Changeset 2497

Timestamp:

Aug 8, 2006, 3:43:08 PM (17 years ago)

Author:

Nicklas Nordborg

Message:

Better performance when creating a root bioassayset by fetching the reporters in
the main query.

Location:

trunk/src/core/net/sf/basedb

Files:

• core/data/FeatureData.java (modified) (1 diff)
• core/query/Hql.java (modified) (4 diffs)
• core/query/HqlLeftJoin.java (modified) (3 diffs)
• util/IntensityCalculatorUtil.java (modified) (8 diffs)

trunk/src/core/net/sf/basedb/core/data/FeatureData.java

@@ -128 +128 @@
   /**
     Get the reporter of the feature.
-    This property is mapped in the hibernate-properties-AbstractFeatureData.xml file since
+    This property is mapped in the hibernate-properties-FeatureData.xml file since
     it must be mapped with a cascade="evict" which is not supported by XDoclet.
   */

trunk/src/core/net/sf/basedb/core/query/Hql.java

@@ -272 +272 @@
   
   /**
-    Same as <code>leftJoin(null, propert, joinedAlias, null)</code>
-    @see #leftJoin(String, String, String, Restriction)
+    Same as <code>leftJoin(null, propert, joinedAlias, null, false)</code>
+    @see #leftJoin(String, String, String, Restriction, boolean)
   */
   public static Join leftJoin(String property, String joinedAlias)
     throws InvalidDataException
   {
-    return leftJoin(null, property, joinedAlias, null);
+    return leftJoin(null, property, joinedAlias, null, false);
   }
 
@@ -304 +304 @@
 </pre>
 
+    <p>
+    The <code>fetch</code> parameter is used to fetch the joined data in the
+    same query. This is useful to 
+    avoid subsequent queries to the database when you know that you are
+    going to access the joined items in your code. If you are joining a
+    collection the {@link Query#setFirstResult(int)} and {@link Query#setMaxResults(int)}
+    shouldn't be used since the join will create multiple rows for the same
+    root item.
+
+    @param alias The alias to resolve the property against, or null to resolve the
+      property against the root entity
+    @param property The property name of the associated entity (required)
+    @param joinedAlias The alias to give the joined entity (required)
+    @param on Optional extra restriction that is used in the <code>ON</code> clause
+      of the generated query
+    @param fetch If the joined items should be prefetched or not
+    @return A join query element
+    @throws InvalidDataException If the property or joined alias parameter
+      are null or if any of the parameters contains invalid characters
+  */
+  public static Join leftJoin(String alias, String property, String joinedAlias, Restriction on, boolean fetch)
+    throws InvalidDataException
+  {
+    if (property == null) throw new InvalidUseOfNullException("property");
+    if (joinedAlias == null) throw new InvalidUseOfNullException("alias");
+    if (!PROPERTY_REGEXP.matcher(property).matches()) 
+    {
+      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
+    }
+    if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
+    {
+      throw new InvalidDataException("Alias '"+alias+"' has one or more invalid characters. Only a-z, A-Z and 0-9 is allowed.");
+    }
+    if (!ALIAS_REGEXP.matcher(joinedAlias).matches()) 
+    {
+      throw new InvalidDataException("Alias '"+joinedAlias+"' has one or more invalid characters. Only a-z, A-Z and 0-9 is allowed.");
+    }
+    return new HqlLeftJoin(alias, property, joinedAlias, on, fetch);
+  }
+
+  /**
+    Same as <code>rightJoin(null, propert, joinedAlias, null)</code>
+    @see #rightJoin(String, String, String, Restriction)
+  */
+  public static Join rightJoin(String property, String joinedAlias)
+    throws InvalidDataException
+  {
+    return rightJoin(null, property, joinedAlias, null);
+  }
+
+  /**
+    Create a right join query element. A right join selects all items
+    from the joined association even if they don't have an associated item in 
+    the root entity. The property must reference an association to another 
+    item or collection of values. 
+
     @param alias The alias to resolve the property against, or null to resolve the
       property against the root entity
@@ -314 +370 @@
       are null or if any of the parameters contains invalid characters
   */
-  public static Join leftJoin(String alias, String property, String joinedAlias, Restriction on)
+  public static Join rightJoin(String alias, String property, String joinedAlias, Restriction on)
     throws InvalidDataException
   {
@@ -331 +387 @@
       throw new InvalidDataException("Alias '"+joinedAlias+"' has one or more invalid characters. Only a-z, A-Z and 0-9 is allowed.");
     }
-    return new HqlLeftJoin(alias, property, joinedAlias, on);
-  }
-
-  /**
-    Same as <code>rightJoin(null, propert, joinedAlias, null)</code>
-    @see #rightJoin(String, String, String, Restriction)
-  */
-  public static Join rightJoin(String property, String joinedAlias)
-    throws InvalidDataException
-  {
-    return rightJoin(null, property, joinedAlias, null);
-  }
-
-  /**
-    Create a right join query element. A right join selects all items
-    from the joined association even if they don't have an associated item in 
-    the root entity. The property must reference an association to another 
-    item or collection of values. 
-
-    @param alias The alias to resolve the property against, or null to resolve the
-      property against the root entity
-    @param property The property name of the associated entity (required)
-    @param joinedAlias The alias to give the joined entity (required)
-    @param on Optional extra restriction that is used in the <code>ON</code> clause
-      of the generated query
-    @return A join query element
-    @throws InvalidDataException If the property or joined alias parameter
-      are null or if any of the parameters contains invalid characters
-  */
-  public static Join rightJoin(String alias, String property, String joinedAlias, Restriction on)
-    throws InvalidDataException
-  {
-    if (property == null) throw new InvalidUseOfNullException("property");
-    if (joinedAlias == null) throw new InvalidUseOfNullException("alias");
-    if (!PROPERTY_REGEXP.matcher(property).matches()) 
-    {
-      throw new InvalidDataException("Property '"+property+"' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.");
-    }
-    if (alias != null && !ALIAS_REGEXP.matcher(alias).matches()) 
-    {
-      throw new InvalidDataException("Alias '"+alias+"' has one or more invalid characters. Only a-z, A-Z and 0-9 is allowed.");
-    }
-    if (!ALIAS_REGEXP.matcher(joinedAlias).matches()) 
-    {
-      throw new InvalidDataException("Alias '"+joinedAlias+"' has one or more invalid characters. Only a-z, A-Z and 0-9 is allowed.");
-    }
     return new HqlRightJoin(alias, property, joinedAlias, on);
   }

trunk/src/core/net/sf/basedb/core/query/HqlLeftJoin.java

@@ -47 +47 @@
   private final String joinedAlias;
   private final Restriction on;
+  private final boolean fetch;
 
-  HqlLeftJoin(String alias, String property, String joinedAlias, Restriction on)
+  HqlLeftJoin(String alias, String property, String joinedAlias, Restriction on, boolean fetch)
   {
     assert property != null : "property == null";
@@ -56 +57 @@
     this.joinedAlias = joinedAlias;
     this.on = on;
+    this.fetch = fetch;
   }
 
@@ -67 +69 @@
     if (query.getQueryType() == QueryType.HQL)
     {
-      return "LEFT JOIN "+(alias == null ? query.getRootAlias() : alias) + "." + property + " " + joinedAlias +
+      return "LEFT JOIN " + (fetch && !query.isCounting() ? "FETCH " : "") +
+        (alias == null ? query.getRootAlias() : alias) + "." + property + " " + joinedAlias +
         (on == null ? "" : " WITH " + on.toQl(query, dc));
     }

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

@@ -24 +24 @@
 package net.sf.basedb.util;
 
+import net.sf.basedb.core.DataQuery;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Item;
 import net.sf.basedb.core.RawDataType;
 import net.sf.basedb.core.ArrayDesign;
@@ -46 +48 @@
 import net.sf.basedb.core.data.RawData;
 import net.sf.basedb.core.data.ReporterData;
+import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Selects;
 import net.sf.basedb.core.query.Select;
@@ -275 +278 @@
       progress.display(10, "Generating spot intensities (0 done)...");
     }
+    
+    /*
+    long total = -System.nanoTime();
+    long calc = 0;
+    long data = 0;
+    long cnew = 0;
+    long chit = 0;
+    long batt = 0;
+    long brep = 0;
+    long braw = 0;
+    */
+    
     for (RawBioAssay rba : rawBioAssays)
     {
@@ -286 +301 @@
     
       // Load raw data for current raw bioassay
-      DataResultIterator<RawData> rawData = rba.getRawData().iterate(dc);
+      DataQuery<RawData> rawQuery = rba.getRawData();
+      rawQuery.join(Hql.leftJoin(null, "reporter", Item.REPORTER.getAlias(), null, true));
+      if (rba.getArrayDesign() != null)
+      {
+        rawQuery.join(Hql.leftJoin(null, "feature", Item.REPORTER.getAlias(), null, true));
+      }
+      
+      DataResultIterator<RawData> rawData = rawQuery.iterate(dc);
+      //data -= System.nanoTime();
       while (rawData.hasNext())
       {
@@ -292 +315 @@
         int position = rd.getPosition();
         ReporterData reporter = rd.getReporter();
+        //data += System.nanoTime();
         
         // Calculate intensities
+        //calc -= System.nanoTime();
         float[] intensities = iCalc.calculateIntensities(rd);
+        //calc += System.nanoTime();
+        
         if (intensities != null)
         {
@@ -300 +327 @@
           if (positionCache.containsKey(position))
           {
+            //chit -= System.nanoTime();
             // A mapping already exists, check if same reporter
             ReporterData cached = positionCache.get(position);
-            if ((reporter == null && cached != null) || (reporter != null && !reporter.equals(cached)))
+            int reporterId = reporter == null ? 0 : reporter.getId();
+            int cachedId = cached == null ? 0 : cached.getId();
+            if (reporterId != cachedId)
             {
               // Same position but different reporter, must assign different position
@@ -330 +360 @@
               positionCache.put(position, reporter);
             }
+            //chit += System.nanoTime();
           }
           else
           {
             // New position, insert reporter mapping
+            //brep -= System.nanoTime();
             posBatcher.insert(position, reporter);
+            //brep += System.nanoTime();
+            //cnew -= System.nanoTime();
             positionCache.put(position, reporter);
+            //cnew += System.nanoTime();
           }
+          //braw -= System.nanoTime();
           // Insert mapping to raw data spot
           rawBatcher.insert(column, position, rd);
+          //braw += System.nanoTime();
           // Insert intensities
+          //batt -= System.nanoTime();
           spotBatcher.insert(column, position, intensities);
+          //batt += System.nanoTime();
         }
         if (progress != null)
@@ -351 +390 @@
           }
         }
-      }
+        //data -= System.nanoTime();
+      }
+      //data += System.nanoTime();
     }
     if (progress != null) progress.display(100, "Generating spot intensities ("+totalSpots+" done)...\n");
 
+    //total += System.nanoTime();
+
+    /*
+    System.out.println("Total time: " + (total / 1000000) + " ms");
+    System.out.println("Intensity : " + (calc / 1000000) + " ms");
+    System.out.println("Load data : " + (data / 1000000) + " ms");
+    System.out.println("New pos   : " + (cnew / 1000000) + " ms");
+    System.out.println("Cached pos: " + (chit / 1000000) + " ms");
+    System.out.println("Batch data: " + (batt / 1000000) + " ms");
+    System.out.println("Batch rep : " + (brep / 1000000) + " ms");
+    System.out.println("Batch raw : " + (braw / 1000000) + " ms");
+    */
+    
     // Close batchers and clean up
     positionCache.clear();