Changeset 3647

Timestamp:

Aug 9, 2007, 11:11:10 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #718: BioAssaySet? tries to calculate number of spots and reporter on non-existing table

Location:

trunk/src

Files:

• core/net/sf/basedb/core/BioAssaySet.java (modified) (2 diffs)
• test/TestExperiment.java (modified) (4 diffs)

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

@@ -313 +313 @@
     if (action == Transactional.Action.CREATE)
     {
+      checkAndCreateTables();
       countSpotsAndReporters();
     }
@@ -1177 +1178 @@
   }
   
+  private void checkAndCreateTables()
+  {
+    VirtualDb vdb = getVirtualDb();
+    vdb.createTables(VirtualTable.SPOT, VirtualTable.POSITION);
+    if (getDataCubeFilterNo() != 0)
+    {
+      vdb.createTables(VirtualTable.FILTER);
+    }
+  }
+  
   /**
     Called when a bioassayset is about to be deleted. Finds which data cubes, layers, 

trunk/src/test/TestExperiment.java

@@ -38 +38 @@
 import net.sf.basedb.util.ConsoleProgressReporter;
 
+import java.util.Collections;
 import java.util.Date;
 import java.util.Set;
@@ -88 +89 @@
     test_list_rawbioassays(id, 2);
 
+    int emptyRootId = test_create_empty_root_bioassayset(id, rbaId1, rbaId2);
+    
     int rootBasId = test_create_root_bioassayset_using_calculator(id, "mean", rbaId1, rbaId2);
     int rootBasId2 = test_create_root_bioassayset_using_query(id, "mean", rbaId1, rbaId2);
@@ -109 +112 @@
     //int mergedBasId = test_merge_bioassays(filterBasId);
     
-    test_list_bioassaysets(id, 7);
+    test_list_bioassaysets(id, 8);
     
     test_list_bioassays(basId, 2);
@@ -600 +603 @@
     return id;
   }
+  
+  static int test_create_empty_root_bioassayset(int experimentId, int... rawBioAssays)
+  {
+    if (experimentId == 0) return 0;
+    int id = 0;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Experiment e = Experiment.getById(dc, experimentId);
+      
+      Set<RawBioAssay> rbaCollection = new HashSet<RawBioAssay>();
+      for (int rbaId : rawBioAssays)
+      {
+        rbaCollection.add(RawBioAssay.getById(dc, rbaId));  
+      }
+      
+      Transformation t = e.newTransformation(null, rbaCollection);
+      BioAssaySet root = t.newProduct("new", "new", false);
+      root.setName("No spots");
+      dc.saveItem(t);
+      dc.saveItem(root);
+      
+      for (RawBioAssay rba : rbaCollection)
+      {
+        // Create a new BioAssay for each raw bioassay
+        BioAssay ba = root.newRootBioAssay(Collections.singleton(rba));
+        ba.setName(rba.getName());
+        dc.saveItem(ba);
+      }
+      dc.commit();
+
+      int numSpots = root.getNumSpots();
+      id = root.getId();
+      dc = TestUtil.getDbControl();
+      dc.reattachItem(root);
+      write_item(0, root);
+      write("--Create empty root bioassayset OK ("+numSpots+" spots inserted)");
+    }
+    catch (Throwable ex)
+    {
+      write("--Create empty root bioassayset FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+    return id;
+  }
+  
   
   static int test_create_bioassayset(int bioAssaySetId)