Changeset 2128

Timestamp:

Mar 30, 2006, 8:01:48 AM (18 years ago)

Author:

Gregory Vincic

Message:

Merged base/trunk revision 2116:2127 with base/branches/rf1

Location:

branches/rf1

Files:

• src/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java (modified) (8 diffs)
• src/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) (8 diffs)
• www/admin/clients/help (copied) (copied from trunk/www/admin/clients/help)
• www/admin/clients/help/edit_help.jsp (copied) (copied from trunk/www/admin/clients/help/edit_help.jsp)
• www/admin/clients/help/index.jsp (copied) (copied from trunk/www/admin/clients/help/index.jsp)
• www/admin/clients/help/list_help.jsp (copied) (copied from trunk/www/admin/clients/help/list_help.jsp)
• www/admin/clients/help/view_help.jsp (copied) (copied from trunk/www/admin/clients/help/view_help.jsp)
• www/admin/clients/view_client.jsp (modified) (3 diffs)
• www/common/plugin/configure.jsp (modified) (6 diffs)
• www/exception/exception.jsp (modified) (3 diffs)
• www/views/experiments/bioassaysets/create_root_bioassayset.jsp (deleted)
• www/views/experiments/bioassaysets/index.jsp (modified) (1 diff)
• www/views/experiments/bioassaysets/list_bioassaysets.jsp (modified) (3 diffs)
• www/views/formulas/edit_formula.jsp (modified) (4 diffs)

branches/rf1/src/core/net/sf/basedb/plugins/IntensityCalculatorPlugin.java

@@ -27 +27 @@
 import net.sf.basedb.core.ProgressReporter;
 
+import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.Formula;
+import net.sf.basedb.core.Include;
+import net.sf.basedb.core.InvalidDataException;
+import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemParameterType;
+import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.PluginParameter;
+import net.sf.basedb.core.RequestInformation;
+import net.sf.basedb.core.StringParameterType;
 import net.sf.basedb.core.Transformation;
 import net.sf.basedb.core.BioAssaySet;
@@ -37 +47 @@
 import net.sf.basedb.core.plugin.AboutImpl;
 import net.sf.basedb.core.plugin.AbstractPlugin;
+import net.sf.basedb.core.plugin.GuiContext;
 import net.sf.basedb.core.plugin.Plugin;
+import net.sf.basedb.core.plugin.InteractivePlugin;
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
-import net.sf.basedb.core.IntensityFormula;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.util.IntensityCalculator;
 import net.sf.basedb.util.IntensityCalculatorUtil;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
+import java.util.Set;
 
 /**
-   This plugin provides methods to calculate the intensity for a root bioassayset using different formulas.
-   It needs the following parameters
+   This plugin provides methods to calculate the intensity for a root bioassayset 
+   using different formulas. It needs the following parameters:
 
    <pre>
-   String              : name 
-   Experiment          : experiment
-   List<RawBioAssay>   : rawBioAssays  
-   String              : formula
+   String              : name; The name of the new bioassayset
+   Experiment          : experiment; The experiment we are working on
+   List&gt;RawBioAssay&lt;   : rawBioAssays; The raw bioassays to create bioassays for
+     (must be part of the experiment)
+   Formula             : formula; The formula to use to for calculating intesities
    </pre>
 
-   @author Gregory
+   @author Gregory, Nicklas
+   @version 2.0
+   @base.modified $Date$
 */
 public class IntensityCalculatorPlugin
   extends AbstractPlugin
-  implements Plugin  
+  implements InteractivePlugin 
 {
 
@@ -70 +90 @@
           new AboutImpl
     (
-      "Intensity calculator",
-      "This plugin is used to calculate intensities from raw data creating an initial raw bioassay.",
-      "1.0",
+      "Formula intensity calculator",
+      "This plugin is used to calculate intensities from raw data creating an initial root bioassay set. "+
+      "The intensities are calculated using Formula objects registered for the experiment's raw data type. " +
+      "Thus, the functionality of this plugin can be extended by adding more formula objects to the database.",
+      "2.0",
       "2006, Department of Theoretical Physics, Lund University",
       null,
@@ -79 +101 @@
     );
 
-
+  private static final Set<GuiContext> guiContexts = 
+    Collections.singleton(new GuiContext(Item.BIOASSAYSET, GuiContext.Type.LIST));
+
+  private static final RequestInformation configurePlugin = new RequestInformation
+  (
+    Request.COMMAND_CONFIGURE_PLUGIN,
+    "Configure intensity calculator",
+    "This plugin has no configuration options.",
+    null
+  );
+
+  private static final StringParameterType nameType = 
+    new StringParameterType(BioAssaySet.MAX_NAME_LENGTH, "New bioassayset", true);
+  private static final PluginParameter<String> nameParameter = new PluginParameter<String>(
+    "name", "Bioassay set name", "The name of the root bioassayset", nameType);
+
+  private ItemParameterType<Experiment> experimentType;
+  private PluginParameter<Experiment> experimentParameter;
+
+  private ItemParameterType<RawBioAssay> rawBioAssaysType;
+  private PluginParameter<RawBioAssay> rawBioAssaysParameter;
+
+  private ItemParameterType<Formula> formulaType;
+  private PluginParameter<Formula> formulaParameter;
+
+  private RequestInformation configureJob;
+  
   /**
      Constructor should be empty. 
@@ -86 +134 @@
   {}
   
-
-  /* 
-    Plugin interface implementation 
-    -------------------------------
+  /*
+    From the Plugin interface
+    -------------------------------------------
   */
   public About getAbout()
@@ -95 +142 @@
     return about;
   }
-
-
   /**
      Returns the main plugin type this plugin belongs to.
@@ -106 +151 @@
   }
 
-
-  /**
-     @param request 
-     @param response 
-     @param progress
-  */
   @SuppressWarnings("unchecked")
   public void run(Request request, Response response, ProgressReporter progress)
@@ -118 +157 @@
     try
     {
-      /* name parameter */
+      // name parameter
       String name = (String)job.getValue("name");
   
-      /* experiment parameter*/
-  
-      Integer experimentId = (Integer)job.getValue("experiment_id");
-      if(experimentId != null)
-      {
-        Experiment experiment = Experiment.getById(dc, experimentId.intValue());
-  
-        /* rawBioAssays parameter*/
-        List<RawBioAssay> sources = (List<RawBioAssay>)job.getValues("rawBioAssays");
-        for (RawBioAssay rba : sources)
-        {
-          dc.reattachItem(rba);
-        }
-  
-        /* formula parameter */
-        String formula = (String)job.getValue("formula");
-  
-        /* intensity calculation */
-        RawDataType rdt = experiment.getRawDataType();
-        IntensityFormula intensityFormula = rdt.getIntensityFormula( formula );
-        IntensityCalculator iCalc = IntensityCalculatorUtil.createJepIntensityCalculator(dc, rdt, intensityFormula.getExpressions());
-        int jobId = job.getId();
-        Job thisJob = Job.getById(dc, jobId);
-        BioAssaySet rootBas = IntensityCalculatorUtil.createRootBioAssaySet(dc, experiment, sources, thisJob, iCalc, progress);
-        rootBas.setName(name);
-        Transformation t = rootBas.getTransformation();
-        t.setName(intensityFormula.getTitle());
-        dc.commit();
-        response.setDone("Done");
+      // experiment parameter
+      Experiment experiment = (Experiment)job.getValue("experiment");
+      
+      // To avoid disconnection/reconnection issues
+      experiment = Experiment.getById(dc, experiment.getId());
+  
+      // rawBioAssays parameter
+      List<RawBioAssay> sources = (List<RawBioAssay>)job.getValues("rawBioAssays");
+      for (RawBioAssay rba : sources)
+      {
+        dc.reattachItem(rba);
       }
-      else
-      {
-        response.setError("Experiment id is null", null);
+
+      // Formula parameter
+      Formula formula = (Formula)job.getValue("formula");
+      formula = Formula.getById(dc, formula.getId());
+  
+      // intensity calculation
+      RawDataType rdt = experiment.getRawDataType();
+
+      // IntensityFormula intensityFormula = rdt.getIntensityFormula( formula );
+      IntensityCalculator iCalc = 
+        IntensityCalculatorUtil.createJepIntensityCalculator(dc, rdt, 
+        formula.getFormulas().toArray(new String[formula.getNumFormulas()]));
+      int jobId = job.getId();
+      Job thisJob = Job.getById(dc, jobId);
+
+      BioAssaySet rootBas = IntensityCalculatorUtil.createRootBioAssaySet(dc, experiment, sources, thisJob, iCalc, progress);
+      rootBas.setName(name);
+      Transformation t = rootBas.getTransformation();
+      t.setName(formula.getName());
+      dc.commit();
+      response.setDone("Done");
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+  // -------------------------------------------
+
+  /*
+    From the InteractivePlugin interface
+    -------------------------------------------
+  */
+  public Set<GuiContext> getGuiContexts()
+  {
+    return guiContexts;
+  }
+  /**
+    Always false, since plugin doesn't operate on individual items.
+  */
+  public boolean isInContext(GuiContext context, Object item)
+  {
+    return false;
+  }
+  /**
+    The {@link Request#COMMAND_CONFIGURE_PLUGIN} command will not ask for
+    any parameters.
+    The {@link Request#COMMAND_CONFIGURE_JOB} command will ask for
+    the parameters mentioned in the class documentation.
+  */
+  public RequestInformation getRequestInformation(GuiContext context, String command)
+    throws BaseException
+  {
+    RequestInformation requestInformation = null;
+    if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN))
+    {
+      requestInformation = configurePlugin;
+    }
+    else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
+    {
+      requestInformation = getConfigureJobParameters();
+    }
+    return requestInformation;
+  }
+  /**
+    Store configuration settings for {@link Request#COMMAND_CONFIGURE_PLUGIN}, 
+    and {@link Request#COMMAND_CONFIGURE_JOB}.
+  */
+  @SuppressWarnings("unchecked")
+  public void configure(GuiContext context, Request request, Response response)
+  {
+    String command = request.getCommand();
+    
+    try
+    {
+      if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN))
+      {
+        response.setDone("No configuration needed.");
       }
-    }
-    finally
-    {
-      if (dc != null) dc.close();
-    }
-  }
+      else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
+      {
+        List<Throwable> errors = validateRequestParameters(configureJob.getParameters(), request);
+        if (errors != null)
+        {
+          response.setError(errors.size()+" invalid parameter(s) were found in the request", errors);
+          return;
+        }
+        
+        Experiment experiment = (Experiment)request.getParameterValue("experiment");
+        DbControl dc = sc.newDbControl();
+        int numSpots = 0;
+        try
+        {
+          experiment = Experiment.getById(dc, experiment.getId());
+          List<RawBioAssay> rawBioAssays = (List<RawBioAssay>)request.getParameterValues("rawBioAssays");
+          for (RawBioAssay rba : rawBioAssays)
+          {
+            if (!experiment.isUsing(rba))
+            {
+              throw new InvalidDataException("Raw bioassay '" + rba.getName() + 
+                "' is not part of the experiment '" + experiment.getName()+"'");
+            }
+            numSpots += rba.getSpots();
+          }
+        }
+        finally
+        {
+          if (dc != null) dc.close();
+        }
+        
+        Formula formula = (Formula)request.getParameterValue("formula");
+        if (formula.getFormulaType() != Formula.Type.INTENSITY_EXPRESSION)
+        {
+          throw new InvalidDataException("The selected formula is not an intensity expression formula: " + 
+            formula.getName());
+        }
+        if (formula.getRawDataType() != experiment.getRawDataType())
+        {
+          throw new InvalidDataException("The selected formula '"+formula.getName()+
+            "' uses a different raw data type than the experiment '" + experiment.getName()+"'");
+        }
+        
+        storeValue(job, request, nameParameter);
+        storeValue(job, request, experimentParameter);
+        storeValues(job, request, rawBioAssaysParameter);
+        storeValue(job, request, formulaParameter);
+        
+        Job.ExecutionTime execTime = Job.ExecutionTime.SHORT;
+        // TODO - this should be configurable in some way
+        if (numSpots > 1000000 && numSpots < 10000000)
+        {
+          execTime = Job.ExecutionTime.MEDIUM;
+        }
+        else
+        {
+          execTime = Job.ExecutionTime.LONG;
+        }
+        
+        response.setDone("Job configuration complete", execTime);
+      }
+    }
+    catch (Throwable ex)
+    {
+      response.setError(ex.getMessage(), Arrays.asList(ex));
+      ex.printStackTrace();
+    }
+  }
+
+  
+  private RequestInformation getConfigureJobParameters()
+  {
+    if (configureJob == null)
+    {
+      List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
+      
+      experimentType = new ItemParameterType<Experiment>(Experiment.class, null, true, 1, null);
+      experimentParameter = new PluginParameter<Experiment>(
+        "experiment", "Experiment", "The experiment we are working with", experimentType);
+      
+      parameters.add(experimentParameter);
+      parameters.add(nameParameter);
+      
+      DbControl dc = sc.newDbControl();
+      try
+      {
+        int experimentId = sc.getCurrentContext(Item.EXPERIMENT).getId();
+        Experiment experiment = Experiment.getById(dc, experimentId);
+        
+        ItemQuery<RawBioAssay> rawBioAssayQuery = experiment.getRawBioAssays();
+        rawBioAssayQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
+        rawBioAssayQuery.order(Orders.asc(Hql.property("name")));
+        List<RawBioAssay> rawBioAssays = new ArrayList<RawBioAssay>(rawBioAssayQuery.list(dc));
+        rawBioAssaysType = new ItemParameterType<RawBioAssay>(RawBioAssay.class, null, true, 0, rawBioAssays);
+        rawBioAssaysParameter = new PluginParameter<RawBioAssay>(
+          "rawBioAssays", "Raw bioassays", "Select the raw bioassays to use when creating the root bioassay set",
+          rawBioAssaysType);
+        
+        parameters.add(rawBioAssaysParameter);
+        
+        ItemQuery<Formula> formulaQuery = Formula.getQuery(Formula.Type.INTENSITY_EXPRESSION, 
+            experiment.getRawDataType());
+        formulaQuery.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
+        formulaQuery.order(Orders.asc(Hql.property("name")));
+        List<Formula> formulas = new ArrayList<Formula>(formulaQuery.list(dc));
+        formulaType = new ItemParameterType<Formula>(Formula.class, null, true, 1, formulas);
+        formulaParameter = new PluginParameter<Formula>(
+          "formula", "Formula", "Select the expression to use for calculating the intensities",
+          formulaType);
+        parameters.add(formulaParameter);
+      }
+      finally
+      {
+        if (dc != null) dc.close();
+      }     
+      configureJob = new RequestInformation
+      (
+        Request.COMMAND_CONFIGURE_JOB,
+        "Intensity calculation options",
+        "Select which raw bioassays to use and a formula for the calculations",
+        parameters
+      );
+    }
+    return configureJob;
+  }
+
 }

branches/rf1/src/core/net/sf/basedb/plugins/MedianRatioNormalization.java

@@ -48 +48 @@
 import net.sf.basedb.core.SpotBatcher;
 import net.sf.basedb.core.Transformation;
+import net.sf.basedb.core.Type;
 import net.sf.basedb.core.VirtualColumn;
 import net.sf.basedb.core.plugin.About;
@@ -58 +59 @@
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
+import net.sf.basedb.core.query.Aggregations;
 import net.sf.basedb.core.query.Dynamic;
 import net.sf.basedb.core.query.Expressions;
@@ -102 +104 @@
     "highExclude",
     "Exclude top",
-    "Exclude top %",
+    "A percentage of the highest values that are ignored when calculating the median.",
     new FloatParameterType(0F, 100F, 5F, true)
   );
@@ -110 +112 @@
     "lowExclude",
     "Exclude low",
-    "Exclude low %",
+    "A percentage of the lowest values that are ignored when calculating the median.",
     new FloatParameterType(0F, 100F, 5F, true)
   );
@@ -185 +187 @@
       try
       {
+        int blockGroupSize = (Integer) job.getValue(blockGroupParameter.getName());
         BioAssaySet bioAssaySet = (BioAssaySet) job.getValue(bioAssaySetParameter.getName());
         bioAssaySet = BioAssaySet.getById(dc, bioAssaySet.getId());
@@ -193 +196 @@
         child.setName(bioAssaySet.getName());
         dc.saveItem(child);
-
         batcher = child.getSpotBatcher();
 
@@ -201 +203 @@
 
         Select ratio = Selects.expression(Expressions.divide(Dynamic.column(VirtualColumn.channel(1)), Dynamic.column(VirtualColumn.channel(2))), "ratio");
-
+        Restriction intensityRestriction = Restrictions.and
+        (
+          Restrictions.gt(Dynamic.column(VirtualColumn.channel(1)), Expressions.aFloat((Float) job.getValue(minIntensityParameter.getName()))), 
+          Restrictions.gt(Dynamic.column(VirtualColumn.channel(2)), Expressions.aFloat((Float) job.getValue(minIntensityParameter.getName())))
+        );
+        float lowExclude = (Float) job.getValue(lowExcludeParameter.getName());
+        float highExclude = (Float) job.getValue(highExcludeParameter.getName());
+        
+        DynamicSpotQuery query;
+        DynamicResultIterator resultIter;
         List<BioAssay> assays = bioAssaySet.getBioAssays().list(dc);
         for (BioAssay assay : assays)
         {
           //TODO use block numbers to create subgroups
-          DynamicSpotQuery query = getQuery(assay.getSpotData());
-          query.select(ratio);
-          query.order(Orders.asc(Expressions.selected(ratio)));
-
-          int count = query.count(dc);
-          numSpots -= assay.getNumSpots() - count;
-          progress.display((normalizedSpots * 100) / numSpots, (assay.getNumSpots() - count)+ " spots removed from assay " + assay.getName());
-
-          // check count > 0
-          double median;
-          if (count % 2 == 0)
-          {
-            query.setFirstResult((count/2)-1);
-            query.setMaxResults(2);
-            DynamicResultIterator iter = query.iterate(dc);
-            median = Math.sqrt(iter.next().getFloat(iter.getIndex("ratio"))*iter.next().getFloat(iter.getIndex("ratio")));
-          }
-          else
-          {
-            query.setFirstResult((count-1)/2);
-            query.setMaxResults(1);
-            DynamicResultIterator iter = query.iterate(dc);
-            median = iter.next().getFloat(iter.getIndex("ratio"));
-          }
-          
-          float sqrtMedRatio = (float) Math.sqrt(median);
-          float invSqrtMedRatio = 1/sqrtMedRatio;
-          Select newCh1 = Selects.expression
-          (
-            Expressions.multiply(Expressions.selected(Dynamic.select(VirtualColumn.channel(1))), Expressions.aFloat(invSqrtMedRatio)),
-            "newCh1"
-          );
-          Select newCh2 = Selects.expression
-          (
-            Expressions.multiply(Expressions.selected(Dynamic.select(VirtualColumn.channel(2))), Expressions.aFloat(sqrtMedRatio)),
-            "newCh2"
-          );
-
-          query = getQuery(assay.getSpotData());
-          query.select(Dynamic.select(VirtualColumn.COLUMN));
-          query.select(Dynamic.select(VirtualColumn.POSITION));
-          query.select(newCh1);
-          query.select(newCh2);
-          
           dc.saveItem(child.newBioAssay(assay));
           
-          DynamicResultIterator iter = query.iterate(dc);
-          int column = iter.getIndex(VirtualColumn.COLUMN.getName());
-          int position = iter.getIndex(VirtualColumn.POSITION.getName());
-          int ch1 = iter.getIndex("newCh1");
-          int ch2 = iter.getIndex("newCh2");
-          while (iter.hasNext())
+          query = assay.getSpotData();
+          query.restrict(intensityRestriction);
+          query.joinRawData(JoinType.LEFT);
+          query.select(Selects.expression(Aggregations.max(Expressions.selected(Dynamic.selectRawData("block"))), "max"));
+          resultIter = query.iterate(dc);
+          int maxBlock = resultIter.next().getInt(resultIter.getIndex("max"));
+
+          for (int i = 0; i < maxBlock; i += blockGroupSize)
           {
-            SqlResult r = iter.next();
-            batcher.insert(r.getShort(column), r.getInt(position), r.getFloat(ch1), r.getFloat(ch2));
-            normalizedSpots++;
-            progress.display((normalizedSpots * 100) / numSpots, normalizedSpots + " spots normalized");
+            Restriction blockRestriction = Restrictions.between
+            ( 
+              Expressions.selected(Dynamic.selectRawData("block")),
+              Expressions.integer(i),
+              Expressions.integer(i+blockGroupSize)
+            );
+            
+            query = assay.getSpotData();
+            query.joinRawData(JoinType.LEFT);
+            query.select(Dynamic.select(VirtualColumn.channel(1)));
+            query.select(Dynamic.select(VirtualColumn.channel(2)));
+            query.select(Dynamic.selectRawData("block"));
+            query.select(ratio);
+            query.restrict(intensityRestriction);
+            query.restrict(blockRestriction);
+            query.order(Orders.asc(Expressions.selected(ratio)));
+            
+            int count = query.count(dc);
+            if (count <= 0) continue;
+            int lowCount = (int) Math.floor(count * lowExclude / 100);
+            int highCount = (int) Math.floor(count * highExclude / 100);
+            numSpots -= assay.getNumSpots() - count;
+            progress.display((normalizedSpots * 100) / numSpots, (assay.getNumSpots() - count) + " spots removed from assay " + assay.getName());
+
+            // check count > 0
+            int include = count - lowCount - highCount;
+            if (include <= 0) continue;
+            double median;
+            if (include % 2 == 0)
+            {
+              query.setFirstResult((include / 2) - 1 + lowCount);
+              query.setMaxResults(2);
+              DynamicResultIterator iter = query.iterate(dc);
+              median = Math.sqrt(iter.next().getFloat(iter.getIndex("ratio")) * iter.next().getFloat(iter.getIndex("ratio")));
+            }
+            else
+            {
+              query.setFirstResult(((include - 1) / 2) + lowCount);
+              query.setMaxResults(1);
+              DynamicResultIterator iter = query.iterate(dc);
+              median = iter.next().getFloat(iter.getIndex("ratio"));
+            }
+
+            float sqrtMedRatio = (float) Math.sqrt(median);
+            float invSqrtMedRatio = 1 / sqrtMedRatio;
+            Select newCh1 = Selects.expression(Expressions.multiply(Expressions.selected(Dynamic.select(VirtualColumn.channel(1))),
+              Expressions.aFloat(invSqrtMedRatio)), "newCh1");
+            Select newCh2 = Selects.expression(Expressions.multiply(Expressions.selected(Dynamic.select(VirtualColumn.channel(2))),
+              Expressions.aFloat(sqrtMedRatio)), "newCh2");
+
+            query = assay.getSpotData();
+            query.joinRawData(JoinType.LEFT);
+            query.select(Dynamic.select(VirtualColumn.COLUMN));
+            query.select(Dynamic.select(VirtualColumn.POSITION));
+            query.select(newCh1);
+            query.select(newCh2);
+            query.restrict(intensityRestriction);
+            query.restrict(blockRestriction);
+            query.setParameter("low", new Integer(i), Type.INT);
+            query.setParameter("high", new Integer(i + blockGroupSize), Type.INT);
+
+            DynamicResultIterator iter = query.iterate(dc);
+            int column = iter.getIndex(VirtualColumn.COLUMN.getName());
+            int position = iter.getIndex(VirtualColumn.POSITION.getName());
+            int ch1 = iter.getIndex("newCh1");
+            int ch2 = iter.getIndex("newCh2");
+            while (iter.hasNext())
+            {
+              SqlResult r = iter.next();
+              batcher.insert(r.getShort(column), r.getInt(position), r.getFloat(ch1), r.getFloat(ch2));
+              normalizedSpots++;
+              progress.display((normalizedSpots * 100) / numSpots, normalizedSpots + " spots normalized");
+            }
           }
         }
@@ -358 +396 @@
   }
   // -------------------------------------------
-
-  private DynamicSpotQuery getQuery(DynamicSpotQuery query)
-  {
-    Restriction restriction = Restrictions.and
-    (
-      Restrictions.gt(Dynamic.column(VirtualColumn.channel(1)), Expressions.aFloat((Float) job.getValue(minIntensityParameter.getName()))), 
-      Restrictions.gt(Dynamic.column(VirtualColumn.channel(2)), Expressions.aFloat((Float) job.getValue(minIntensityParameter.getName())))
-    );
-
-    query.restrictPermanent(restriction);
-    query.joinRawData(JoinType.LEFT);
-    query.selectPermanent(Dynamic.select(VirtualColumn.channel(1)));
-    query.selectPermanent(Dynamic.select(VirtualColumn.channel(2)));
-    query.selectPermanent(Dynamic.selectRawData("block"));
-    return query;
-  }
 }

branches/rf1/www/admin/clients/view_client.jsp

@@ -106 +106 @@
       Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&item_id=<%=itemId%>', 'RunPlugin'+cmd, 740, 540);
     }
+    function viewHelp()
+    {
+      location.href = 'help/index.jsp?ID=<%=ID%>&cmd=List&client_id=<%=itemId%>';
+    }
+    function switchTab(tabControlId, tabId)
+    {
+      if (tabId == 'help')
+      {
+        viewHelp();
+      }
+      else
+      {
+        TabControl.setActiveTab(tabControlId, tabId);
+      }
+    }
     </script>
   </base:head>
@@ -115 +130 @@
     </p:path>
     
-    <t:tabcontrol id="main" active="properties">
+    <t:tabcontrol id="main" active="properties" switch="switchTab">
     <t:tab id="properties" title="Properties">
     
@@ -207 +222 @@
     </div>
       </t:tab>
+      
+      <t:tab id="help" title="Help" tooltip="View and manage help texts for this client application" />
       </t:tabcontrol>
 

branches/rf1/www/common/plugin/configure.jsp

@@ -129 +129 @@
             }
             // Finally we use the parameters default value
-            if (values == null || values.size() == 0)
+            if ((values == null || values.size() == 0) && pType.getDefaultValue() != null)
             {
               values = Collections.singletonList(pType.getDefaultValue());
@@ -579 +579 @@
                   {
                     %>
-                    <select name="<%=inputName%>" multiple size="10"
+                    <select name="<%=inputName%>" multiple size="10" style="width: 30em;"
                       onchange="setEnumValues('<%=inputName%>')">
                     <%
@@ -587 +587 @@
                     String listValue = "";
                     String listText = "";
+                    String listTitle = "";
                     if (value instanceof Date) 
                     {
@@ -596 +597 @@
                       BasicItem item = (BasicItem)value;
                       listValue = Integer.toString(item.getId());
-                      listText = HTML.encodeTags(item instanceof Nameable ? ((Nameable)item).getName() : item.toString());
+                      if (item instanceof Nameable)
+                      {
+                        Nameable nameable = (Nameable)item;
+                        listText = HTML.encodeTags(nameable.getName());
+                        listTitle = HTML.encodeTags(nameable.getDescription());
+                      }
+                      else
+                      {
+                        listText = item.toString();
+                      }
                     }
                     else
@@ -604 +614 @@
                     }
                     %>
-                    <option value="<%=listValue%>"><%=listText%>
+                    <option value="<%=listValue%>" title="<%=listTitle%>"><%=listText%>
                     <%
                   }
@@ -786 +796 @@
                   if (cc.getId() != 0)
                   {
+                    BasicItem item = parameterItemType.getById(dc, cc.getId());
+                    String display = "";
+                    if (item instanceof Nameable)
+                    {
+                      Nameable nameable = (Nameable)item;
+                      display = nameable.getName();
+                    }
+                    else 
+                    {
+                      display = item.toString();
+                    }
                     %>
-                    <%=parameterItemType.getById(dc, cc.getId()).toString()%>
+                    <b><%=HTML.encodeTags(param.getLabel())%></b><br>
+                    <input class="text disabled" size="50" type="text" disabled value="<%=HTML.encodeTags(display)%>">
                     <%
                   }

branches/rf1/www/exception/exception.jsp

@@ -36 +36 @@
 --%>
 <%@ page
+  import="net.sf.basedb.core.Application"
+  import="net.sf.basedb.core.Config"
   import="net.sf.basedb.core.NotLoggedInException"
   import="net.sf.basedb.core.PermissionDeniedException"
@@ -111 +113 @@
 <base:body onload="fixWindow()">
   <base:note type="error" title="<%=exceptionClassName + " on page "+request.getAttribute("javax.servlet.error.request_uri")%>" style="width:90%;">
-    <%=HTML.formatLineBreaks(HTML.encodeTags(ex.getMessage(), ""))%>
+    <table border="0" cellpadding="0" cellspacing="0" class="form">
+    <tr>
+      <td class="prompt">Base version</td>
+      <td><%=Application.getMajorVersion() + "." +Application.getMinorVersion() + " (build #" + Application.getBuild()+")"%></td>
+    </tr>
+    <tr>
+      <td class="prompt">Web server</td>
+      <td><%=application.getServerInfo()%></td>
+    </tr>
+    <tr>
+      <td class="prompt">Database Dialect</td>
+      <td><%=Config.getString("db.dialect")%></td>
+    </tr>
+    <tr>
+      <td class="prompt">JDBC Driver</td>
+      <td><%=Config.getString("db.driver")%></td>
+    </tr>
+    <tr>
+      <td class="prompt">Browser</td>
+      <td><%=HTML.encodeTags(request.getHeader("User-Agent"))%></td>
+    </tr>
+    <tr>
+      <td class="prompt">Error message</td>
+      <td><%=HTML.formatLineBreaks(HTML.encodeTags(ex.getMessage(), ""))%></td>
+    </tr>
+    <tr>
+      <td class="prompt">Stack trace</td>
+      <td></td>
+    </tr>
+    </table>
+    
     <%
     StackTraceElement[] st = ex.getStackTrace();
@@ -151 +183 @@
     <base:button id="goback" onclick="<%="history.go(-1)"%>" title="Go back"/>
     <base:button id="close" onclick="<%="window.close()"%>" title="Close"/>
-    <base:button id="reportbug" onclick="<%="window.open('"+reportbuglink+"','Reportbug')"%>" title="Report bug"
+    <base:button id="reportbug" onclick="<%="window.open('"+reportbuglink+"','Reportbug')"%>" 
+      title="Report bug&hellip;"
     visible="<%=HTML.isValidUrl(reportbuglink)%>"/>
   </base:buttongroup>

branches/rf1/www/views/experiments/bioassaysets/index.jsp

@@ -83 +83 @@
 final String viewPage = "view_bioassayset.jsp?ID="+ID+"&experiment_id="+experimentId;
 final String editPage = "edit_bioassayset.jsp?ID="+ID+"&experiment_id="+experimentId;
-final String newPage = "create_root_bioassayset.jsp?ID="+ID+"&experiment_id="+experimentId;
+
+final String newPage = "../../../common/plugin/index.jsp?ID="+ID
+  +"&cmd=SelectPlugin&main_type=INTENSITY&item_type=BIOASSAYSET&context_type=LIST&title=Create+root+bioassay+set";
+
+sc.getCurrentContext(Item.EXPERIMENT).setId(experimentId);
 
 String forward = null;

branches/rf1/www/views/experiments/bioassaysets/list_bioassaysets.jsp

@@ -166 +166 @@
     function newItem()
     {
-      Main.openPopup('index.jsp?ID=<%=ID%>&cmd=NewItem&experiment_id=<%=experimentId%>', 'NewBioAssaySet', 600, 400);
+      Main.openPopup('index.jsp?ID=<%=ID%>&cmd=NewItem&experiment_id=<%=experimentId%>', 'NewBioAssaySet', 740, 540);
     }
     function editItem(itemId)
@@ -210 +210 @@
     function runPlugin(cmd)
     {
-      Table.submitToPopup(formId, cmd, 540, 460);
+      Table.submitToPopup(formId, cmd, 740, 540);
     }
     function returnSelected()
@@ -455 +455 @@
           title="New root bioassay set&hellip;" 
           tooltip="<%=createPermission ? "Create new event" : "You do not have permission to create events"%>" 
+          visible="<%=pluginCount.containsKey(Plugin.MainType.INTENSITY)%>"
         />
         <tbl:button 

branches/rf1/www/views/formulas/edit_formula.jsp

@@ -36 +36 @@
   import="net.sf.basedb.core.RawDataType"
   import="net.sf.basedb.core.RawDataTypes"
+  import="net.sf.basedb.core.RawDataProperty"
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.clients.web.Base"
@@ -158 +159 @@
       %>
       rawDataTypes['<%=rdt.getId()%>'] = <%=rdt.getChannels()%>;
+      var a = new Array();
+      <%
+      for (RawDataProperty rp : rdt.getProperties())
+      {
+        %>
+        a['<%=rp.getName()%>'] = 1;
+        <%
+      }
+      %>
+      rawDataTypes['<%=rdt.getId()%>.properties'] = a;
       <%
     }
@@ -219 +230 @@
     }
     
+    function validateOnClick()
+    {
+      var frm = document.forms['formula'];
+      if (frm.expression.value != '')
+      {
+        try
+        {
+          var result = eval(frm.expression.value);
+          alert('The expressions seems to be ok.\nNote! This feature is experimental and may not be 100% correct.');
+        }
+        catch (er)
+        {
+          alert(er + '\nNote! This feature is experimental and may not be 100% correct.');
+        }
+      }
+    }
+    function raw(property)
+    {
+      var frm = document.forms['formula'];
+      var rdt = frm.rawdatatype[frm.rawdatatype.selectedIndex].value;
+      if (!property) throw 'Property must be specified for function raw()';
+      if (rdt == '') throw 'Cannot use function raw(). No raw data type selected';
+      if (!rawDataTypes[rdt+'.properties'][property]) throw 'Property '+property+' not found for raw data type ' + rdt;
+      return Math.random() * 100;
+    }
+    function mean(property)
+    {
+      var frm = document.forms['formula'];
+      var rdt = frm.rawdatatype[frm.rawdatatype.selectedIndex].value;
+      if (!property) throw 'Property must be specified for function mean()';
+      if (rdt == '') throw 'Cannot use function mean(). No raw data type selected';
+      if (!rawDataTypes[rdt+'.properties'][property]) throw 'Property '+property+' not found for raw data type ' + rdt;
+      return Math.random() * 100;
+    }
+    function ch(channel)
+    {
+      var frm = document.forms['formula'];
+      var type = frm.type[frm.type.selectedIndex].value;
+      if (type == '<%=Formula.Type.INTENSITY_EXPRESSION.name()%>' || type == '<%=Formula.Type.INTENSITY_TRANSFORMATION.name()%>')
+      {
+        // Channel function not available
+        throw 'Function ch() is not available for ' + frm.type[frm.type.selectedIndex].text;
+      }
+
+      var channels = parseInt(frm.channels.value);
+      if (!channel || channel <= 0 || channel > channels) throw 'Invalid channel: ' + channel + '; must be between 1 and '+ channels;
+      return channel;
+    }
+    function log(value)
+    {
+      return Math.log(value);
+    }
+    function log2(value)
+    {
+      return Math.log(value);
+    }
+    function ln(value)
+    {
+      return Math.log(value);
+    }
+    function sqrt(value)
+    {
+      return Math.sqrt(value);
+    }
     </script>
   </base:head>
@@ -324 +399 @@
             <base:button onclick="addOnClick()" title="Add" />
           </td>
+          <td>
+            <base:button onclick="validateOnClick()" title="Validate&hellip;" 
+              tooltip="Validate the selected expression. EXPERIMENTAL!!" />
+          </td>
           </table>
         </td>