Changeset 7302

Timestamp:

Mar 1, 2017, 2:22:26 PM (6 years ago)

Author:

Nicklas Nordborg

Message:

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

This should hopefully fix the second problem with back-links going to a parent extract higher up in the overview tree. The same fix was needed for both derived and raw bioassays.

Location:

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

Files:

• DerivedBioAssayLoader.java (modified) (6 diffs)
• RawBioAssayLoader.java (modified) (4 diffs)

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

@@ -40 +40 @@
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.util.listable.ExtractToParentExtractTransformer;
+import net.sf.basedb.util.listable.SourceItemTransformer;
+import net.sf.basedb.util.listable.TransformContext;
 import net.sf.basedb.util.overview.Fix;
 import net.sf.basedb.util.overview.Node;
@@ -211 +214 @@
     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(
@@ -216 +223 @@
           Restrictions.in(Hql.property("extract"), Expressions.parameter("extracts"))
         ));
-      query.setParameter("extracts", extractIds, Type.INT);
+      query.setParameter("extracts", allParents, Type.INT);
     }
 
@@ -250 +257 @@
     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(
@@ -255 +266 @@
           Restrictions.in(Hql.property("extract"), Expressions.parameter("extracts"))
         ));
-      query.setParameter("extracts", extractIds, Type.INT);
+      query.setParameter("extracts", allParents, Type.INT);
     }
 
@@ -399 +410 @@
   }
   
+  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

@@ -22 +22 @@
 package net.sf.basedb.util.overview.loader;
 
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 import net.sf.basedb.core.DbControl;
@@ -32 +36 @@
 import net.sf.basedb.core.ItemResultIterator;
 import net.sf.basedb.core.RawBioAssay;
+import net.sf.basedb.core.Type;
+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.listable.ExtractToParentExtractTransformer;
+import net.sf.basedb.util.listable.SourceItemTransformer;
+import net.sf.basedb.util.listable.TransformContext;
 import net.sf.basedb.util.overview.Node;
 import net.sf.basedb.util.overview.NodeAttribute;
@@ -194 +203 @@
     ItemQuery<RawBioAssay> query = context.initQuery(bioAssay.getRawBioAssays(), "name");
 
-    // If there is an extract node in the parent chain we should only load
-    // raw bioassays with the same or a null extract
-    Node extractNode = bioAssayNode.getFirstNode(new ItemTypeFilter(Item.EXTRACT));
-    Extract extract = null;
-    if (extractNode != null)
-    {
-      extract = (Extract)extractNode.getItem();
-      query.restrict(Restrictions.or(
-          Restrictions.eq(Hql.property("parentExtract"), Hql.entity(extract)), 
-          Restrictions.eq(Hql.property("parentExtract"), null))
-        );
-    }
-    
+    // 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);
+    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(
+          Restrictions.eq(Hql.property("parentExtract"), null),
+          Restrictions.in(Hql.property("parentExtract"), Expressions.parameter("extracts"))
+        ));
+      query.setParameter("extracts", allParents, Type.INT);
+    }
+  
     ItemResultIterator<RawBioAssay> it = query.iterate(dc);
     while (it.hasNext())
@@ -243 +256 @@
   }
   
+  private Set<Integer> getExtractChain(Node node)
+  {
+    List<Node> extractNodes = node.findAll(new ItemTypeFilter(Item.EXTRACT));
+    Set<Integer> extractIds = new HashSet<Integer>(extractNodes.size());
+    for (Node n : extractNodes)
+    {
+      extractIds.add(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);
+  }
+
 }