Changeset 5026

Timestamp:

Jul 28, 2009, 11:06:46 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #1350: Update to Hibernate 3.3.2

• Made ArrayDesignBlockData?, FeatureData?, ReporterData? and RawData? lazy="true".
• Changed queries to only join information that we need.
• Added test that changes the array design for a raw bioassay

Location:

trunk

Files:

• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/data/ArrayDesignBlockData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/FeatureData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ReporterData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/templates/hibernate-properties-RawData.xml (modified) (1 diff)
• src/core/net/sf/basedb/util/IntensityCalculatorUtil.java (modified) (3 diffs)
• src/test/TestArrayDesign.java (modified) (3 diffs)
• src/test/TestRawBioAssay.java (modified) (6 diffs)
• www/lims/arraydesigns/features/list_features.jsp (modified) (2 diffs)
• www/views/rawbioassays/rawdata/list_rawdata.jsp (modified) (2 diffs)

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

@@ -1309 +1309 @@
       if (progress != null) progress.display(10, "Loading raw data from raw bioassay...");
       DataQuery<RawData> rawQuery = getRawData();
-      // NOTE!! Due to an issue in Hibernate we must join all three
-      // tables or we will get an AssertionFailure: possible non-threadsafe access to the session
-      // The query also works if don't join at all, but that will generate a lot
-      // of extra queries for each iteration
       rawQuery.join(Hql.leftJoin(null, "reporter", "rep", null, true));
       rawQuery.join(Hql.leftJoin(null, "feature", "feat", null, true));
-      rawQuery.join(Hql.leftJoin("feat", "arrayDesignBlock", "bl", null, true));
 
       DataResultIterator<RawData> result = rawQuery.iterate(dc);
@@ -1327 +1322 @@
         // Get the feature identifier for the current raw data
         FeatureData oldFeature = raw.getFeature();
-        String externalFeatureId = oldFeature == null ? null : oldFeature.getExternalId();;
+        String externalFeatureId = oldFeature == null ? null : oldFeature.getExternalId();
         Object rawFeatureId = fiMethod.getIdentifier(raw, externalFeatureId);
         

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

@@ -34 +34 @@
   @see <a href="../../../../../../html/developerdoc/api/data_api.arrays.html">Array LIMS - arrays overview</a>
   @base.modified $Date$
-  @hibernate.class table="`ArrayDesignBlocks`" lazy="false"
+  @hibernate.class table="`ArrayDesignBlocks`" lazy="true"
 */
 public class ArrayDesignBlockData 

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

@@ -31 +31 @@
   @see <a href="../../../../../../html/developerdoc/api/data_api.arrays.html">Array LIMS - arrays overview</a>
   @base.modified $Date$
-  @hibernate.class table="`Features`" lazy="false"
+  @hibernate.class table="`Features`" lazy="true"
  */
 public class FeatureData

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

@@ -47 +47 @@
   @see net.sf.basedb.core.ExtendedProperties
   @see <a href="../../../../../../html/developerdoc/api/data_api.reporters.html">Reporter overview</a>
-  @hibernate.class table="`Reporters`" lazy="false"
+  @hibernate.class table="`Reporters`" lazy="true"
 */
 public class ReporterData

trunk/src/core/net/sf/basedb/core/templates/hibernate-properties-RawData.xml

@@ -37 +37 @@
     dynamic-update="false"
     dynamic-insert="false"
-    lazy="false"
+    lazy="true"
     >
     <id

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

@@ -25 +25 @@
 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;
@@ -48 +47 @@
 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;
@@ -348 +346 @@
       // Load raw data for current raw bioassay
       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.FEATURE.getAlias(), null, true));
-        // The joins below are needed to avoid extra SELECT statements for each spot 
-        // that is loaded
-        rawQuery.join(Hql.leftJoin(Item.FEATURE.getAlias(), "reporter", "ftrep", null, true));
-        rawQuery.join(Hql.leftJoin(Item.FEATURE.getAlias(), "arrayDesignBlock", "ftrbl", null, true));
-      }
-      
       DataResultIterator<RawData> rawData = rawQuery.iterate(dc);
       ThreadSignalHandler.checkInterrupted();

trunk/src/test/TestArrayDesign.java

@@ -26 +26 @@
 import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BlockInfo;
+import net.sf.basedb.core.DataQuery;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Feature;
@@ -47 +48 @@
 import net.sf.basedb.core.data.FeatureData;
 import net.sf.basedb.core.data.ReporterData;
+import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.parser.FlatFileParser;
@@ -512 +514 @@
       ArrayDesign ad = ArrayDesign.getById(dc, arrayDesignId);
       
-      DataResultIterator<FeatureData> it = ad.getFeatures().iterate(dc);
+      DataQuery<FeatureData> query = ad.getFeatures();
+      query.join(Hql.innerJoin(null, "arrayDesignBlock", "blk", null, true));
+      query.join(Hql.leftJoin(null, "reporter", "rpt", null, true));
+      DataResultIterator<FeatureData> it = query.iterate(dc);
       int counter = 0;
       while (it.hasNext())

trunk/src/test/TestRawBioAssay.java

@@ -24 +24 @@
 import net.sf.basedb.core.*;
 import net.sf.basedb.core.data.RawData;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.util.ConsoleProgressReporter;
 import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.Values;
@@ -54 +56 @@
     int scanId = TestScan.test_create(hybridizationId, 0, 0, false);
     int arrayDesignId = TestArrayDesign.test_create(Platform.GENERIC, false);
+    int arrayDesignId2 = TestArrayDesign.test_create(Platform.GENERIC, false);
+    
     TestReporter.test_import_from_file("data/test.rawdata.import.txt", 
       "\"Block\"\\t\"Column\"\\t\"Row\"\\t\"Name\"\\t\"ID\".*", "\\t", 4, 3);
     TestArrayDesign.test_import_from_file(arrayDesignId, "data/test.rawdata.import.txt", 
       "\"Block\"\\t\"Column\"\\t\"Row\"\\t\"Name\"\\t\"ID\".*", null, 0, 2, 1, 4);
+    TestArrayDesign.test_import_from_file(arrayDesignId2, "data/test.rawdata.import.txt", 
+        "\"Block\"\\t\"Column\"\\t\"Row\"\\t\"Name\"\\t\"ID\".*", null, 0, 2, 1, 4);
+    
     int softwareId = TestSoftware.test_create(SystemItems.getId(SoftwareType.FEATURE_EXTRACTION), null, false);
     int protocolId = TestProtocol.test_create(SystemItems.getId(ProtocolType.FEATURE_EXTRACTION), null, false);
@@ -76 +83 @@
     test_list_raw_data(id, 10, 5, 0, true);
     
+    // Test switch array design
+    test_change_arraydesign(id, arrayDesignId2);
+    
     // Test adding raw data -- stored in files
     int celId = TestFile.test_create("data/test.affymetrix.cel", false, false);
@@ -94 +104 @@
     TestHybridization.test_delete(hybridizationId);
     TestArrayDesign.test_delete(arrayDesignId);
+    TestArrayDesign.test_delete(arrayDesignId2);
     TestSoftware.test_delete(softwareId);
     TestProtocol.test_delete(protocolId);
@@ -413 +424 @@
       RawBioAssay rba = RawBioAssay.getById(dc, rawBioAssayId);
       DataQuery<RawData> query = rba.getRawData();
+      query.join(Hql.leftJoin(null, "feature", "ft", null, true));
+      query.join(Hql.leftJoin(null, "reporter", "rep", null, true));
       query.setMaxResults(limit);
       query.setFirstResult(offset);
@@ -647 +660 @@
       if (dc != null) dc.close();
     }
-  } 
+  }
+  
+  static void test_change_arraydesign(int id, int arrayDesignId)
+  {
+    if (id == 0 || arrayDesignId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      RawBioAssay rba = RawBioAssay.getById(dc, id);
+      ArrayDesign ad = ArrayDesign.getById(dc, arrayDesignId);
+      ProgressReporter progress = TestUtil.getSilent() ?
+          null : new ConsoleProgressReporter();
+      rba.updateArrayDesign(ad, null, progress);
+      dc.commit();
+      write("--Change array design OK");
+    }
+    catch (Throwable ex)
+    {
+      write("--Change array design FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
 }

trunk/www/lims/arraydesigns/features/list_features.jsp

@@ -126 +126 @@
   try
   {
-    query.join(Hql.leftJoin(null, "reporter", "rpt", null, false));
+    query.join(Hql.leftJoin(null, "reporter", "rpt", null, true));
     cc.configureQuery(dc, query, true);
     if (!"row".equals(cc.getSortProperty())) query.order(Orders.asc(Hql.property("row")));
@@ -135 +135 @@
   {
     cc.setMessage(t.getMessage());
+    t.printStackTrace();
   }
   int numListed = 0;

trunk/www/views/rawbioassays/rawdata/list_rawdata.jsp

@@ -104 +104 @@
   query.join(Hql.leftJoin(null, "reporter", "r", null, true));
   query.join(Hql.leftJoin(null, "feature", "f", null, true));
-  query.join(Hql.leftJoin("f", "arrayDesignBlock", "b", null, true));
   cc.configureQuery(dc, query, true);
   if (!"row".equals(cc.getSortProperty())) query.order(Orders.asc(Hql.property("row")));
@@ -135 +134 @@
   {
     cc.setMessage(t.getMessage());
+    t.printStackTrace();
   }
   int numListed = 0;