Changeset 4829

Timestamp:

Mar 23, 2009, 3:28:03 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #903: Experiment Explorer is slow

Store list of position in the static file cache. Removed index on 'position' column.

Location:

trunk/src

Files:

• clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java (modified) (3 diffs)
• core/net/sf/basedb/core/VirtualColumn.java (modified) (1 diff)
• core/net/sf/basedb/core/VirtualTable.java (modified) (1 diff)
• core/net/sf/basedb/util/StaticCache.java (modified) (5 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java

@@ -36 +36 @@
 import javax.servlet.jsp.PageContext;
 
+import net.sf.basedb.util.StaticCache;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.clients.web.formatter.FormatterFactory;
 import net.sf.basedb.clients.web.taglib.table.TableColumn;
 import net.sf.basedb.core.AnnotationType;
+import net.sf.basedb.core.Application;
 import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BioAssay;
@@ -848 +850 @@
   }
   
+  @SuppressWarnings("unchecked")
   private void initReporterCache(DbControl dc)
   {
@@ -854 +857 @@
     if (posCache == null)
     {
-      Select spotPos = Dynamic.select(VirtualTable.SPOT, VirtualColumn.POSITION);
-      DynamicSpotQuery posQuery = bas.getSpotData();
-      posQuery.select(spotPos);
-      posQuery.order(Orders.asc(Expressions.selected(spotPos)));
-      posQuery.setDistinct(true);
-      DynamicResultIterator it = posQuery.iterate(dc);
-      List<Integer> posList = new ArrayList<Integer>(bas.getNumReporters());
-      try
-      {
-        while (it.hasNext())
+      StaticCache staticCache = Application.getStaticCache();
+      String cacheKey = "explorer/bioassayset." + bas.getId() + "/poslist.ser";
+      List<Integer> posList = (List<Integer>)staticCache.load(cacheKey, 100);
+      if (posList == null)
+      {
+        Select spotPos = Dynamic.select(VirtualTable.SPOT, VirtualColumn.POSITION);
+        DynamicSpotQuery posQuery = bas.getSpotData();
+        posQuery.select(spotPos);
+        posQuery.order(Orders.asc(Expressions.selected(spotPos)));
+        posQuery.setDistinct(true);
+        DynamicResultIterator it = posQuery.iterate(dc);
+        posList = new ArrayList<Integer>(bas.getNumReporters());
+        try
         {
-          posList.add(it.next().getInt(1));
+          while (it.hasNext())
+          {
+            posList.add(it.next().getInt(1));
+          }
+          staticCache.store(cacheKey, posList, 100);
         }
-      }
-      catch (SQLException ex)
-      {
-        throw new BaseException(ex);
-      }
-      finally
-      {
-        it.close();
+        catch (SQLException ex)
+        {
+          throw new BaseException(ex);
+        }
+        finally
+        {
+          it.close();
+        }
       }
       posCache = new int[posList.size()];

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

@@ -92 +92 @@
       !INDEXED, !NULLABLE, PRIMARY_KEY);
 
-  /**
-    This column stores the (indexed) data cube position coordinate.
-  */
-  public static final VirtualColumn INDEXED_POSITION = 
-    new VirtualColumn("position", "position", Hibernate.INTEGER, 0, 
-      INDEXED, !NULLABLE, PRIMARY_KEY);
-  
   /**
     This column stores the data cube filter number.

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

@@ -57 +57 @@
     VirtualColumn.LAYER,
     VirtualColumn.COLUMN,
-    VirtualColumn.INDEXED_POSITION
+    VirtualColumn.POSITION
   )
   {

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

@@ -53 +53 @@
   with the any of the {@link #read(String, int)} or {@link #write(String, InputStream, int)}
   methods and their variants. It can also be used to store any {@link Serializable}
-  object with {@link #store(String, Serializable, int)} and {@link #load(String, int)}.
+  object with {@link #store(String, Object, int)} and {@link #load(String, int)}.
   <p>
   
@@ -305 +305 @@
     
     @param key The cache key
-    @param object The object to store in the cache
+    @param object The object to store in the cache, it must be a
+      {@link Serializable} object
     @param timeout A timeout in milliseconds to wait for a write lock
       on the requested cache entry
     @return TRUE if the object could be stored, FALSE otherwise
   */
-  public boolean store(String key, Serializable object, int timeout)
-    throws IOException
+  public boolean store(String key, Object object, int timeout)
   {
     if (disabled) return false;
     OutputStream out = null;
+    boolean stored = false;
     try
     {
@@ -323 +324 @@
         oos.writeObject(object);
         oos.flush();
-      }
+        stored = true;
+      }
+    }
+    catch (IOException ex)
+    {
+      log.warn("Could not store cached entry: " + key, ex);
     }
     finally
     {
-      if (out != null) out.close();
-    }
-    return true;
+      if (out != null) 
+      {
+        try
+        {
+          out.close();
+        }
+        catch (IOException ex)
+        {}
+      }
+    }
+    return stored;
   }
   
@@ -341 +355 @@
       exists or if a read lock couldn't be aquired
   */
-  public Serializable load(String key, int timeout)
-    throws IOException
+  public Object load(String key, int timeout)
   {
     if (disabled) return null;
@@ -363 +376 @@
       }
     }
+    catch (IOException ex)
+    {
+      log.warn("Could not load cached entry: " + key, ex);
+    }
     finally
     {
-      if (in != null) in.close();
+      if (in != null) 
+      {
+        try
+        {
+          in.close();
+        }
+        catch (IOException ex)
+        {}
+      }
     }
     return object;