Changeset 4358

Timestamp:

Jul 1, 2008, 11:08:43 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1075: Lowess normaliztion fails on trunk but works on latest 2.7-stable

Location:

trunk/src

Files:

• core/net/sf/basedb/core/AbstractEntityQuery.java (modified) (1 diff)
• core/net/sf/basedb/core/AbstractQuery.java (modified) (3 diffs)
• core/net/sf/basedb/core/DynamicQuery.java (modified) (1 diff)
• plugins/core/net/sf/basedb/plugins/LowessNormalization.java (modified) (2 diffs)
• plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) (2 diffs)

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

@@ -266 +266 @@
   public boolean isReadonly()
   {
-    return lastMainQuery != null;
+    return super.isReadonly() || lastMainQuery != null;
   }
   

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

@@ -439 +439 @@
   }
   
+  public boolean isReadonly()
+  {
+    return hasAutoJoined;
+  }
+  
   /**
     Resets the query, allowing you to add more restrictions, joins, order objects
@@ -818 +823 @@
     if (autoJoiners == null || hasAutoJoined) return;
     
-    hasAutoJoined = true;
     Iterator<QueryElement> iterator = new NestedIterator<QueryElement>(
       selects, permanentSelects, temporarySelects,
@@ -844 +848 @@
       }
     }
+    hasAutoJoined = true;
   }
   

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

@@ -83 +83 @@
     return HibernateUtil.quote(rootTable.getAlias());
   }
-  public boolean isReadonly()
-  {
-    return false;
-  }
   // -------------------------------------------
   

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

@@ -408 +408 @@
     // Count number of spots that is going to be normalized
     DynamicSpotQuery query = source.getSpotData();
-    query.restrict(intensityRestriction);
+    query.restrictPermanent(intensityRestriction);
     checkInterrupted();
     long numSpots = query.count(dc);
-    
+    query.reset();
+
     long normalizedSpots = 0;
     if (progress != null) progress.display((int)(normalizedSpots / numSpots * 100), normalizedSpots + " spots normalized");
@@ -435 +436 @@
     query.restrict(bioAssayRestriction);
     query.order(Orders.asc(block));
-      
+    
     // Normalize one bioassay at a time
     List<BioAssay> assays = source.getBioAssays().list(dc);

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

@@ -442 +442 @@
     // Get the number of spots to be normalized
     DynamicSpotQuery query = source.getSpotData();
-    query.restrict(intensityRestriction);
+    query.restrictPermanent(intensityRestriction);
     long numSpots = query.count(dc);
+    query.reset();
     long normalizedSpots = 0;
     if (progress != null)
@@ -551 +552 @@
     // Count number of spots that is going to be normalized
     DynamicSpotQuery query = source.getSpotData();
-    query.restrict(intensityRestriction);
+    query.restrictPermanent(intensityRestriction);
     checkInterrupted();
     long numSpots = query.count(dc);
+    query.reset();
     long normalizedSpots = 0;
     if (progress != null) progress.display((int)(normalizedSpots / numSpots * 100), normalizedSpots + " spots normalized");