Changeset 5314

Timestamp:

Apr 16, 2010, 12:46:12 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

References #1397: Function to inherit annotations for all experimental factors in the experimental factors table

Fixed a NullPointerException? that happened when the item to inherit annotations to doesn't have any annotations already.

Updated test documentation to reflect changes in the gui.

Location:

branches/2.15-stable

Files:

• doc/test/roles/index.html (modified) (1 diff)
• src/core/net/sf/basedb/core/AnnotationSet.java (modified) (1 diff)
• src/core/net/sf/basedb/core/snapshot/SnapshotManager.java (modified) (2 diffs)

branches/2.15-stable/doc/test/roles/index.html

@@ -1778 +1778 @@
     Inherit the annotations from the scans, samples and biosource for each raw bioassay.
     Use the <i>auto-inherit</i> function that exists on the experiment properties
-    tab. The <i>Status</i> column in <i>Experimental factors</i> table should indicate
-    the number of raw bioassays that is missing a value. Click on this warning to
-    automatically inherit annotations from the parents. Note! The <i>Dye swap</i>
+    tab. Make sure that all experimental factors are selected by the check boxes,
+    then click on the <i>Auto-inherit</i> link in the column header. 
+    Note! The <i>Dye swap</i>
     annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i>
-    data set doesn't have any parents with annotations.
+    data set is missing biomaterial parents with annotations.
     <p>
 

branches/2.15-stable/src/core/net/sf/basedb/core/AnnotationSet.java

@@ -791 +791 @@
     AnnotationSetSnapshot snapshot = manager.getSnapshot(dc, getId());
     AnnotationTypeFilter atFilter = new AnnotationTypeFilter();
-    for (AnnotationType at : annotationTypes)
-    {
-      atFilter.setAnnotationType(at);
-      if (manager.findAnnotations(dc, snapshot, atFilter, true).size() == 0)
+    if (snapshot == null)
+    {
+      // If snapshot==null this annotation set is new and unsaved 
+      // and doesn't have any annotations
+      missing.addAll(annotationTypes);
+    }
+    else
+    {
+      for (AnnotationType at : annotationTypes)
       {
-        missing.add(at);
+        atFilter.setAnnotationType(at);
+        if (manager.findAnnotations(dc, snapshot, atFilter, true).size() == 0)
+        {
+          missing.add(at);
+        }
       }
     }

branches/2.15-stable/src/core/net/sf/basedb/core/snapshot/SnapshotManager.java

@@ -90 +90 @@
       the database cache
     @param annotationSetId The id of the annotation set
-    @return A snapshot
+    @return A snapshot, or null if the annotation set with the given
+     id doesn't exists
   */
   public AnnotationSetSnapshot getSnapshot(DbControl dc, int annotationSetId)
@@ -106 +107 @@
       // As a last resort, create a new snapshot and cache it
       snapshot = AnnotationSet.createSnapshot(dc, annotationSetId);
-      cache.store(cacheKey, snapshot, 1000);
+      if (snapshot != null) cache.store(cacheKey, snapshot, 1000);
     }
     snapshots.put(annotationSetId, snapshot);