/views/jobs/view_job.jsp (modified) (1 diff)
• www/views/physicalbioassays/bioassays.js (modified) (1 diff)

trunk/credits.txt

@@ -1 +1 @@
 $Id$
 
-The current BASE team is (at BASE 3.3.1 release)
+The current BASE team is (at BASE 3.3.2 release)
 {{{
 Jari Häkkinen
@@ -21 +21 @@
 Peter Johansson
 David Lindgren
+Bob MacCallum
 Olle Månsson
 Peter Mörck

trunk/doc/src/docbook/developer/documentation.xml

@@ -989 +989 @@
           All screen shots are from Firefox and Windows 7. Popup windows in Firefox should not have the 
           navigation toolbar (nor any other toolbars). Full windows should have the navigation toolbar.
-          Replace the URL with <userinput>base2.thep.lu.se/demo/</userinput>. Avoid extra toolbar buttons,
+          Replace the URL with <userinput>base.onk.lu.se/demo/</userinput>. Avoid extra toolbar buttons,
           etc. that are from plug-ins you may have installed in Firefox.
           </para>

trunk/doc/src/docbook/developer/migrate_2_3.xml

@@ -133 +133 @@
       You'll need to make sure that your build system can handle this.
       The BASE JAR files can be downloaded from 
-      <ulink url="http://base2.thep.lu.se/base/jars/">http://base2.thep.lu.se/base/jars/</ulink>.
+      <ulink url="http://base.thep.lu.se/chrome/site/files/base/jars/">http://base.thep.lu.se/chrome/site/files/base/jars/</ulink>.
     </note>
     

trunk/doc/src/docbook/developer/plugins.xml

@@ -355 +355 @@
         <note>
           <para>
-          The installation wizard can only install configurations that belong to 
-          plug-ins defined by the same package. It is currently not possible to,
-          for example, include configuration for core plug-ins.
+          As of BASE 3.3.2 the installation wizard can also install configurations
+          for plug-ins defined by the BASE core or other extensions. Simply include
+          the configuration settings for the plug-in as you would do with a configuration
+          for a plug-in defined by your own extension.
           </para>
         </note>

trunk/doc/src/docbook/overview/resources.xml

@@ -211 +211 @@
       explore BASE without having to install it. Follow the link on
       BASE web site to the demo server or go directly to
-      <ulink url="http://base2.thep.lu.se/demo/">
-        http://base2.thep.lu.se/demo/
-      </ulink>
+      <ulink url="http://base.onk.lu.se/demo/">
+        http://base.onk.lu.se/demo/
+      </ulink>. NOTE! The demo server is currently down!
     </para>
     <para>

trunk/doc/src/docbook/user/webclient.xml

@@ -47 +47 @@
         <para>
           You may, for example, try the BASE demo server. Go to the
-          URL <ulink url="http://base2.thep.lu.se/demo/">http://base2.thep.lu.se/demo/</ulink>
+          URL <ulink url="http://base.onk.lu.se/demo/">http://base.onk.lu.se/demo/</ulink>
           and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
-          for the password.
+          for the password. NOTE! The demo server is currently down!
         </para>
         

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/WebClientRegisterExtensionsProcessor.java

@@ -23 +23 @@
 
 import net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter;
+import net.sf.basedb.clients.web.taglib.Head;
 import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.util.Values;
@@ -98 +99 @@
       ContentSecurityPolicyFilter.setSafeResources(xtFile.getName(), safeResources);
     }
+    // Register the version of this extension so
+    // we can append ?version to script and css URLs
+    if (about != null && about.getVersion() != null)
+    {
+      Head.setExtensionVersion(xtFile.getName(), about.getVersion());
+    }
 
     super.processFile(manager, wFile);

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/FixedMenuItemFactory.java

@@ -23 +23 @@
 
 import net.sf.basedb.clients.web.extensions.AbstractJspActionFactory;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.extensions.InvokationContext;
@@ -55 +56 @@
   private String submenuId;
   private String icon;
+  @Deprecated
   private String onClick;
   private String style;
@@ -190 +192 @@
   
   @VariableSetter
+  @Deprecated
   public void setOnClick(String onClick) 
   {
     this.onClick = onClick;
+    DeprecationLogger.warn("MenuItemAction", "onclick", "3.5");
   }
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/MenuItemBean.java

@@ -23 +23 @@
 
 import net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 
 /**
@@ -42 +43 @@
   private String submenuId;
   private String icon;
+  @Deprecated
   private String onClick;
   private String clazz;
@@ -183 +185 @@
   {
     this.onClick = onClick;
+    DeprecationLogger.warn("MenuItemAction", "onclick", "3.5");
   }
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/PermissionMenuItemFactory.java

@@ -24 +24 @@
 import net.sf.basedb.clients.web.extensions.AbstractJspActionFactory;
 import net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.Permission;
@@ -69 +70 @@
   private String disabledClazz;
   
+  @Deprecated
   private String onClick;
   private MenuType type;
@@ -230 +232 @@
   {
     this.onClick = onClick;
+    DeprecationLogger.warn("MenuItemAction", "onclick", "3.5");
   }
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/tabcontrol/FixedTabFactory.java

@@ -23 +23 @@
 
 import net.sf.basedb.clients.web.extensions.AbstractJspActionFactory;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.extensions.InvokationContext;
@@ -202 +203 @@
   {
     this.onValidate = onValidate;
+    DeprecationLogger.warn("TabAction", "onvalidate", "3.5");
   }
 
@@ -209 +211 @@
   {
     this.onActivate = onActivate;
+    DeprecationLogger.warn("TabAction", "onactivate", "3.5");
   }
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/tabcontrol/IncludeContentTabFactory.java

@@ -28 +28 @@
 import net.sf.basedb.clients.web.extensions.AbstractJspActionFactory;
 import net.sf.basedb.clients.web.extensions.JspContext;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 import net.sf.basedb.clients.web.util.HTML;
 import net.sf.basedb.util.Values;
@@ -143 +144 @@
   {
     this.onValidate = onValidate;
+    DeprecationLogger.warn("TabAction", "onvalidate", "3.5");
   }
 
@@ -150 +152 @@
   {
     this.onActivate = onActivate;
+    DeprecationLogger.warn("TabAction", "onactivate", "3.5");
   }
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/tabcontrol/TabBean.java

@@ -23 +23 @@
 
 import net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 
 /**
@@ -165 +166 @@
   {
     this.onValidate = onValidate;
+    DeprecationLogger.warn("TabAction", "onvalidate", "3.5");
   }
   
@@ -171 +173 @@
   {
     this.onActivate = onActivate;
+    DeprecationLogger.warn("TabAction", "onactivate", "3.5");
   }
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/ButtonBean.java

@@ -23 +23 @@
 
 import net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 
 /**
@@ -40 +41 @@
   private String icon;
   private String id;
+  @Deprecated
   private String onClick;
   private String style;
@@ -137 +139 @@
   {
     this.onClick = onClick;
+    DeprecationLogger.warn("ButtonAction", "onclick", "3.5");
   }
 

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/FixedButtonFactory.java

@@ -23 +23 @@
 
 import net.sf.basedb.clients.web.extensions.AbstractJspActionFactory;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.extensions.InvokationContext;
@@ -59 +60 @@
   private String clazz;
   private String icon;
+  @Deprecated
   private String onClick;
   private String style;
@@ -176 +178 @@
   {
     this.onClick = onClick;
+    DeprecationLogger.warn("ButtonAction", "onclick", "3.5");
   }
 

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

@@ -161 +161 @@
   {
     this.onLoad = onLoad;
+    DeprecationLogger.warn("base:body", "onload", "3.5");
   }
   @Deprecated

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

@@ -259 +259 @@
   {
     this.onClick = onClick;
+    DeprecationLogger.warn("base:button", "onclick", "3.5");
   }
   @Deprecated

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

@@ -37 +37 @@
 
   public CalendarButton()
+  {}
+  
+  
+  @Override
+  protected void initDefaultAttributes() 
   {
     super.setTitle("Calendar…");
@@ -43 +48 @@
     setDynamicAttribute(null, "data-auto-init", "calendar");
   }
-  
+
   public void setTextarea(String textarea)
   {

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

@@ -23 +23 @@
 package net.sf.basedb.clients.web.taglib;
 
+import net.sf.basedb.clients.web.extensions.ExtensionsControl;
+import net.sf.basedb.clients.web.util.HTML;
 import net.sf.basedb.core.SessionControl;
+import net.sf.basedb.core.Version;
 import net.sf.basedb.util.Values;
 
+import java.util.HashMap;
 import java.util.LinkedHashSet;
 import java.util.Arrays;
-
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.servlet.http.HttpServletRequest;
 import javax.servlet.jsp.JspException;
 import javax.servlet.jsp.JspTagException;
+import javax.servlet.jsp.PageContext;
 import javax.servlet.jsp.tagext.TagSupport;
 
@@ -91 +100 @@
   private static final long serialVersionUID = 948719986796860767L;
 
+  // Contain the file name of extension JAR files mapped to versions
+  private static final Map<String, String> xtVersions = new HashMap<String, String>();
+
+  // Match files under /base-root/extensions path. group 1 is the JAR file name
+  private static final Pattern PATH_MATCH = 
+      Pattern.compile("/?[^/]*" + ExtensionsControl.RESOURCES_URL + "/([^/]+)/(.*)");
+
+  /**
+    Register the version for an exteniosn JAR file.
+    Used for appending a query parameter to all scripts and style sheets
+    to prevent that browsers cache the old version.
+    @see #getVersionParameter(String)
+    @since 3.3.2
+  */
+  public static void setExtensionVersion(String jarName, String version)
+  {
+    synchronized (xtVersions)
+    {
+      xtVersions.put(jarName, "v="+HTML.urlEncode(version));
+    }
+  }
+
+  /**
+    Get query parameter to the given absolute path (including root directory).
+    If the path points to a file in the /base-root/extensions/ directory the version
+    of the extension is used, otherwise the BASE version is used. The
+    returned parameter is of the form v=<version>.
+    @param absolutePath An absolute path with or without the base-root directory
+    @since 3.3.2
+  */
+  public static final String getVersionParameter(String absolutePath)
+  {
+    Matcher m = PATH_MATCH.matcher(absolutePath);
+    String version = globalVersion;
+    if (m.matches())
+    {
+      String jarFile = m.group(1);
+      if (xtVersions.containsKey(jarFile))
+      {
+        version = xtVersions.get(jarFile);
+      }
+    }
+    return version;
+  }
+
+  
   /**
     The parent &lt;base:page&gt; tag.
@@ -105 +160 @@
   */
   private String scripts = null;
+  
+  private static final String globalVersion = "v=" + Version.getMajor()+"."+Version.getMinor()+"."+Version.getMaintenance();
+  private String localVersion;
   
   /*
@@ -143 +201 @@
     for (String style : allStyles)
     {
+      char pp = style.indexOf('?') == -1 ? '?' : '&';
       sb.append("\t<link rel=\"stylesheet\" type=\"text/css\" href=\"");
       if (style.startsWith(appRoot))
       {
         // Full absolute path 
-        sb.append(style);
+        sb.append(style).append(pp).append(getVersionParameter(style));
       }
       else if (style.startsWith("/"))
       {
-        // Absolute path is relative the page root (eg. /foo/bar.css --> /base/foo/bar.css)
-        sb.append(appRoot).append(style.substring(1));
+        sb.append(appRoot).append(style.substring(1)).append(pp).append(getVersionParameter(style));
       }
       else if (style.startsWith("~"))
       {
         // Relative path is relative the current page (eg. ~bar.css --> bar.css)
-        sb.append(style.substring(1));
+        sb.append(style.substring(1)).append(pp).append(localVersion);
       }
       else
       {
         // All other style sheets are in the /include/styles folder
-        sb.append(appRoot).append("include/styles/").append(style);
+        sb.append(appRoot).append("include/styles/").append(style).append(pp).append(globalVersion);
       }
       sb.append("\">\n");
@@ -192 +250 @@
     for (String script : allScripts)
     {
+      char pp = script.indexOf('?') == -1 ? '?' : '&';
       sb.append("\t<script type=\"text/javascript\" charset=\"UTF-8\" src=\"");
       if (script.startsWith(appRoot))
       {
         // Full absolute path 
-        sb.append(script);
+        sb.append(script).append(pp).append(getVersionParameter(script));
       }
       else if (script.startsWith("/"))
       {
         // Absolute path that is relative the BASE root (eg. /foo/bar.js --> /base/foo/bar.js)
-        sb.append(appRoot).append(script.substring(1));
+        sb.append(appRoot).append(script.substring(1)).append(pp).append(getVersionParameter(script));
       }
       else if (script.startsWith("~"))
       {
         // Relative path is relative the current page (eg. ~bar.js --> bar.js)
-        sb.append(script.substring(1));
+        sb.append(script.substring(1)).append(pp).append(localVersion);
       }
       else
       {
         // All other scripts are in the /include/scripts folder
-        sb.append(appRoot).append("include/scripts/").append(script);
+        sb.append(appRoot).append("include/scripts/").append(script).append(pp).append(globalVersion);
       }
       sb.append("\"></script>\n");
@@ -217 +276 @@
   }
 
+  @Override
+  public void setPageContext(PageContext pageContext) 
+  {
+    super.setPageContext(pageContext);
+    HttpServletRequest req = (HttpServletRequest)pageContext.getRequest();
+    // If we are on /extension subpage, the localVersion is the
+    // version for the extension, otherwise we use the global version
+    localVersion = getVersionParameter(req.getServletPath());
+  }
+  
+  
   @Override
   public int doStartTag()

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

@@ -235 +235 @@
     this.onClick = onClick;
     if (!setEnabledIsCalled) this.enabled = onClick != null;
+    DeprecationLogger.warn("base:icon", "onclick", "3.5");
   }
   @Deprecated

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

@@ -495 +495 @@
   {
     this.onChange = onChange;
+    DeprecationLogger.warn("base:select", "onchange", "3.5");
   }
   @Deprecated
@@ -506 +507 @@
   {
     this.onSelect = onSelect;
+    DeprecationLogger.warn("base:select", "onselect", "3.5");
   }
   @Deprecated

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

@@ -76 +76 @@
     super.setPageContext(pageContext);
     dynamicAttributes = null;
-  }
-
+    initDefaultAttributes();
+  }
+
+  /**
+    Initialize default attributes. Can be called multiple times (once before each tag is used/re-used).
+    This default implementation does nothing.
+    @since 3.3.2
+  */
+  protected void initDefaultAttributes()
+  {}
+  
   public void setClazz(String clazz)
   {

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/extensions/Scripts.java

@@ -34 +34 @@
 
 import net.sf.basedb.clients.web.extensions.JspContext;
+import net.sf.basedb.clients.web.taglib.Head;
 
 /**
@@ -92 +93 @@
     for (String script : scripts)
     {
+      char pp = script.indexOf('?') == -1 ? '?' : '&';
       sb.append("<script type=\"text/javascript\" src=\"");
-      sb.append(script);
+      sb.append(script).append(pp).append(Head.getVersionParameter(script));
       sb.append("\" charset=\"UTF-8\"></script>\n");
     }

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/extensions/Stylesheets.java

@@ -34 +34 @@
 
 import net.sf.basedb.clients.web.extensions.JspContext;
+import net.sf.basedb.clients.web.taglib.Head;
 
 /**
@@ -93 +94 @@
     for (String stylesheet : stylesheets)
     {
+      char pp = stylesheet.indexOf('?') == -1 ? '?' : '&';
       sb.append("<link rel=\"stylesheet\" type=\"text/css\" href=\"");
-      sb.append(stylesheet);
+      sb.append(stylesheet).append(pp).append(Head.getVersionParameter(stylesheet));
       sb.append("\">\n");
     }

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/menu/Menuitem.java

@@ -30 +30 @@
 
 import net.sf.basedb.clients.web.extensions.DynamicActionAttribute;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 import net.sf.basedb.clients.web.taglib.StylableTag;
 
@@ -191 +192 @@
     Javascript statment to execute when the user clicks the menu.
   */
+  @Deprecated
   private String onclick = null;
     
@@ -234 +236 @@
   {
     this.onclick = onclick;
+    DeprecationLogger.warn("base:menu", "onclick", "3.5");
   }
   @Deprecated

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/Tab.java

@@ -35 +35 @@
 import net.sf.basedb.clients.web.extensions.DynamicActionAttributes;
 import net.sf.basedb.clients.web.extensions.tabcontrol.TabAction;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 
 /**
@@ -279 +280 @@
   {
     this.validate = validate;
+    DeprecationLogger.warn("t:tab", "validate", "3.5");
   }
   @Override
@@ -294 +296 @@
   {
     this.activate = activate;
+    DeprecationLogger.warn("t:tab", "activate", "3.5");
   }
   /**

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/TabControl.java

@@ -28 +28 @@
 import net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport;
 import net.sf.basedb.clients.web.extensions.tabcontrol.TabAction;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 import net.sf.basedb.clients.web.taglib.StylableTag;
 import net.sf.basedb.util.extensions.ExtensionsInvoker;
@@ -273 +274 @@
   {
     this.switchtab = s;
+    DeprecationLogger.warn("t:tabcontrol", "switch", "3.5");
   }
   @Deprecated

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Button.java

@@ -29 +29 @@
 import net.sf.basedb.clients.web.extensions.toolbar.ButtonAction;
 import net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer;
+import net.sf.basedb.clients.web.taglib.DeprecationLogger;
 import net.sf.basedb.clients.web.taglib.StylableTag;
 
@@ -237 +238 @@
   {
     this.onClick = onClick;
+    DeprecationLogger.warn("tbl:button", "onclick", "3.5");
   }
   @Deprecated

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

@@ -904 +904 @@
         {
           throw new ItemNotFoundException(HibernateUtil.getShortEntityName(ex.getEntityName())+
-            "[id="+ex.getIdentifier()+"]");
+            "[id="+ex.getIdentifier()+"]", ex);
         }
       }

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

@@ -511 +511 @@
   
   /**
+    Set the version of the plugin that executes the job.
+    NOTE! This is automatically called for jobs that are executed by
+    plug-ins but should be called excplicitely for other types of jobs
+    @param pluginVersion
+    @since 3.3.2
+  */
+  public void setPluginVersion(String pluginVersion)
+  {
+    checkPermission(Permission.WRITE);
+    getData().setPluginVersion(StringUtil.setNullableString(pluginVersion, "pluginVersion", JobData.MAX_PLUGIN_VERSION_LENGTH));
+  }
+  
+  /**
     Get the version number of the configuration parameters used for this job.
   */
@@ -1049 +1062 @@
       data.setJobAgentId(agent == null ? null : agent.getId());
       PluginDefinitionData plugin = data.getPluginDefinition();
-      data.setPluginVersion(plugin == null ? null : plugin.getVersionString());
+      if (plugin != null) data.setPluginVersion(plugin.getVersionString());
     }
 

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

@@ -47 +47 @@
 import java.util.Set;
 import java.util.Collections;
+
+import org.hibernate.Hibernate;
 
 /**
@@ -933 +935 @@
 
     Class dataClass = itemType.getDataClass();
-    for (BasicData data : defaultItems.getValues())
-    {
+    Iterator<BasicData> it = defaultItems.getValues().iterator();
+    while (it.hasNext())
+    {
+      BasicData data = it.next();
       if (dataClass.isInstance(data))
       {
+        // Check if item has been removed
+        try
+        {
+          Hibernate.initialize(data);
+        }
+        catch (org.hibernate.ObjectNotFoundException ex)
+        {
+          it.remove();
+          continue;
+        }
+        
         // Found an item of the correct item type... get it's subtype
         ItemSubtypeData otherSubtype = null;
@@ -985 +1000 @@
     
     Class dataClass = itemType.getDataClass();
-    for (BasicData data : defaultItems.getValues())
-    {
+    Iterator<BasicData> it = defaultItems.getValues().iterator();
+    while (it.hasNext())
+    {
+      BasicData data = it.next();
       if (dataClass.isInstance(data))
       {
+        // Check if item has been removed
+        try
+        {
+          Hibernate.initialize(data);
+        }
+        catch (org.hibernate.ObjectNotFoundException ex)
+        {
+          it.remove();
+          continue;
+        }
+
         // Found an item of the correct item type... get it's subtype
         ItemSubtypeData otherSubtype = null;

trunk/src/core/net/sf/basedb/core/query/CaseExpression.java

@@ -74 +74 @@
     {
       sb.append("WHEN ").append(when.getCondition().toQl(query, dc));
-      sb.append(" THEN ").append(when.getValue().toQl(query, dc));
+      sb.append(" THEN ").append(when.getValue() == null ? "null" : when.getValue().toQl(query, dc));
       sb.append("\n");
     }
@@ -95 +95 @@
     {
       all.add(when.getCondition());
-      all.add(when.getValue());
+      if (when.getValue() != null) all.add(when.getValue());
     }
     if (elseExpression != null) all.add(elseExpression);

trunk/src/core/net/sf/basedb/core/query/Hql.java

@@ -56 +56 @@
   
   /**
-    A property can only contain the characters a-zA-Z0-9, period(.) or hash (#)
+    A property can only contain the characters a-zA-Z0-9, period(.), underscore(_) or hash (#)
     It cannot begin or end with a period/hash and cannot have two periods/hashes in a sequence.
     A hash indicates a path to a component while a period indicates a path to another
     entity.
   */
-  public static final Pattern PROPERTY_REGEXP = Pattern.compile("[a-zA-Z0-9]+((\\.|\\#)[a-zA-Z0-9]+)*");
+  public static final Pattern PROPERTY_REGEXP = Pattern.compile("[a-zA-Z0-9_]+((\\.|\\#)[a-zA-Z0-9_]+)*");
 
   /**
@@ -199 +199 @@
       if (!PROPERTY_REGEXP.matcher(property).matches()) 
       {
-        throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+        throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
       }
       if (property.endsWith("affyChip"))
@@ -234 +234 @@
     if (property != null && !PROPERTY_REGEXP.matcher(property).matches()) 
     {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
     }
     if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
@@ -260 +260 @@
     if (!PROPERTY_REGEXP.matcher(property).matches()) 
     {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
     }
     if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
@@ -287 +287 @@
     if (!PROPERTY_REGEXP.matcher(property).matches()) 
     {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
     }
     if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
@@ -365 +365 @@
     if (!PROPERTY_REGEXP.matcher(property).matches()) 
     {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
     }
     if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
@@ -438 +438 @@
     if (!PROPERTY_REGEXP.matcher(property).matches()) 
     {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
     }
     if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
@@ -484 +484 @@
     if (!PROPERTY_REGEXP.matcher(property).matches()) 
     {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
     }
     if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
@@ -535 +535 @@
     if (!PROPERTY_REGEXP.matcher(property).matches()) 
     {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
     }
     if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
@@ -557 +557 @@
     if (!PROPERTY_REGEXP.matcher(property).matches()) 
     {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9, _ and . is allowed.");
     }
     return Restrictions.eq(

trunk/src/core/net/sf/basedb/core/query/WhenStatement.java

@@ -23 +23 @@
 
 import net.sf.basedb.core.InvalidUseOfNullException;
+import net.sf.basedb.util.EqualsHelper;
 
 /**
@@ -45 +46 @@
       value is returned or not, null is not allowed
     @param value The value to return if the condition is TRUE, 
-      null is not allowed
+      null is allowed
   */
   public WhenStatement(Restriction condition, Expression value)
   {
     if (condition == null) throw new InvalidUseOfNullException("condition");
-    if (value == null) throw new InvalidUseOfNullException("value");
     this.condition = condition;
     this.value = value;
@@ -82 +82 @@
     StringBuilder sb = new StringBuilder();
     sb.append("WHEN ").append(getCondition().toString());
-    sb.append(" THEN ").append(getValue().toString());
+    sb.append(" THEN ").append(getValue() == null ? "null" : getValue().toString());
     return sb.toString();
   }
@@ -96 +96 @@
     if (other == null || this.getClass() != other.getClass()) return false;
     WhenStatement o = (WhenStatement)other;
-    return condition.equals(o.condition) && value.equals(o.value);
+    return condition.equals(o.condition) && EqualsHelper.equals(value, o.value);
   }
 
@@ -102 +102 @@
   public int hashCode()
   {
-    return condition.hashCode() + value.hashCode();
+    return condition.hashCode() + (value == null ? 0 : value.hashCode());
   }
   // -------------------------------------------

trunk/src/core/net/sf/basedb/util/extensions/manager/processor/PluginInstallationProcessor.java

@@ -30 +30 @@
 
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Include;
 import net.sf.basedb.core.ItemKey;
 import net.sf.basedb.core.ItemQuery;
@@ -174 +175 @@
             
             PluginDefinition plugin = allPlugins.get(pluginClassName);
+            if (plugin == null)
+            {
+              try
+              {
+                plugin = PluginDefinition.getByClassName(dc, pluginClassName);
+              }
+              catch (RuntimeException ex)
+              {}
+            }
             if (plugin != null)
             {
@@ -180 +190 @@
               {
                 ItemQuery<PluginConfiguration> query = plugin.getPluginConfigurations();
+                query.setIncludes(Include.ALL);
                 query.restrict(Restrictions.eq(Hql.property("name"), Expressions.parameter("name", name, Type.STRING)));
                 List<PluginConfiguration> existing = query.list(dc);
@@ -202 +213 @@
               }
             }
-  
+            else 
+            {
+              numError++;
+              wFile.setError(true);
+              String msg = "Failed to install plug-in configuration '" + name + "', no plug-in: " + pluginClassName;
+              if (results != null) results.addErrorMessage(xtFile, msg);
+              log.error(msg);
+            }
           }
         }
@@ -213 +231 @@
         if (numInstalled > 0) results.addMessage(xtFile, numInstalled + " plug-in(s) installed.");
         if (numUpdated > 0) results.addMessage(xtFile, numUpdated + " plug-in(s) updated.");
-        if (numConfigurations > 0) results.addMessage(xtFile, numConfigurations + " plug-in configuration(s) created");
+        if (numConfigurations > 0) results.addMessage(xtFile, numConfigurations + " plug-in configuration(s) created.");
         if (numInstalled == 0 && numUpdated == 0 && numProcessed > 0)
         {
-          results.addMessage(xtFile, numProcessed + " plug-in(s) loaded");
+          results.addMessage(xtFile, numProcessed + " plug-in(s) loaded.");
         }
       }

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

@@ -892 +892 @@
       msg.append(" spot(s) skipped due to missing features");
     }
-    if (skippedLines > 0) 
-    {
-      msg.append("; ").append(skippedLines).append(" spot(s) skipped due to errors");
+    if (skippedLines > numSkippedMissingFeature) 
+    {
+      msg.append("; ").append(skippedLines-numSkippedMissingFeature).append(" spot(s) skipped due to errors");
     }
     return msg.toString();

trunk/src/test/TestFile.java

@@ -79 +79 @@
     int baseTracServer = TestFileServer.test_create("base.thep.lu.se", "BASE trac site", 
         "base", "base", null, null, null);
-    int base2DemoServer = TestFileServer.test_create("base2.thep.lu.se", "BASE demo site", null, null, 
-        "data/base2.thep.lu.se.crt", null, null);
+    int base2DemoServer = TestFileServer.test_create("base.onk.lu.se", "BASE demo site", null, null, 
+        "data/base.onk.lu.se.crt", null, null);
     int extId1 = test_create("http://base.thep.lu.se/robots.txt", false, false);
-    int extId2 = test_create("https://base2.thep.lu.se/base/base-2.17.2.tar.gz.MD5", false, false);
+    int extId2 = test_create("https://base.onk.lu.se/onk/images/baselogo.png", false, false);
     int extId3 = test_create("http://base.thep.lu.se/login", false, false);
     test_load(id1);
@@ -96 +96 @@
     test_download(id1, "data/test.upload.txt");
     test_download(extId1, "data/test.download.robots.txt");
-    test_download(extId2, "data/test.download.base-2.17.2.md5");
+    test_download(extId2, "data/test.download.baselogo.png");
     test_download(extId3, null);
     

trunk/src/test/TestFileServer.java

@@ -47 +47 @@
     // Standard tests: create, load, list
     int id = test_create("base.thep.lu.se", "BASE trac site", "base", "base", null, null, null);
-    int id2 = test_create("base2.thep.lu.se", "BASE demo site", null, null, "data/base2.thep.lu.se.crt", null, null);
+    int id2 = test_create("base.onk.lu.se", "BASE demo site", null, null, "data/base.onk.lu.se.crt", null, null);
     test_load(id);
     test_list(-1);

trunk/src/test/TestItemImporter.java

@@ -87 +87 @@
     int childScanId = TestItemSubtype.test_create(Item.DERIVEDBIOASSAY, "ChildScan", SystemItems.getId(DerivedBioAssay.SCAN));
     int allSamplesSubtypeId = TestItemSubtype.test_create(Item.SAMPLE, "All samples");
-    int base2DemoServer = TestFileServer.test_create("base2.thep.lu.se", "BASE demo site", null, null, 
-        "data/base2.thep.lu.se.crt", null, null);
+    int base2DemoServer = TestFileServer.test_create("base.onk.lu.se", "BASE demo site", null, null, 
+        "data/base.onk.lu.se.crt", null, null);
 
     TestProject.test_defaultItem(projectId, Item.PROTOCOL, defaultSamplingProtocolId);
@@ -103 +103 @@
     ok = ok & TestFile.test_list("/file-import", 1);  // 'reporters.txt'
     ok = ok & TestFile.test_list("/file-import/raw", 2);  // 'file1.txt' and 'file2.txt'
-    ok = ok & TestFile.test_list("/file-import/ext", 2);  // 'robots.txt' and '2.17.md5'
+    ok = ok & TestFile.test_list("/file-import/ext", 2);  // 'robots.txt' and 'baselogo.png'
     
     // Import bioplates

trunk/src/test/data/test.batchimport.files.txt

@@ -4 +4 @@
 raw/file2.txt     Raw data    Raw data #2
 /file-import/ext/robots.txt http://base.thep.lu.se/robots.txt     text/plain  Robots file for BASE
-/file-import/ext/2.17.md5 https://base2.thep.lu.se/base/base-2.17.2.tar.gz.MD5  base2.thep.lu.se    
+/file-import/ext/baselogo.png https://base.onk.lu.se/onk/images/baselogo.png  base.onk.lu.se    

trunk/www/biomaterials/extracts/extracts.js

@@ -481 +481 @@
     event.detail.name += ' [-]';
     Link.addItem('extracts', 'EXTRACT', event.detail);
-    frm.parentType[0].checked = false;
-    frm.parentType[1].checked = true;
-    extracts.parentTypeOnClick();
+    if (event.detail.remaining == 0)
+    {
+      frm.parentType[0].checked = false;
+      frm.parentType[1].checked = true;
+      extracts.parentTypeOnClick();
+    }
   }
 

trunk/www/biomaterials/samples/samples.js

@@ -411 +411 @@
     event.detail.name += ' [-]';
     Link.addItem('samples', 'SAMPLE', event.detail);
-    frm.parentType[0].checked = false;
-    frm.parentType[1].checked = true;
-    samples.parentTypeOnClick();
+    if (event.detail.remaining == 0)
+    {
+      frm.parentType[0].checked = false;
+      frm.parentType[1].checked = true;
+      samples.parentTypeOnClick();
+    }
   }
 

trunk/www/common/import/select_file.jsp

@@ -158 +158 @@
           <th>Character set</th>
           <td>
-            <select name="charset">
+            <select name="charset" style="max-width: 98%;">
             <%
             String defaultCharset = Config.getCharset();
@@ -183 +183 @@
             <th>Data files</th>
             <td>
-              <select name="dataFile" id="dataFile">
+              <select name="dataFile" id="dataFile" style="width: 98%;">
               <option value="">
               <%
@@ -225 +225 @@
             <th>Recently used</th>
             <td>
-              <select name="recentFile" id="recentFile">
+              <select name="recentFile" id="recentFile" style="width: 98%;">
               <option value="">
               <%

trunk/www/common/plugin/configure.jsp

@@ -231 +231 @@
   if (helpText == null) helpText = plugin.getDescription();
   List<File> recentFiles = currentContext == null ? null : (List<File>)currentContext.getRecent(dc, Item.FILE);
-  
-  recentFiles = File.getQuery().list(dc);
   
   JSONArray jsonParameters = JsonUtil.toArray(parameters, new JsonConverter<PluginParameter>()
@@ -747 +745 @@
                         id="<%=fieldName%>:recent"
                         name="<%=fieldName%>:recent" 
-                        data-field="<%=fieldName %>">
+                        data-field="<%=fieldName %>"
+                        style="width: 98%;">
                       <option value="">
                       <%

trunk/www/common/share/share.js

@@ -144 +144 @@
     
     Link.addItem('members', 'USER', event.detail);
-    share.membersOnChange();
+    if (event.detail.remaining == 0)
+    {
+      share.membersOnChange();
+    }
   }
 
@@ -174 +177 @@
     
     Link.addItem('members', 'GROUP', event.detail);
-    share.membersOnChange();
+    if (event.detail.remaining == 0)
+    {
+      share.membersOnChange();
+    }
   }
 
@@ -199 +205 @@
     
     Link.addItem('members', 'PROJECT', event.detail);
-    share.membersOnChange();
+    if (event.detail.remaining == 0)
+    {
+      share.membersOnChange();
+    }
   }
   
@@ -218 +227 @@
   {
     Link.addItem('members', 'PERMISSIONTEMPLATE', event.detail);
-    share.membersOnChange();
+    if (event.detail.remaining == 0)
+    {
+      share.membersOnChange();
+    }
   }
 

trunk/www/filemanager/files/files.js

@@ -148 +148 @@
     else if (autoInit == 'file-check')
     {
-      Events.addEventHandler(element, 'click', fileManager.onFileChecked);
+      Events.addEventHandler(element, 'change', fileManager.onFileChecked);
     }
     else if (autoInit == 'directory-item')
@@ -172 +172 @@
       url += '&directory_id='+directoryId;
     }
-    Dialogs.openPopup(url, 'UploadFile', 600, 400);
+    var controller = Items.getController('FILE');
+    Dialogs.openPopup(url, 'UploadFile', controller.width, controller.height);
   }
   

trunk/www/filemanager/select_file.js

@@ -35 +35 @@
   selectFile.setSelectedFile = function(fileId, path)
   {
-    selected[0] = {'id': fileId, 'path': path};
+    selected[0] = {'id': fileId, 'name': path};
     selectFile.updatePath();
   }
@@ -46 +46 @@
     if (selectFile.getSelectedFileIndex(fileId) == -1)
     {
-      selected[selected.length] = {'id': fileId, 'path': path};
+      selected[selected.length] = {'id': fileId, 'name': path};
     }
     selectFile.updatePath();
@@ -73 +73 @@
     {
       if (path != '') path += ', ';
-      path += selected[i].path;
+      path += selected[i].name;
     }
     Doc.element('files').innerHTML = path;
@@ -84 +84 @@
     var callbackMethod = window.opener[callback];
     
+    var remaining = selected.length-1;
     for (var i = 0; i < selected.length; i++)
     {
+      var s = selected[i];
+      s.remaining = remaining--;
       if (notifyTarget)
       {
         // Send event to the target in the opener window
-        Events.sendCustomEvent(notifyTarget, 'base-selected', {'id': selected[i].id, 'name': selected[i].path});
+        Events.sendCustomEvent(notifyTarget, 'base-selected', s);
       }
       else if (callbackMethod)
       {
         // Call the callback method in the opener window
-        callbackMethod.call(null, selected[i].id, selected[i].path);
+        callbackMethod.call(null, s.id, s.path);
       }
     }

trunk/www/footnote.js

@@ -38 +38 @@
     Buttons.addClickHandler('multiMessages', footnote.showAllMessages);
     
-    // Reload the footnote in 60 seconds
-    Footnote.startReloadTimer();
-  }
-  
-  /**
-    Start the reload timer. Timeout parameter (in seconds) is optional.
-    If not given, the default timout is used (60 seconds).
-  */
-  footnote.startReloadTimer = function(timeout)
-  {
-    setTimeout(Footnote.reload, (timeout || pAutoReload) * 1000);
+    Footnote.loadMessages();
   }
   
@@ -54 +44 @@
     Reload the footnote page.
   */
-  footnote.reload = function()
+  footnote.loadMessages = function()
   {
-    location.reload(false);
+    var url = 'ajax.jsp?ID='+App.getSessionId();
+    url += '&cmd=GetFootnoteMessages';
+    var request = Ajax.getXmlHttpRequest();
+    request.open("GET", url, true);
+    Ajax.setReadyStateHandler(request, footnote.messagesLoaded, footnote.messagesNotLoaded);
+    request.send(null);
+  }
+  
+  footnote.messagesLoaded = function(request)
+  {
+    var messages = JSON.parse(request.responseText);
+    
+    Doc.hide('broadcast');
+    Doc.hide('credit');
+    Doc.hide('singleMessage');
+    Doc.hide('multiMessages');
+    if (messages.broadcast)
+    {
+      Doc.show('broadcast');
+      Doc.element('broadcast-title').innerHTML = Strings.encodeTags(messages.broadcast);
+    }
+    else if (messages.newMessages > 1)
+    {
+      Doc.show('multiMessages');
+      Doc.element('num-messages').innerHTML = messages.newMessages;
+    }
+    else if (messages.newMessages == 1)
+    {
+      var msg = messages.message;
+      Doc.show('singleMessage');
+      Data.set('singleMessage', 'message-id', msg.id);
+      Doc.element('message-name').innerHTML = Strings.encodeTags(msg.name);
+      Doc.element('message-from').innerHTML = Strings.encodeTags(msg.from);
+    }
+    else
+    {
+      Doc.show('credit');
+    }
+    setTimeout(footnote.loadMessages, pAutoReload * 1000);
+  }
+
+  footnote.messagesNotLoaded = function(request)
+  {
+    App.debug('Footnote not updated: ' + request.responseText);
+    setTimeout(footnote.loadMessages, pAutoReload * 1000);
   }
   

trunk/www/footnote.jsp

@@ -45 +45 @@
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 <%
-String broadcastTitle = (String)application.getAttribute("broadcast.title");
 SessionControl sc = Base.getSessionControl(pageContext, false);
 String ID = "";
@@ -56 +55 @@
   serverAdminName = Values.getStringOrNull(sc.getClientDefaultSetting("server.admin.name"));
   serverAdminEmail = Values.getStringOrNull(sc.getClientDefaultSetting("server.admin.email"));
-  dc = sc.newDbControl();
 }
-long numNewMessages = 0;
 try
 {
-  if (sc != null && sc.isLoggedIn()) numNewMessages = Message.countUnreadMessages(dc, null, false);
   %>
   <base:page type="iframe" title="">
@@ -68 +64 @@
   <div class="footer">
   <table style="width: 100%; height: 100%;"><tr><td>
-  <% 
-  if (broadcastTitle != null)
-  {
-    String broadcastMessage = (String)application.getAttribute("broadcast.message");
-    %>
-    <div class="message">
+
+    <div class="message" id="broadcast" style="display: none;">
     <base:icon id="broadcast" image="warning.png" tooltip="Read more&hellip;"
-      style="font-weight: bold;">&nbsp;<%=HTML.encodeTags(broadcastTitle) %></base:icon>
+      style="font-weight: bold;">
+      <span id="broadcast-title"></span>
+    </base:icon>
     </div>
-    <% 
-  }
-  else if (numNewMessages == 0)
-  {
-    %>
-    <div class="credit">
+    
+    <div class="credit" id="credit">
       The development of BASE is currently supported by Lund
       University through SCIBLU. Previous patrons of the BASE project
@@ -108 +98 @@
       %>
     </div>
-    <%
-  }
-  else if (numNewMessages == 1)
-  {
-    User user = User.getById(dc, sc.getLoggedInUserId());
-    ItemQuery<Message> query = Message.getQuery(user);
-    query.restrict(
-      Restrictions.eq(
-        Hql.property("read"),
-        Expressions.parameter("read")
-      )
-    );
-    query.setParameter("read", false, Type.BOOLEAN);
-    ItemResultList<Message> messages = query.list(dc);
-    Message message = messages.get(0);
-    %>
-    <base:icon id="singleMessage" image="message.png" tooltip="Read the message"
-      data-message-id="<%=message.getId()%>"
-      >&nbsp;<%=HTML.encodeTags(message.getName())%> (From: <%=HTML.encodeTags(message.getFrom())%>)
+
+    <base:icon id="singleMessage" style="display: none;" image="message.png" tooltip="Read the message">
+      <span id="message-name"></span> (From: <span id="message-from"></span>)
     </base:icon>
-    <%
-  }
-  else
-  {
-    %>
-    <base:icon id="multiMessages" image="message.png" tooltip="Read the messages"
-      >&nbsp;<b>You have <%=numNewMessages%> new messages</b></base:icon>
-    <%
-  }
-  %>
+    <base:icon id="multiMessages" style="display: none;" image="message.png" tooltip="Read the messages">
+      <b>You have <span id="num-messages"></span> new messages</b>
+    </base:icon>
   </td></tr></table>
   </div>

trunk/www/include/menu.jsp

@@ -1224 +1224 @@
         else if (action.getType() == MenuItemAction.MenuType.MENUITEM)
         {
-          %>
-          <m:menuitem 
-            id="<%=action.getId() %>"
-            subclass="<%=action.getClazz() %>"
-            style="<%=action.getStyle()%>"
-            title="<%=action.getTitle()%>"
-            icon="<%=action.getIcon()%>"
-            tooltip="<%=action.getTooltip()%>"
-            enabled="<%=action.isEnabled()%>"
-            visible="<%=action.isVisible()%>"
-            onclick="<%=action.getOnClick()%>"
-            dynamic="<%=dynamicAttributes%>"
-          />
-          <%
+          if (action.getOnClick() != null)
+          {
+            %>
+            <m:menuitem 
+              id="<%=action.getId() %>"
+              subclass="<%=action.getClazz() %>"
+              style="<%=action.getStyle()%>"
+              title="<%=action.getTitle()%>"
+              icon="<%=action.getIcon()%>"
+              tooltip="<%=action.getTooltip()%>"
+              enabled="<%=action.isEnabled()%>"
+              visible="<%=action.isVisible()%>"
+              onclick="<%=action.getOnClick()%>"
+              dynamic="<%=dynamicAttributes%>"
+            />
+            <%
+          }
+          else
+          {
+            %>
+            <m:menuitem 
+              id="<%=action.getId() %>"
+              subclass="<%=action.getClazz() %>"
+              style="<%=action.getStyle()%>"
+              title="<%=action.getTitle()%>"
+              icon="<%=action.getIcon()%>"
+              tooltip="<%=action.getTooltip()%>"
+              enabled="<%=action.isEnabled()%>"
+              visible="<%=action.isVisible()%>"
+              dynamic="<%=dynamicAttributes%>"
+            />
+            <%
+          }
         }
         else if (action.getType() == MenuItemAction.MenuType.SUBMENU)

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

@@ -75 +75 @@
   app.getScale = function()
   {
-    return Data.int(document.body, 'gui-scale');
+    return Data.float(document.body, 'gui-scale');
   }
   
@@ -226 +226 @@
   {
     console.log(message);
+  }
+  
+  /**
+    Log usage of a deprecated method. A call to this method
+    should be included as the first line in a deprecated method.
+    @param method The name of the method (eg. Main.openPopup())
+    @param voidVersion The version number of BASE in which the method will be removed
+   */
+  app.deprecatedMethod = function(method, voidVersion)
+  {
+    var msg = 'Deprecated method "' + method + '" will be removed in BASE ' + voidVersion;
+    console.error(msg);
   }
   
@@ -755 +767 @@
   events.integerOnly = function(event)
   {
-    var charCode = event.charCode || event.keyCode;
+    var charCode = event.charCode;
     // <31 for tab, delete, etc. 48-57=key 0-9, 45= '-'
     var allow = charCode <= 31 || (charCode >= 48 && charCode <= 57) || charCode == 45;
@@ -767 +779 @@
   events.numberOnly = function(event)
   {
-    var charCode = event.charCode || event.keyCode;
+    var charCode = event.charCode;
     // <31 for tab, delete, etc. 48-57=key 0-9, 45= '-', 46='.', 69/101=E/e
     var allow = charCode <= 31 || (charCode >= 48 && charCode <= 57) || charCode == 45 || charCode == 46 || charCode == 69 || charCode == 101;
@@ -1261 +1273 @@
       // If no last position is know, use the specified settings
       position = {};
-      // Rescale according to user settings
+      // Rescale according to user settings -- but not larger than current screen
       var scale = App.getScale();
-      position.width = width * scale;
-      position.height = height * scale;
+      position.width = Math.ceil(Math.min(width * scale, screen.availWidth));
+      position.height = Math.ceil(Math.min(height * scale, screen.availHeight));
       
       //  Try to position the popup window in the center of the parent window.
       var pos = App.getWindowPosition(window.top);
-      var top = Math.ceil(pos.top+(pos.height-height) / 2);
-      var left = Math.ceil(pos.left+(pos.width-width) / 2);
+      var top = Math.ceil(pos.top+(pos.height-position.height) / 2);
+      var left = Math.ceil(pos.left+(pos.width-position.width) / 2);
       position.top = (top < 0 && pos.top >= 0) ? 0 : top;
       position.left = (left < 0 && pos.left >= 0) ? 0 : left;
@@ -1938 +1950 @@
     controllers['EXTRAVALUETYPE'] = { url:'admin/extravaluetypes/index.jsp', width:600, height:400 };
     controllers['FEATURE'] = { url:'lims/arraydesigns/features/index.jsp', width:750, height:500, popup:true, edit:false, noAnyToAny:true };
-    controllers['FILE'] = { url:'filemanager/index.jsp', iframe:true, width:600, height:400 };
+    controllers['FILE'] = { url:'filemanager/index.jsp', iframe:true, width:750, height:500 };
     controllers['FILESERVER'] = { url:'filemanager/fileservers/index.jsp', width:750, height:500 };
-    controllers['FORMULA'] = { url:'views/formulas/index.jsp', width:750, height:500 };
+    controllers['FORMULA'] = { url:'views/formulas/index.jsp', width:900, height:600 };
     controllers['GROUP'] = { url:'admin/groups/index.jsp', width:600, height:400 };
     controllers['HARDWARE'] = { url:'admin/hardware/index.jsp', width:800, height:500 };
@@ -2216 +2228 @@
   
   // Kept for backwards compatibility
+  // @Deprecated
   forms.createHidden = function(frm, name, value, doc)
   {
+    App.deprecatedMethod('Forms.createHidden()', '3.5');
     Forms.addHidden(frm, name, value);
   }
@@ -2302 +2316 @@
       if (element.type == 'checkbox' && !element.disabled && element.name.match(nameRegexp))
       {
+        var was = element.checked;
         if (first == null)
         {
@@ -2311 +2326 @@
           element.checked = first.checked;
         }
+        if (was != element.checked) Events.sendChangeEvent(element);
       }
     }
@@ -2883 +2899 @@
 
   // Kept for backwards compatibility
+  // @Deprecated
   numbers.numberOnly = function(event)
   {
+    App.deprecatedMethod('Numbers.numberOnly()', '3.5');
     Events.numberOnly(event);
   }
   
   // Kept for backwards compatibility
+  // @Deprecated
   numbers.integerOnly = function(event)
   {
+    App.deprecatedMethod('Numbers.integerOnly()', '3.5');
     Events.integerOnly(event);
   }
@@ -3361 +3381 @@
     @param callback Deprecated, onchange event is sent instead
   */
+  // @Deprecated
   dates.selectDate = function(title, form, input, callback, format)
   {
+    App.deprecatedMethod('Dates.selectDate()', '3.5');
     var textarea = document.forms[form][input];
     if (!textarea.id) textarea.id = 't'+(new Date()).getTime();
@@ -3378 +3400 @@
     @param callback Deprecated, onchange event is sent instead
   */
+  // @Deprecated
   dates.selectDateTime = function(title, form, input, callback, format)
   {
+    App.deprecatedMethod('Dates.selectDateTime()', '3.5');
     var textarea = document.forms[form][input];
     if (!textarea.id) textarea.id = 't'+(new Date()).getTime();

trunk/www/include/scripts/main.js

@@ -29 +29 @@
 */
 
+
 /**
   Get the root URL path of this BASE installation. Always ends with a '/' (eg. /base/)
 */
+// @Deprecated
 function getRoot()
 {
+  App.deprecatedMethod('getRoot()', '3.5');
   return App.getRoot();
 }
@@ -41 +44 @@
   (should only happen on the top frameset of the login page)
 */
+//@Deprecated
 function getSessionId()
 {
+  App.deprecatedMethod('getSessionId()', '3.5');
   return App.getSessionId();
 }
@@ -50 +55 @@
   require scaling to fit).
 */
+//@Deprecated
 function getScale()
 {
+  App.deprecatedMethod('getScale()', '3.5');
   return App.getScale();
 }
@@ -60 +67 @@
   value of '0' disable the rewriting.
 */
+//@Deprecated
 function getMaxUrlLength()
 {
+  App.deprecatedMethod('getMaxUrlLength()', '3.5');
   return App.getMaxUrlLength();
 }
@@ -77 +86 @@
     in the reverse order as they were added to this method.
   */
+  // @Deprecated
   this.onLoad = function(f)
   {
+    App.deprecatedMethod('Main.onLoad()', '3.5');
     Doc.onLoad(f);
   }
@@ -95 +106 @@
     @see http://devedge.netscape.com/library/manuals/2000/javascript/1.3/reference/window.html#1202731
   */
+  // @Deprecated
   this.openPopup = function(url, name, width, height, options, parentWin)
   {
+    App.deprecatedMethod('Main.openPopup()', '3.5');
     Dialogs.openPopup(url, name, width, height);
   }
@@ -103 +116 @@
     Brings a named window to focus.
   */
+  // @Deprecated
   this.focusWindow = function(windowName)
   {
+    App.deprecatedMethod('Main.focusWindow()', '3.5');
     var win = this.getWindow(windowName);
     if (win) win.focus();
@@ -114 +129 @@
     the current window is returned.
    */
+  // @Deprecated
   this.getWindow = function(windowName)
   {
+    App.deprecatedMethod('Main.getWindow()', '3.5');
     var win = Dialogs.getDialog(windowName);
     if (!win || win.closed) win = window;
@@ -130 +147 @@
     @param textarea The name of the textarea to zoom
   */
+  // @Deprecated
   this.zoom = function(title, form, textarea, disabled, callback)
   {
+    App.deprecatedMethod('Main.zoom()', '3.5');
     var tmp = document.forms[form][textarea];
     if (!tmp.id) tmp.id = 'z'+(new Date()).getTime();
@@ -148 +167 @@
       instead of by setting the form field
   */
+  // @Deprecated
   this.selectColor = function(title, form, input, callback)
   {
+    App.deprecatedMethod('Main.selectColor()', '3.5');
     var tmp = document.forms[form][input];
     if (!tmp.id) tmp.id = 'z'+(new Date()).getTime();
@@ -161 +182 @@
       @param helpid The id of the helptext to be displayed.
   */
+  // @Deprecated
   this.openHelp = function(ID, helpid)  
   {
+    App.deprecatedMethod('Main.openHelp()', '3.5');
     Dialogs.openHelp(helpid);
   }
@@ -175 +198 @@
         used if the current tab doesn't specify a help id
   */
+  // @Deprecated
   this.openTabControlHelp = function(ID, tabcontrol, helpId)  
   {
+    App.deprecatedMethod('Main.openTabControlHelp()', '3.5');
     Dialogs.openTabControlHelp(tabcontrol, helpId);
   }
@@ -189 +214 @@
     @param maxLength The maximum length
   */
+  // @Deprecated
   this.cutString = function(value, maxLength)
   {
+    App.deprecatedMethod('Main.cutString()', '3.5');
     return Strings.cut(value, maxLength);
   }
@@ -199 +226 @@
     @return The trimmed string
   */
+  // @Deprecated
   this.trimString = function(value)
   {
+    App.deprecatedMethod('Main.trimString()', '3.5');
     return Strings.trim(value);
   }
   
   // Show or hide an element with the given ID attribute as a block element
+  // @Deprecated
   this.showHide = function(id, show)
   {
+    App.deprecatedMethod('Main.showHide()', '3.5');
     Doc.showHide(id, show);
   }
   
   // Shows an element with the given ID attribute as a block element
+  // @Deprecated
   this.show = function(id)
   {
+    App.deprecatedMethod('Main.show()', '3.5');
     Doc.show(id);
   }
   // Shows an element with the given ID attribute as an inline element
+  // @Deprecated
   this.showInline = function(id)
   {
+    App.deprecatedMethod('Main.showInline()', '3.5');
     Doc.show(id, 'inline');
   }
   // Hides an element with the given ID attribute
+  // @Deprecated
   this.hide = function(id)
   {
+    App.deprecatedMethod('Main.hide()', '3.5');
     Doc.hide(id);
   }
   
+  // @Deprecated
   this.addClass = function(obj, className)
   {
+    App.deprecatedMethod('Main.addClass()', '3.5');
     Doc.addClass(obj, className);
   }
   
+  // @Deprecated
   this.removeClass = function(obj, className)
   {
+    App.deprecatedMethod('Main.removeClass()', '3.5');
     Doc.removeClass(obj, className);
   }
   
+  // @Deprecated
   this.addOrRemoveClass = function(obj, className, addIfTrue)
   {
+    App.deprecatedMethod('Main.addOrRemoveClass()', '3.5');
     Doc.addOrRemoveClass(obj, className, addIfTrue);
   }
   
+  // @Deprecated
   this.toggleClass = function(obj, className)
   {
+    App.deprecatedMethod('Main.toggleClass()', '3.5');
     Doc.addOrRemoveClass(obj, className);
   }
@@ -248 +293 @@
   // Get the character code of an event that invloves a key, returns 0 if no code can be found
   // Use this method for onKeyPress events only. See also: getEventKeyCode()
+  // @Deprecated
   this.getEventCharCode = function(event)
   {
+    App.deprecatedMethod('Main.getEventCharCode()', '3.5');
     var charCode = event.charCode;
     if (event.ctrlKey) 
@@ -273 +320 @@
   // Get the key code of an event that invloves a key, returns 0 if no code can be found
   // Use this method for onKeyDown and onKeyUp events only. See also: getEventCharCode();
+  // @Deprecated
   this.getEventKeyCode = function(event)
   {
+    App.deprecatedMethod('Main.getEventKeyCode()', '3.5');
     return event.keyCode;
   }
@@ -280 +329 @@
   // Handle keypress events on focused elements:
   //  * Send a 'click' event to the same target if the 'ENTER' key was pressed
+  // @Deprecated
   this.handleFocusedKeypress = function(event)
   {
+    App.deprecatedMethod('Main.handleFocusedKeypress()', '3.5');
     Events.handleFocusedKeypress(event);
   }
   
   // Try to get the window height
+  // @Deprecated
   this.getWindowHeight = function(theWin)
   {
+    App.deprecatedMethod('Main.getWindowHeight()', '3.5');
     return App.getWindowPosition(theWin).height;
   }
   
   // Try to get the window width
+  // @Deprecated
   this.getWindowWidth = function(theWin)
   {
+    App.deprecatedMethod('Main.getWindowWidth()', '3.5');
     return App.getWindowPosition(theWin).width;
   }
@@ -300 +355 @@
   // returns an object with 'left', 'top', 'width' and 'height' properties
   // If 'rightAndBottom' is true, then 'right' and 'bottom' properties are also calculated
+  // @Deprecated
   this.getElementPosition = function(theElement, rightAndBottom)
   {
+    App.deprecatedMethod('Main.getElementPosition()', '3.5');
     return Doc.getElementPosition(theElement);
   }
   
   
+  // @Deprecated
   this.encodeURI = function(value)
   {
+    App.deprecatedMethod('Main.encodeURI()', '3.5');
     return encodeURIComponent(value);
   }
 
+  // @Deprecated
   this.encodeTags = function(value)
   {
+    App.deprecatedMethod('Main.encodeTags()', '3.5');
     return Strings.encodeTags(value);
   }
   
+  // @Deprecated
   this.viewFile = function(ID, fileId)
   {
+    App.deprecatedMethod('Main.viewFile()', '3.5');
     Files.viewFile(fileId);
   }
 
+  // @Deprecated
   this.downloadFile = function(ID, fileId)
   {
+    App.deprecatedMethod('Main.downloadFile()', '3.5');
     Files.downloadFile(fileId);
   }
   
   
+  // @Deprecated
   this.getController = function(itemType)
   {
+    App.deprecatedMethod('Main.getController()', '3.5');
     return Items.getController(itemType);
   }
   
+  // @Deprecated
   this.listItems = function(ID, itemType, extraUrl)
   {
+    App.deprecatedMethod('Main.listeItems()', '3.5');
     Items.list(itemType, extraUrl);
   }
     
+  // @Deprecated
   this.viewOrEditItem = function(ID, itemType, itemId, edit, extraUrl, popupOptions)
   {
+    App.deprecatedMethod('Main.viewOrEditItem()', '3.5');
     if (edit)
     {
@@ -350 +421 @@
   }
   
+  // @Deprecated
   this.selectItem = function(ID, itemType, mode, callback, extraUrl, popupOptions)
   {
+    App.deprecatedMethod('Main.selectItem()', '3.5');
     Dialogs.selectItem(itemType, callback, mode.indexOf('ultiple') > 0, extraUrl);
   }
   
+  // @Deprecated
   this.deleteItemPermanently = function(ID, ask, itemType, itemId, extraUrl, popupOptions)
   {
+    App.deprecatedMethod('Main.deleteItemPermanently()', '3.5');
     Items.deleteItemPermanently(itemType, itemId, ask);
   }
 
+  // @Deprecated
   this.showUsingItems = function(ID, itemType, itemId, extraUrl)
   {
+    App.deprecatedMethod('Main.showUsingItems()', '3.5');
     Items.showUsingItems(itemType, itemId);
   }
@@ -369 +446 @@
     @return A request object or null if the browser doesn't support ajax
   */
+  // @Deprecated
   this.getAjaxRequest = function()
   {
+    App.deprecatedMethod('Main.getAjaxRequest()', '3.5');
     return Ajax.getXmlHttpRequest();
   }
@@ -388 +467 @@
       (only if url is not too long)
   */
+  // @Deprecated
   this.safeSetLocation = function(url, win, replace)
   {
+    App.deprecatedMethod('Main.safeSetLocation()', '3.5');
     App.safeSetLocation(url, win, replace);
   }
@@ -396 +477 @@
     Check if the URL is longer than the configured max URL length.
   */
+  // @Deprecated
   this.isTooLongURL = function(url)
   {
+    App.deprecatedMethod('Main.isTooLongURL()', '3.5');
     return App.isTooLongUrl(url);
   }
@@ -412 +495 @@
       window.
   */
+  // @Deprecated
   this.convertToPostForm = function(url, win)
   {
+    App.deprecatedMethod('Main.convertToPostForm()', '3.5');
     return Forms.convertUrlToForm(url, win);
   }
@@ -420 +505 @@
     Save a key-value pair for a page.
   */
+  // @Deprecated
   this.setPageValue = function(page, key, value)
   {
+    App.deprecatedMethod('Main.setPageValue()', '3.5');
     Data.setPageValue(key, value, page);
   }
@@ -428 +515 @@
     Get the saved value for the given key on a page
   */
+  // @Deprecated
   this.getPageValue = function(page, key)
   {
+    App.deprecatedMethod('Main.getPageValue()', '3.5');
     return Data.getPageValue(key,  page);
   }
 
 
+  // @Deprecated
   this.debug = function(message, clearOutput)
   {
+    App.deprecatedMethod('Main.debug()', '3.5');
     App.debug(message);
   }
   
+  // @Deprecated
   this.hideDebug = function()
-  {}
+  {
+    App.deprecatedMethod('Main.hideDebug()', '3.5');
+  }
   
 }

trunk/www/include/scripts/popup.js

@@ -42 +42 @@
   {
     saveDialogPosition = window.top.name && App.rememberDialogPositions();
-    if (saveDialogPosition) setTimeout(internal.initPosition, 500);
+    if (saveDialogPosition) setTimeout(internal.initPosition, 200);
   }
   
@@ -51 +51 @@
     var key = 'dialog-position-req:'+window.top.name;
     var rpos = JSON.parse(App.getLocal(key));
-//    alert('['+window.screenX+', '+window.screenY+'], ['+rpos.width+', ' + rpos.height+'], ['+window.innerWidth+', ' + window.innerHeight+'], [' + window.outerWidth+', '+window.outerHeight+']');
     if (rpos)
     {
       App.removeLocal(key);
       var cpos = App.getWindowPosition(window.top);
-      dx = rpos.width-cpos.width;
-      dy = rpos.height-cpos.height;
+      dx = Math.min(rpos.width, screen.availWidth) - cpos.width;
+      dy = Math.min(rpos.height, screen.availHeight) - cpos.height;
+//      window.top.opener.App.debug('requested:'+JSON.stringify(rpos));
+//      window.top.opener.App.debug('actual:'+JSON.stringify(cpos));
+//      window.top.opener.App.debug('delta:'+dx+','+dy);
+//      window.top.opener.App.debug('screen:'+screen.availWidth+','+screen.availHeight);
     }
   }

trunk/www/include/scripts/table.js

@@ -422 +422 @@
     url += '&table_id='+tableDiv.id+'&item_type='+itemType+'&subcontext='+subContext;
     if (settingName) url += '&settingName='+settingName;
-    Dialogs.openPopup(url, 'ConfigureColumns', 600, 400);
+    Dialogs.openPopup(url, 'ConfigureColumns', 750, 450);
   }
 
@@ -658 +658 @@
       {
         element.checked = !element.checked;
+        Events.sendChangeEvent(element);
         return element;
       }
@@ -736 +737 @@
     }
     
-    var numSelected = 0;
+    var selected = [];
     if (frm.item_id)
     {
@@ -744 +745 @@
       {
         var id = element.value.match(/^\d+$/) ? parseInt(element.value) : element.value;
-        if (notifyTarget)
-        {
-          // Send event to the target in the opener window
-          Events.sendCustomEvent(notifyTarget, 'base-selected', {'id': id, 'name': element.title, 'itemType': itemType});
-        }
-        else if (callbackMethod)
-        {
-          // Call the callback method in the opener window
-          callbackMethod.call(null, id, element.title);
-        }
-        numSelected = 1;
+        selected[selected.length] = {'id': id, 'name': element.title, 'itemType': itemType};
       }
     }
@@ -766 +757 @@
         {
           var id = element.value.match(/^\d+$/) ? parseInt(element.value) : element.value;
-          if (notifyTarget)
-          {
-            // Send event to the target in the opener window
-            Events.sendCustomEvent(notifyTarget, 'base-selected', {'id': id, 'name': element.title, 'itemType': itemType});
-          }
-          else if (callbackMethod)
-          {
-            // Call the callback method in the opener window
-            callbackMethod.call(null, id, element.title);
-          }
-          numSelected++;
+          selected[selected.length] = {'id': id, 'name': element.title, 'itemType': itemType};
         }
       }
     }
-    return numSelected;
+    
+    var remaining = selected.length-1;
+    for (var i = 0; i < selected.length; i++)
+    {
+      var s = selected[i];
+      s.remaining = remaining--;
+      if (notifyTarget)
+      {
+        // Send event to the target in the opener window
+        Events.sendCustomEvent(notifyTarget, 'base-selected', s);
+      }
+      else if (callbackMethod)
+      {
+        // Call the callback method in the opener window
+        callbackMethod.call(null, s.id, s.name);
+      }
+    }
+
+    return selected.length;
   }
 

trunk/www/login.js

@@ -48 +48 @@
     login.initForm();
     
+    var footNoteFrame = App.topWindow().frames['footnote'];
+    if (footNoteFrame)
+    {
+      footNoteFrame.location.reload();      
+    }
+    
     if (Exception) Exception.fixWindow();
   }

trunk/www/views/jobs/view_job.jsp

@@ -239 +239 @@
         <th>Plugin</th>
         <td>
-          <base:propertyvalue item="<%=job%>" property="pluginDefinition.name" /> 
+          <base:propertyvalue item="<%=job%>" property="pluginDefinition.name" nulltext="<i>External</i>"/> 
           <%=job.getPluginVersion() == null ?
-            "" : "(version " + HTML.encodeTags(job.getPluginVersion()) + ")"%>
+            "" : "(" + HTML.encodeTags(job.getPluginVersion()) + ")"%>
         </td>
       </tr>

trunk/www/views/physicalbioassays/bioassays.js

@@ -353 +353 @@
     event.detail.value = ':1';
     Link.addItem('extracts', 'EXTRACT', event.detail);
-    bioassays.extractsOnChange();
+    if (event.detail.remaining == 0)
+    {
+      bioassays.extractsOnChange();
+    }
   }