Changeset 4544

Timestamp:

Sep 25, 2008, 9:01:30 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #792: Add support for units to annotation values

• Made it possible to select a default unit for an annotation type
• Display annotations with units on the "Annotations" tab in the single-item view
• Test for displaying annotations with units in list pages on the Array designs list page

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/formatter/FormatterFactory.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/CellValue.java (modified) (6 diffs)
• src/core/net/sf/basedb/core/Annotation.java (modified) (9 diffs)
• src/core/net/sf/basedb/core/AnnotationType.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/data/AnnotationTypeData.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/data/UnitData.java (modified) (1 diff)
• src/core/net/sf/basedb/util/formatter/PrefixSuffixFormatter.java (added)
• src/core/net/sf/basedb/util/formatter/ToStringFormatter.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/units (added)
• src/core/net/sf/basedb/util/units/IdentityUnitConverter.java (added)
• src/core/net/sf/basedb/util/units/LinearUnitConverter.java (added)
• src/core/net/sf/basedb/util/units/UnitConverter.java (added)
• src/test/TestAnnotation.java (modified) (6 diffs)
• src/test/TestAnnotationFlatFileImporter.java (modified) (2 diffs)
• src/test/TestAnnotationType.java (modified) (5 diffs)
• src/test/TestAnnotationTypeCategory.java (modified) (1 diff)
• src/test/TestExperiment.java (modified) (1 diff)
• src/test/TestWebservices.java (modified) (1 diff)
• src/webservices/server/net/sf/basedb/ws/server/ReporterService.java (modified) (2 diffs)
• www/WEB-INF/table.tld (modified) (1 diff)
• www/admin/annotationtypes/edit_annotationtype.jsp (modified) (9 diffs)
• www/admin/annotationtypes/index.jsp (modified) (3 diffs)
• www/admin/annotationtypes/list_annotationtypes.jsp (modified) (4 diffs)
• www/admin/annotationtypes/view_annotationtype.jsp (modified) (1 diff)
• www/common/annotations/list_annotations.jsp (modified) (7 diffs)
• www/include/scripts/linkitems.js (modified) (2 diffs)
• www/lims/arraydesigns/list_designs.jsp (modified) (2 diffs)

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

@@ -212 +212 @@
     Formatter<Boolean> booleanFormatter = FormatterFactory.getBooleanFormatter(sc);
     Formatter<String> stringFormatter = FormatterFactory.getStringFormatter(sc);
-    Formatter<Object> defaultFormatter = new ToStringFormatter();
+    Formatter<Object> defaultFormatter = new ToStringFormatter<Object>();
     while (result.hasNext())
     {

trunk/src/clients/web/net/sf/basedb/clients/web/formatter/FormatterFactory.java

@@ -25 +25 @@
 
 import net.sf.basedb.clients.web.Base;
+import net.sf.basedb.core.Annotation;
+import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Coloring;
 import net.sf.basedb.core.ExtendedProperty;
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.Type;
+import net.sf.basedb.core.Unit;
 import net.sf.basedb.util.ColorGenerator;
 import net.sf.basedb.util.formatter.BooleanFormatter;
@@ -35 +38 @@
 import net.sf.basedb.util.formatter.IntegerFormatter;
 import net.sf.basedb.util.formatter.NumberFormatter;
+import net.sf.basedb.util.formatter.PrefixSuffixFormatter;
 
 /**
@@ -310 +314 @@
   }
 
+  /**
+    Get a formatter for nice formatting of annotation values, including units.
+    A base formatter is created by {@link #getTypeFormatter(SessionControl, Type)}
+    using the value type of the annotation. This formatter is wrapped by
+    a {@link PrefixSuffixFormatter} if a unit is supplied or the annotation has
+    a unit.
+    
+    @param sc The logged in user's session control
+    @param a The annotation to get a formatter for
+    @param unit The unit, or null to use the unit from the annotation 
+      ({@link Annotation#getUnit()}.
+    @return A formatter object
+    @since 2.9
+  */
+  public static Formatter<?> getAnnotationFormatter(SessionControl sc, Annotation a, Unit unit)
+  {
+    AnnotationType at = a.getAnnotationType();
+    Formatter<?> f = getTypeFormatter(sc, a.getValueType());
+    return a.getUnitFormatter(f, unit);
+  }
+  
 }

trunk/src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java

@@ -244 +244 @@
     boolean annotatable = itemType.getItemClass() != null && 
       Annotatable.class.isAssignableFrom(itemType.getItemClass());
-    MultiFormatter formatter = new MultiFormatter(new ToStringFormatter(), true);
+    MultiFormatter formatter = new MultiFormatter(new ToStringFormatter<Object>(), true);
     formatter.registerFormatter(Date.class, FormatterFactory.getDateFormatter(sc));
     for (String column : columns)

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

@@ -40 +40 @@
       list=...
       separator=...
+      prefix=...
+      suffix=...
    >
 </pre>
@@ -71 +73 @@
   </tr>
   <tr>
-    <td>list</td>
+    <td>separator</td>
     <td>; </td>
     <td>no</td>
     <td>
       A separator to use between each value in a list.
+    </td>
+  </tr>
+  <tr>
+    <td>prefix</td>
+    <td></td>
+    <td>no</td>
+    <td>
+      A prefix that is added before each value. Since 2.9.
+    </td>
+  </tr>
+  <tr>
+    <td>suffix</td>
+    <td></td>
+    <td>no</td>
+    <td>
+      A suffix that is added after each value. Since 2.9.
     </td>
   </tr>
@@ -99 +117 @@
   private Object value = null;
   private Iterable<?> list = null;
+  private String prefix = "";
+  private String suffix = "";
   private String separator = "; ";
 
@@ -132 +152 @@
   {
     return separator;
+  }
+
+  /**
+    @since 2.9
+  */
+  public void setPrefix(String prefix)
+  {
+    this.prefix = prefix == null ? "" : prefix;
+  }
+  /**
+    @since 2.9
+  */
+  public String getPrefix()
+  {
+    return prefix;
+  }
+  /**
+    @since 2.9
+  */
+  public void setSuffix(String suffix)
+  {
+    this.suffix = suffix == null ? "" : suffix;
+  }
+  /**
+    @since 2.9
+  */
+  public String getSuffix()
+  {
+    return suffix;
   }
 
@@ -149 +198 @@
     if (value != null)
     {
-      output.append(formatter.format(value));
+      output.append(prefix).append(formatter.format(value)).append(suffix);
       theSeparator = separator;
     }
@@ -158 +207 @@
         if (o != null)
         {
-          output.append(theSeparator).append(formatter.format(o));
+          output.append(theSeparator).append(prefix).append(formatter.format(o)).append(suffix);
           theSeparator = separator;
         }

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

@@ -24 +24 @@
 
 import net.sf.basedb.core.data.AnnotationData;
+import net.sf.basedb.core.data.UnitData;
 import net.sf.basedb.core.query.EntityQuery;
-
+import net.sf.basedb.util.formatter.Formatter;
+import net.sf.basedb.util.formatter.PrefixSuffixFormatter;
+import net.sf.basedb.util.units.LinearUnitConverter;
+import net.sf.basedb.util.units.UnitConverter;
+
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Collections;
@@ -74 +80 @@
     data.setAnnotationSet(annotationSet.getData());
     data.setAnnotationType(annotationType.getData());
+    data.setUnit(annotationType.getData().getDefaultUnit());
     data.setValues(annotationType.getValueType().newParameterValueData());
     return a;
@@ -199 +206 @@
   }
   
+  /**
+    Checks if the values in this annotation has a unit.
+    @return TRUE if a unit is used, FALSE otherwise
+    @since 2.9
+  */
+  public boolean hasUnit()
+  {
+    return getData().getUnit() != null;
+  }
+  
+  /**
+    Get the unit used for the values in this annotation.
+    @return A unit, or null if this annotation doesn't use units
+    @since 2.9
+  */
+  public Unit getUnit()
+  {
+    return getDbControl().getItem(Unit.class, getData().getUnit());
+  }
+  
+  /**
+    Get a converter for converting the values in this annotation to
+    a specific unit. 
+    
+    @param unit The unit to convert the values to, or null
+      to convert the values to the unit specified by {@link #getUnit()}
+    @return A unit converter, or null if this annotation doesn't use units, or
+      if the specified unit is the same as the default unit of the annotation
+      type (see {@link AnnotationType#getDefaultUnit()}
+    @since 2.9
+  */
+  public UnitConverter getUnitConverter(Unit unit)
+  {
+    UnitConverter converter = null;
+    UnitData unitData = unit == null ? getData().getUnit() : unit.getData();
+    if (unitData != null)
+    {
+      UnitData reference = getData().getAnnotationType().getDefaultUnit();
+      if (!unitData.equals(reference))
+      {
+        converter = new LinearUnitConverter(
+            unitData.getReferenceFactor(), unitData.getReferenceOffset(),
+            reference.getReferenceFactor(), reference.getReferenceOffset());
+      }
+    }
+    return converter;
+  }
+
+  /**
+    Wrap a parent formatter with a formatter for units. NOTE!
+    Values should be retrived with the same unit using 
+    {@link #getValues(Unit)} to be correctly formatted with the
+    returned formatter.
+    
+    @param parent The parent formatter, which should be of the
+      correct type for the annotation values
+    @param unit The unit to use for formatting, or null to
+      use the annotation's unit
+    @return A formatter object
+    @since 2.9
+  */
+  public <T> Formatter<T> getUnitFormatter(Formatter<T> parent, Unit unit)
+  {
+    Formatter<T> formatter = parent;
+    UnitData unitData = unit == null ? getData().getUnit() : unit.getData();
+    if (unitData == null) 
+    {
+      unitData = getData().getAnnotationType().getDefaultUnit();
+    }
+    if (unitData != null)
+    {
+      formatter = new PrefixSuffixFormatter<T>("", parent, 
+          PrefixSuffixFormatter.NBSP + unitData.getDisplaySymbol());
+    }
+    return formatter;
+  }
+  
+  /**
+    Shortcut for <code>Unit.getDisplaySymbol()</code>, but also
+    checks the default unit of the annotation type.
+    @param unit The unit to get the symbol for, or null to use
+      the annotation's unit
+    @return The unit symbol, or null if this annotation doesn't use
+      units
+    @since 2.9
+  */
+  public String getUnitSymbol(Unit unit)
+  {
+    UnitData unitData = unit == null ? getData().getUnit() : unit.getData();
+    if (unitData == null) 
+    {
+      unitData = getData().getAnnotationType().getDefaultUnit();
+    }
+    return unitData == null ? null : unitData.getDisplaySymbol();
+  }
   
   /**
@@ -215 +317 @@
     {@link Type} appropriate for the given annotation type, ie. Integer object
     for an integer annotation type. All objects in the list are of the same type.
+    If this is an annotation with units, the values are returned in the unit
+    of the annotation type ({@link AnnotationType#getDefaultUnit()}). Use
+    {@link #getValues(Unit)} to get the values in a different unit, including the
+    specific unit used on this annotation.
     @see AnnotationType#getValueType()
     @return A list of objects
@@ -225 +331 @@
     return Collections.unmodifiableList(values);
   }
+  
+  /**
+    Get the values for this annotation in a specific unit. The values are of a
+    {@link Type} appropriate for the given annotation type, ie. Integer object
+    for an integer annotation type. All objects in the list are of the same type.
+    
+    @param unit The unit to convert the values to, or null to get the values
+      in the unit used on this annotation
+    @see AnnotationType#getValueType()
+    @return A list of objects
+    @throws BaseException If there is an error
+  */
+  public List<?> getValues(Unit unit)
+    throws BaseException
+  {
+    List<?> values = Values.getItemValues(getDbControl(), getData().getValues().getValues());
+    UnitConverter converter = getUnitConverter(null);
+    if (converter != null)
+    {
+      List<Object> convertedValues = new ArrayList<Object>(values.size());
+      Type valueType = getValueType();
+      for (Object value : values)
+      {
+        if (value instanceof Number)
+        {
+          value = valueType.convertNumber(converter.convertToSpecificUnit(((Number)value).doubleValue()));
+        }
+        convertedValues.add(value);
+      }
+      values = convertedValues;
+    }
+    return Collections.unmodifiableList(values);
+  }
+  
   
   /**
@@ -238 +378 @@
   }
 
+  public void setValue(Object value)
+    throws PermissionDeniedException, InvalidDataException, BaseException
+  {
+    setValue(value, null);
+  }
+  
   /**
     Set the value of the annotation, replacing any previous values.
     @param value The new value
+    @param unit The unit of the value, or null to use the default unit of
+      the annotation type
     @throws PermissionDeniedException If the logged in user doesn't have
       write permission for the annotation or read permission for the annotation
@@ -247 +395 @@
       annotation type, see {@link AnnotationType#validateAnnotationValue(Object)}
     @throws BaseException If there is another error
-  */
-  public void setValue(Object value)
+    @since 2.9
+  */
+  public void setValue(Object value, Unit unit)
     throws PermissionDeniedException, InvalidDataException, BaseException
   {
     checkPermission(Permission.WRITE);
     AnnotationType annotationType = getAnnotationType();
+    if (unit == null) unit = annotationType.getDefaultUnit();
+    UnitConverter converter = getUnitConverter(unit);
+    if (converter != null && value instanceof Number)
+    {
+      value = converter.convertToReferenceUnit(((Number)value).doubleValue());
+    }
     annotationType.validateAnnotationValue(value);
+    if (unit != null) getData().setUnit(unit.getData());
     getData().getValues().setSingleValue(Values.getDataValue(value));
   }
 
+  public void setValues(List<?> values)
+    throws PermissionDeniedException, InvalidDataException, BaseException
+  {
+    setValues(values, null);
+  }
+  
   /**
     Set the values of the annotation, replacing any previous values.
     @param values A list containing the new values
+    @param unit The unit of the value, or null to use the default unit of
+      the annotation type
     @throws PermissionDeniedException If the logged in user doesn't have
       write permission for the annotation or read permission for the annotation
@@ -269 +433 @@
     @throws BaseException If there is another error
   */
-  public void setValues(List<?> values)
+  public void setValues(List<?> values, Unit unit)
     throws PermissionDeniedException, InvalidDataException, BaseException
   {
     checkPermission(Permission.WRITE);
     AnnotationType annotationType = getAnnotationType();
+    if (unit == null) unit = annotationType.getDefaultUnit();
     int multiplicity = annotationType.getMultiplicity();
     if (multiplicity > 0 && values.size() > multiplicity)
@@ -279 +444 @@
       throw new InvalidDataException("Too many values. Max "+multiplicity+" value(s) are allowed for this annotation type");
     }
+    UnitConverter converter = getUnitConverter(unit);
+    List<Object> convertedValues = new ArrayList<Object>(values.size());
+    Type valueType = getValueType();
     for (Object value : values)
     {
+      if (converter != null && value instanceof Number) 
+      {
+        value = valueType.convertNumber(converter.convertToReferenceUnit(((Number)value).doubleValue()));
+      }
       annotationType.validateAnnotationValue(value);
-    }
-    getData().getValues().replaceValues(Values.getDataValues(values));
+      convertedValues.add(value);
+    }
+    if (unit != null) getData().setUnit(unit.getData());
+    getData().getValues().replaceValues(Values.getDataValues(convertedValues));
   }
 

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

@@ -26 +26 @@
 import net.sf.basedb.core.data.ParameterValueData;
 import net.sf.basedb.core.data.AnnotationTypeData;
+import net.sf.basedb.core.data.QuantityData;
+import net.sf.basedb.core.data.UnitData;
 
 import net.sf.basedb.core.query.Restrictions;
@@ -300 +302 @@
 
   /**
+    Get the quantity for this annotation type. If the quantity is null,
+    units are not used with this annotation type. An annotation type without
+    units can be changed to use units with the {@link #setDefaultUnit(Unit)}
+    method. Once a unit has been configured, it is not possible to change
+    the {@link Quantity}. 
+    @return The quantity, or null
+    @since 2.9
+  */
+  public Quantity getQuantity()
+  {
+    return getDbControl().getItem(Quantity.class, getData().getQuantity());
+  }
+  
+  /**
+    Get the default unit for this annotation type.
+    @return The default unit, or null if this annotation type
+      doesn't use units
+    @since 2.9
+  */
+  public Unit getDefaultUnit()
+  {
+    return getDbControl().getItem(Unit.class, getData().getDefaultUnit());
+  }
+  
+  /**
+    Set the default unit to use for this annotation type. If the
+    annotation type doesn't have any current default unit, any
+    unit can be used. If there already is a default unit, the new
+    unit must be from the same {@link Quantity} as the existing unit.
+    <p>
+    Note! Changing units will result in a convertion of existing
+    annotation values to the new unit. This may result in loss
+    of precision due to rounding or truncation errors.
+    @param defaultUnit The new default unit
+    @since 2.9
+  */
+  public void setDefaultUnit(Unit defaultUnit)
+  {
+    checkPermission(Permission.WRITE);
+    if (isInDatabase())
+    {
+      // Make sure that the current quantity is null or the same as for the new unit
+      QuantityData quantity = getData().getQuantity();
+      if (quantity != null)
+      {
+        if (defaultUnit == null)
+        {
+          throw new InvalidUseOfNullException("defaultUnit");
+        }
+        else if (!quantity.equals(defaultUnit.getData().getQuantity()))
+        {
+          throw new InvalidDataException("The unit '" + defaultUnit.getName() + 
+          "' is not of the expected quantity: " + quantity.getName());
+        }
+        if (defaultUnit.getId() != getData().getDefaultUnit().getId())
+        {
+          // TODO - recalculate annotation values
+        }
+      }
+    }
+    getData().setDefaultUnit(defaultUnit == null ? null : defaultUnit.getData());
+    getData().setQuantity(defaultUnit == null ? null : defaultUnit.getData().getQuantity());
+  }
+  
+  /**
+    Get a query for returning the units that are considered
+    "usable" for this annotation type. This is typically used by client
+    applications to limit the list of choices in the graphical interface.
+    If this query doesn't return any items, all units should be
+    consiedered usable.
+    
+    @return A query
+    @since 2.9
+  */
+  public ItemQuery<Unit> getUsableUnits()
+  {
+    ItemQuery<Unit> query = Unit.getQuery();
+    query.joinPermanent(Hql.innerJoin("usedUnits", Item.ANNOTATIONTYPE.getAlias()));
+    query.restrictPermanent(
+      Restrictions.eq(
+        Hql.alias(Item.ANNOTATIONTYPE.getAlias()),
+        Hql.entity(this)
+      )
+    );
+    return query;
+  }
+  
+  /**
+    Checks if the given unit is a unit that has been specified as
+    a "usable" unit for this annotation type.
+    @param unit The unit to check
+    @return TRUE if the unit is "usable", FALSE otherwise
+    @since 2.9
+  */
+  public boolean isUsableUnit(Unit unit)
+  {
+    if (unit == null) return false;
+    return getData().getUsableUnits().contains(unit.getData());
+  }
+  
+  /**
+    Add a unit to be used with this annotation type. Note! This doesn't
+    prevent other units (from the same {@link Quantity}) from being
+    used. This is just a recommendation to allow client applications
+    to limit the list of choices in the graphical interface.
+    
+    @param unit The unit to add
+    @throws PermissionDeniedException If the logged in user 
+      doesn't have write permission for the annotation type or 
+      use permission  for the unit
+    @throws InvalidDataException If the unit is null
+    @since 2.9
+  */
+  public void addUsableUnit(Unit unit)
+  {
+    checkPermission(Permission.WRITE);
+    if (unit == null) throw new InvalidUseOfNullException("unit");
+    unit.checkPermission(Permission.USE);
+    getData().getUsableUnits().add(unit.getData());
+  }
+  
+  /**
+    Remove a unit from this annotation type. This will not affect 
+    already existing annotation with this unit.
+    @param unit The unit to remove from the set of usable units
+    @throws PermissionDeniedException If the
+      logged in user doesn't have {@link Permission#WRITE}
+      permission for the annotation type
+    @throws InvalidDataException If the unit is null
+    @since 2.9
+  */
+  public void removeUsableUnit(Unit unit)
+  {
+    checkPermission(Permission.WRITE);
+    if (unit == null) throw new InvalidUseOfNullException("unit");
+    getData().getUsableUnits().remove(unit.getData());
+  }
+
+  /**
+    Clear all units.
+    @since 2.9
+  */
+  public void clearUsableUnits()
+  {
+    checkPermission(Permission.WRITE);
+    getData().getUsableUnits().clear();
+  }
+
+  /**
     Get the external id of the annotation type. This value can be used to link
     with information in external databases. It is not used by the BASE core
@@ -852 +1003 @@
     return pv == null ? null : Collections.unmodifiableList(Values.getItemValues(getDbControl(), pv.getValues()));
   }
+  
   /**
     Set the list of allowed values for an enumerated annotation type.

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

@@ -49 +49 @@
     Get the quantity this annotation type uses. Can't be changed
     after creation.
-    @hibernate.many-to-one column="`quantity_id`" not-null="false" outer-join="false" 
-      update="false"
+    @hibernate.many-to-one column="`quantity_id`" not-null="false" outer-join="false"
     @since 2.9
   */
@@ -97 +96 @@
   public Set<UnitData> getUsableUnits()
   {
+    if (usableUnits == null) usableUnits = new HashSet<UnitData>();
     return usableUnits;
   }
+  
   /**
     @since 2.9

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

@@ -177 +177 @@
   }
 
+  private Set<AnnotationTypeData> usedUnits;
+  /**
+    This is the inverse end. It has lazy="false" because we need
+    automatic deletion from the AnnotationTypeUnits table
+    @see AnnotationTypeData#getUsableUnits()
+    @hibernate.set table="`AnnotationTypeUnits`" lazy="true" 
+    @hibernate.collection-key column="`unit_id`"
+    @hibernate.collection-many-to-many column="`annotationtype_id`" 
+      class="net.sf.basedb.core.data.AnnotationTypeData"
+  */
+  Set<AnnotationTypeData> getUsedUnits()
+  {
+    return usedUnits;
+  }
+  void setUsedUnits(Set<AnnotationTypeData> usedUnits)
+  {
+    this.usedUnits = usedUnits;
+  }
+  
 }

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

@@ -31 +31 @@
   @base.modified $Date$
 */
-public class ToStringFormatter
-  implements Formatter<Object>
+public class ToStringFormatter<T>
+  implements Formatter<T>
 {
 
@@ -45 +45 @@
     -------------------------------------------
   */
-  public String format(Object value)
+  public String format(T value)
   {
     return value == null ? "" : value.toString();
   }
-  public Number parseString(String value)
+  public T parseString(String value)
   {
     throw new UnsupportedOperationException("parseString");

trunk/src/test/TestAnnotation.java

@@ -48 +48 @@
     write("++Testing annotations");
     write_header();
+    
+    int celsiusId = TestUnit.test_load_by_symbol(SystemItems.getId(Quantity.TEMPERATURE), "C");
+    int fahrenheitId = TestUnit.test_load_by_symbol(SystemItems.getId(Quantity.TEMPERATURE), "F");
+    int meterId = TestUnit.test_load_by_symbol(SystemItems.getId(Quantity.LENGTH), "m");
+    int millimeterId = TestUnit.test_load_by_symbol(SystemItems.getId(Quantity.LENGTH), "mm");
+
     // Create annotation types and array design
-
-    int intId = TestAnnotationType.test_create(null, Type.INT, 10, null, Item.ARRAYDESIGN, 1, null, true);
-    int longId = TestAnnotationType.test_create(null, Type.LONG, 1056567756767l, null, Item.ARRAYDESIGN, 1, null, true);
-    int floatId = TestAnnotationType.test_create(null, Type.FLOAT, 10.1f, null, Item.ARRAYDESIGN, 1, null, true);
-    int doubleId = TestAnnotationType.test_create(null, Type.DOUBLE, 8.13454646d, null, Item.ARRAYDESIGN, 1, null, true);
-    int dateId = TestAnnotationType.test_create(null, Type.DATE, new Date(), null, Item.ARRAYDESIGN, 1, null, true);
-    int textId = TestAnnotationType.test_create(null, Type.TEXT, "default value", null, Item.ARRAYDESIGN, 1, null, true);
-    int stringId = TestAnnotationType.test_create(null, Type.STRING, "default value", null, Item.ARRAYDESIGN, 1, null, true);
-    int booleanId = TestAnnotationType.test_create(null, Type.BOOLEAN, true, null, Item.ARRAYDESIGN, 1, null, true);
-    int enumId = TestAnnotationType.test_create(null, Type.INT, 3, null, Item.ARRAYDESIGN, 1, new Object[] { 1, 2, 3, 4, 5 }, false);
+    int intId = TestAnnotationType.test_create(null, Type.INT, 0, 10, null, Item.ARRAYDESIGN, 1, null, true);
+    int longId = TestAnnotationType.test_create(null, Type.LONG, 0, 1056567756767l, null, Item.ARRAYDESIGN, 1, null, true);
+    int floatId = TestAnnotationType.test_create("Temperature", Type.FLOAT, celsiusId, 10.1f, null, Item.ARRAYDESIGN, 1, null, true);
+    int doubleId = TestAnnotationType.test_create("Size", Type.DOUBLE, meterId, 8.13454646d, null, Item.ARRAYDESIGN, 1, null, true);
+    int dateId = TestAnnotationType.test_create(null, Type.DATE, 0, new Date(), null, Item.ARRAYDESIGN, 1, null, true);
+    int textId = TestAnnotationType.test_create(null, Type.TEXT, 0, "default value", null, Item.ARRAYDESIGN, 1, null, true);
+    int stringId = TestAnnotationType.test_create(null, Type.STRING, 0, "default value", null, Item.ARRAYDESIGN, 1, null, true);
+    int booleanId = TestAnnotationType.test_create(null, Type.BOOLEAN, 0, true, null, Item.ARRAYDESIGN, 1, null, true);
+    int enumId = TestAnnotationType.test_create(null, Type.INT, 0, 3, null, Item.ARRAYDESIGN, 1, new Object[] { 1, 2, 3, 4, 5 }, false);
     int arrayDesignId = TestArrayDesign.test_create(Platform.GENERIC, true);
+    int arrayDesignId2 = TestArrayDesign.test_create(Platform.AFFYMETRIX, true);
 
     // Annotate the array design and list the annotations
-    int intAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, intId, 10);
-    int longAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, longId, 1023456789012345l);
-    int floatAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, floatId, 11.365789456857f);
-    int doubleAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, doubleId, 11.365789456857d);
-    int dateAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, dateId, new Date());
-    int textAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, textId, "a text annotation");
-    int stringAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, stringId, "a string annotation");
-    int booleanAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, booleanId, false);
-    int enumAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, enumId, 4);
+    int intAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, intId, 0, 10);
+    int longAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, longId, 0, 1023456789012345l);
+    int floatAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, floatId, celsiusId, 11.365789456857f);
+    int doubleAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, doubleId, meterId, 11.365789456857d);
+    int floatAnnotationId2 = test_annotatate(Item.ARRAYDESIGN, arrayDesignId2, floatId, fahrenheitId, 11.365789456857f);
+    int doubleAnnotationId2 = test_annotatate(Item.ARRAYDESIGN, arrayDesignId2, doubleId, millimeterId, 11.365789456857d);
+    int dateAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, dateId, 0, new Date());
+    int textAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, textId, 0, "a text annotation");
+    int stringAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, stringId, 0, "a string annotation");
+    int booleanAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, booleanId, 0, false);
+    int enumAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId, enumId, 0, 4);
     test_list_annotations(Item.ARRAYDESIGN, arrayDesignId, 9);
+    test_list_annotations(Item.ARRAYDESIGN, arrayDesignId2, 2);
 
     // Test: inherit annotations
@@ -102 +111 @@
     // Delete annotation types and array design
     TestArrayDesign.test_delete(arrayDesignId);
+    TestArrayDesign.test_delete(arrayDesignId2);
     TestAnnotationType.test_delete(intId);
     TestAnnotationType.test_delete(longId);
@@ -116 +126 @@
   }
   
-  static int test_annotatate(Item itemType, int itemId, int annotationTypeId, Object... value)
+  static int test_annotatate(Item itemType, int itemId, int annotationTypeId, int unitId, Object... value)
   {
     if (itemId == 0 || annotationTypeId == 0) return 0;
@@ -132 +142 @@
       List<Object> l = new ArrayList<Object>();
       l.addAll(Arrays.asList(value));
-      a.setValues(l);
+      Unit unit = unitId != 0 ? Unit.getById(dc, unitId) : null;
+      a.setValues(l, unit);
       dc.commit();
       id = a.getId();
@@ -215 +226 @@
     if (!TestUtil.getSilent())
     {
-      write("   \tID \tAnnotation type\tAnnotation set\tValues");
-      write("-- \t-- \t---------------\t--------------\t------");
+      write("   \tID \tAnnotation type\tAnnotation set\tValues\tUnit\tRaw values");
+      write("-- \t-- \t---------------\t--------------\t------\t----\t----------");
     }
   }
@@ -223 +234 @@
   {
     if (!TestUtil.getSilent()) 
-      write(i+":\t"+a.getId()+"\t"+a.getAnnotationType()+"\t"+a.getAnnotationSet()+"\t"+a.getValues());
+      write(i+":\t"+a.getId()+"\t"+a.getAnnotationType()+"\t"+a.getAnnotationSet()+"\t"+
+          a.getValues(null) + "\t" + a.getUnit() + "\t" + a.getValues());
   }
   static void write_item(int i, AnnotationSet as)

trunk/src/test/TestAnnotationFlatFileImporter.java

@@ -56 +56 @@
     // Create annotation types, samples and upload file
     
-    int timeId = TestAnnotationType.test_create("Time (hours)", Type.INT, null, 25, Item.SAMPLE, 1, null, false);
-    int ageId = TestAnnotationType.test_create("Age (years)", Type.INT, null, 100, Item.SAMPLE, 1, null, false);
-    int commentId = TestAnnotationType.test_create("Comment", Type.STRING, null, 20, Item.SAMPLE, 0, null, false);
-    int enumId = TestAnnotationType.test_create("Subtype", Type.STRING, null, null, Item.SAMPLE, 
-      1, new String[] { "alfa", "beta", "gamma" }, false);
+    int timeId = TestAnnotationType.test_create("Time (hours)", Type.INT, 0, null, 25, Item.SAMPLE, 1, null, false);
+    int ageId = TestAnnotationType.test_create("Age (years)", Type.INT, 0, null, 100, Item.SAMPLE, 1, null, false);
+    int commentId = TestAnnotationType.test_create("Comment", Type.STRING, 0, null, 20, Item.SAMPLE, 0, null, false);
+    int enumId = TestAnnotationType.test_create("Subtype", Type.STRING, 0, null, null, 
+      Item.SAMPLE, 1, new String[] { "alfa", "beta", "gamma" }, false);
 
     int sample1 = TestSample.test_create(0, "Sample #1", false);
@@ -69 +69 @@
     int sampleDup2 = TestSample.test_create(0, "Sample dup", false);
     
-    TestAnnotation.test_annotatate(Item.SAMPLE, sample4, timeId, 12);
-    TestAnnotation.test_annotatate(Item.SAMPLE, sample4, ageId, 2);
-    TestAnnotation.test_annotatate(Item.SAMPLE, sample4, enumId, "gamma");
-    TestAnnotation.test_annotatate(Item.SAMPLE, sample4, commentId, "A comment from code");
+    TestAnnotation.test_annotatate(Item.SAMPLE, sample4, timeId, 0, 12);
+    TestAnnotation.test_annotatate(Item.SAMPLE, sample4, ageId, 0, 2);
+    TestAnnotation.test_annotatate(Item.SAMPLE, sample4, enumId, 0, "gamma");
+    TestAnnotation.test_annotatate(Item.SAMPLE, sample4, commentId, 0, "A comment from code");
     
     int fileId = TestFile.test_create("data/test.annotation.import.txt", false, false);

trunk/src/test/TestAnnotationType.java

@@ -44 +44 @@
     write("++Testing annotation types");
     write_header();
+    
+    int celsiusId = TestUnit.test_load_by_symbol(SystemItems.getId(Quantity.TEMPERATURE), "C");
+    int meterId = TestUnit.test_load_by_symbol(SystemItems.getId(Quantity.LENGTH), "m");
+    
     // Standard tests: create, load, list
-    int id_int = test_create(null, Type.INT, 10, null, Item.SAMPLE, 1, null, true);
-    int id_long = test_create(null, Type.LONG, 123456789123456l, null, Item.SAMPLE, 1, null, true);
-    int id_float = test_create(null, Type.FLOAT, 10.1, null, Item.SAMPLE, 1, null, false);
-    int id_double = test_create(null, Type.DOUBLE, 8.13459187745, null, Item.SAMPLE, 1, null, false);
-    int id_date = test_create(null, Type.DATE, new Date(), null, Item.SAMPLE, 1, null, false);
-    int id_text = test_create(null, Type.TEXT, "default value", null, Item.SAMPLE, 1, null, false);
-    int id_string = test_create(null, Type.STRING, "default value", null, Item.SAMPLE, 1, null, false);
-    int id_boolean = test_create(null, Type.BOOLEAN, true, null, Item.SAMPLE, 1, null, false);
-    int id_enum = test_create(null, Type.INT, 3, null, Item.SAMPLE, 1, new Object[] { 1, 2, 3, 4, 5 }, false);
-    int id2_enum = test_create(null, Type.STRING, "one", null, Item.SAMPLE, 1, new String[] { "one", "two ", "three" }, false);
+    int id_int = test_create(null, Type.INT, 0, 10, null, Item.SAMPLE, 1, null, true);
+    int id_long = test_create(null, Type.LONG, 0, 123456789123456l, null, Item.SAMPLE, 1, null, true);
+    int id_float = test_create("Temperature", Type.FLOAT, celsiusId, 10.1, null, Item.SAMPLE, 1, null, false);
+    int id_double = test_create("Size", Type.DOUBLE, meterId, 8.13459187745, null, Item.SAMPLE, 1, null, false);
+    int id_date = test_create(null, Type.DATE, 0, new Date(), null, Item.SAMPLE, 1, null, false);
+    int id_text = test_create(null, Type.TEXT, 0, "default value", null, Item.SAMPLE, 1, null, false);
+    int id_string = test_create(null, Type.STRING, 0, "default value", null, Item.SAMPLE, 1, null, false);
+    int id_boolean = test_create(null, Type.BOOLEAN, 0, true, null, Item.SAMPLE, 1, null, false);
+    int id_enum = test_create(null, Type.INT, 0, 3, null, Item.SAMPLE, 1, new Object[] { 1, 2, 3, 4, 5 }, false);
+    int id2_enum = test_create(null, Type.STRING, 0, "one", null, Item.SAMPLE, 1, new String[] { "one", "two ", "three" }, false);
     test_load(id_int);
     test_load(id_long);
@@ -99 +103 @@
   }
   
-  static int test_create(String name, Type type, Object defaultValue, Number maxValue, Item itemType, int multiplicity, Object[] enumValues, boolean setAll)
+  static int test_create(String name, Type type, int unitId, 
+      Object defaultValue, Number maxValue, Item itemType, int multiplicity, Object[] enumValues, boolean setAll)
   {
     if (!TestUtil.hasPermission(Permission.CREATE, Item.ANNOTATIONTYPE)) return 0;
@@ -119 +124 @@
       at.setMultiplicity(multiplicity);
       if (name != null) at.setName(name);
+      if (unitId != 0)
+      {
+        at.setDefaultUnit(Unit.getById(dc, unitId));
+      }
       if (enumValues != null)
       {
@@ -241 +250 @@
     if (!TestUtil.getSilent())
     {
-      write("   \tID \tName      \tDescription\tValue type\tMultiplicity\tExternal ID\tWidth\tHeight\tMiame\tDefault value\tItem types\tEnumeration values");
-      write("-- \t-- \t--------- \t-----------\t----------\t------------\t-----------\t-----\t------\t-----\t-------------\t----------\t------------------");
+      write("   \tID \tName      \tDescription\tValue type\tDefault unit\tMultiplicity\tExternal ID\tWidth\tHeight\tMiame\tDefault value\tItem types\tEnumeration values");
+      write("-- \t-- \t--------- \t-----------\t----------\t------------\t------------\t-----------\t-----\t------\t-----\t-------------\t----------\t------------------");
     }
   }
@@ -250 +259 @@
     if (!TestUtil.getSilent()) 
       write(i+":\t"+at.getId()+"\t"+at.getName()+"\t"+at.getDescription()+"\t"+at.getValueType()+
+      "\t" + at.getDefaultUnit()+ 
       "\t"+at.getMultiplicity()+"\t"+at.getExternalId()+"\t"+at.getWidth()+"\t"+at.getHeight()+"\t"+at.isRequiredForMiame()+
       "\t"+at.getDefaultValue()+"\t"+at.getEnabledItems()+"\t"+at.getValues());

trunk/src/test/TestAnnotationTypeCategory.java

@@ -58 +58 @@
 
     // extra test: add categories to annotation type
-    int id_int = TestAnnotationType.test_create(null, Type.INT, 10, null, Item.SAMPLE, 1, null, true);
+    int id_int = TestAnnotationType.test_create(null, Type.INT, 0, 10, null, Item.SAMPLE, 1, null, true);
     test_add_categories(id_int, id, id2);
     test_list_categories(id_int, 2);

trunk/src/test/TestExperiment.java

@@ -73 +73 @@
     
     // Experimental factors
-    int factorId1 = TestAnnotationType.test_create("Drug resistance", Type.STRING, null, null, Item.RAWBIOASSAY, 1, new String[] { "high", "medium", "low" }, false);
-    int factorId2 = TestAnnotationType.test_create("Temperature", Type.FLOAT, null, null, Item.RAWBIOASSAY, 1, null, false);
+    int factorId1 = TestAnnotationType.test_create("Drug resistance", Type.STRING, 0, null, null, Item.RAWBIOASSAY, 1, new String[] { "high", "medium", "low" }, false);
+    int factorId2 = TestAnnotationType.test_create("Temperature", Type.FLOAT, 0, null, null, Item.RAWBIOASSAY, 1, null, false);
     test_add_experimental_factors(id, factorId1, factorId2);
     test_list_experimental_factors(id, 2);

trunk/src/test/TestWebservices.java

@@ -127 +127 @@
     TestExperiment.test_add_rawbioassay(experimentId2, rawBioAssayId4);
     
-    int factorId1 = TestAnnotationType.test_create("Drug resistance", Type.STRING, null, null, Item.RAWBIOASSAY, 1, new String[] { "high", "medium", "low" }, false);
-    int factorId2 = TestAnnotationType.test_create("Temperature", Type.FLOAT, null, null, Item.RAWBIOASSAY, 1, null, false);
+    int factorId1 = TestAnnotationType.test_create("Drug resistance", Type.STRING, 0, null, null, Item.RAWBIOASSAY, 1, new String[] { "high", "medium", "low" }, false);
+    int factorId2 = TestAnnotationType.test_create("Temperature", Type.FLOAT, 0, null, null, Item.RAWBIOASSAY, 1, null, false);
     
     TestExperiment.test_add_experimental_factors(experimentId1, factorId1, factorId2);
-    TestAnnotation.test_annotatate(Item.RAWBIOASSAY, rawBioAssayId1, factorId1, "medium");
-    TestAnnotation.test_annotatate(Item.RAWBIOASSAY, rawBioAssayId1, factorId2, 12.5f);
-    TestAnnotation.test_annotatate(Item.RAWBIOASSAY, rawBioAssayId2, factorId1, "high");
-    TestAnnotation.test_annotatate(Item.RAWBIOASSAY, rawBioAssayId2, factorId2, 20.3f);
+    TestAnnotation.test_annotatate(Item.RAWBIOASSAY, rawBioAssayId1, factorId1, 0, "medium");
+    TestAnnotation.test_annotatate(Item.RAWBIOASSAY, rawBioAssayId1, factorId2, 0, 12.5f);
+    TestAnnotation.test_annotatate(Item.RAWBIOASSAY, rawBioAssayId2, factorId1, 0, "high");
+    TestAnnotation.test_annotatate(Item.RAWBIOASSAY, rawBioAssayId2, factorId2, 0, 20.3f);
     
     //Tests

trunk/src/webservices/server/net/sf/basedb/ws/server/ReporterService.java

@@ -108 +108 @@
     
     boolean annotatable = false;
-    MultiFormatter formatter = new MultiFormatter(new ToStringFormatter(), true);
+    MultiFormatter formatter = new MultiFormatter(new ToStringFormatter<Object>(), true);
     formatter.registerFormatter(Date.class, FormatterFactory.getDateFormatter(sc));
     List<ExportedProperty> exportedProperties = new ArrayList<ExportedProperty>(extPropInfos.length);   
@@ -173 +173 @@
     
     boolean annotatable = false;
-    MultiFormatter formatter = new MultiFormatter(new ToStringFormatter(), true);
+    MultiFormatter formatter = new MultiFormatter(new ToStringFormatter<Object>(), true);
     formatter.registerFormatter(Date.class, FormatterFactory.getDateFormatter(sc));
     List<ExportedProperty> exportedProperties = new ArrayList<ExportedProperty>(extPropInfos.length);   

trunk/www/WEB-INF/table.tld

@@ -672 +672 @@
       <rtexprvalue>true</rtexprvalue>
     </attribute>
+    <attribute>
+      <name>prefix</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>suffix</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
   </tag>
 

trunk/www/admin/annotationtypes/edit_annotationtype.jsp

@@ -35 +35 @@
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.AnnotationTypeCategory"
+  import="net.sf.basedb.core.Quantity"
+  import="net.sf.basedb.core.Unit"
   import="net.sf.basedb.core.SystemItems"
   import="net.sf.basedb.core.Metadata"
@@ -67 +69 @@
   AnnotationType annotationType = null;
   ItemQuery<AnnotationTypeCategory> categoryQuery = null;
+  ItemQuery<Unit> unitQuery = null;
   Type valueType = null;
+  boolean readCurrentQuantity = true;
+  int currentQuantityId = 0;
+  boolean readCurrentUnit = true;
+  int currentUnitId = 0;
 
   if (itemId == 0)
@@ -73 +80 @@
     title = "Create annotation type";
     valueType = Type.valueOf(request.getParameter("value_type"));
+    unitQuery = Unit.getQuery();
+    
+    int recentQuantityId = Values.getInt(cc.getRecent(Item.QUANTITY.name(), 0));
+    currentQuantityId = Values.getInt(cc.getPropertyValue("quantity"), recentQuantityId);
+
+    if (cc.getPropertyFilter("defaultUnit.name") != null)
+    {
+      Unit currentUnit = Base.getFirstMatching(dc, Unit.getQuery(), "name", cc.getPropertyFilter("defaultUnit.name"));
+      if (currentUnit != null) currentUnitId = currentUnit.getId();
+    }
+    if (currentUnitId == 0) currentUnitId = Values.getInt(cc.getRecent(Item.UNIT.name(), 0));
     cc.removeObject("item");
   }
@@ -85 +103 @@
     categoryQuery.include(Include.ALL);
     categoryQuery.order(Orders.asc(Hql.property("name")));
+    try
+    {
+      Quantity quantity = annotationType.getQuantity();
+      if (quantity != null) 
+      {
+        currentQuantityId = quantity.getId();
+        unitQuery = quantity.getUnits();
+      }
+      else
+      {
+        unitQuery = Unit.getQuery();
+      }
+      Unit unit = annotationType.getDefaultUnit();
+      if (unit != null) currentUnitId = unit.getId();
+    }
+    catch (PermissionDeniedException ex)
+    {
+      readCurrentQuantity = false;
+      readCurrentUnit = false;
+    }
   }
+  // Query to retrieve quantities types
+  final ItemQuery<Quantity> quantityQuery = Quantity.getQuery();
+  quantityQuery.include(Include.ALL);
+  quantityQuery.order(Orders.asc(Hql.property("name")));
+  
+  unitQuery.include(Include.ALL);
+  unitQuery.order(Orders.asc(Hql.property("quantity.name")));
+  unitQuery.order(Orders.asc(Hql.property("referenceFactor")));
+  unitQuery.order(Orders.asc(Hql.property("name")));
   
   final String clazz = "class=\"text\"";
@@ -95 +142 @@
   %>
   <base:page type="popup" title="<%=title%>">
-  <base:head scripts="tabcontrol.js,linkitems.js" styles="tabcontrol.css">
+  <base:head scripts="tabcontrol.js,linkitems.js,units.js" styles="tabcontrol.css">
     <script language="JavaScript">
     // Validate the "Annotation type" tab
@@ -116 +163 @@
     
     function validateItemTypes()
+    {
+      return true;
+    }
+
+    function validateUnits()
     {
       return true;
@@ -138 +190 @@
         frm.addCategories.value = Link.getActionIds(1, 'C').join(',');
         frm.removeCategories.value = Link.getActionIds(-1, 'C').join(',');
+        frm.addUsableUnits.value = Link.getActionIds(1, 'U').join(',');
+        frm.removeUsableUnits.value = Link.getActionIds(-1, 'U').join(',');
         frm.submit();
       }
@@ -156 +210 @@
       initItemTypes();
       initCategories();
+      initUnits();
       interfaceOnClick();
     }
+
+    function initUnits()
+    {
+      var frm = document.forms['annotationType'];
+      var quantityList = frm.quantity_id;
+      var unitList = frm.unit_id;
+      var quantity;
+      <%
+      if (unitQuery != null)
+      {
+        List<Unit> units = unitQuery.list(dc);
+        Quantity prevQuantity = null;
+        for (Unit unit : units)
+        {
+          Quantity quantity = unit.getQuantity();
+          if (!quantity.equals(prevQuantity))
+          {
+            %>
+            quantity = new Quantity(<%=quantity.getId()%>, '<%=HTML.javaScriptEncode(quantity.getName())%>');
+            <%
+            prevQuantity = quantity;
+          }
+          %>
+          quantity.addUnit(<%=unit.getId()%>, '<%=HTML.javaScriptEncode(unit.getName())%>', '<%=HTML.javaScriptEncode(unit.getDisplaySymbol())%>');
+          <%
+        }
+      }
+      %>
+      Quantities.populateLists(quantityList, unitList, <%=currentQuantityId%>, <%=currentUnitId%>);
+      Quantities.updateUnitsList(quantityList[quantityList.selectedIndex].quantity, frm.allUnits);
+      var usableUnits = new Array();
+      <%
+      if (annotationType != null)
+      {
+        ItemQuery<Unit> usableQuery = annotationType.getUsableUnits();
+        usableQuery.include(Include.ALL);
+        usableQuery.order(Orders.asc(Hql.property("referenceFactor")));
+        usableQuery.order(Orders.asc(Hql.property("name")));
+        
+        ItemResultList<Unit> usableUnits = usableQuery.list(dc);
+        for (Unit u : usableUnits)
+        {
+          %>
+          usableUnits['ID<%=u.getId()%>'] = true;
+          <%
+        }
+      }
+      %>
+      addUsableUnits(usableUnits);
+    }
+    
+    function quantityOnChange()
+    {
+      var frm = document.forms['annotationType'];
+      var quantityList = frm.quantity_id;
+      var unitList = frm.unit_id;
+      var quantity = quantityList[quantityList.selectedIndex].quantity;
+      Quantities.updateUnitsList(quantity, unitList, <%=currentUnitId%>);
+      Quantities.updateUnitsList(quantity, frm.allUnits);
+    }
+
+    function addUsableUnits(usableUnits)
+    {
+      var frm = document.forms['annotationType'];
+      for (var i = 0; i < frm.allUnits.length; i++)
+      {
+        var option = frm.allUnits[i];
+        if (option.selected || (usableUnits && usableUnits['ID'+option.value]))
+        {
+          addUsableUnit(option.value, option.text, usableUnits);
+          frm.allUnits[i--] = null;
+        }
+      }
+    }
+
+    function addUsableUnit(unitId, name, asNew)
+    {
+      var item = Link.getItem('U', unitId);
+      if (!item) item = new Item('U', unitId, name);
+      if (asNew)
+      {
+        Link.addNewItem(document.forms['annotationType'].usableUnits, item);
+      }
+      else
+      {
+        Link.addItem(document.forms['annotationType'].usableUnits, item);
+      }
+    }
+    function removeUsableUnits()
+    {
+      var frm = document.forms['annotationType'];
+      Link.removeSelected(frm.usableUnits, frm.allUnits);
+    }
+    
     function initItemTypes()
     {
@@ -682 +831 @@
     </t:tab>
     
+    <t:tab id="units" title="Units" validate="validateUnits()" 
+      visible="<%=valueType.isNumerical()%>" helpid="annotationtype.edit.units">
+    
+      <table class="form" cellspacing="0">
+      <tr valign="top">
+        <td class="prompt">Quantity</td>
+        <td>
+          <select name="quantity_id" onchange="quantityOnChange()"
+            <%=!readCurrentQuantity || (annotationType != null && currentQuantityId != 0) ? 
+                "disabled readonly class=\"disabled\"" : "class=\"unchangeable\""%>>
+            <option value="">- do not use units -
+          </select>
+        </td>
+      </tr>
+      <tr valign="top">
+        <td class="prompt">Default unit</td>
+        <td>
+          <select name="unit_id" 
+            <%=!readCurrentQuantity ? "disabled readonly class=\"disabled\"" : ""%>>
+          </select>
+        </td>
+      </tr>
+      </table>
+
+      <base:note type="warning" style="background: #ffffd8;"  visible="<%=annotationType != null %>">
+      Changing the default unit triggers a conversion of existing annotation values
+      to the new unit. This may result in loss of precision due to rounding or 
+      truncation.
+      </base:note>
+
+      <table class="form" cellspacing="0">
+      <tr valign="top">
+        <td class="prompt">Use units</td>
+        <td></td>
+        <td class="prompt">Do not use</td>
+      </tr>
+      <tr>
+        <td>
+          <select name="usableUnits" size="5" multiple style="width: 15em;">
+          </select>
+        </td>
+        <td>
+           <br>
+          <base:button
+            onclick="addUsableUnits()"
+            title="<img src='../../images/move_left.gif' alt='' style='vertical-align: middle;'>" 
+            tooltip="Enable the annotation type for the selected unit(s)" 
+          /><p>
+          <base:button 
+            onclick="removeUsableUnits()"
+            title="<img src='../../images/move_right.gif' alt='' style='vertical-align: middle;'>" 
+            tooltip="Disable the annotation type for the selected unit(s)" 
+          />
+          <br>
+        </td>
+        <td>
+          <select name="allUnits" size="5" multiple style="width: 15em;">
+          </select>
+          <input type="hidden" name="removeUsableUnits" value="">
+          <input type="hidden" name="addUsableUnits" value="">
+        </td>
+      </tr>
+      </table>
+
+      <div align=right>
+        <i><base:icon image="unchangeable.gif" /> = can't be changed later</i>
+      </div>
+
+    </t:tab>
+
     <t:tab id="categories" title="Categories" validate="validateCategories()" 
       helpid="annotationtype.edit.categories">

trunk/www/admin/annotationtypes/index.jsp

@@ -31 +31 @@
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.AnnotationTypeCategory"
+  import="net.sf.basedb.core.Quantity"
+  import="net.sf.basedb.core.Unit"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.Permission"
@@ -132 +134 @@
     // Update the properties on an item (will close the popup)
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext);
+    final int maxRecent = Base.getMaxRecent(sc);
     dc = sc.newDbControl();
     AnnotationType annotationType = (AnnotationType)cc.getObject("item");
@@ -245 +248 @@
     }
     
+    // Units tab
+    if (valueType.isNumerical())
+    {
+      int unitId = Values.getInt(request.getParameter("unit_id"), -1);
+      if (unitId >= 0) // < 0 = denied or unchanged
+      {
+        Unit unit = unitId == 0 ? null : Unit.getById(dc, unitId);
+        annotationType.setDefaultUnit(unit);
+        if (unit != null) cc.setRecent(unit, maxRecent);
+      }
+      
+      String[] removeUnits = Values.getString(request.getParameter("removeUsableUnits")).split(",");
+      for (int i = 0; i < removeUnits.length; ++i)
+      {
+        int uId = Values.getInt(removeUnits[i], -1);
+        if (uId != -1) annotationType.removeUsableUnit(Unit.getById(dc, uId));
+      }
+      
+      String[] addUnits = Values.getString(request.getParameter("addUsableUnits")).split(",");
+      for (int i = 0; i < addUnits.length; ++i)
+      {
+        int uId = Values.getInt(addUnits[i], -1);
+        if (uId != -1) annotationType.addUsableUnit(Unit.getById(dc, uId));
+      }
+    }
+    
     // Categories tab
     String[] removeCategories = Values.getString(request.getParameter("removeCategories")).split(",");

trunk/www/admin/annotationtypes/list_annotationtypes.jsp

@@ -30 +30 @@
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.AnnotationTypeCategory"
+  import="net.sf.basedb.core.Quantity"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.Include"
@@ -100 +101 @@
   categoryQuery.order(Orders.asc(Hql.property("name"))); 
 
+  // Get all quantities
+  final ItemQuery<Quantity> quantityQuery = Quantity.getQuery();
+  quantityQuery.order(Orders.asc(Hql.property("name")));
+  quantityQuery.setCacheResult(true);
+
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
   try
@@ -285 +291 @@
         enumeration="<%=types%>"
         title="Value type"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <%
+      Enumeration<String, String> quantities = new Enumeration<String, String>();
+      quantities.add("", "- none -");
+      for (Quantity q : quantityQuery.list(dc))
+      {
+        quantities.add(Integer.toString(q.getId()), q.getName());
+      }
+      %>
+      <tbl:columndef 
+        id="quantity"
+        property="quantity"
+        sortproperty="quantity.name"
+        exportproperty="quantity.name"
+        datatype="int"
+        enumeration="<%=quantities%>"
+        title="Quantity"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
+        id="defaultUnit"
+        property="defaultUnit.name"
+        datatype="string"
+        title="Default unit"
         sortable="true" 
         filterable="true"
@@ -541 +576 @@
                 <tbl:cell column="externalId"><%=HTML.encodeTags(item.getExternalId())%></tbl:cell>
                 <tbl:cell column="valueType"><%=item.getValueType()%></tbl:cell>
+                <tbl:cell column="quantity"><base:propertyvalue 
+                    item="<%=item%>" 
+                    property="quantity"
+                    enableEditLink="<%=mode.hasEditLink()%>" 
+                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
+                  /></tbl:cell>
+                <tbl:cell column="defaultUnit"><base:propertyvalue 
+                    item="<%=item%>" 
+                    property="defaultUnit"
+                    enableEditLink="<%=mode.hasEditLink()%>" 
+                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
+                  /></tbl:cell>
                 <tbl:cell column="isEnumeration"><%=item.isEnumeration() ? 
                   HTML.encodeTags(Values.getString(item.getValues(), ", ", true)) : 

trunk/www/admin/annotationtypes/view_annotationtype.jsp

@@ -247 +247 @@
         <td class="prompt">Value type</td>
         <td><%=annotationType.getValueType()%></td>
+      </tr>
+      <tr>
+        <td class="prompt">Default unit</td>
+        <td><base:propertyvalue item="<%=annotationType%>" property="quantity" />
+          <base:icon image="submenu.gif" style="vertical-align: baseline;"/>
+          <base:propertyvalue item="<%=annotationType%>" property="defaultUnit" />
+        </td>
       </tr>
       <tr>

trunk/www/common/annotations/list_annotations.jsp

@@ -34 +34 @@
   import="net.sf.basedb.core.Annotatable"
   import="net.sf.basedb.core.AnnotatableProxy"
+  import="net.sf.basedb.core.Unit"
   import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.ItemQuery"
@@ -43 +44 @@
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.formatter.Formatter"
+  import="net.sf.basedb.util.formatter.PrefixSuffixFormatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
   import="net.sf.basedb.util.Values"
@@ -102 +104 @@
     inheritedAnnotations = inheritedQuery.list(dc);
   }
-  %>
+%>
   <base:page type="include">
   <base:body>
@@ -163 +165 @@
             for (AnnotationType at : annotationTypes)
             {
-              Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
-              List<?> values = as == null || !as.hasAnnotation(at) ? 
-                null : as.getAnnotation(at).getValues();
+              Annotation a = as != null && as.hasAnnotation(at) ? as.getAnnotation(at) : null;
+              List<?> values = null;
+              Formatter formatter = null;
+              if (a != null)
+              {
+                values = a.getValues(null);
+                formatter = FormatterFactory.getAnnotationFormatter(sc, a, null);
+              }
               if (values != null || !at.isRemoved())
               {
-                %>
+              %>
                 <tbl:row>
                   <tbl:cell column="annotation"><base:icon 
@@ -198 +205 @@
         <%
       }
+      char nbsp = 0xA0;
       %>
-
+      :<%="a" + nbsp + "b" %>:
       <%
       if (protocolParameters != null )
@@ -241 +249 @@
               for (AnnotationType at : protocolParameters)
               {
-                Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
-                List<?> values = as == null || !as.hasAnnotation(at) ? 
-                  null : as.getAnnotation(at).getValues();
+                Annotation a = as != null && as.hasAnnotation(at) ? as.getAnnotation(at) : null;
+                Formatter formatter = null;
+                List<?> values = null;
+                if (a != null)
+                {
+                  values = a.getValues(null);
+                  formatter = FormatterFactory.getAnnotationFormatter(sc, a, null);
+                }
                 if (values != null || !at.isRemoved())
                 {
@@ -329 +342 @@
               boolean writeInherited = false;
               String icon = "joust/annotation.gif";
-              Formatter formatter = FormatterFactory.getTypeFormatter(sc, a.getValueType());
+              Formatter formatter = FormatterFactory.getAnnotationFormatter(sc, a, null);
               try
               {

trunk/www/include/scripts/linkitems.js

@@ -132 +132 @@
     the links are also registered.
     @param list The list object
-  */
-  this.removeSelected = function(list)
+    @param addTo An optional list item to add the removed items to
+  */
+  this.removeSelected = function(list, addTo)
   {
     for (var i = 0; i < list.length; i++)
@@ -143 +144 @@
         listItem.value = 0;
         list[i--] = null;
+        if (addTo)
+        {
+          addTo[addTo.length] = new Option(listItem.name, listItem.id, false, true);
+        }
       }
     }

trunk/www/lims/arraydesigns/list_designs.jsp

@@ -36 +36 @@
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.AnnotationSet"
+  import="net.sf.basedb.core.Annotation"
   import="net.sf.basedb.core.Job"
   import="net.sf.basedb.core.ItemQuery"
@@ -699 +700 @@
                     if (as.hasAnnotation(at))
                     {
+                      Annotation a = as.getAnnotation(at);
                       %>
-                      <tbl:cell column="<%="at"+at.getId()%>"
+                      <tbl:cell 
+                        column="<%="at"+at.getId()%>"
                         ><tbl:cellvalue 
-                        list="<%=as.getAnnotation(at).getValues()%>" 
+                          list="<%=a.getValues(null)%>"
+                          suffix="<%="&nbsp;"+a.getUnitSymbol(null)%>"
                       /></tbl:cell>
                       <%