Changeset 3562

Timestamp:

Jul 16, 2007, 2:35:29 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #649 and #674

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java (modified) (10 diffs)
• src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java (modified) (5 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/TableColumn.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/ExtendedProperties.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/ExtendedProperty.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/RawDataProperty.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawDataTypes.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/ExtendableData.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/dtd/extended-properties.dtd (modified) (1 diff)
• src/core/net/sf/basedb/core/dtd/raw-data-types.dtd (modified) (1 diff)
• www/views/experiments/explorer/view/view.jsp (modified) (2 diffs)

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

@@ -70 +70 @@
     Formatter<Number> intFormatter = FormatterFactory.getIntFormatter(sc);
     columns.add(new TableColumn("POSITION", "POSITION", null, Type.INT, 
-      "Position", "Spot position", "always", true, true, true, false, intFormatter));
+      "Position", "Spot position", "always", true, true, true, 
+      Formula.AverageMethod.NONE, intFormatter));
     for (int channel = 1; channel <= channels; ++channel)
     {
       TableColumn tc = new TableColumn("ch"+channel, "%"+channel, "ch("+channel+")", 
-        Type.FLOAT, "Ch "+channel, "Channel " + channel + " intensity");
-      tc.setFormatter(numberFormatter);
+        Type.FLOAT, "Ch "+channel, "Channel " + channel + " intensity", "auto", true, true, true,
+        Formula.AverageMethod.ARITHMETIC_MEAN, numberFormatter);
       columns.add(tc);
     }
@@ -87 +88 @@
       Formatter<Number> intFormatter = FormatterFactory.getIntFormatter(sc);
       columns.add(new TableColumn(idPrefix + "position", propertyPrefix+"position", "raw('position')", 
-        Type.INT, titlePrefix+"Position", "Raw spot position", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Position", "Raw spot position", "auto", true, true, true, 
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "block", propertyPrefix+"block", "raw('block')", 
-        Type.INT, titlePrefix+"Block", "Block number", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Block", "Block number", "auto", true, true, true, 
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "metaGridX", propertyPrefix+"metaGridX", "raw('metaGridX')", 
-        Type.INT, titlePrefix+"Meta grid X", "Meta X coordinate", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Meta grid X", "Meta X coordinate", "auto", true, true, true, 
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "metaGridY", propertyPrefix+"metaGridY", "raw('metaGridY')", 
-        Type.INT, titlePrefix+"Meta grid Y", "Meta Y coordinate", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Meta grid Y", "Meta Y coordinate", "auto", true, true, true, 
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "row", propertyPrefix+"row", "raw('row')", Type.INT, 
-        titlePrefix+"Row", "Row number", "auto", true, true, true, false, intFormatter));
+        titlePrefix+"Row", "Row number", "auto", true, true, true, 
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "column", propertyPrefix+"column", "raw('column')", 
-        Type.INT, titlePrefix+"Column", "Column number", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Column", "Column number", "auto", true, true, true, 
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "x", propertyPrefix+"x", "raw('x')", Type.INT, 
-        titlePrefix+"X", "X coordinate", "auto", true, true, true, false, intFormatter));
+        titlePrefix+"X", "X coordinate", "auto", true, true, true, 
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "y", propertyPrefix+"y", "raw('y')", Type.INT, 
-        titlePrefix+"Y", "Y coordinate", "auto", true, true, true, false, intFormatter));
+        titlePrefix+"Y", "Y coordinate", "auto", true, true, true, 
+        Formula.AverageMethod.NONE, intFormatter));
   
       List<RawDataProperty> rdpList = rawDataType.getProperties();
@@ -109 +118 @@
         TableColumn tc = new TableColumn(idPrefix+rdpName, propertyPrefix+rdpName, "raw('"+rdpName+"')", rdp.getType(), 
           titlePrefix + rdp.getTitle(), rdp.getDescription(), "auto", true, true, true, 
-          rdp.isAveragable(), FormatterFactory.getExtendedPropertyFormatter(sc, rdp));
+          rdp.getAverageMethod(), FormatterFactory.getExtendedPropertyFormatter(sc, rdp));
         columns.add(tc);
       }
@@ -121 +130 @@
     Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
     columns.add(new TableColumn(idPrefix + "name", propertyPrefix+"name", "rep('name')", 
-      Type.STRING, titlePrefix + "Name", "Reporter name", "auto", true, true, true, false, stringFormatter));
+      Type.STRING, titlePrefix + "Name", "Reporter name", "auto", true, true, true, 
+      Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "externalId", propertyPrefix+"externalId", "rep('externalId')", 
-      Type.STRING, titlePrefix + "ID", "Reporter ID", "auto", true, true, true, false, stringFormatter));
+      Type.STRING, titlePrefix + "ID", "Reporter ID", "auto", true, true, true, 
+      Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "symbol", propertyPrefix+"symbol", "rep('symbol')", 
-      Type.STRING, titlePrefix + "Gene symbol", "Gene symbol", "auto", true, true, true, false, stringFormatter));
+      Type.STRING, titlePrefix + "Gene symbol", "Gene symbol", "auto", true, true, true, 
+      Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "description", propertyPrefix+"description", "rep('description')", 
-      Type.STRING, titlePrefix + "Description", "Reporter description", "auto", true, true, true, false, stringFormatter));
+      Type.STRING, titlePrefix + "Description", "Reporter description", "auto", true, true, true, 
+      Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "lastUpdate", propertyPrefix+"lastUpdate", "rep('lastUpdate')", 
-      Type.DATE, titlePrefix + "Last update", "Last updateded", "auto", true, true, true, false, dateFormatter));
+      Type.DATE, titlePrefix + "Last update", "Last updateded", "auto", true, true, true, 
+      Formula.AverageMethod.NONE, dateFormatter));
 
     List<ExtendedProperty> extended = ExtendedProperties.getProperties("ReporterData");
@@ -138 +152 @@
         String name = ep.getName();
         TableColumn tc = new TableColumn(idPrefix + name, propertyPrefix + name, "rep('"+name+"')", 
-          ep.getType(), titlePrefix + ep.getTitle(), ep.getDescription());
-        tc.setFormatter(FormatterFactory.getExtendedPropertyFormatter(sc, ep));
+          ep.getType(), titlePrefix + ep.getTitle(), ep.getDescription(), "auto", true, true, true,
+          ep.getAverageMethod(), FormatterFactory.getExtendedPropertyFormatter(sc, ep));
         columns.add(tc);
       }
@@ -158 +172 @@
       int id = ev.getId();
       TableColumn tc = new TableColumn(idPrefix+id, propertyPrefix + id, "xtra('" + evt.getExternalId() + "')", ev.getValueType(), 
-        titlePrefix+evt.getName(), evt.getDescription());
+        titlePrefix+evt.getName(), evt.getDescription(), "auto", true, true, true, evt.getAverageMethod(), null);
       Formatter<?> formatter = FormatterFactory.getTypeFormatter(sc, evt.getValueType());
       if (evt.getValueType().isNumerical())
       {
-        // Numerical types *should* return a numberic formatter which is required by the color formatter
+        // Numerical types *should* return a numeric formatter which is required by the color formatter
         formatter = FormatterFactory.getColorFormatter(sc, evt.getColoring(), 
           (Formatter<Number>)formatter);
@@ -188 +202 @@
       {
         TableColumn tc = new TableColumn(idPrefix+f.getId(), "="+jepExpression, jepExpression, Type.FLOAT, 
-            titlePrefix + f.getName(), f.getDescription());
+            titlePrefix + f.getName(), f.getDescription(), "auto", true, true, true, 
+            f.getAverageMethod(), null);
         tc.setFormatter(FormatterFactory.getColorFormatter(sc, f.getColoring(), numberFormatter));
         columns.add(tc);
@@ -200 +215 @@
     List<String> selectedIds = new ArrayList<String>(columns.size());
     List<String> selectedProperties = new ArrayList<String>(columns.size());
+    List<TableColumn> selectedColumns = new ArrayList<TableColumn>(columns.size());
     
     String visibleColumns = cc.getSetting("columns");
@@ -213 +229 @@
           selectedProperties.add(tc.getProperty());
           selectedIds.add(tc.getId());
+          selectedColumns.add(tc);
         }
       }
     }
-    return new SelectedInfo(selectedProperties, selectedIds);
+    return new SelectedInfo(selectedProperties, selectedIds, selectedColumns);
   } 
   
@@ -223 +240 @@
     public final List<String> selectedProperties;
     public final List<String> selectedIds;
+    public final List<TableColumn> selectedColumns;
     
-    private SelectedInfo(List<String> properties, List<String> ids)
+    private SelectedInfo(List<String> properties, List<String> ids, List<TableColumn> columns)
     {
       this.selectedIds = ids;
       this.selectedProperties = properties;
+      this.selectedColumns = columns;
     }
   }

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

@@ -36 +36 @@
 import net.sf.basedb.util.Values;
 import net.sf.basedb.clients.web.formatter.FormatterFactory;
+import net.sf.basedb.clients.web.taglib.table.TableColumn;
 import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.BaseException;
@@ -712 +713 @@
     @return A query
   */
-  public DynamicSpotQuery getSpotQuery(DbControl dc, ReporterData reporter, int positionIndex, List<String> selectionList)
+  public DynamicSpotQuery getSpotQuery(DbControl dc, ReporterData reporter, int positionIndex, List<TableColumn> selectionList)
   {
     BioAssaySet bioAssaySet = getBioAssaySet(dc);
@@ -780 +781 @@
     // Set additional selected columns
     int i = 0;
-    for (String selectProperty : selectionList)
+    for (TableColumn tc : selectionList)
     {
       // Skip channel intensities since they are already selected
-      if (!selectProperty.startsWith("%"))
+      if (!tc.getProperty().startsWith("%"))
       {
-        Expression select = ItemContext.getDynamicExpression(dc, selectProperty);
+        Expression select = ItemContext.getDynamicExpression(dc, tc.getProperty());
         if (select != null)
         {
@@ -791 +792 @@
           if (positionIndex == SPOT_AVG)
           {
-            select = Aggregations.mean(select);
+            select = tc.getAverageMethod().getAverageExpression(select);
           }
           spotQuery.select(Selects.expression(select, "e" + i));
@@ -809 +810 @@
         if (positionIndex == SPOT_AVG)
         {
-          sortby = Aggregations.mean(sortby);
+          // Find TableColumn to know which average method to use
+          boolean found = false;
+          for (TableColumn tc : selectionList)
+          {
+            if (sortProperty.equals(tc.getProperty()))
+            {
+              sortby = tc.getAverageMethod().getAverageExpression(sortby);
+              found = true;
+              break;
+            }
+          }
+          if (!found) sortby = null;
         }
         if (sortby != null)

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

@@ -25 +25 @@
 package net.sf.basedb.clients.web.taglib.table;
 
+import net.sf.basedb.core.Formula;
 import net.sf.basedb.core.Type;
 import net.sf.basedb.util.formatter.Formatter;
@@ -71 +72 @@
   private final boolean exportable;
   private final String show;
-  private final boolean averagable;
+  private final Formula.AverageMethod averageMethod;
   private Formatter<?> formatter;
   
+  /**
+    Create TableColumn.
+    @param id
+    @param property
+    @param jepExpression
+    @param datatype
+    @param title
+    @param description
+    @deprecated
+   */
   public TableColumn(String id, String property, String jepExpression, Type datatype, String title, String description)
   {   
-    this(id, property, jepExpression, datatype, title, description, "auto", true, true, true, datatype.isNumerical(), null);
+    this(id, property, jepExpression, datatype, title, description, "auto", true, true, true, 
+      datatype.isNumerical() ? Formula.AverageMethod.ARITHMETIC_MEAN : null, null);
   }
   
   public TableColumn(String id, String property, String jepExpression, Type datatype, String title, String description, String show,
-    boolean sortable, boolean filterable, boolean exportable, boolean averagable, Formatter<?> formatter)
+    boolean sortable, boolean filterable, boolean exportable, Formula.AverageMethod averageMethod, Formatter<?> formatter)
   {   
     this.id = id;
@@ -92 +104 @@
     this.filterable = filterable;
     this.exportable = exportable;
-    this.averagable = datatype.isNumerical() && averagable;
+    this.averageMethod = averageMethod;
     this.formatter = formatter;
   }
@@ -148 +160 @@
   public boolean isAveragable()
   {
-    return averagable;
+    return averageMethod != null && averageMethod != Formula.AverageMethod.NONE;
   }
 
+  /**
+    @since 2.4
+  */
+  public Formula.AverageMethod getAverageMethod()
+  {
+    return averageMethod;
+  }
+  
   /**
      @since 2.0.2

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

@@ -205 +205 @@
       if (type == Type.STRING && length > 255) type = Type.TEXT;
       boolean nullable = XMLUtil.getBooleanAttribute(property, "null", true);
-      boolean insertable = XMLUtil.getBooleanAttribute(property, "insert", true);;
-      boolean updateable = XMLUtil.getBooleanAttribute(property, "update", true);;
+      boolean insertable = XMLUtil.getBooleanAttribute(property, "insert", true);
+      boolean updateable = XMLUtil.getBooleanAttribute(property, "update", true);
       boolean averagable = XMLUtil.getBooleanAttribute(property, "averagable", type.isNumerical());
+      String avgMethod = property.getAttributeValue("averagemethod");
+      Formula.AverageMethod averageMethod = null;
+      if (avgMethod != null) 
+      {
+        averageMethod = Formula.AverageMethod.valueOf(avgMethod.toUpperCase());
+      }
+      else if (averagable) 
+      {
+        averageMethod = Formula.AverageMethod.ARITHMETIC_MEAN;
+      }
+      else
+      {
+        averageMethod = Formula.AverageMethod.NONE;       
+      }
       
       List<Element> links = (List<Element>)property.getChildren("link");
@@ -221 +235 @@
         }
       }
-      properties.add(new ExtendedProperty(name, title, description, column, type, length, nullable, insertable, updateable, averagable, epLinks));
+      properties.add(new ExtendedProperty(name, title, description, column, type, length, nullable, insertable, updateable, averageMethod, epLinks));
     }
     return properties;

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

@@ -46 +46 @@
   private final boolean insertable;
   private final boolean updateable;
-  private final boolean isAveragable;
+  private final Formula.AverageMethod averageMethod;
   private final List<ExtendedPropertyLinker> linkers;
 
@@ -55 +55 @@
   ExtendedProperty(String name, String title, String description, String column,
     Type type, int length, boolean nullable, boolean insertable, boolean updateable, 
-    boolean isAveragable, List<ExtendedPropertyLinker> linkers)
+    Formula.AverageMethod averageMethod, List<ExtendedPropertyLinker> linkers)
   {
     this.name = name;
@@ -66 +66 @@
     this.insertable = insertable;
     this.updateable = updateable;
-    this.isAveragable = type.isNumerical() && isAveragable;
+    this.averageMethod = averageMethod;
     this.linkers = linkers;
   }
@@ -161 +161 @@
     values. By default all numerical values are averagable.
     @return TRUE if it makes sense to take the average, FALSE otherwise
+    @see #getAverageMethod()
   */
   public boolean isAveragable()
   {
-    return isAveragable;
+    return averageMethod != null && averageMethod != Formula.AverageMethod.NONE;
+  }
+  
+  /**
+    Which method to use when calculating the average of a set of values.
+    Prior to 2.4 only arithmetic mean was supported.
+    @return The average method to use
+    @since 2.4
+  */
+  public Formula.AverageMethod getAverageMethod()
+  {
+    return averageMethod;
   }
   

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

@@ -42 +42 @@
   */
   RawDataProperty(String name, String title, String description, String column,
-    Type type, int length, boolean nullable, boolean averagable, int channel)
+    Type type, int length, boolean nullable, Formula.AverageMethod averageMethod, int channel)
   {
-    super(name, title, description, column, type, length, nullable, true, false, averagable, null);
+    super(name, title, description, column, type, length, nullable, true, false, averageMethod, null);
     this.channel = channel;
   }

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

@@ -177 +177 @@
       boolean nullable = XMLUtil.getBooleanAttribute(property, "null", true);
       boolean averagable = XMLUtil.getBooleanAttribute(property, "averagable", type.isNumerical());
+      String avgMethod = property.getAttributeValue("averagemethod");
+      Formula.AverageMethod averageMethod = null;
+      if (avgMethod != null) 
+      {
+        averageMethod = Formula.AverageMethod.valueOf(avgMethod.toUpperCase());
+      }
+      else if (averagable) 
+      {
+        averageMethod = Formula.AverageMethod.ARITHMETIC_MEAN;
+      }
+      else
+      {
+        averageMethod = Formula.AverageMethod.NONE;       
+      }
       int channel = XMLUtil.getIntAttribute(property, "channel", 0);
-      properties.add(new RawDataProperty(name, title, description, column, type, length, nullable, averagable, channel));
+      properties.add(new RawDataProperty(name, title, description, column, type, length, nullable, averageMethod, channel));
     }
     return properties;

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

@@ -45 +45 @@
          update="true"
          insert="true"
-         averagable="false"
+         averagemethod="geometric_mean"
          description="An extra property for all reporters"
       />
@@ -156 +156 @@
     <td>averagable</td>
     <td>
+      <b>This attribute has been deprecated and is replaced by <code>averagemethod</code>!</b>
+      <br>
       If it makes sense to take the average of multiple values for this
       property. By default all numerical columns are averagable. For non-numerical
-      columns, this attribute is ignored.
+      columns, this attribute is ignored. The default method is to calculate the
+      arithmetic mean.
       <ul>
       <li>true 
@@ -164 +167 @@
       </ul>
       See {@link net.sf.basedb.core.ExtendedProperty#isAveragable()}.
+    </td>
+  </tr>
+  <tr valign="top">
+    <td>averagemethod</td>
+    <td>
+      The method to use when calculating the average of a set of values.
+      This attribute replaces the <code>averagable</code> attribute.
+      The following values can be used:
+      <ul>
+      <li>none: do not use this property when calculating averages
+      <li>arithmetic_mean: calculate the arithmetic mean
+      <li>geometric_mean: calculate the geometric mean
+      <li>min: use the minimum value among the values in the set
+      <li>max: use the maximum value among the values in the set
+      </ul>
+      If no value is given to this attribute the default is to use arithmetic
+      mean for all numerical value types.
+      See {@link net.sf.basedb.core.ExtendedProperty#getAverageMethod()}.
     </td>
   </tr>

trunk/src/core/net/sf/basedb/core/dtd/extended-properties.dtd

@@ -43 +43 @@
   update (true|false) "true"
   averagable (true|false) #IMPLIED
+  averagemethod (none|arithmetic_mean|geometric_mean|min|max) #IMPLIED
 >
 

trunk/src/core/net/sf/basedb/core/dtd/raw-data-types.dtd

@@ -46 +46 @@
   null (true|false) "true"
   averagable (true|false) #IMPLIED
+  averagemethod (none|arithmetic_mean|geometric_mean|min|max) #IMPLIED
   channel CDATA #IMPLIED
 >

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

@@ -120 +120 @@
     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, 
+      "[Raw] Spotimage", "", "auto", false, false, false, null, 
       new SpotImageFormatter(dc, rawDataType, root)));
   }
@@ -162 +162 @@
     try
     {
-      DynamicSpotQuery spotQuery = explorer.getSpotQuery(dc, reporter, positionIndex, selected.selectedProperties);
+      DynamicSpotQuery spotQuery = explorer.getSpotQuery(dc, reporter, positionIndex, selected.selectedColumns);
       spotData = spotQuery.iterate(dc);
     }