Changeset 4371

Timestamp:

Jul 3, 2008, 7:51:08 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 2.7.2 to the trunk.

Location:

trunk

Files:

• bin/onetimefix.bat (copied) (copied from tags/2.7.2/bin/onetimefix.bat)
• bin/onetimefix.sh (copied) (copied from tags/2.7.2/bin/onetimefix.sh)
• doc/src/docbook/admindoc/installation_upgrade.xml (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/ColumnDef.java (modified) (1 diff)
• src/core/net/sf/basedb/util/IntensityCalculatorUtil.java (modified) (5 diffs)
• src/core/net/sf/basedb/util/formatter/MultiFormatter.java (modified) (3 diffs)
• src/install/net/sf/basedb/install/OneTimeFix.java (copied) (copied from tags/2.7.2/src/install/net/sf/basedb/install/OneTimeFix.java)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (7 diffs)
• src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java (modified) (5 diffs)
• src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) (9 diffs)
• www/views/experiments/explorer/view/view.jsp (modified) (1 diff)
• www/views/experiments/spotdata/list_spotdata.jsp (modified) (1 diff)

trunk/doc/src/docbook/admindoc/installation_upgrade.xml

@@ -66 +66 @@
   <sect1 id="installation_upgrade.upgrade">
     <title>Upgrade instructions</title>
+
+    <important id="lowess_bug">
+      <title>Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1</title>
+      <para>
+      BASE 2.7.2 fixes a serious bug in the LOWESS plug-in shipped
+      as a part of the BASE package. The bug is found in all
+      BASE versions between 2.0 and 2.7.1, and has caused incorrect normalization values to be 
+      calculated. All data that has been normalized with the LOWESS plug-in prior 
+      to BASE 2.7.2 should be considered invalid and needs to be re-normalized with
+      the fixed version. Downstream analysis steps that has used the incorrectly
+      normalized data also needs to be redone. For more information about the bug see 
+      <ulink url="http://base.thep.lu.se/ticket/1077">http://base.thep.lu.se/ticket/1077</ulink>
+      </para>
+      
+      <para>
+      BASE 2.7.2 includes a utility for finding all experiments/bioassay sets that
+      includes data normalized with the LOWESS plug-in. An administrator can use
+      this utility to extract a list of all experiments/bioassay sets that needs to be fixed.
+      The utility can also tag the name of the found experiments/bioassay sets with
+      <code>FIX LOWESS</code> to make it easier to find data that needs to be fixed.
+      </para>
+      
+      <para>
+      The utility can't see any difference between data normalized with the 
+      old version and the fixed version. It will simply report all data that
+      has been normalized with the LOWESS plug-in. Only use the utility a single
+      time right after the upgrade to BASE 2.7.2.
+      </para>
+      
+      <para>
+      The utility is a command line program that should be executed on the BASE
+      application (web) server.
+      </para>
+      
+      <programlisting>
+<![CDATA[
+cd <base-dir>/bin
+./onetimefix.sh lowess_warn -u <login> -p <password> -f
+]]>
+</programlisting>
+      
+      <para>
+        We recommend running the utility as the root user. The <option>-f</option>
+        option is optional. If it is included the found experiments/bioassay sets
+        are tagged with <code>FIX LOWESS</code>, otherwise only a list with the
+        information is generated. 
+      </para>
+      
+    </important>
 
     <important id="tomcat6">

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

@@ -45 +45 @@
 import net.sf.basedb.clients.web.taglib.table.TableColumn;
 import net.sf.basedb.util.formatter.Formatter;
+import net.sf.basedb.util.formatter.MultiFormatter;
+import net.sf.basedb.util.formatter.ToStringFormatter;
 
 import java.util.ArrayList;
@@ -207 +209 @@
     ItemResultIterator<Formula> result = query.iterate(dc);
     SessionControl sc = dc.getSessionControl();
-    Formatter<Number> numberFormatter = FormatterFactory.getNumberFormatter(sc);
+    Formatter<Number> floatFormatter = FormatterFactory.getNumberFormatter(sc);
+    Formatter<Number> intFormatter = FormatterFactory.getIntFormatter(sc);
+    Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
+    Formatter<Boolean> booleanFormatter = FormatterFactory.getBooleanFormatter(sc);
+    Formatter<String> stringFormatter = FormatterFactory.getStringFormatter(sc);
+    Formatter<Object> defaultFormatter = new ToStringFormatter();
     while (result.hasNext())
     {
@@ -217 +224 @@
             titlePrefix + f.getName(), f.getDescription(), "auto", true, true, true, 
             f.getAverageMethod(), null);
-        tc.setFormatter(FormatterFactory.getColorFormatter(sc, f.getColoring(), numberFormatter));
+        Formatter<Number> intColorFormatter = FormatterFactory.getColorFormatter(sc, f.getColoring(), intFormatter);
+        Formatter<Number> floatColorFormatter = FormatterFactory.getColorFormatter(sc, f.getColoring(), floatFormatter);
+        MultiFormatter multiFormatter = new MultiFormatter(defaultFormatter, true);
+        multiFormatter.registerFormatter(Integer.class, intColorFormatter);
+        multiFormatter.registerFormatter(Long.class, intColorFormatter);
+        multiFormatter.registerFormatter(Number.class, floatColorFormatter);
+        multiFormatter.registerFormatter(Date.class, dateFormatter);
+        multiFormatter.registerFormatter(Boolean.class, booleanFormatter);
+        multiFormatter.registerFormatter(String.class, stringFormatter);
+        tc.setFormatter(multiFormatter);
         columns.add(tc);
       }

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/ColumnDef.java

@@ -616 +616 @@
 
         sb.append("<span class=\"link\" onclick=\"Table.setSortOrder(event, '").append(table.getId()).append("', '");
-        sb.append(getSortproperty()).append("', '").append(direction.name()).append("')\" title=\"");
+        sb.append(HTML.javaScriptEncode(getSortproperty())).append("', '").append(direction.name()).append("')\" title=\"");
         sb.append(theTooltip).append("\">").append(getTitle()).append("</span>").append(image);
         

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

@@ -47 +47 @@
 import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.InvalidUseOfNullException;
+import net.sf.basedb.core.data.FeatureData;
 import net.sf.basedb.core.data.RawData;
 import net.sf.basedb.core.data.ReporterData;
@@ -305 +306 @@
 
     // A cache holding already seen position --> reporter mappings
-    Map<Integer, ReporterData> positionCache = new HashMap<Integer, ReporterData>();
+    Map<Integer, Integer> positionCache = new HashMap<Integer, Integer>();
+    // A cache holding already seen feature->position mappings
+    Map<Integer, Integer> featureCache = new HashMap<Integer, Integer>();
     
     // The max position number in the raw bioassays -- only calculated if needed (see below)
@@ -350 +353 @@
       if (rba.getArrayDesign() != null)
       {
-        rawQuery.join(Hql.leftJoin(null, "feature", Item.REPORTER.getAlias(), null, true));
+        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));
       }
       
@@ -362 +369 @@
         int position = rd.getPosition();
         ReporterData reporter = rd.getReporter();
+        FeatureData feature = rd.getFeature();
         //data += System.nanoTime();
         
@@ -371 +379 @@
         if (intensities != null)
         {
-          // Insert mapping position --> reporter
-          if (positionCache.containsKey(position))
+          // If we have a feature check the feature cache if a position has
+          // already been assigned to it
+          Integer cachedFeaturePosition = feature == null ?
+            null : featureCache.get(feature.getId());
+          if (cachedFeaturePosition != null)
           {
-            //chit -= System.nanoTime();
-            // A mapping already exists, check if same reporter
-            ReporterData cached = positionCache.get(position);
-            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
-              if (maxPosition == 0)
-              {
-                // We must find the maximum position among all raw bioassays unless we havn't done that already
-                try
-                {
-                  for (RawBioAssay rbaMax : rawBioAssays)
-                  {
-                    DynamicRawDataQuery query = rbaMax.getDynamicRawData();
-                    query.select(Selects.expression(Aggregations.max(Dynamic.rawData("position")), "maxPosition"));
-                    DynamicResultIterator result = query.iterate(dc);
-                    int thisMaxPosition = result.next().getInt(1);
-                    if (thisMaxPosition > maxPosition) maxPosition = thisMaxPosition;
-                    result.close();
-                  }
-                }
-                catch (SQLException ex)
-                {
-                  throw new BaseException(ex);
-                }
-              }
-              maxPosition++;
-              position = maxPosition;
-              posBatcher.insert(position, reporter);
-              positionCache.put(position, reporter);
-            }
-            //chit += System.nanoTime();
+            position = cachedFeaturePosition;
           }
           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();
+            // We have no feature or the feautre has no position; 
+            // check if the position has same reporter
+            if (positionCache.containsKey(position))
+            {
+              Integer cachedReporterId = positionCache.get(position);
+              Integer reporterId = reporter == null ? null : reporter.getId();
+              if (reporterId == null && cachedReporterId != null || 
+                reporterId != null && !reporterId.equals(cachedReporterId))
+              {
+                // Reporters don't match, we need a new position
+                if (maxPosition == 0)
+                {
+                  // We must find the maximum position among all raw bioassays unless we havn't done that already
+                  try
+                  {
+                    for (RawBioAssay rbaMax : rawBioAssays)
+                    {
+                      DynamicRawDataQuery query = rbaMax.getDynamicRawData();
+                      query.select(Selects.expression(Aggregations.max(Dynamic.rawData("position")), "maxPosition"));
+                      DynamicResultIterator result = query.iterate(dc);
+                      int thisMaxPosition = result.next().getInt(1);
+                      if (thisMaxPosition > maxPosition) maxPosition = thisMaxPosition;
+                      result.close();
+                    }
+                  }
+                  catch (SQLException ex)
+                  {
+                    throw new BaseException(ex);
+                  }
+                }
+                maxPosition++;
+                position = maxPosition;
+                posBatcher.insert(position, reporter);
+                positionCache.put(position, reporterId);
+                if (feature != null) featureCache.put(feature.getId(), position);
+              }
+            }
+            else
+            {
+              // This position is not used, map it to the current reporter
+              posBatcher.insert(position, reporter);
+              positionCache.put(position, reporter == null ? null : reporter.getId());
+              if (feature != null) featureCache.put(feature.getId(), position);
+            }
           }
+          
           //braw -= System.nanoTime();
           // Insert mapping to raw data spot

trunk/src/core/net/sf/basedb/util/formatter/MultiFormatter.java

@@ -46 +46 @@
   private final boolean checkSuperclass;
   private final Map<Class<?>, Formatter<?>> formatters;
+  private final boolean decideOnFirst;
+  private Formatter formatter;
   
   /**
@@ -56 +58 @@
   public MultiFormatter(Formatter<Object> defaultFormatter, boolean checkSuperclass)
   {
+    this(defaultFormatter, checkSuperclass, false);
+  }
+  
+  /**
+    Create a new multi formatter.
+    @param defaultFormatter The formatter to use if the object's class
+      isn't found among the registered formatters
+    @param checkSuperclass If the superclass of the object should be
+      checked in case there is no exact match
+    @param decideOnFirst If TRUE, the first non-null value decides which parent
+      formatter to use. All subsequent calls to {@link #format(Object)} uses
+      the same formatetter. This is useful when you know that the formatter will
+      only use the same class of objects, but not which class.
+    @since 2.7.2
+  */
+  public MultiFormatter(Formatter<Object> defaultFormatter, boolean checkSuperclass, 
+    boolean decideOnFirst)
+  {
     this.defaultFormatter = defaultFormatter;
     this.formatters = new HashMap<Class<?>, Formatter<?>>();
     this.checkSuperclass = checkSuperclass;
+    this.decideOnFirst = decideOnFirst;
   }
   
@@ -70 +91 @@
     if (value == null) return "";
     Class c = value.getClass();
-    Formatter f = formatters.get(c);
-    if (f == null && checkSuperclass)
+    Formatter f = formatter;
+    if (f == null)
     {
-      c = c.getSuperclass();
-      while (f == null && c != null)
+      f = formatters.get(c);
+      if (f == null && checkSuperclass)
       {
-        f = formatters.get(c);
         c = c.getSuperclass();
+        while (f == null && c != null)
+        {
+          f = formatters.get(c);
+          c = c.getSuperclass();
+        }
       }
+      if (f == null) f = defaultFormatter;
+      if (decideOnFirst) formatter = f;
     }
-    if (f == null) f = defaultFormatter;
     return f.format(value);
   }

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -128 +128 @@
 import java.util.TreeMap;
 import java.util.regex.Pattern;
+import java.util.regex.Matcher;
 
 /**
@@ -843 +844 @@
       Boolean mergeReporters = (Boolean) configuration.getValue(geneAveragesParameter.getName());
       
+      TreeMap<String, JobParameter> base1parametertype = getJobParameterObjectsFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName())), true);
       ListMap<String, String> parameters = new ListMap<String, String>();
       for (PluginParameter<?> pp : getJobParametersFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName())), true))
@@ -848 +850 @@
         String name = pp.getName();
         Object value = job.getValue(name);
-        parameters.put(name, value == null ? "" : value.toString());
+        String valueString = (value == null) ? "" : value.toString();
+        JobParameter jp=base1parametertype.get(name);
+        // replacing line breaks for Base1 TEXT and STRING types
+        if (jp.getType() == Base1JobParameterType.STRING ||
+            jp.getType() == Base1JobParameterType.TEXT)
+        {
+          Pattern p=Pattern.compile("\r");
+          Matcher m=p.matcher(valueString);
+          valueString = m.replaceAll("\\\\r");
+          m.usePattern(Pattern.compile("\n"));
+          m.reset(valueString);
+          valueString = m.replaceAll("\\\\n");
+        }
+        parameters.put(name, valueString);
       }
       
@@ -1010 +1025 @@
     return headers;
   }
-  
-  
+
+
   @SuppressWarnings({ "unchecked", "serial" })
-  private List<PluginParameter<?>> getJobParametersFromXML(String xml, boolean hideRemoved)
+  private TreeMap<String, JobParameter>
+    getJobParameterObjectsFromXML(String xml, boolean hideRemoved)
   {
     try
@@ -1031 +1047 @@
         }
       });
-      
-      TreeMap<Integer, PluginParameter<?>> positionParameter = new TreeMap<Integer, PluginParameter<?>>();
+
+      TreeMap<String, JobParameter> pars= new TreeMap<String, JobParameter>();
       while (it.hasNext())
       {
@@ -1039 +1055 @@
         if (!jp.isRemoved())
         {
+          if (pars.containsKey(jp.getName()))
+          {
+            throw new BaseException("Duplicate parameter at position "+jp.getPosition());
+          }
+          pars.put(jp.getName(), jp);
+        }
+      }
+      return pars;
+    }
+    catch (JDOMException e1)
+    {
+      throw new BaseException(e1.getCause());
+    }
+    catch (IOException e1)
+    {
+      throw new BaseException(e1);
+    }
+  }
+
+
+  @SuppressWarnings({ "unchecked", "serial" })
+  private List<PluginParameter<?>> getJobParametersFromXML(String xml, boolean hideRemoved)
+  {
+    try
+    {
+      String doctype = "<!DOCTYPE jobparameters SYSTEM \"base1-plugin-configuration-file.dtd\">";
+      Document doc = XMLUtil.getValidatedXml(doctype+xml, dtdFile);
+      Iterator<Element> it = doc.getDescendants(new Filter()
+      {
+        public boolean matches(Object o)
+        {
+          if (o instanceof Element)
+          {
+            Element e = (Element) o;
+            return e.getName().equals("parameter");
+          }
+          return false;
+        }
+      });
+      
+      TreeMap<Integer, PluginParameter<?>> positionParameter = new TreeMap<Integer, PluginParameter<?>>();
+      while (it.hasNext())
+      {
+        Element e = it.next();
+        JobParameter jp = new JobParameter(e);
+        if (!jp.isRemoved())
+        {
           if (positionParameter.containsKey(jp.getPosition()))
           {
@@ -1057 +1120 @@
     }
   }
-  
-  
+
+
   /**
     Creates a boolean from a string.

trunk/src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java

@@ -138 +138 @@
   (
     "delta",
-    "Minimum log(intensity) step",
+    "Minimum log10(intensity) step",
     "",
-    new FloatParameterType(0F, null, 0.1F, true)
+    new FloatParameterType(0F, null, 0.043F, true)
   );
   
@@ -510 +510 @@
               checkInterrupted();
               SpotData spot = toNormalize.get(j);
-              double factor = Math.exp(smoothCurve.get(j) * 0.5);
+              double factor = Math.pow(2,smoothCurve.get(j) * 0.5);
               batcher.insert(bioassayColumn, spot.position, (float)(spot.ch1/factor), (float)(spot.ch2*factor));
             }
@@ -611 +611 @@
         // while distance from windowStart to i is greater then distance from i to windowEnd: move window
         while ((windowStart + windowSize < dataSize) && 
-            (Ai - data.get(windowStart).A > data.get(windowStart + windowSize).A - Ai))
+            (Ai - data.get(windowStart).A > data.get(windowStart + windowSize-1).A - Ai))
         {
           windowStart++;
@@ -657 +657 @@
       {
         double w = Math.abs((smoothCurve[j] - data.get(j).M) * invYWRange);
-        wFit.set(j, w < 1 ? Math.pow(Math.pow(1 - w, 2), 2) : 0);
+        wFit.set(j, w < 1 ? Math.pow(1D - w*w, 2) : 0);
       }
     }
@@ -675 +675 @@
       double v1 = temp.get((temp.size() / 2) - 1);
       double v2 = temp.get((temp.size() / 2));
-      return 0.5 * v1 * v2; 
-    }
-    else
-    {
-      return temp.get((temp.size() - 1) / 2);
-    }
+      return 0.5 * (v1 + v2);
+    }
+    return temp.get(temp.size() / 2);
   }
 

trunk/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java

@@ -238 +238 @@
     if (command.equals(Request.COMMAND_EXECUTE))
     {
-      if (progress != null) progress.display(0, "Preparing to normalize...");
-
       DbControl dc = null;
       try
@@ -251 +249 @@
         float highExclude = (Float) job.getValue(highExcludeParameter.getName());
         Job thisJob = getCurrentJob(dc);
-
-        // Create Transformation
-        Transformation t = source.newTransformation(getCurrentJob(dc));
-        t.setName(about.getName());
-        dc.saveItem(t);
-
-        // Create the normalized bioassay set
-        BioAssaySet child = t.newProduct(null, "new", true);
-        dc.saveItem(child);
-
-        // Batcher for inserting normalized data
-        SpotBatcher batcher = child.getSpotBatcher();
-
-        int nofChannels=source.getRawDataType().getChannels();
-        switch (nofChannels)
+        
+        BioAssaySet child = null;
+        int rawChannels = source.getRawDataType().getChannels();
+        switch (rawChannels)
         {
-            case 1:
-              String method = (String) job.getValue(methodParameter.getName());
-              normalize1ch(dc, source, batcher, minIntensity, lowExclude,
-                           highExclude, method.equals("Scale"), progress);
+          case 1:
+            String method = (String) job.getValue(methodParameter.getName());
+            child = normalize1ch(dc, source, thisJob, minIntensity, lowExclude,
+                    highExclude, method.equals("Scale"), progress);
+            break;
+          case 2:
+            int blockGroupSize =
+              (Integer) job.getValue(blockGroupParameter.getName());
+            child = normalize(dc, source, thisJob, minIntensity, lowExclude, 
+                highExclude, blockGroupSize, progress);
               break;
-            case 2:
-              int blockGroupSize =
-                (Integer) job.getValue(blockGroupParameter.getName());
-              normalize2ch(dc, source, batcher, minIntensity, lowExclude,
-                           highExclude, blockGroupSize, progress);
-              break;
-            default:
-              throw new InvalidDataException(nofChannels +
-                                             "-channel arrays not supported");
-        }
-
-        batcher.close();
+          default:
+              throw new InvalidDataException(rawChannels + 
+                "-channel arrays not supported");
+        }
+        
         child.setName(childName);
         child.setDescription(childDescription);
         dc.commit();
-
         int normalizedSpots = child.getNumSpots();
         response.setDone(normalizedSpots + " spots normalized, " + (source.getNumSpots() - normalizedSpots) + " spots removed");
@@ -421 +406 @@
     @since 2.7
   */
-  private void
-  normalize1ch(DbControl dc, BioAssaySet source, SpotBatcher batcher,
+  private BioAssaySet
+  normalize1ch(DbControl dc, BioAssaySet source, Job job,
                float minIntensity, float lowExclude, float highExclude,
                boolean scale, ProgressReporter progress)
   {
+    // Create Transformation
+    Transformation t = source.newTransformation(job);
+    t.setName(about.getName());
+    dc.saveItem(t);
+
+    // Create the normalized bioassay set
+    BioAssaySet child = t.newProduct(null, "new", true);
+    dc.saveItem(child);
+
+    // Batcher for inserting normalized data
+    SpotBatcher batcher = child.getSpotBatcher();
+    
     // Expressions used to get data
     Expression ch1 = Dynamic.column(VirtualColumn.channel(1));
@@ -510 +507 @@
       throw new BaseException(e);
     }
+    return child;
   }
 
   /**
-    Normalise the source bioassay set using MEDIAN-RATIO normalization.
+    Normalise the source bioassay set using MEDIAN-RATIO normalization. NOTE!
+    This normalization method only works with 2-channel data.
+    
     @param dc The DbControl to use for database access
     @param source The source bioassay set that is going to be normalized
+    @param job The job that is doing the normalization, or null
     @param minIntensity All spots which have a lower intensity value in either channel
       will be filtered out
@@ -525 +526 @@
     @param progress Progress reporter for the caller to keep track of the plugin's progress. Null is allowed. 
     @return The normalized bioassayset
-    @since 2.5
-  */
-  private void
-  normalize2ch(DbControl dc, BioAssaySet source, SpotBatcher batcher,
-               float minIntensity, float lowExclude, float highExclude,
-               int blockGroupSize, ProgressReporter progress)
-  {
+    @since 2.5; This method was removed in 2.7.0 by accident, added in 2.7.2 again
+  */
+  public BioAssaySet normalize(DbControl dc, BioAssaySet source, Job job, 
+      float minIntensity, float lowExclude, float highExclude, 
+      int blockGroupSize, ProgressReporter progress)
+  {
+    if (progress != null) progress.display(0, "Preparing to normalize...");
+  
+    // Create Transformation
+    Transformation t = source.newTransformation(job);
+    t.setName(about.getName());
+    dc.saveItem(t);
+    
+    // Create the normalized bioassay set
+    BioAssaySet child = t.newProduct(null, "new", true);
+    dc.saveItem(child);
+    
+    // Batcher for inserting normalized data
+    SpotBatcher batcher = child.getSpotBatcher();
+    
     // Expressions used to get data
     Expression block = Dynamic.rawData("block");
@@ -567 +581 @@
     query.restrict(bioAssayRestriction);
     query.order(Orders.asc(block));
-
+  
     // Normalize one bioassay at a time
     List<BioAssay> assays = source.getBioAssays().list(dc);
@@ -575 +589 @@
       {
         checkInterrupted();
-
+  
         // Prepare list for holding data
         int assaySpots = assay.getNumSpots();
@@ -657 +671 @@
           fromBlock = toBlock + 1;
         }
-        batcher.flush();
-      }
+      }
+      batcher.flush();
       batcher.close();
     }
@@ -665 +679 @@
       throw new BaseException(e);
     }
+    return child;
   }
   

trunk/www/views/experiments/explorer/view/view.jsp

@@ -616 +616 @@
           property="<%=tc.getProperty()%>"
           datatype="<%=tc.getDatatype().getStringValue()%>"
-          title="<%=tc.getTitle()%>"
+          title="<%=HTML.encodeTags(tc.getTitle())%>"
           sortable="<%=tc.getSortable()%>"
           filterable="<%=tc.getFilterable()%>"

trunk/www/views/experiments/spotdata/list_spotdata.jsp

@@ -258 +258 @@
           property="<%=tc.getProperty()%>"
           datatype="<%=tc.getDatatype().getStringValue()%>"
-          title="<%=tc.getTitle()%>"
+          title="<%=HTML.encodeTags(tc.getTitle())%>"
           sortable="<%=tc.getSortable()%>"
           filterable="<%=tc.getFilterable()%>"