Changeset 6937

Timestamp:

Aug 7, 2015, 8:34:06 AM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #1941: Store experimental factor values as part experiments

Removing the annotation on a parent item will nullify the link from cloned annotations instead of removing the clones.

Other changes are related to fixing various NullPointerExceptions and other problems resulting from having "inherited" annotations without a parent item.

But more work is needed on this since the cloned annotations now end up in a state that is almost impossible to manage via the gui. The "batch inherit annotations" can be used to remove or update cloned annotation.

Location:

trunk

Files:

• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/Annotation.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/AnnotationSet.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/snapshot/AnnotationSnapshot.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/snapshot/SnapshotManager.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/annotations/InheritAnnotationsManager.java (modified) (2 diffs)
• www/common/annotations/inherit.jsp (modified) (1 diff)
• www/common/annotations/list_annotations.jsp (modified) (3 diffs)

trunk/src/core/common-queries.xml

@@ -1958 +1958 @@
   </query>
   
+  <query id="NULLIFY_LINK_FROM_CLONES" type="HQL">
+    <sql>
+      UPDATE AnnotationData ad
+      SET ad.inheritedFrom = null
+      WHERE ad.inheritedFrom = :targetId
+      AND ad.source = 2
+    </sql>
+    <description>
+      A HQL query that nullify the link from all cloned annotations
+      to a specified target annotation.
+    </description>
+  </query>
+  
   <query id="UPDATE_BYTES_FOR_EXPERIMENT" type="HQL">
     <sql>

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

@@ -23 +23 @@
 package net.sf.basedb.core;
 
+import net.sf.basedb.core.Transactional.Action;
 import net.sf.basedb.core.data.AnnotationData;
 import net.sf.basedb.core.data.AnnotationTypeData;
@@ -218 +219 @@
     super.initPermissions(granted, denied);
   }
+  
+  /**
+    Nullify links to this annotation from cloned annotations when this annotation is deleted
+    (since the cloned annotation should not be deleted).
+  */
+  @Override
+  void onBeforeCommit(Action action) 
+    throws BaseException 
+  {
+    super.onBeforeCommit(action);
+    if (action == Action.DELETE && getSource() == Annotation.Source.PRIMARY)
+    {
+      org.hibernate.Session session = getDbControl().getHibernateSession();
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+        "NULLIFY_LINK_FROM_CLONES");
+      /*
+        UPDATE AnnotationData ad
+        SET ad.inheritedFrom = null
+        WHERE ad.inheritedFrom = :targetId
+        AND ad.source = CLONED
+      */
+      query.setInteger("targetId", getId());
+      HibernateUtil.executeUpdate(query);
+    }
+  }
+
   @Override
   PluginPermission getPluginPermissions()

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

@@ -855 +855 @@
   
   /**
-    Remove an inherited an annotation.
+    Remove an inherited an annotation. The specified annotation can be
+    either a CLONED or INHERITED annotation in this set or the PRIMARY
+    annotation of another annotation set that is inherited/cloned by
+    this set.
+    
     @param annotation The annotation to remove
     @throws PermissionDeniedException If the logged in user
@@ -870 +874 @@
     AnnotationData toRemove = annotation.getData();
     Iterator<AnnotationData> it = getData().getAnnotations().iterator();
+    boolean checkInherited = annotation.getSource() == Annotation.Source.PRIMARY;
+    
     while (it.hasNext())
     {
       AnnotationData ad = it.next();
-      if (toRemove.equals(ad.getInheritedFrom()))
+      boolean remove = checkInherited ? toRemove.equals(ad.getInheritedFrom()) : toRemove.equals(ad);
+      if (remove)
       {
         Annotation a = dc.getItem(Annotation.class, ad);

trunk/src/core/net/sf/basedb/core/snapshot/AnnotationSnapshot.java

@@ -127 +127 @@
   public boolean isInherited()
   {
-    return inheritedFromId != 0;
+    return getSource() != Annotation.Source.PRIMARY;
   }
   
@@ -605 +605 @@
   {
     this.inheritedFrom = inheritedFrom;
+    if (inheritedFrom == null)
+    {
+      this.inheritedFromId = 0;
+      this.inheritedFromSetId = 0;
+    }
   }
 

trunk/src/core/net/sf/basedb/core/snapshot/SnapshotManager.java

@@ -198 +198 @@
         {
           shot.setItem(snapshot.getItemId(), snapshot.getItemType());
-          result.add(shot);
           
           AnnotationSetSnapshot recursive = getSnapshot(dc, shot.getInheritedAnnotationSetId());
+          AnnotationSnapshot inheritedFrom = null;
           if (recursive != null)
           {
@@ -211 +211 @@
             if (primary.size() > 0)
             {
-              shot.setInheritedFrom(primary.get(0));
+              inheritedFrom = primary.get(0);
             }
+          }
+          shot.setInheritedFrom(inheritedFrom);
+          if (inheritedFrom != null || shot.getSource() == Annotation.Source.CLONED)
+          {
+            result.add(shot);
           }
         }

trunk/src/core/net/sf/basedb/util/annotations/InheritAnnotationsManager.java

@@ -99 +99 @@
       for (AnnotationSnapshot inherited : snapshotManager.findAnnotations(dc, snapshot, removeFilter, false, true))
       {
-        as.removeInheritedAnnotation(inherited.getInheritedAnnotation(dc));
+        as.removeInheritedAnnotation(inherited.getThisAnnotation(dc));
       }
       
@@ -155 +155 @@
                     {
                       // We only remove the annotation if it is not the same we are going to add later
-                      as.removeInheritedAnnotation(e.getInheritedAnnotation(dc));
+                      as.removeInheritedAnnotation(e.getThisAnnotation(dc));
                     }
                     else

trunk/www/common/annotations/inherit.jsp

@@ -246 +246 @@
   final AnnotationSet as = item != null && item.isAnnotated() ? item.getAnnotationSet() : null;
   Set<Annotation> inheritedAnnotations = null;
+  
   if (as != null)
   {
-    ItemQuery<Annotation> inheritedQuery = as.getInheritedAnnotations();
+    ItemQuery<Annotation> inheritedQuery = as.getAnnotations(null);
+    inheritedQuery.restrict(
+        Restrictions.neq(
+          Hql.property("source"), 
+          Expressions.integer(Annotation.Source.PRIMARY.ordinal())
+      ));
+    
     inheritedQuery.order(Orders.asc(Hql.property("annotationSet")));
     inheritedQuery.order(Orders.asc(Hql.property("annotationType.name")));
-    inheritedAnnotations = new HashSet<Annotation>(inheritedQuery.list(dc));
-    for (Annotation a : inheritedAnnotations)
-    {
-      AnnotationSet from = a.getAnnotationSet();
-      if (!parentAnnotations.contains(from) && from.hasPermission(Permission.USE))
-      {
-        parentAnnotations.add(from);
-        nonParents.add(from);
+    inheritedAnnotations = new HashSet<Annotation>();
+    for (Annotation a : inheritedQuery.list(dc))
+    {
+      a = a.getInheritedFrom();
+      if (a != null)
+      {
+        inheritedAnnotations.add(a);
+        AnnotationSet from = a.getAnnotationSet();
+        if (!parentAnnotations.contains(from) && from.hasPermission(Permission.USE))
+        {
+          parentAnnotations.add(from);
+          nonParents.add(from);
+        }
       }
     }

trunk/www/common/annotations/list_annotations.jsp

@@ -119 +119 @@
     {
       AnnotationType at = a.getAnnotationType(dc);
-      if (!a.isInherited())
+      if (a.getSource() == Annotation.Source.PRIMARY)
       {
         existing.put(a.getAnnotationType(dc), a);
@@ -470 +470 @@
           />
           <tbl:columndef 
+            id="values"
+            title="Values"
+          />
+          <tbl:columndef 
             id="source"
             title="Cloned"
@@ -476 +480 @@
             id="item"
             title="From item"
-          />
-          <tbl:columndef 
-            id="values"
-            title="Values"
           />
           <tbl:columndef