Changeset 999

Timestamp:

Mar 27, 2009, 3:35:14 PM (15 years ago)

Author:

Jari Häkkinen

Message:

Restructured result storage.

File:

• plugins/base2/net.sf.basedb.pluginutilities/trunk/src/net/sf/basedb/plugins/AbstractRunBinaryPlugin.java (modified) (5 diffs)

plugins/base2/net.sf.basedb.pluginutilities/trunk/src/net/sf/basedb/plugins/AbstractRunBinaryPlugin.java

@@ -2 +2 @@
   $Id$
 
-  Copyright (C) 2008 Jari Hakkinen
+  Copyright (C) 2008, 2009 Jari Hakkinen
 
   This file is part of the PluginUtilities
@@ -29 +29 @@
 import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
-import net.sf.basedb.core.Experiment; // Jari, remove this?
-import net.sf.basedb.core.InvalidUseOfNullException; // Jari, remove this?
 import net.sf.basedb.core.Job;
 import net.sf.basedb.core.PluginDefinition;
 import net.sf.basedb.core.PluginParameter;
 import net.sf.basedb.core.ProgressReporter;
-import net.sf.basedb.core.RawBioAssay; // Jari, remove this?
 import net.sf.basedb.core.RequestInformation;
+import net.sf.basedb.core.SpotBatcher;
+import net.sf.basedb.core.Transformation;
+import net.sf.basedb.util.Values;
 
 import net.sf.basedb.core.plugin.About;
@@ -283 +283 @@
     DbControl dc=sc.newDbControl();
     try {
-      String name=(String)job.getValue("name");
-      if (name==null)
-        name="New bioassay set";
       if (sourceBAS==null)
         sourceBAS = getSourceBioAssaySet(dc);
       runBinary();
-      storeResult(dc,name);
+      storeResult(dc);
 //      dc.commit();
       response.setDone("Plug-in ended successfully");
@@ -323 +320 @@
 
 
-  abstract protected void storeResult(DbControl dc, String name);
+  private void storeResult(DbControl dc)
+  {
+    // Create Transformation
+    Transformation t = sourceBAS.newTransformation(this.getCurrentJob(dc));
+    t.setName(about.getName());
+    dc.saveItem(t);
+
+    // Create the normalized bioassay set
+    BioAssaySet child = t.newProduct(null, "new", true);
+    child.setName(Values.getString((String)job.getValue(CHILD_NAME),
+                                   sourceBAS.getName()));
+    child.setDescription((String)job.getValue(CHILD_DESCRIPTION));
+    dc.saveItem(child);
+
+    // Batcher for inserting normalized data
+    SpotBatcher batcher = child.getSpotBatcher();
+    storeResult(batcher);
+  }
+
+
+  abstract protected void storeResult(SpotBatcher batcher)
+    throws BaseException;
 
 
@@ -339 +357 @@
   protected String subprocess_stdin=null;
   protected String subprocess_stdout=null;
+  protected String metadata=null;
 
   private String binaryPath=null;