Changeset 728

Timestamp:

Jul 17, 2008, 4:20:07 PM (15 years ago)

Author:

Martin Svensson

Message:

Re-arrange the files.
Created the plug-in body for average and cubic spline, without the algorithms.

Location:

plugins/base2/net.sf.basedb.normalizations/trunk/src/net/sf/basedb

Files:

• normalizations (added)
• normalizations/Normalizations.java (added)
• plugins/AbstractNormalizationPlugin.java (added)
• plugins/AverageNormalization.java (copied) (copied from plugins/base2/net.sf.basedb.normalizations/trunk/src/net/sf/basedb/plugins/average/AverageNormalization.java) (3 diffs)
• plugins/CubicSplineNormalization.java (added)
• plugins/average (deleted)
• plugins/cubicspline (deleted)
• plugins/rankinvariant (deleted)

plugins/base2/net.sf.basedb.normalizations/trunk/src/net/sf/basedb/plugins/AverageNormalization.java

@@ -24 +24 @@
 */
 
-package net.sf.basedb.plugins.average;
+package net.sf.basedb.plugins;
 
 import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.BioAssay;
+import net.sf.basedb.core.BioAssaySet;
+import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.PluginParameter;
 import net.sf.basedb.core.ProgressReporter;
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.core.plugin.AboutImpl;
-import net.sf.basedb.core.plugin.AbstractPlugin;
 import net.sf.basedb.core.plugin.GuiContext;
 import net.sf.basedb.core.plugin.InteractivePlugin;
@@ -37 +40 @@
 import net.sf.basedb.core.plugin.Response;
 import net.sf.basedb.core.signal.SignalHandler;
+import net.sf.basedb.core.signal.SignalReceivedException;
 import net.sf.basedb.core.signal.SignalTarget;
-
-import java.util.Set;
+import net.sf.basedb.core.signal.ThreadSignalHandler;
+import net.sf.basedb.normalizations.Normalizations;
+import net.sf.basedb.util.Values;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 /**
@@ -50 +59 @@
  */
 public class AverageNormalization 
-  extends AbstractPlugin 
-  implements SignalTarget, InteractivePlugin
+  extends AbstractNormalizationPlugin
+  implements InteractivePlugin, SignalTarget
 {
+  /**
+    Use to abort a running job
+   */
+  private ThreadSignalHandler signalHandler;
+  
+  /**
+    Holds the configured job parameters
+  */
+  private RequestInformation configureJob = null;
+  
   
   private final About about = new AboutImpl
   (
     "Average normalization plug-in",
-    "",
-    "",
-    "",
-    "",
-    "", 
-    ""
+    "This normalization plug-in uses the average algorithm to adjust sample signals.\n" +
+    "\n" +
+    "This plug-in is part of the BASE 2 normalization package.",
+    Normalizations.PACKAGE_VERSION,
+    Normalizations.COPYRIGHT,
+    null,
+    Normalizations.EMAIL, 
+    Normalizations.URL
   );
-
-  /*  (non-Javadoc)
-      @see net.sf.basedb.core.signal.SignalTarget#getSignalHandler()
+    
+  /*
+    From SignalTarget interface
+  */
+  @Override
+  public SignalHandler getSignalHandler()
+  {
+    signalHandler = new ThreadSignalHandler();
+    return signalHandler;
+  }
+  /*
+   ---------------------------------------------------------
+  */
+
+
+  /*
+    From InteractivePlugin interface
    */
   @Override
-  public SignalHandler getSignalHandler()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*  (non-Javadoc)
-      @see net.sf.basedb.core.plugin.InteractivePlugin#configure(net.sf.basedb.core.plugin.GuiContext, net.sf.basedb.core.plugin.Request, net.sf.basedb.core.plugin.Response)
-   */
-  @Override
-  public void configure(GuiContext arg0, Request arg1, Response arg2)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  /*  (non-Javadoc)
-      @see net.sf.basedb.core.plugin.InteractivePlugin#getGuiContexts()
-   */
-  @Override
-  public Set<GuiContext> getGuiContexts()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*  (non-Javadoc)
-      @see net.sf.basedb.core.plugin.InteractivePlugin#getRequestInformation(net.sf.basedb.core.plugin.GuiContext, java.lang.String)
-   */
-  @Override
-  public RequestInformation getRequestInformation(GuiContext context, String arg1)
+  public void configure(GuiContext context, Request request, Response response)
+  {
+    String command = request.getCommand();
+    if (command.equals(Request.COMMAND_CONFIGURE_JOB))
+    {
+      try
+      {
+        RequestInformation ri = getConfiguredJobParameters();
+        List<Throwable> errors = validateRequestParameters(ri.getParameters(), request);
+        if (errors != null)
+        {
+          response.setError(errors.size() + " invalid parameter(s) were found in the request", errors);
+          return;
+        }
+
+        // Source bioassay set
+        storeValue(job, request, ri.getParameter(SOURCE_BIOASSAYSET));
+                
+        // Child name, description and transformation
+        storeValue(job, request, ri.getParameter(CHILD_NAME));
+        storeValue(job, request, ri.getParameter(CHILD_DESCRIPTION));
+        
+        //TODO Store Average Normalization specific parameters
+      }
+      catch (SignalReceivedException signalException)
+      {
+        response.setError("Aborted by user.", Arrays.asList(signalException));
+      }
+      catch (Throwable ex)
+      {
+        response.setError(ex.getMessage(), Arrays.asList(ex));
+      }
+    }
+  }
+
+
+  @Override
+  public RequestInformation getRequestInformation(GuiContext context, String command)
       throws BaseException
   {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*  (non-Javadoc)
-      @see net.sf.basedb.core.plugin.InteractivePlugin#isInContext(net.sf.basedb.core.plugin.GuiContext, java.lang.Object)
-   */
-  @Override
-  public String isInContext(GuiContext arg0, Object arg1)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*  (non-Javadoc)
-      @see net.sf.basedb.core.plugin.Plugin#getAbout()
-   */
+    RequestInformation requestInformation = null;
+    if (command.equals(Request.COMMAND_CONFIGURE_JOB))
+    {
+      requestInformation = getConfiguredJobParameters();
+    }
+    return requestInformation;
+  }
+  /*
+   ---------------------------------------------------------
+  */
+  
+  /*
+    From Plugin interface
+  */
   @Override
   public About getAbout()
   {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*  (non-Javadoc)
-      @see net.sf.basedb.core.plugin.Plugin#getMainType()
-   */
-  @Override
-  public MainType getMainType()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*  (non-Javadoc)
-      @see net.sf.basedb.core.plugin.Plugin#run(net.sf.basedb.core.plugin.Request, net.sf.basedb.core.plugin.Response, net.sf.basedb.core.ProgressReporter)
-   */
-  @Override
-  public void run(Request arg0, Response arg1, ProgressReporter arg2)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
+    return about;
+  }
+
+  @Override
+  public void run(Request request, Response response, ProgressReporter progress)
+  {
+    String command = request.getCommand();
+    if (command.equals(Request.COMMAND_EXECUTE))
+    {
+      if (signalHandler != null) 
+      {
+        signalHandler.setWorkerThread(null);
+      }
+      DbControl dc = null;
+      try
+      {
+        dc = sc.newDbControl();
+        BioAssaySet source = getSourceBioAssaySet(dc);
+        String childName = Values.getString((String)job.getValue(CHILD_NAME), source.getName());
+        String childDescription = (String)job.getValue(CHILD_DESCRIPTION);
+        
+        List<BioAssay> referenceGroup = getReferenceGroup(dc);
+        //TODO Implement things specific for the algortihm.
+      }
+      catch (Throwable ex)
+      {
+        response.setError(ex.getMessage(), Arrays.asList(ex));
+      }
+      finally
+      {
+        if (dc != null) dc.close();
+      }
+    }
+  }
+  /*
+   ---------------------------------------------------------
+  */
+  
+  private RequestInformation getConfiguredJobParameters()
+  {
+    DbControl dc = null;
+    try
+    {
+      if (configureJob == null)
+      {
+        dc = sc.newDbControl();
+        BioAssaySet bas = getCurrentBioAssaySet(dc);
+        List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>(3);
+        
+        // Source and child bioassay set parameters
+        parameters.add(getSourceBioAssaySetParameter(null, null));
+        parameters.add(getChildNameParameter(null, null, bas.getName()));
+        parameters.add(getChildDescriptionParameter(null, null, null)); 
+
+        //Reference group
+        parameters.add(getReferenceGroupParameter(null, null));
+        //TODO Configure Average Normalization specific parameters.
+      }
+    }
+    finally
+    {
+      if (dc != null ) dc.close();
+    }
+    
+    return configureJob;
+  }
 }