Changeset 6456

Timestamp:

May 9, 2014, 11:21:36 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1806: Fail to load upstream extracts from physical bioassays when inheriting annotations

Location:

trunk/src/core/net/sf/basedb

Files:

• core/MeasuredBioMaterial.java (modified) (5 diffs)
• util/AnnotationUtil.java (modified) (7 diffs)

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

@@ -24 +24 @@
 package net.sf.basedb.core;
 
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
+import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
@@ -36 +38 @@
 import net.sf.basedb.core.log.ChangeType;
 import net.sf.basedb.core.log.LoggingInterceptor;
+import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.util.EqualsHelper;
+import net.sf.basedb.util.collections.BasicItemToIdTransformer;
 
 /**
@@ -189 +195 @@
     throws BaseException
   {
+    return getAnnotatableParents(null);
+  }
+  // -------------------------------------------
+
+  /**
+    Get the annotable parents, possible only a given set of specific parents items.
+    @param parents If not null or empty, only include the given parent items (for pooled items only)
+    @since 3.3
+  */
+  public Set<Annotatable> getAnnotatableParents(Collection<? extends MeasuredBioMaterial> parents)
+    throws BaseException
+  {
     Set<Annotatable> annotatable = super.getAnnotatableParents();
     try
@@ -200 +218 @@
         ItemQuery<? extends BioMaterial> query = getCreationEvent().getSources();
         query.include(Include.ALL);
+        if (parents != null && parents.size() > 0)
+        {
+          query.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("parents")));
+          Set<Integer> parentIds = new HashSet<Integer>();
+          new BasicItemToIdTransformer().transform(parents, parentIds);
+          query.setParameter("parents", parentIds, Type.INT);
+        }
         annotatable.addAll(query.list(getDbControl()));
       }
@@ -211 +236 @@
     return annotatable;
   }
-  // -------------------------------------------
-
-  
+
   /*
     From the Subtypable interface

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

@@ -39 +39 @@
 import net.sf.basedb.core.PhysicalBioAssay;
 import net.sf.basedb.core.RawBioAssay;
+import net.sf.basedb.util.biomaterial.ChildrenTransformer;
+import net.sf.basedb.util.extensions.events.AllEventsFilter;
 import net.sf.basedb.util.filter.Filter;
 
@@ -115 +117 @@
       {
         // ...and queue the parents items for processing...
-        unprocessed.addAll(toProcess.getAnnotatableParentWrappers());
+        unprocessed.addAll(toProcess.getAnnotatableParentWrappers(dc));
       }
     }
@@ -170 +172 @@
     private final Annotatable item;
     private final Set<Extract> extractsInChain;
+    private Set<Extract> allChildExtractsInChain;
     private final AnnotatableWrapper chain;
     private final Cache cache;
@@ -181 +184 @@
       this.extract = getExtract(item);
       this.extractsInChain = loadExtracts();
+      this.allChildExtractsInChain = null;
     }
     
@@ -190 +194 @@
       this.extract = getExtract(item);
       this.extractsInChain = loadExtracts();
+      this.allChildExtractsInChain = chain.allChildExtractsInChain;
     }
     
@@ -233 +238 @@
       Get all annotatable parents wrapped inside AnnotatableWrapper:s
     */
-    Set<AnnotatableWrapper> getAnnotatableParentWrappers() 
+    Set<AnnotatableWrapper> getAnnotatableParentWrappers(DbControl dc) 
       throws BaseException
     {
@@ -247 +252 @@
         if (item instanceof PhysicalBioAssay)
         {
-          parents = ((PhysicalBioAssay)item).getAnnotatableParents(0, extractsInChain);
+          allChildExtractsInChain = new HashSet<Extract>();
+          if (extractsInChain.size() > 0)
+          {
+            // Only load parents that eventually lead up to one of the extracts in the chain
+            ChildrenTransformer<Extract> transformer = new ChildrenTransformer<Extract>(dc, true, Extract.getQuery());
+            transformer.transform(extractsInChain, allChildExtractsInChain);
+          }
+          parents = ((PhysicalBioAssay)item).getAnnotatableParents(0, allChildExtractsInChain);
+        }
+        else if (item instanceof Extract)
+        {
+          if (extractsInChain.contains(item))
+          {
+            // When we have reached one of the items in the chain, we no longed need to restrict the loading of parent items
+            allChildExtractsInChain = null;
+          }
+          parents = ((Extract)item).getAnnotatableParents(allChildExtractsInChain);
         }
         else