Changeset 5120

Timestamp:

Oct 8, 2009, 2:30:00 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #1374: Caching of experimental factors

The cache is now working. #1400, #1401 and some other enhancements indicate that the initial caching can be 2-3 times quicker than the old code. The performance gain with the cache seems to be about 5-7 times. The end result is about 15-20 times quicker than the old code. Note that this was for a very simple experiment with 4 raw data sets and 5 experimental factors and almost no other data in the database. This should be tested in real-world scenario.

IMPORTANT NOTE!! Cache invalidation has not yet been implemented. What goes into the cache stays in the cache. Updates and changes to annotations will not be visible!

Location:

trunk

Files:

• src/core/net/sf/basedb/core/Annotation.java (modified) (1 diff)
• src/core/net/sf/basedb/core/AnnotationSet.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/snapshot (added)
• src/core/net/sf/basedb/core/snapshot/AnnotationSetSnapshot.java (added)
• src/core/net/sf/basedb/core/snapshot/AnnotationSnapshot.java (added)
• src/core/net/sf/basedb/core/snapshot/SnapshotManager.java (added)
• www/views/experiments/view_experiment.jsp (modified) (6 diffs)

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

@@ -194 +194 @@
   }
 
+  /**
+    Get the date and time the values in this annotation was last
+    updated.
+    @since 2.14
+  */
+  public Date getLastUpdate()
+  {
+    return DateUtil.copy(getData().getLastUpdate());
+  }
+  
   /**
     Check if this annotation belongs to the primaray annotations for a specified annotation set.

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

@@ -23 +23 @@
 package net.sf.basedb.core;
 
+import java.io.Serializable;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Date;
@@ -35 +37 @@
 import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.snapshot.AnnotationSetSnapshot;
+import net.sf.basedb.core.snapshot.AnnotationSnapshot;
+import net.sf.basedb.core.snapshot.SnapshotManager;
 
 import net.sf.basedb.core.data.AnnotationData;
@@ -40 +45 @@
 import net.sf.basedb.core.data.AnnotationTypeData;
 import net.sf.basedb.util.AnnotationUtil;
+import net.sf.basedb.util.StaticCache;
 import net.sf.basedb.util.filter.Filter;
 
@@ -797 +803 @@
   }
   
+  /**
+    Create a new annotation snapshot for the given annotation set.
+    NOTE! This method will create a new snapshot from the database.
+    Snapshots can be cached as files which are much quicker to load.
+    It is recommended that {@link SnapshotManager#getSnapshot(int)} 
+    is used instead of this method.
+    
+    @param dc A DbControl to use for database access
+    @param annotationSetId The ID of the annotation set
+    @return A snapshot, or null if the annotation set with the given
+      id doens't exist
+    @since 2.14
+  */
+  public static AnnotationSetSnapshot createSnapshot(DbControl dc, int annotationSetId)
+  {
+
+    AnnotationSetData set = HibernateUtil.loadData(dc.getHibernateSession(), AnnotationSetData.class, annotationSetId);
+    if (set == null) return null;
+    
+    AnnotationSetSnapshot snapshot = new AnnotationSetSnapshot();
+    snapshot.init(set);
+    return snapshot;
+  }
+
+  
   private static class QueryRuntimeFilterImpl
     implements QueryRuntimeFilter

trunk/www/views/experiments/view_experiment.jsp

@@ -57 +57 @@
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="net.sf.basedb.core.snapshot.SnapshotManager"
+  import="net.sf.basedb.core.snapshot.AnnotationSetSnapshot"
+  import="net.sf.basedb.core.snapshot.AnnotationSnapshot"
   import="net.sf.basedb.util.formatter.Formatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
@@ -545 +548 @@
       else
       {
+        long time = 0;
         %>
         <base:section 
@@ -582 +586 @@
           <tbl:rows>
           <%
+          time -= System.currentTimeMillis();
+          SnapshotManager manager = new SnapshotManager();
           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>
@@ -600 +610 @@
                 
                 String value = "<i>- none -</i>";
-                List<Annotation> all = as == null ? null : as.findAnnotations(dc, at, true);
+                //System.out.println("load annotations: " + at);
+                List<AnnotationSnapshot> all = snapshot == null ? 
+                    null : manager.findAnnotations(dc, snapshot, at, true);
+                //System.out.println("loaded annotations: " + at);
                 Map<Annotatable, List> factorValues = new HashMap<Annotatable, List>();
                 if (all != null && all.size() > 0)
                 {
-                  for (Annotation a : all)
+                  for (AnnotationSnapshot a : all)
                   {
                     List values = a.getValues();
@@ -612 +625 @@
                     try
                     {
-                      aItem = a.getAnnotationSet().getItem();
+                      //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)
@@ -653 +668 @@
             <%
           }
+          time += System.currentTimeMillis();
           %>
           </tbl:rows>
         </tbl:data>
         </tbl:table>
+        <%=time %> ms
         </base:section>
         <%