Changeset 2993

Timestamp:

Dec 1, 2006, 3:34:35 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #215: Incorrect use of DynamicSpotQuery? in table view, plot function, filter function, etc.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/servlet/PlotServlet.java (modified) (3 diffs)
• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/BioAssaySet.java (modified) (1 diff)
• src/core/net/sf/basedb/core/DataCube.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ItemContext.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Update.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/data/DataCubeData.java (modified) (1 diff)
• src/core/net/sf/basedb/util/BioAssaySetUtil.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/IntensityCalculatorUtil.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/jep/ChannelFunction.java (modified) (1 diff)
• src/core/net/sf/basedb/util/jep/ExtraValueFunction.java (modified) (1 diff)
• src/core/net/sf/basedb/util/jep/InReporterListFunction.java (modified) (1 diff)
• src/core/net/sf/basedb/util/jep/NotInReporterListFunction.java (modified) (1 diff)
• src/core/net/sf/basedb/util/jep/RawFunction.java (modified) (6 diffs)
• src/core/net/sf/basedb/util/jep/ReporterFunction.java (modified) (1 diff)
• src/core/net/sf/basedb/util/jep/ScoreFunction.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/JepExtraValueCalculator.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/JepIntensityTransformer.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) (1 diff)
• src/test/TestExperiment.java (modified) (1 diff)
• src/test/TestJep.java (modified) (3 diffs)
• www/common/expression_builder.jsp (modified) (4 diffs)
• www/plugins/net/sf/basedb/plugins/jep_extra_value_calculator.jsp (modified) (4 diffs)
• www/plugins/net/sf/basedb/plugins/jep_filter.jsp (modified) (3 diffs)
• www/plugins/net/sf/basedb/plugins/jep_intensity_transformer.jsp (modified) (5 diffs)
• www/views/experiments/bioassaysets/index.jsp (modified) (1 diff)
• www/views/experiments/explorer/view/view.jsp (modified) (2 diffs)
• www/views/experiments/plotter/index.jsp (modified) (3 diffs)
• www/views/experiments/spotdata/list_spotdata.jsp (modified) (1 diff)

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

@@ -172 +172 @@
   }
   
-  public static void addFormulaColumns(List<TableColumn> columns, DbControl dc, RawDataType rawDataType, Formula.Type type, String idPrefix, String titlePrefix)
+  public static void addFormulaColumns(List<TableColumn> columns, DbControl dc, 
+    RawDataType rawDataType, Formula.Type type, String idPrefix, String titlePrefix, boolean allowRawFunction)
   {
     ItemQuery<Formula> query = Formula.getQuery(type, rawDataType);
@@ -184 +185 @@
       Formula f = result.next();
       String jepExpression = f.getFormula(0);
-      TableColumn tc = new TableColumn(idPrefix+f.getId(), "="+jepExpression, jepExpression, Type.FLOAT, 
-        titlePrefix + f.getName(), f.getDescription());
-      tc.setFormatter(FormatterFactory.getColorFormatter(sc, f.getColoring(), numberFormatter));
-      columns.add(tc);
+      if (allowRawFunction || !jepExpression.contains("raw("))
+      {
+        TableColumn tc = new TableColumn(idPrefix+f.getId(), "="+jepExpression, jepExpression, Type.FLOAT, 
+            titlePrefix + f.getName(), f.getDescription());
+        tc.setFormatter(FormatterFactory.getColorFormatter(sc, f.getColoring(), numberFormatter));
+        columns.add(tc);
+      }
     }
     result.close();

trunk/src/clients/web/net/sf/basedb/clients/web/servlet/PlotServlet.java

@@ -376 +376 @@
         // Filter
         Restriction filter = filterFormula == null ? 
-          null : BioAssaySetUtil.createJepRestriction(dc, bas, filterFormula);
+          null : BioAssaySetUtil.createJepRestriction(dc, bas, filterFormula, false);
         
         // Convert formulas to Expression:s
@@ -386 +386 @@
           for (int i = 0; i < xFormulas.length; ++i)
           {
-            x[i] = BioAssaySetUtil.createJepExpression(dc, bas, xFormulas[i]);
+            x[i] = BioAssaySetUtil.createJepExpression(dc, bas, xFormulas[i], false);
             if (xLog) x[i] = Expressions.log2(x[i]);
           }
@@ -394 +394 @@
           for (int i = 0; i < yFormulas.length; ++i)
           {
-            y[i] = BioAssaySetUtil.createJepExpression(dc, bas, yFormulas[i]);
+            y[i] = BioAssaySetUtil.createJepExpression(dc, bas, yFormulas[i], false);
             if (yLog) y[i] = Expressions.log2(y[i]);
           }

trunk/src/core/common-queries.xml

@@ -2485 +2485 @@
   </query>
 
+  <query id="SET_MAX_MAPPING_ON_DATACUBES" type="HQL">
+    <sql>
+      UPDATE DataCubeData dcd
+      SET dcd.maxRawMappingsForSpot = -1
+      WHERE dcd.maxRawMappingsForSpot IS NULL
+    </sql>
+    <description>
+      A HQL query that sets the maxRawMappingsForSpot on all data cubes with a
+      null value to -1. This is required so we can load them by Hibernate.
+    </description>
+  </query>
+
+
+  <query id="SET_MAX_MAPPING_ON_DATACUBE" type="HQL">
+    <sql>
+      UPDATE DataCubeData dcd
+      SET dcd.maxRawMappingsForSpot = :mapCount
+      WHERE dcd.id = :dataCube
+    </sql>
+    <description>
+      A HQL query that sets the maxRawMappingsForSpot on a data cube.
+    </description>
+  </query>
+
 </predefined-queries>

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

@@ -414 +414 @@
   {
     return getData().getNumSpots();
+  }
+  
+  /**
+    Get the number of mappings to raw data spots for the spot with
+    the most number of mappings. For most bioassay sets this value is 
+    probably 1. After a merge, the count can be higher which may require some
+    plugins to behave differently when using values from the raw data table.
+    @since 2.2
+  */
+  public int getMaxRawMappingsForSpot()
+  {
+    return getData().getDataCubeLayer().getDataCube().getMaxRawMappingsForSpot();
   }
   

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

@@ -24 +24 @@
 package net.sf.basedb.core;
 
+import java.sql.SQLException;
+
 import net.sf.basedb.core.data.DataCubeData;
 import net.sf.basedb.core.data.SharedData;
+import net.sf.basedb.core.query.Aggregations;
+import net.sf.basedb.core.query.Dynamic;
+import net.sf.basedb.core.query.Expression;
+import net.sf.basedb.core.query.Orders;
+import net.sf.basedb.core.query.Select;
+import net.sf.basedb.core.query.Selects;
+import net.sf.basedb.core.query.SqlResult;
 
 /**
@@ -160 +169 @@
     {
       getData().setBytes(addedBytes);
+      getData().setMaxRawMappingsForSpot(countSpotMappings());
     }
     else if (action == Transactional.Action.UPDATE && addedBytes != 0)
@@ -559 +569 @@
   
   /**
+    Get the number of mappings to raw data spots for the spot with
+    the most number of mappings. For most data cubes this value is 
+    probably 1. After a merge, the count can be higher which may require some
+    plugins to behave differently when using values from the raw data table.
+    @since 2.2
+  */
+  public int getMaxRawMappingsForSpot()
+  {
+    return getData().getMaxRawMappingsForSpot();
+  }
+  
+  /**
       Gets the number of bytes the analysed data in this cube occupies on disk.
   */
@@ -627 +649 @@
   }
 
+  /**
+    Count the number of raw data mappings for the spot with the most
+    mappings.
+    @since 2.2
+  */
+  int countSpotMappings()
+  {
+    DynamicQuery query = new RawMappingQuery(this);
+    Expression count = Aggregations.count(null, false);
+    query.select(
+      Selects.expression(count, "mapCount")
+    );
+    query.group(Dynamic.column(VirtualColumn.COLUMN));
+    query.group(Dynamic.column(VirtualColumn.POSITION));
+    query.order(Orders.desc(count));
+    query.setMaxResults(1);
+    /*
+      SELECT COUNT(*) AS mapCount 
+      FROM Dymamic#RawParents raw
+      WHERE raw.cube = ?
+      GROUP BY raw.column, raw.position
+      ORDER BY COUNT(*) DESC
+      LIMIT 1
+    */
+    DynamicResultIterator result = query.iterate(getDbControl());
+    try
+    {
+      int maxCount = 0;
+      if (result.hasNext())
+      {
+        SqlResult r = result.next();
+        maxCount = r.getInt(result.getIndex("mapCount"));
+      }
+      return maxCount;
+    }
+    catch (SQLException ex)
+    {
+      throw new BaseException(ex);
+    }
+    finally
+    {
+      result.close();
+    }
+  }
+
+  /**
+    Select data from Dynamic#RawParents table. Used for counting
+    number of mappings between spots and raw data.
+  
+    @version 2.2
+  */
+  private static final class RawMappingQuery
+    extends DynamicQuery
+  {
+    
+    private RawMappingQuery(DataCube dataCube)
+    {
+      super(dataCube, VirtualTable.RAWPARENTS);
+    }
+    
+    /*
+      From the AbstractSqlQuery class
+      -------------------------------------------
+    */
+    Select[] getDefaultSelects()
+    {
+      return null;
+    }
+    // -------------------------------------------
+  }
+  
 }

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

@@ -102 +102 @@
     method.
   */
-  public static final int NEW_SCHEMA_VERSION = 27;
+  public static final int NEW_SCHEMA_VERSION = 28;
 
   public static synchronized void createTables(boolean update, final ProgressReporter progress)

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

@@ -159 +159 @@
   // For parsing JEP expressions
   private static final JepFunction ch = new ChannelFunction();
-  private static final JepFunction raw = new RawFunction();
+  private static final JepFunction raw = new RawFunction(true);
   private static final JepFunction rep = new ReporterFunction();
   

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

@@ -33 +33 @@
 import org.hibernate.mapping.Table;
 
+import net.sf.basedb.core.data.DataCubeData;
 import net.sf.basedb.core.data.FormulaData;
 import net.sf.basedb.core.data.PlateData;
@@ -326 +327 @@
       <li>Added {@link net.sf.basedb.core.data.ProjectData#getProjectDefaults()}.
       </ul>
+    </td>
+  </tr>
+  
+  <tr>
+    <td>28</td>
+    <td>
+      <ul>
+      <li>Added {@link net.sf.basedb.core.data.DataCubeData#getMaxRawMappingsForSpot()}.
+      </ul>
+      The update must query the dynamic database and set this value for
+      all existing data cubes.
     </td>
   </tr>
@@ -442 +454 @@
       }
 
+      // Schemaversion 20-23 only updates the version number 
       if (schemaVersion < 23)
       {
@@ -464 +477 @@
       if (schemaVersion < 26)
       {
-        if (progress != null) progress.display((int)(25*progress_factor), "--Updating schema version: " + schemaVersion + " -> 26...");
-        schemaVersion = setSchemaVersionInTransaction(session, 26);
-      }
-      
-      if (schemaVersion < 27)
-      {
-        if (progress != null) progress.display((int)(26*progress_factor), "--Updating schema version: " + schemaVersion + " -> 27...");
+        if (progress != null) progress.display((int)(25*progress_factor), "--Updating schema version: " + schemaVersion + " -> 27...");
         schemaVersion = setSchemaVersionInTransaction(session, 27);
       }
       
+      if (schemaVersion < 28)
+      {
+        if (progress != null) progress.display((int)(27*progress_factor), "--Updating schema version: " + schemaVersion + " -> 28...");
+        updateToSchemaVersion28(sc);
+      }
+      
       /*
-      if (schemaVersion < 28)
-      {
-        if (progress != null) progress.display((int)(27*progress_factor), "--Updating schema version: " + schemaVersion + " -> 28...");
-        schemaVersion = setSchemaVersionInTransaction(session, 28);
+      if (schemaVersion < 29)
+      {
+        if (progress != null) progress.display((int)(28*progress_factor), "--Updating schema version: " + schemaVersion + " -> 29...");
+        schemaVersion = setSchemaVersionInTransaction(session, 29);
         - or - 
-        schemaVersion = updateToSchemaVersion28(session);
+        schemaVersion = updateToSchemaVersion29(session);
       }
       ... etc... 
@@ -756 +769 @@
     finally
     {
-      if (dc != null) dc.close(); 
+      if (dc != null) dc.close();
     }
     return schemaVersion;
@@ -981 +994 @@
       log.error("updateToSchemaVersion25: FAILED", ex);
       throw ex;
+    }
+    return schemaVersion;
+  }
+
+  /**
+    Find the number of raw mappings for the spot with the maximum number
+    for each data cube
+    @return The new schema version (=28)
+  */
+  private static int updateToSchemaVersion28(SessionControl sc)
+    throws BaseException
+  {
+    final int schemaVersion = 28;
+    DbControl dc = null;
+    try
+    {
+      dc = sc.newDbControl();
+      org.hibernate.Session session = dc.getHibernateSession();
+      
+      // Query for loading all data cubes
+      org.hibernate.Query query = HibernateUtil.createQuery(session, 
+        "FROM DataCubeData dcd WHERE dcd.maxRawMappingsForSpot = -1");
+      org.hibernate.Query updateQuery = HibernateUtil.getPredefinedQuery(session, 
+        "SET_MAX_MAPPING_ON_DATACUBE");
+      /*
+        UPDATE DataCubeData dcd
+        SET dcd.maxRawMappingsForSpot = :mapCount
+        WHERE dcd.id = :dataCube
+      */
+      for (DataCubeData cubeData : HibernateUtil.loadList(DataCubeData.class, query))
+      {
+        DataCube cube = dc.getItem(DataCube.class, cubeData);
+        int mapCount = cube.countSpotMappings();
+        updateQuery.setInteger("mapCount", mapCount);
+        updateQuery.setInteger("dataCube", cube.getId());
+        HibernateUtil.executeUpdate(updateQuery);
+      }
+
+      // Update the shcema version number
+      setSchemaVersion(session, schemaVersion);
+  
+      // Commit the changes
+      dc.commit();
+      log.info("updateToSchemaVersion28: OK");
+    }
+    catch (BaseException ex)
+    {
+      log.error("updateToSchemaVersion28: FAILED", ex);
+      throw ex;
+    }
+    finally
+    {
+      if (dc != null) dc.close(); 
     }
     return schemaVersion;
@@ -1200 +1266 @@
         }
       
+        if (schemaVersion < 28)
+        {
+          // Set maxRawMappingsForSpot to -1 for all data cubes with a null value
+          org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+              "SET_MAX_MAPPING_ON_DATACUBES");
+          /*
+            UPDATE DataCubeData dcd
+            SET dcd.maxRawMappingsForSpot = -1
+            WHERE dcd.maxRawMappingsForSpot IS NULL
+          */
+          HibernateUtil.executeUpdate(query);
+        }
+        
         //  Commit the changes
         HibernateUtil.commit(tx);

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

@@ -161 +161 @@
     this.numPositions = numPositions;
   }
+  
+  private int maxRawMappings;
+  /**
+    The maximum number of raw data spots a single spot in this data cube
+    is mapped to.
+    @hibernate.property column="`max_raw_spots`" type="int" not-null="true" update="false"
+  */
+  public int getMaxRawMappingsForSpot()
+  {
+    return maxRawMappings;
+  }
+  public void setMaxRawMappingsForSpot(int maxRawMappings)
+  {
+    this.maxRawMappings = maxRawMappings;
+  }
 
   private Set<DataCubeLayerData> layers;

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

@@ -140 +140 @@
     by JEP (see {@link Jep#getFunctions()}) this method defines the following functions:
     <ul>
-    <li>all functions defined by the {@link #createJepExpression(DbControl, BioAssaySet, String)} 
-      method
+    <li>all functions defined by the {@link #createJepExpression(DbControl, BioAssaySet, 
+      String, boolean)} method
     <li>inList(list): Checks if the reporter is included in the specified list
     <li>notInList(list): Checks if the reporter isn't included in the specified list
@@ -147 +147 @@
     @see net.sf.basedb.util.jep.Jep
   */
-  public static Restriction createJepRestriction(DbControl dc, BioAssaySet bioAssaySet, String formula)
+  public static Restriction createJepRestriction(DbControl dc, BioAssaySet bioAssaySet, 
+    String formula, boolean allowRawIfMultipleMappings)
     throws InvalidDataException, BaseException
   {
     if (bioAssaySet == null) throw new InvalidUseOfNullException("bioAssaySet");
     if (formula == null) throw new InvalidUseOfNullException("formula");
-    RawFunction raw = new RawFunction();
+    RawFunction raw = new RawFunction(bioAssaySet.getMaxRawMappingsForSpot() == 1 || 
+      allowRawIfMultipleMappings);
     ChannelFunction ch = new ChannelFunction();
     ReporterFunction reporter = new ReporterFunction();
@@ -167 +169 @@
     by JEP (see {@link Jep#getFunctions()}) this method defines the following functions:
     <ul>
-    <li>raw(property): The value of the specified raw data property
+    <li>raw(property): The value of the specified raw data property. The use of this function
+      can be denied if the bioassayset contains spots that are mapped to more than one 
+      raw data spot. The <code>allowRawIfMultipleMappings</code> parameter controls
+      this.
     <li>rep(property): The value of the specified reporter property
     <li>pos: The position of a spot. Note that this is not the same as raw(position)
@@ -178 +183 @@
     @see net.sf.basedb.util.jep.Jep
   */
-  public static Expression createJepExpression(DbControl dc, BioAssaySet bioAssaySet, String formula)
+  public static Expression createJepExpression(DbControl dc, BioAssaySet bioAssaySet, 
+    String formula, boolean allowRawIfMultipleMappings)
     throws InvalidDataException, BaseException
   {
     if (bioAssaySet == null) throw new InvalidUseOfNullException("bioAssaySet");
     if (formula == null) throw new InvalidUseOfNullException("formula");
-    RawFunction raw = new RawFunction();
+    RawFunction raw = new RawFunction(bioAssaySet.getMaxRawMappingsForSpot() == 1 || 
+      allowRawIfMultipleMappings);
     ChannelFunction ch = new ChannelFunction();
     PositionFunction pos = new PositionFunction();

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

@@ -485 +485 @@
     }
     JEP[] jeps = new JEP[channels];
-    RawFunction raw = new RawFunction(dc, rawDataType);
+    RawFunction raw = new RawFunction(dc, rawDataType, true);
     MeanFunction mean = new MeanFunction(dc);
     for (int i = 0; i < channels; ++i)
@@ -501 +501 @@
   {
     Expression[] expressions = new Expression[formulas.length];
-    RawFunction raw = new RawFunction(dc, rawDataType);
+    RawFunction raw = new RawFunction(dc, rawDataType, true);
     MeanFunction mean = new MeanFunction(dc);
     for (int i = 0; i < formulas.length; ++i)

trunk/src/core/net/sf/basedb/util/jep/ChannelFunction.java

@@ -70 +70 @@
   @base.modified $Date$
   @see Jep
-  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String)
+  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String, boolean)
 */
 public class ChannelFunction

trunk/src/core/net/sf/basedb/util/jep/ExtraValueFunction.java

@@ -55 +55 @@
   @base.modified $Date$
   @see Jep
-  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String)
+  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String, boolean)
 */
 public class ExtraValueFunction

trunk/src/core/net/sf/basedb/util/jep/InReporterListFunction.java

@@ -51 +51 @@
   @base.modified $Date$
   @see Jep
-  @see BioAssaySetUtil#createJepRestriction(DbControl, BioAssaySet, String)
+  @see BioAssaySetUtil#createJepRestriction(DbControl, BioAssaySet, String, boolean)
 */
 public class InReporterListFunction

trunk/src/core/net/sf/basedb/util/jep/NotInReporterListFunction.java

@@ -51 +51 @@
   @base.modified $Date$
   @see Jep
-  @see BioAssaySetUtil#createJepRestriction(DbControl, BioAssaySet, String)
+  @see BioAssaySetUtil#createJepRestriction(DbControl, BioAssaySet, String, boolean)
 */
 public class NotInReporterListFunction

trunk/src/core/net/sf/basedb/util/jep/RawFunction.java

@@ -26 +26 @@
 import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BioAssaySet;
+import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.RawDataType;
 import net.sf.basedb.core.DbControl;
@@ -72 +73 @@
   @base.modified $Date$
   @see Jep
-  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String)
+  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String, boolean)
 */
 public class RawFunction
@@ -81 +82 @@
   private final Metadata<RawData> metaData;
   private final DbControl dc;
+  private final boolean allowUse;
   private int numParameters;
   private RawData rawData;
@@ -90 +92 @@
     @see Jep#formulaToExpression(String, JepFunction[])
   */
-  public RawFunction()
+  public RawFunction(boolean allowUse)
   {
     this.dc = null;
     this.metaData = null;
     this.rawDataType = null;
+    this.allowUse = allowUse;
   }
   
@@ -102 +105 @@
     @param rawDataType The type of raw data this function uses
   */
-  public RawFunction(DbControl dc, RawDataType rawDataType)
+  public RawFunction(DbControl dc, RawDataType rawDataType, boolean allowUse)
   {
     this.dc = dc;
     this.rawDataType = rawDataType;
     this.metaData = Metadata.getInstance(RawData.class, rawDataType.getEntityName());
+    this.allowUse = allowUse;
   }
   
@@ -131 +135 @@
   public Expression toExpression(Node node)
   {
+    if (!allowUse)
+    {
+      throw new PermissionDeniedException("Not allowed to use 'raw' function with merged data");
+    }
     int numChildren = node.jjtGetNumChildren();
     if (numChildren != 1)

trunk/src/core/net/sf/basedb/util/jep/ReporterFunction.java

@@ -71 +71 @@
   @base.modified $Date$
   @see Jep
-  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String)
+  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String, boolean)
 */
 public class ReporterFunction

trunk/src/core/net/sf/basedb/util/jep/ScoreFunction.java

@@ -52 +52 @@
   @base.modified $Date$
   @see Jep
-  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String)
+  @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String, boolean)
 */
 public class ScoreFunction

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

@@ -253 +253 @@
         {
           ++aliasIndex;
-          query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, field), aliasIndex.toString()));
+          query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, field, true), aliasIndex.toString()));
           aliases.put(field, aliasIndex.toString());
         }
@@ -259 +259 @@
         {
           ++aliasIndex;
-          query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, field),
+          query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, field, true),
             aliasIndex.toString()));
           aliases.put(field, aliasIndex.toString());

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

@@ -176 +176 @@
       
       // Parse filter expression
-      Restriction filter = BioAssaySetUtil.createJepRestriction(dc, source, expression);
+      Restriction filter = BioAssaySetUtil.createJepRestriction(dc, source, expression, false);
 
       if (includeLimit != null || excludeLimit != null)

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

@@ -160 +160 @@
       query.select(Dynamic.select(VirtualColumn.COLUMN));
       query.select(Dynamic.select(VirtualColumn.POSITION));
-      Expression extraExpression = BioAssaySetUtil.createJepExpression(dc, source, expression);
+      Expression extraExpression = BioAssaySetUtil.createJepExpression(dc, source, expression, false);
       query.select(Selects.expression(extraExpression, "xtra"));
 

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

@@ -171 +171 @@
         if (expression != null)
         {
-          chExpression = BioAssaySetUtil.createJepExpression(dc, source, expression);
+          chExpression = BioAssaySetUtil.createJepExpression(dc, source, expression, false);
         }
         else

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

@@ -388 +388 @@
         message = "Lowess normalization requires 2-channel data, not " + channels + "-channel.";
       }
+      if (bas.getMaxRawMappingsForSpot() != 1)
+      {
+        message = "Lowess normalization can't be done on merged data.";
+      }
     }
     return message;

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

@@ -373 +373 @@
         message = "Normalization requires 2-channel data, not " + channels + "-channel.";
       }
+      if (bas.getMaxRawMappingsForSpot() != 1)
+      {
+        message = "Normalization can't be done on merged data.";
+      }
     }
     return message;

trunk/src/test/TestExperiment.java

@@ -570 +570 @@
       RawDataType rdt = e.getRawDataType();
       String[] formulas = rdt.getIntensityFormula(intensityFormulaName).getExpressions();
-      RawFunction raw = new RawFunction(dc, e.getRawDataType());
+      RawFunction raw = new RawFunction(dc, e.getRawDataType(), true);
       Expression ch1 = Jep.formulaToExpression(formulas[0], raw);
       Expression ch2 = Jep.formulaToExpression(formulas[1], raw);

trunk/src/test/TestJep.java

@@ -71 +71 @@
     try
     {
-      Jep.newJep(formula, new RawFunction(null, RawDataTypes.getRawDataType("genepix")));
+      Jep.newJep(formula, new RawFunction(null, RawDataTypes.getRawDataType("genepix"), true));
       write("--Parse formula: "+formula+" OK");
     }
@@ -86 +86 @@
     try
     {
-      Expression e = Jep.formulaToExpression(formula, new RawFunction(null, RawDataTypes.getRawDataType("genepix")));
+      Expression e = Jep.formulaToExpression(formula, new RawFunction(null, RawDataTypes.getRawDataType("genepix"), true));
       write(e);
       write("--Jep to Expression: "+formula+" OK");
@@ -102 +102 @@
     try
     {
-      Restriction r = Jep.formulaToRestriction(formula, new RawFunction(null, RawDataTypes.getRawDataType("genepix")));
+      Restriction r = Jep.formulaToRestriction(formula, 
+        new RawFunction(null, RawDataTypes.getRawDataType("genepix"), true));
       write(r);
       write("--Jep to Restriction: "+formula+" OK");

trunk/www/common/expression_builder.jsp

@@ -68 +68 @@
   {
     BioAssaySet bas = bioAssaySetId == -1 ? null : BioAssaySet.getById(dc, bioAssaySetId);
+    int maxRawMappings = bas == null ? 1 : bas.getMaxRawMappingsForSpot();
 
     List<TableColumn> spotProperties = new LinkedList<TableColumn>();
@@ -74 +75 @@
     if (rawDataType != null)
     {
-      DynamicUtil.addFormulaColumns(spotProperties, dc, rawDataType, Formula.Type.COLUMN_EXPRESSION, "", "");
+      DynamicUtil.addFormulaColumns(spotProperties, dc, rawDataType, Formula.Type.COLUMN_EXPRESSION, "", "", maxRawMappings == 1);
       if (bas != null) DynamicUtil.addExtraColumns(spotProperties, dc, bas, "", "", "[Xtra] ");
-      DynamicUtil.addRawDataColumns(rawProperties, dc, rawDataType, "", "", "");
+      if (maxRawMappings == 1) DynamicUtil.addRawDataColumns(rawProperties, dc, rawDataType, "", "", "");
     }
     List<TableColumn> reporterProperties = new LinkedList<TableColumn>();
@@ -206 +207 @@
     function raw(property)
     {
+      <%
+      if (maxRawMappings != 1)
+      {
+        %>
+        throw 'Cannot use function raw() for bioassayset that has multiple mappings to raw data';
+        <%
+      }
+      %>
       var rdt = '<%=rawDataType == null ? "" : rawDataType.getId()%>';
       if (!property) throw 'Property must be specified for function raw()';
@@ -412 +421 @@
           </td>
           <%
-          if (rawDataType != null && rawDataType.isStoredInDb())
+          if (rawDataType != null && rawDataType.isStoredInDb() && rawProperties.size() > 0)
           {
             %>

trunk/www/plugins/net/sf/basedb/plugins/jep_extra_value_calculator.jsp

@@ -75 +75 @@
   if (source == null) throw new WebException("popup", "No current bioassay set", 
     "Could not find any current bioassay set. Please select a bioassay set before trying again");
+  int maxRawMappings = source.getMaxRawMappingsForSpot();
 
   RawDataType rdt = source.getRawDataType();
@@ -91 +92 @@
   for (Formula f : formulas)
   {
-    addFormulaOption(formulaOptions, f.getFormula(0), f.getName(), f.getDescription());
+    String formula = f.getFormula(0);
+    if (maxRawMappings == 1 || !formula.contains("raw("))
+    {
+      addFormulaOption(formulaOptions, formula, f.getName(), f.getDescription());
+    }
   }
   
   // Load recently used items
   List<ExtraValueType> recentExtraValueTypes = (List<ExtraValueType>)cc.getRecent(dc, Item.EXTRAVALUETYPE);
-  
   %>
   <base:page type="popup" title="Calculate extra value">
@@ -143 +147 @@
     function openExpressionBuilder()
     {
-      Main.expressionBuilder('<%=ID%>', 'Expression', 'extraValue', 'parameter:expression', 'COLUMN_EXPRESSION', '<%=rdt.getId()%>', <%=rdt.getChannels()%>, false);
+      Main.expressionBuilder('<%=ID%>', 'Expression', 'extraValue', 'parameter:expression', 'COLUMN_EXPRESSION', '<%=rdt.getId()%>', <%=rdt.getChannels()%>, false, <%=source.getId()%>);
     }
     function validate()
@@ -159 +163 @@
         return false;
       }
+      <%
+      if (maxRawMappings != 1)
+      {
+        %>
+        else if (frm['parameter:expression'].value.search(/raw\(/) != -1)
+        {
+          alert('Can\'t use function raw() for bioassaysets with multiple mappings to raw data');
+          frm['parameter:expression'].focus();
+          return false;
+        }
+        <%
+      }
+      %>
       return true;
     }

trunk/www/plugins/net/sf/basedb/plugins/jep_filter.jsp

@@ -82 +82 @@
   RawDataType rdt = source.getRawDataType();
   long numBioAssays = source.getBioAssays().count(dc);
+  int maxRawMappings = source.getMaxRawMappingsForSpot();
   
   // Find selected bioassays
@@ -117 +118 @@
   for (Formula f : formulas)
   {
-    addFormulaOption(formulaOptions, f.getFormula(0), f.getName(), f.getDescription());
+    String formula = f.getFormula(0);
+    if (maxRawMappings == 1 || !formula.contains("raw("))
+    {
+      addFormulaOption(formulaOptions, formula, f.getName(), f.getDescription());
+    }
   }
   %>
@@ -167 +172 @@
         return false;
       }
+      <%
+      if (maxRawMappings != 1)
+      {
+        %>
+        else if (frm['parameter:expression'].value.search(/raw\(/) != -1)
+        {
+          alert('Can\'t use function raw() for bioassayset with multiple mappings to raw data');
+          frm['parameter:expression'].focus();
+          return false;
+        }
+        <%
+      }
+      %>
       else if (exclude != '' || include != '')
       {

trunk/www/plugins/net/sf/basedb/plugins/jep_intensity_transformer.jsp

@@ -70 +70 @@
   if (source == null) throw new WebException("popup", "No current bioassay set", 
     "Could not find any current bioassay set. Please select a bioassay set before trying again");
+  int maxRawMappings = source.getMaxRawMappingsForSpot();
 
   RawDataType rdt = source.getRawDataType();
@@ -110 +111 @@
     function openExpressionBuilder(title, inputName)
     {
-      Main.expressionBuilder('<%=ID%>', title, 'transformation', inputName, 'INTENSITY_TRANSFORMATION', '<%=rdt.getId()%>', <%=rdt.getChannels()%>, false);
+      Main.expressionBuilder('<%=ID%>', title, 'transformation', inputName, 'INTENSITY_TRANSFORMATION', '<%=rdt.getId()%>', <%=rdt.getChannels()%>, false, '<%=source.getId()%>');
     }
     function validate()
@@ -124 +125 @@
           return false;
         }
+        else if (<%=maxRawMappings != 1 ? "true" : "false"%> && frm[inputName].value.search(/raw\(/) != -1)
+        {
+          alert('Can\'t use function raw() for bioassaysets with multiple mappings to raw data');
+          frm[inputName].focus();
+          return false;
+        }
       }
       return true;
@@ -144 +151 @@
         for (int ch = 1; ch <= rdt.getChannels(); ++ch)
         {
+          String formula = f.getFormula(ch-1);
           %>
-          formulas['<%=f.getId()%>.<%=ch%>'] = '<%=HTML.javaScriptEncode(f.getFormula(ch-1))%>';
+          formulas['<%=f.getId()%>.<%=ch%>'] = '<%=HTML.javaScriptEncode(formula)%>';
           <%
         }
@@ -234 +242 @@
             for (Formula f : formulas)
             {
-              %>
-              <option value="<%=f.getId()%>" title="<%=HTML.encodeTags(f.getDescription())%>"
-                ><%=HTML.encodeTags(f.getName())%>
-              <%
+              boolean ok = true;
+              if (maxRawMappings != 1)
+              {
+                for (String formula : f.getFormulas())
+                {
+                  ok &= !formula.contains("raw(");
+                }
+              }
+              if (ok)
+              {
+                %>
+                <option value="<%=f.getId()%>" title="<%=HTML.encodeTags(f.getDescription())%>"
+                  ><%=HTML.encodeTags(f.getName())%>
+                <%
+              }
             }
             %>

trunk/www/views/experiments/bioassaysets/index.jsp

@@ -69 +69 @@
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 <%!
-  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,transformation,spots,reporters,date,tools");
+  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,spots,reporters,date,tools");
   private static final Item itemType = Item.BIOASSAYSET;
   

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

@@ -104 +104 @@
   final int channels = rawDataType.getChannels();
   final boolean hasRatio = channels == 2;
+  final int maxRawMappings = bioAssaySet.getMaxRawMappingsForSpot();
   
   final ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bioAssaySet);
@@ -111 +112 @@
   
   List<TableColumn> columns = new LinkedList<TableColumn>();
-  DynamicUtil.addFormulaColumns(columns, dc, rawDataType, Formula.Type.COLUMN_EXPRESSION, "frm.", "");
+  DynamicUtil.addFormulaColumns(columns, dc, rawDataType, Formula.Type.COLUMN_EXPRESSION, 
+    "frm.", "", maxRawMappings == 1);
   DynamicUtil.addExtraColumns(columns, dc, bioAssaySet, "ev", "#", "[Xtra] ");
-  DynamicUtil.addRawDataColumns(columns, dc, rawDataType, "raw.", "$", "[Raw] ");
-  columns.add(new TableColumn("raw.spotimage", "$id", "raw('id')", Type.INT, 
-    "[Raw] Spotimage", "", "auto", false, false, false, false, 
-    new SpotImageFormatter(dc, rawDataType, root)));
+  if (maxRawMappings == 1)
+  {
+    DynamicUtil.addRawDataColumns(columns, dc, rawDataType, "raw.", "$", "[Raw] ");
+    columns.add(new TableColumn("raw.spotimage", "$id", "raw('id')", Type.INT, 
+      "[Raw] Spotimage", "", "auto", false, false, false, false, 
+      new SpotImageFormatter(dc, rawDataType, root)));
+  }
 
   final int matchingReporters = explorer.getMatchingReporters(dc);

trunk/www/views/experiments/plotter/index.jsp

@@ -78 +78 @@
   RawDataType rdt = bas.getRawDataType();
   Experiment experiment = bas.getExperiment();
+  int maxRawMappings = bas.getMaxRawMappingsForSpot();
   
   List<TableColumn> formulas = new LinkedList<TableColumn>();
   DynamicUtil.addSpotColumns(formulas, dc, rdt.getChannels());
-  DynamicUtil.addFormulaColumns(formulas, dc, rdt, Formula.Type.COLUMN_EXPRESSION, "", "");
+  DynamicUtil.addFormulaColumns(formulas, dc, rdt, Formula.Type.COLUMN_EXPRESSION, "", "", maxRawMappings == 1);
   DynamicUtil.addExtraColumns(formulas, dc, bas, "ev", "#", "[Xtra] ");
-  DynamicUtil.addRawDataColumns(formulas, dc, rdt, "", "", "[Raw] ");
+  if (maxRawMappings == 1)
+  {
+    DynamicUtil.addRawDataColumns(formulas, dc, rdt, "", "", "[Raw] ");
+  }
   
   StringBuilder formulaOptions = new StringBuilder();
@@ -90 +94 @@
     if (tc.getJepExpression() != null && tc.getDatatype().isNumerical())
     {
-      addFormulaOption(formulaOptions, tc.getJepExpression(), tc.getTitle(), tc.getDescription());
+      String jepExpression = tc.getJepExpression();
+      addFormulaOption(formulaOptions, jepExpression, tc.getTitle(), tc.getDescription());
     }
   }
@@ -100 +105 @@
   for (Formula formula : formulaQuery.list(dc))
   {
-    addFormulaOption(filterOptions, formula.getFormulas().get(0), 
-      formula.getName(), formula.getDescription());
+    String f = formula.getFormulas().get(0);
+    if (maxRawMappings == 1 || !f.contains("raw("))
+    {
+      addFormulaOption(filterOptions, f, 
+        formula.getName(), formula.getDescription());
+    }
   }
   

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

@@ -97 +97 @@
   List<TableColumn> columns = new LinkedList<TableColumn>();
   DynamicUtil.addSpotColumns(columns, dc, rawDataType.getChannels());
-  DynamicUtil.addFormulaColumns(columns, dc, rawDataType, Formula.Type.COLUMN_EXPRESSION, "frm.", "");
+  DynamicUtil.addFormulaColumns(columns, dc, rawDataType, Formula.Type.COLUMN_EXPRESSION, "frm.", "", true);
   DynamicUtil.addExtraColumns(columns, dc, bioAssaySet, "ev", "#", "[Xtra] ");
   DynamicUtil.addRawDataColumns(columns, dc, rawDataType, "raw.", "$", "[Raw] ");