Changeset 5131

Timestamp:

Oct 14, 2009, 9:44:14 AM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1374 and #1403: Caching of annotations, etc...

Made some changes to the API to make it more useful in other contexts. For example, the ability to find annotation snapshots by annotation id is needed by #1404.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/snapshot/AnnotationFilter.java (added)
• src/core/net/sf/basedb/core/snapshot/AnnotationSnapshot.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/snapshot/AnnotationTypeFilter.java (added)
• src/core/net/sf/basedb/core/snapshot/SnapshotManager.java (modified) (7 diffs)
• src/core/net/sf/basedb/util/BioAssaySetUtil.java (modified) (3 diffs)
• www/views/experiments/view_experiment.jsp (modified) (7 diffs)

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

@@ -36 +36 @@
 import net.sf.basedb.core.data.AnnotationData;
 import net.sf.basedb.core.data.AnnotationSetData;
+import net.sf.basedb.util.filter.Filter;
 import net.sf.basedb.util.units.UnitConverter;
 
@@ -197 +198 @@
     Get the annotation values. NOTE! The values are only available
     for primary annotations and for inherited annotations returned by
-    {@link SnapshotManager#findAnnotations(DbControl, AnnotationSetSnapshot, AnnotationType, boolean)}
+    {@link SnapshotManager#findAnnotations(DbControl, AnnotationSetSnapshot, Filter, boolean)}
     
     @return A list with the values
@@ -233 +234 @@
     Get the id of the item this annotation belongs to. NOTE! this value
     is only available on annotations returned from the call to:
-    {@link SnapshotManager#findAnnotations(DbControl, AnnotationSetSnapshot, AnnotationType, boolean)}
+    {@link SnapshotManager#findAnnotations(DbControl, AnnotationSetSnapshot, Filter, boolean)}
   */
   public int getItemId()
@@ -252 +253 @@
     Get the item type of the item this annotation belongs to. 
     NOTE! this value is only available on annotations returned from the call to:
-    {@link SnapshotManager#findAnnotations(DbControl, AnnotationSetSnapshot, AnnotationType, boolean)}
+    {@link SnapshotManager#findAnnotations(DbControl, AnnotationSetSnapshot, Filter, boolean)}
 
     @return The item type, or null if not known

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

@@ -30 +30 @@
 import net.sf.basedb.core.Annotatable;
 import net.sf.basedb.core.AnnotationSet;
-import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Application;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.util.StaticCache;
+import net.sf.basedb.util.filter.Filter;
+import net.sf.basedb.util.filter.StaticFilter;
 
 /**
@@ -110 +111 @@
   }
 
+
   /**
     Search in a snapshot for all annotations of a specified annotation type.
@@ -118 +120 @@
       exists for an inherited annotation set
     @param snapshot The snapshot to search
-    @param at The annotation type to look for, or null to return
-      annotations of any type
+    @param filter A filter that should match the wanted annotation snapshots
+      or null to match all annotations
     @param searchInherited TRUE if inherited annotations should be searched, 
       FALSE to only search primary annotations
@@ -125 +127 @@
   */
   public List<AnnotationSnapshot> findAnnotations(DbControl dc, AnnotationSetSnapshot snapshot, 
-    AnnotationType at, boolean searchInherited)
+      Filter<? super AnnotationSnapshot> filter, boolean searchInherited)
   {
     List<AnnotationSnapshot> result = new ArrayList<AnnotationSnapshot>();
-    int id = at == null ? 0 : at.getId();
+    if (filter == null) filter = new StaticFilter<AnnotationSnapshot>(true);
     for (AnnotationSnapshot shot : snapshot.getAnnotations())
     {
@@ -134 +136 @@
       {
         if (!searchInherited) continue; // with the next snapshot in the list
-        // Is this a specific inherited annotation or a complete annotation set?
-        if (shot.getAnnotationTypeId() == id || shot.getAnnotationId() == 0)
+        
+        // If this is an inherited annotation set or if it matches the filter we
+        // must recursively load the inherited annotations
+        if (shot.getAnnotationId() == 0 || filter.evaluate(shot))
         {
-          // Load the snapshot for the inherited annotation set and search the
-          // primary annotations only 
           AnnotationSetSnapshot recursive = getSnapshot(dc, shot.getAnnotationSetId());
           if (recursive != null)
           {
-            for (AnnotationSnapshot primary : findAnnotations(dc, recursive, at, false))
+            for (AnnotationSnapshot primary : findAnnotations(dc, recursive, filter, false))
             {
               AnnotationSnapshot copy = new AnnotationSnapshot();
@@ -154 +156 @@
       {
         // Primary annotation
-        if (shot.getAnnotationTypeId() == id || id == 0) 
+        if (filter.evaluate(shot)) 
         {
           shot.setItem(snapshot.getItemId(), snapshot.getItemType());
@@ -170 +172 @@
       item doesn't have any annotations)
     @see #getSnapshot(DbControl, int)
-    @see #findAnnotations(DbControl, AnnotationSetSnapshot, AnnotationType, boolean)
+    @see #findAnnotations(DbControl, AnnotationSetSnapshot, Filter, boolean)
   */
   public List<AnnotationSnapshot> findAnnotations(DbControl dc, Annotatable item, 
-    AnnotationType at, boolean searchInherited)
-  {
-    if (!item.isAnnotated()) return Collections.emptyList();
-    AnnotationSetSnapshot snapshot = getSnapshot(dc, item.getAnnotationSet().getId());
-    return findAnnotations(dc, snapshot, at, searchInherited);
-  }
+      Filter<? super AnnotationSnapshot> filter, boolean searchInherited)
+    {
+      if (!item.isAnnotated()) return Collections.emptyList();
+      AnnotationSetSnapshot snapshot = getSnapshot(dc, item.getAnnotationSet().getId());
+      return findAnnotations(dc, snapshot, filter, searchInherited);
+    }
+
 }

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

@@ -36 +36 @@
 import net.sf.basedb.core.query.Restriction;
 import net.sf.basedb.core.snapshot.AnnotationSnapshot;
+import net.sf.basedb.core.snapshot.AnnotationTypeFilter;
 import net.sf.basedb.core.snapshot.SnapshotManager;
+import net.sf.basedb.util.filter.Filter;
 import net.sf.basedb.util.jep.ChannelFunction;
 import net.sf.basedb.util.jep.ExtraValueFunction;
@@ -109 +111 @@
     Set<Object> allValues = new TreeSet<Object>();
     if (snapshotManager == null) snapshotManager = new SnapshotManager();
-    for (AnnotationSnapshot a : snapshotManager.findAnnotations(dc, bioAssay, annotationType, true))
+    Filter<AnnotationSnapshot> filter = new AnnotationTypeFilter(annotationType);
+    for (AnnotationSnapshot a : snapshotManager.findAnnotations(dc, bioAssay, filter, true))
     {
       if (a != null) allValues.addAll(a.getValues());
@@ -117 +120 @@
     for (RawBioAssay rb : rbaQuery.list(dc))
     {
-      for (AnnotationSnapshot a : snapshotManager.findAnnotations(dc, rb, annotationType, true))
+      for (AnnotationSnapshot a : snapshotManager.findAnnotations(dc, rb, filter, true))
       {
         if (a != null) allValues.addAll(a.getValues());

trunk/www/views/experiments/view_experiment.jsp

@@ -60 +60 @@
   import="net.sf.basedb.core.snapshot.AnnotationSetSnapshot"
   import="net.sf.basedb.core.snapshot.AnnotationSnapshot"
+  import="net.sf.basedb.core.snapshot.AnnotationTypeFilter"
   import="net.sf.basedb.util.formatter.Formatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
@@ -532 +533 @@
       }
       %>
-      
       <%
       ItemQuery<RawBioAssay> rbaQuery = experiment.getRawBioAssays();
@@ -579 +579 @@
         }
         %>
-        
         <tbl:data>
           <tbl:columns>
@@ -586 +585 @@
           <%
           SnapshotManager manager = new SnapshotManager();
+          AnnotationTypeFilter annotationTypeFilter = new AnnotationTypeFilter();
           for (RawBioAssay item : rawBioAssays)
           {
-            //System.out.println("processing rba: " + item);
             AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
-            //System.out.println("got annotation set: " + as);
             AnnotationSetSnapshot snapshot = as == null ? null : manager.getSnapshot(dc, as.getId());
-            //System.out.println("got snapshot: " + snapshot);
             %>
             <tbl:row>
@@ -608 +605 @@
                 
                 String value = "<i>- none -</i>";
-                //System.out.println("load annotations: " + at);
+                annotationTypeFilter.setAnnotationType(at);
                 List<AnnotationSnapshot> all = snapshot == null ? 
-                    null : manager.findAnnotations(dc, snapshot, at, true);
-                //System.out.println("loaded annotations: " + at);
+                    null : manager.findAnnotations(dc, snapshot, annotationTypeFilter, true);
                 Map<Annotatable, List> factorValues = new HashMap<Annotatable, List>();
                 if (all != null && all.size() > 0)
@@ -623 +619 @@
                     try
                     {
-                      //System.out.println("load item: "+ a.getItemType() + a.getItemId());
                       aItem = a.getItem(dc);
-                      //System.out.println("loaded item: "+ a.getItemType() + a.getItemId());
                     }
                     catch (Throwable t)
@@ -638 +632 @@
                   }
                 }
-                
                 %>
                 <tbl:cell column="<%="at"+at.getId()%>"