Changeset 2998

Timestamp:

Dec 4, 2006, 10:28:39 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

References #215: Incorrect use of DynamicSpotQuery?...

Fixed problem with DataCube?.onBeforeCommit() never beeing called, and no spot count was generated.

Location:

trunk/src/core/net/sf/basedb

Files:

• core/AnnotatedItem.java (modified) (1 diff)
• core/AnnotationSet.java (modified) (1 diff)
• core/BioAssay.java (modified) (1 diff)
• core/BioAssaySet.java (modified) (1 diff)
• core/DbControl.java (modified) (5 diffs)
• core/DynamicResultIterator.java (modified) (2 diffs)
• core/RawBioAssay.java (modified) (1 diff)
• core/Transformation.java (modified) (2 diffs)
• core/Well.java (modified) (1 diff)
• core/data/BioAssaySetData.java (modified) (1 diff)
• core/data/DataCubeLayerData.java (modified) (1 diff)
• util/BioAssaySetFilterUtil.java (modified) (2 diffs)

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

@@ -59 +59 @@
       as = AnnotationSet.getNew(dc, this);
       getData().setAnnotationSet(as.getData());
-      dc.saveItemIf(this, as);
+      dc.saveItemIf(this, as, false);
     }
     return as;

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

@@ -280 +280 @@
       a = Annotation.getNew(dc, annotationType, this);
       getData().getAnnotations().put(annotationType.getData(), a.getData());
-      dc.saveItemIf(this, a); 
+      dc.saveItemIf(this, a, false); 
     }
     return a;

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

@@ -186 +186 @@
       as = AnnotationSet.getNew(dc, this);
       getData().setAnnotationSet(as.getData());
-      dc.saveItemIf(this, as);
+      dc.saveItemIf(this, as, false);
     }
     return as;

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

@@ -245 +245 @@
       as = AnnotationSet.getNew(dc, this);
       getData().setAnnotationSet(as.getData());
-      dc.saveItemIf(this, as);
+      dc.saveItemIf(this, as, false);
     }
     return as;

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

@@ -96 +96 @@
     @see #saveItemIf(BasicItem, BasicItem)
   */
-  private Map<BasicItem, List<BasicItem>> saveIfQueue;
+  private Map<BasicItem, List<SaveIf>> saveIfQueue;
   
   /**
@@ -815 +815 @@
     item.initPermissions(0, 0);
     item.checkPermission(Permission.CREATE);
+
+    // Check save-if queue
+    List<SaveIf> saveIfItems = saveIfQueue == null ? null : saveIfQueue.remove(item);
+    
+    // Save items with before=TRUE
+    if (saveIfItems != null)
+    {
+      for (SaveIf ifItem : saveIfItems)
+      {
+        if (ifItem.before && !ifItem.item.isInDatabase())
+        {
+          saveItem(ifItem.item);
+        }
+      }
+    }
+    
+    // Save the item
     commitQueue.put(item, Transactional.Action.CREATE);
     
-    // Check save-if queue
-    if (saveIfQueue != null)
-    {
-      List<BasicItem> items = saveIfQueue.remove(item);
-      if (items != null)
-      {
-        for (BasicItem cItem : items)
-        {
-          if (!cItem.isInDatabase()) saveItem(cItem);
+    // Save items with before=FALSE
+    if (saveIfItems != null)
+    {
+      for (SaveIf ifItem : saveIfItems)
+      {
+        if (!ifItem.before && !ifItem.item.isInDatabase())
+        {
+          saveItem(ifItem.item);
         }
       }
@@ -842 +858 @@
     @param itemIf The parent item that must be saved
     @param item The item to save when the parent item is saved
+    @param before TRUE if the <code>item</code> should be saved before the <code>itemIf</code>,
+      FALSE to save <code>itemIf</code> first
     @see #saveItem(BasicItem)
-   */
-  public void saveItemIf(BasicItem itemIf, BasicItem item)
+  */
+  public void saveItemIf(BasicItem itemIf, BasicItem item, boolean before)
   {
     if (itemIf == null || item == null) return;
@@ -853 +871 @@
     else
     {
-      if (saveIfQueue == null) saveIfQueue = new HashMap<BasicItem, List<BasicItem>>();
-      List<BasicItem> items = saveIfQueue.get(itemIf);
+      if (saveIfQueue == null) saveIfQueue = new HashMap<BasicItem, List<SaveIf>>();
+      List<SaveIf> items = saveIfQueue.get(itemIf);
       if (items == null)
       {
-        items = new LinkedList<BasicItem>();
+        items = new LinkedList<SaveIf>();
         saveIfQueue.put(itemIf, items);
       }
-      items.add(item);
+      items.add(new SaveIf(item, before));
     }
   }
@@ -1029 +1047 @@
   }
   
+  private static class SaveIf
+  {
+    private final BasicItem item;
+    private final boolean before;
+    
+    private SaveIf(BasicItem item, boolean before)
+    {
+      this.item = item;
+      this.before = before;
+    }
+  }
+  
+  
 }

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

@@ -45 +45 @@
 
   /**
+    Logger.
+  */
+  private static final org.apache.log4j.Logger log = 
+    org.apache.log4j.LogManager.getLogger("net.sf.basedb.core.query.DynamicResultIterator");
+  
+  /**
     The results of the query.
   */
@@ -104 +110 @@
       try
       {
+        results.getStatement().close();
         results.close();
-        results.getStatement().close();
       }
       catch (SQLException ex)
       {
-        throw new DatabaseException(ex);
+        log.warn("Exception when closing result set", ex);
       }
     }

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

@@ -492 +492 @@
     {
       spotImages = SpotImages.getNew(getDbControl(), this);
-      getDbControl().saveItemIf(this, spotImages);
+      getDbControl().saveItemIf(this, spotImages, false);
     }
     else

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

@@ -447 +447 @@
     }
     DataCubeLayer layer = namedLayers.get(namedLayer);
+    DbControl dc = getDbControl();
+    DataCube cube = null;
     if (layer == null)
     {
-      DataCube cube = namedCubes.get(namedCube);
+      cube = namedCubes.get(namedCube);
       if (cube == null)
       {
@@ -458 +460 @@
       namedLayers.put(namedLayer, layer);
     }
-    BioAssaySet newBas = BioAssaySet.getNew(getDbControl(), this, layer);
+    BioAssaySet newBas = BioAssaySet.getNew(dc, this, layer);
+    if (cube != null && !cube.isInDatabase()) dc.saveItemIf(newBas, cube, true);
+    if (!layer.isInDatabase()) dc.saveItemIf(newBas, layer, true);
     
     if (namedCube == null && createChildBioAssays)
     {
-      DbControl dc = getDbControl();
       BioAssaySet source = getSource();
       for (BioAssay parentBa : source.getBioAssays().list(dc))
       {
         BioAssay childBa = newBas.newBioAssay(parentBa);
-        dc.saveItemIf(newBas, childBa);
+        dc.saveItemIf(newBas, childBa, false);
       }
     }

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

@@ -128 +128 @@
       as = AnnotationSet.getNew(dc, this);
       getData().setAnnotationSet(as.getData());
-      dc.saveItemIf(this, as);
+      dc.saveItemIf(this, as, false);
     }
     return as;

trunk/src/core/net/sf/basedb/core/data/BioAssaySetData.java

@@ -138 +138 @@
     Get the layer this bioassayset stores it's data in.
     @hibernate.many-to-one column="`datacubelayer_id`" not-null="true" outer-join="false" 
-      update="false" cascade="save-update"
+      update="false"
   */
   public DataCubeLayerData getDataCubeLayer()

trunk/src/core/net/sf/basedb/core/data/DataCubeLayerData.java

@@ -44 +44 @@
     Get the data cube this layer belongs to.
     @hibernate.many-to-one column="`datacube_id`" not-null="true" outer-join="false" 
-      update="false" unique-key="uniquelayer" cascade="save-update"
+      update="false" unique-key="uniquelayer"
   */
   public DataCubeData getDataCube()

trunk/src/core/net/sf/basedb/util/BioAssaySetFilterUtil.java

@@ -130 +130 @@
     {
       BioAssay childBa = child.newBioAssay(parentBa);
-      dc.saveItemIf(child, childBa);
+      dc.saveItemIf(child, childBa, false);
       spotsDone += parentBa.getNumSpots();
       query.setParameter("column", (int)parentBa.getDataCubeColumnNo(), Type.INT);
@@ -193 +193 @@
         BioAssay ba = bioAssays.get(i);
         BioAssay childBa = child.newBioAssay(ba);
-        dc.saveItemIf(child, childBa);
+        dc.saveItemIf(child, childBa, false);
         selectedColumns[i] = Expressions.integer(ba.getDataCubeColumnNo());
         spotsTotal += ba.getNumSpots();