Changeset 3592

Timestamp:

Jul 23, 2007, 2:57:39 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #687: Make it possible for other plug-ins than the FormulaFilter? to be launched by the 'Filter bioassayset' button

Location:

trunk

Files:

• doc/src/docbook/developerdoc/plugin_developer.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/core/plugin/AnalysisFilterPlugin.java (added)
• src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java (modified) (2 diffs)
• www/common/plugin/index.jsp (modified) (1 diff)
• www/views/experiments/bioassaysets/analysis_tree.jsp (modified) (1 diff)
• www/views/experiments/bioassaysets/index.jsp (modified) (1 diff)

trunk/doc/src/docbook/developerdoc/plugin_developer.xml

@@ -2981 +2981 @@
       
     </sect2>
+    
+    <sect2 id="plugin_developer.analyse.filterplugin">
+      <title>The AnalysisFilterPlugin interface</title>
+      
+      <para>
+        The <interfacename>net.sf.basedb.core.plugin.AnalysisFilterPlugin</interfacename> 
+        is a tagging interface with no methods that all analysis plug-ins that only filters
+        data should implement. The benefit is that they will be linked from the
+        <guibutton>Filter bioassay set</guibutton> button and not just
+        the <guibutton>Run analysis</guibutton> button. They will also get
+        a different icon in the experiment outline to make filtering 
+        transformations appear different from other transformations.
+      </para>
+      
+      <para>
+        The interface exists purely for making the user interaction better. There is
+        no harm in not implementing it since the plug-in will always appear in
+        from the <guibutton>Run analysis</guibutton> button. On the other hand,
+        it doesn't cost anything to implement the interface since it doesn't
+        have any methods.
+      </para>
+    
+    </sect2>
 
   </sect1>

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

@@ -581 +581 @@
         "file system  first. For this to work the plugin must also be given 'immediate exection' rights",
         "net.sf.basedb.core.plugin.ImmediateDownloadExporter", null);
-
+      createPluginType("Analysis filter plug-in", "Analysis plug-ins that are pure filter plug-ins should " +
+          "implement this interface. If they do they are linked with the 'Filter bioassayset' button and" +
+          "not just the 'Run analysis plug-in' button.",
+          "net.sf.basedb.core.plugin.AnalysisFilterPlugin", null);
+      
       createPluginDefinition("net.sf.basedb.plugins.Base1PluginExecuter", null, null, true, null, false);
       createPluginDefinition("net.sf.basedb.plugins.BioAssaySetExporter", null, keyEveryoneUse, true, null, true);

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

@@ -41 +41 @@
 import net.sf.basedb.core.plugin.AboutImpl;
 import net.sf.basedb.core.plugin.AbstractAnalysisPlugin;
+import net.sf.basedb.core.plugin.AnalysisFilterPlugin;
 import net.sf.basedb.core.plugin.GuiContext;
 import net.sf.basedb.core.plugin.InteractivePlugin;
@@ -71 +72 @@
 public class FormulaFilter
   extends AbstractAnalysisPlugin
-  implements InteractivePlugin
+  implements InteractivePlugin, AnalysisFilterPlugin
 {
 

trunk/www/common/plugin/index.jsp

@@ -129 +129 @@
     GuiContext context = new GuiContext(itemType, contextType, subContext);
     Plugin.MainType mainType = Plugin.MainType.valueOf(request.getParameter("main_type"));
-
-    ItemQuery<PluginDefinition> pluginQuery = PluginDefinition.getQuery(context, null);
+    String pluginType = request.getParameter("plugin_type");
+
+    ItemQuery<PluginDefinition> pluginQuery = PluginDefinition.getQuery(context, pluginType);
     pluginQuery.restrict(
       Restrictions.eq(

trunk/www/views/experiments/bioassaysets/analysis_tree.jsp

@@ -179 +179 @@
   else if (nodeType == Item.TRANSFORMATION)
   {
+    Transformation t = (Transformation)node;
     folderIcon = "Transformation";
-    name = ((Transformation)node).getName();
+    try
+    {
+      if (t.getJob().getPluginDefinition().supports("net.sf.basedb.core.plugin.AnalysisFilterPlugin"))
+      {
+        folderIcon = "Filter";
+      }
+    }
+    catch (Throwable tt)
+    {}
+    name = t.getName();
   } 
   else if (nodeType == Item.EXTRAVALUE) 

trunk/www/views/experiments/bioassaysets/index.jsp

@@ -358 +358 @@
     // Display the edit page for for filtering a bioassay set (should be opened in a popup)
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
-    redirect = "../../../common/plugin/index.jsp?ID="+ID+"&cmd=NewJob&item_type="+itemType.name()+"&context_type=ITEM&main_type=ANALYZE&title=Filter+bioassay+set&plugin_class=net.sf.basedb.plugins.FormulaFilter";
+    redirect = "../../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=ANALYZE&title=Filter+bioassay+set&plugin_type=net.sf.basedb.core.plugin.AnalysisFilterPlugin";
   }
   else