Changeset 7303

Timestamp:

Mar 1, 2017, 3:36:09 PM (6 years ago)

Author:

Nicklas Nordborg

Message:

References #2058: Item overview is not working when going from extract to derived bioassay

The second fix did not work since it was going up and down among the extracts causing derived bioassays for other libraries in the pool to be loaded when they should not be loaded.

This fix changes the code so that only parent extracts from the root node are considered when loading the derived and raw bioassays.

Location:

trunk/src/core/net/sf/basedb/util/overview/loader

Files:

• DerivedBioAssayLoader.java (modified) (7 diffs)
• RawBioAssayLoader.java (modified) (5 diffs)

trunk/src/core/net/sf/basedb/util/overview/loader/DerivedBioAssayLoader.java

@@ -22 +22 @@
 package net.sf.basedb.util.overview.loader;
 
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -211 +212 @@
     // We should only load derived bioassays that has a null extract or an
     // extract that is found in the parent chain
-    Set<Integer> extractIds = getExtractChain(bioAssayNode);
+    Set<Integer> extractIds = getExtractChain(dc, bioAssayNode);
     if (extractIds.size() > 0)
-    {
-      // Since we don't know exactly how far upstreams the given extracts are we
-      // must first find all parent items (recursively)
-      Set<Integer> allParents = getAllExtractParents(dc, extractIds);
-      
+    {     
       query.restrict(
         Restrictions.or(
@@ -223 +220 @@
           Restrictions.in(Hql.property("extract"), Expressions.parameter("extracts"))
         ));
-      query.setParameter("extracts", allParents, Type.INT);
+      query.setParameter("extracts", extractIds, Type.INT);
     }
 
@@ -254 +251 @@
     // We should only load derived bioassays that has a null extract or an
     // extract that is found in the parent chain
-    Set<Integer> extractIds = getExtractChain(parentNode);
+    Set<Integer> extractIds = getExtractChain(dc, parentNode);
     if (extractIds.size() > 0)
-    {
-      // Since we don't know exactly how far upstreams the given extracts are we
-      // must first find all parent items (recursively)
-      Set<Integer> allParents = getAllExtractParents(dc, extractIds);
-      
+    {     
       query.restrict(
         Restrictions.or(
@@ -266 +259 @@
           Restrictions.in(Hql.property("extract"), Expressions.parameter("extracts"))
         ));
-      query.setParameter("extracts", allParents, Type.INT);
+      query.setParameter("extracts", extractIds, Type.INT);
     }
 
@@ -399 +392 @@
   }
   
-  private Set<Integer> getExtractChain(Node node)
+  private Set<Integer> getExtractChain(DbControl dc, Node node)
   {
     List<Node> extractNodes = node.findAll(new ItemTypeFilter(Item.EXTRACT));
@@ -406 +399 @@
     {
       extractIds.add(n.getItem().getId());
+      if (n.getParent() == null)
+      {
+        // We have reach the root node, continue to load parent extracts from here
+        SourceItemTransformer transformer = new ExtractToParentExtractTransformer(true);
+        extractIds.addAll(transformer.transform(new TransformContext(dc), Collections.singleton(n.getItem().getId())));
+        
+      }
     }
     return extractIds;
   }
-  
-  private Set<Integer> getAllExtractParents(DbControl dc, Set<Integer> extracts)
-  {
-    SourceItemTransformer transformer = new ExtractToParentExtractTransformer(true);
-    return transformer.transform(new TransformContext(dc), extracts);
-  }
 
   

trunk/src/core/net/sf/basedb/util/overview/loader/RawBioAssayLoader.java

@@ -23 +23 @@
 
 
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -205 +206 @@
     // We should only load derived bioassays that has a null extract or an
     // extract that is found in the parent chain
-    Set<Integer> extractIds = getExtractChain(bioAssayNode);
+    Set<Integer> extractIds = getExtractChain(dc, bioAssayNode);
     if (extractIds.size() > 0)
     {
-      // Since we don't know exactly how far upstreams the given extracts are we
-      // must first find all parent items (recursively)
-      Set<Integer> allParents = getAllExtractParents(dc, extractIds);
-      
       query.restrict(
         Restrictions.or(
@@ -217 +214 @@
           Restrictions.in(Hql.property("parentExtract"), Expressions.parameter("extracts"))
         ));
-      query.setParameter("extracts", allParents, Type.INT);
+      query.setParameter("extracts", extractIds, Type.INT);
     }
   
@@ -256 +253 @@
   }
   
-  private Set<Integer> getExtractChain(Node node)
+  private Set<Integer> getExtractChain(DbControl dc, Node node)
   {
     List<Node> extractNodes = node.findAll(new ItemTypeFilter(Item.EXTRACT));
@@ -263 +260 @@
     {
       extractIds.add(n.getItem().getId());
+      if (n.getParent() == null)
+      {
+        // We have reach the root node, continue to load parent extracts from here
+        SourceItemTransformer transformer = new ExtractToParentExtractTransformer(true);
+        extractIds.addAll(transformer.transform(new TransformContext(dc), Collections.singleton(n.getItem().getId())));
+        
+      }
     }
     return extractIds;
   }
-  
-  private Set<Integer> getAllExtractParents(DbControl dc, Set<Integer> extracts)
-  {
-    SourceItemTransformer transformer = new ExtractToParentExtractTransformer(true);
-    return transformer.transform(new TransformContext(dc), extracts);
-  }
 
 }