Changeset 7490

Timestamp:

May 28, 2018, 2:47:24 PM (5 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #2122: Item overview should load more child derived and raw bioassays from extracts

The direct links should now be loaded also for bioassays with a parent as long as that parent doesn't lead to the originating extract. Only the top-most derived bioassay is loaded and directly and children to that are loaded as normal.

Location:

branches/3.12-stable/src/core/net/sf/basedb/util/overview/loader

Files:

• DerivedBioAssayLoader.java (modified) (3 diffs)
• RawBioAssayLoader.java (modified) (4 diffs)

branches/3.12-stable/src/core/net/sf/basedb/util/overview/loader/DerivedBioAssayLoader.java

@@ -50 +50 @@
 import net.sf.basedb.util.overview.OverviewUtil;
 import net.sf.basedb.util.overview.Validator;
+import net.sf.basedb.util.overview.filter.BasicItemFilter;
 import net.sf.basedb.util.overview.filter.ItemTypeFilter;
 import net.sf.basedb.util.overview.node.ChildNodeDirection;
@@ -157 +158 @@
   protected void loadPropertyChildNodes(DbControl dc, OverviewContext context, Node bioAssayNode)
   {
-    getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, bioAssayNode);
+    Extract e = getExtract((DerivedBioAssay)bioAssayNode.getItem());
+    if (e == null || bioAssayNode.getFirstParent(new BasicItemFilter(e)) == null)
+    {
+      // Only load the extract if it is not already a parent node
+      getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, bioAssayNode);
+    }
     getNodeLoader(context, Item.ANNOTATION).createPropertyNode(dc, context, bioAssayNode);
     getNodeLoader(context, Item.FILESETMEMBER).createPropertyNode(dc, context, bioAssayNode);
@@ -281 +287 @@
     NodeFactory<DerivedBioAssay> nf = getNodeFactory(dc, context);
     Node folderNode = null;
+    // Load derived bioassays linked to the 'extract' if:
+    // they have no parent bioassay OR
+    // the parent bioassay has no parent extract OR
+    // the parent bioassay has a different parent extract
     ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
     query.restrict(Restrictions.eq(Hql.property("extract"), Hql.entity(extract)));
     query.join(Hql.leftJoin("parents", "parent"));
-    query.restrict(Restrictions.eq(Hql.alias("parent"), null));
+    query.join(Hql.leftJoin("parent", "extract", "parentExtract", null, false));
+    query.restrict(
+      Restrictions.or(
+        Restrictions.eq(Hql.alias("parent"), null),
+        Restrictions.eq(Hql.alias("parentExtract"), null),
+        Restrictions.neq(Hql.alias("parentExtract"), Hql.entity(extract))
+        ));
+    query.setDistinct(true); // left joins may create multiple hits for items with more than one parent
     context.initQuery(query, "name");
     ItemResultIterator<DerivedBioAssay> it = query.iterate(dc);

branches/3.12-stable/src/core/net/sf/basedb/util/overview/loader/RawBioAssayLoader.java

@@ -47 +47 @@
 import net.sf.basedb.util.overview.NodeAttribute;
 import net.sf.basedb.util.overview.OverviewContext;
+import net.sf.basedb.util.overview.filter.BasicItemFilter;
 import net.sf.basedb.util.overview.filter.ItemTypeFilter;
 import net.sf.basedb.util.overview.node.ChildNodeDirection;
@@ -169 +170 @@
   protected void loadPropertyChildNodes(DbControl dc, OverviewContext context, Node rawBioAssayNode)
   {
-    getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, rawBioAssayNode);
+    Extract e = getExtract((RawBioAssay)rawBioAssayNode.getItem());
+    if (e == null || rawBioAssayNode.getFirstParent(new BasicItemFilter(e)) == null)
+    {
+      // Only load the extract if it is not already a parent node
+      getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, rawBioAssayNode);
+    }
     getNodeLoader(context, Item.ANNOTATION).createPropertyNode(dc, context, rawBioAssayNode);
     getNodeLoader(context, Item.FILESETMEMBER).createPropertyNode(dc, context, rawBioAssayNode);
@@ -235 +241 @@
     NodeFactory<RawBioAssay> nf = getNodeFactory(dc, context);
     Node folderNode = null;
+    // Load raw bioassays linked to the 'extract' if:
+    // they have no parent bioassay OR
+    // the parent bioassay has no parent extract OR
+    // the parent bioassay has a different parent extract
     ItemQuery<RawBioAssay> query = RawBioAssay.getQuery();
     query.restrict(Restrictions.eq(Hql.property("parentExtract"), Hql.entity(extract)));
-    query.restrict(Restrictions.eq(Hql.property("parentBioAssay"), null));
+    query.join(Hql.leftJoin("parentBioAssay", "parent"));
+    query.join(Hql.leftJoin("parent", "extract", "parentExtract", null, false));
+    query.restrict(
+        Restrictions.or(
+          Restrictions.eq(Hql.alias("parent"), null),
+          Restrictions.eq(Hql.alias("parentExtract"), null),
+          Restrictions.neq(Hql.alias("parentExtract"), Hql.entity(extract))
+          ));
     context.initQuery(query, "name");
     ItemResultIterator<RawBioAssay> it = query.iterate(dc);
@@ -253 +270 @@
   }
   
+  /**
+    Get the extract that is associated with the current raw bioassay
+    @return The extract or null if none was found
+  */
+  private Extract getExtract(RawBioAssay bioAssay)
+  {
+    Extract extract = null;
+    try
+    {
+      extract = bioAssay.getParentExtract();
+    }
+    catch (PermissionDeniedException ex)
+    {}
+    return extract;
+  }
+
   private Set<Integer> getExtractChain(DbControl dc, Node node)
   {