Changeset 4822

Timestamp:

Mar 19, 2009, 2:06:45 PM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1255: Make annotation importer handle units

Location:

trunk/src

Files:

• core/net/sf/basedb/core/Annotation.java (modified) (2 diffs)
• core/net/sf/basedb/core/AnnotationType.java (modified) (3 diffs)
• plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java (modified) (13 diffs)
• test/TestAnnotationFlatFileImporter.java (modified) (4 diffs)
• test/data/test.annotation.import.txt (modified) (1 diff)

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

@@ -420 +420 @@
     {
       converter = getUnitConverter(unit);
-      if (converter != null && value instanceof Number)
+      Type valueType = getValueType();
+      if (value instanceof Number)
       {
-        value = converter.convertToReferenceUnit(((Number)value).doubleValue());
+        Number numericValue = (Number)value;
+        if (converter != null) 
+        {
+          numericValue = converter.convertToReferenceUnit(numericValue.doubleValue());
+        }
+        value = valueType.convertNumber(numericValue);
       }
     }
@@ -472 +478 @@
     for (Object value : values)
     {
-      if (converter != null && value instanceof Number) 
+      if (value instanceof Number)
       {
-        value = valueType.convertNumber(converter.convertToReferenceUnit(((Number)value).doubleValue()));
+        Number numericValue = (Number)value;
+        if (converter != null) 
+        {
+          numericValue = converter.convertToReferenceUnit(numericValue.doubleValue());
+        }
+        value = valueType.convertNumber(numericValue);
       }
       annotationType.validateAnnotationValue(value);

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

@@ -1233 +1233 @@
   
   /**
-    Validate an annotation value. We check the following:
+    Validate an annotation value assuming that the value
+    is in the default unit. 
+    @param value The object to be validated 
+    @throws InvalidDataException If the value object can not be used.
+    @see #validateAnnotationValue(Object, Unit)
+    @see #getDefaultUnit()
+  */
+  public void validateAnnotationValue(Object value)
+    throws InvalidDataException
+  {
+    validateAnnotationValue(value, null);
+  }
+  
+  /**
+    Validate an annotation value that can be in a different unit than
+    the default unit. We check the following:
     <ul>
-    <li>The object is of the correct type, ie. <code>Float</code> if {@link #getValueType()} 
-      returns {@link Type#FLOAT}, etc.
+    <li>The object is of the correct type, ie. <code>Float</code> 
+      if {@link #getValueType()} returns {@link Type#FLOAT}, etc.
+      NOTE! If a unit is specified it is only required that the
+      value is a {@link Number}. It will automatically be converted
+      to the correct class after unit conversion has taken place.
     <li>The value is within the min and max bouds if specified
     <li>A string value is not too long
@@ -1243 +1261 @@
     </ul>
     @param value The object to be validated 
+    @param unit The unit if the value, this parameter is ignored if
+      the value type doesn't support units (eg. strings) or if the
+      no default unit has been set for this annotation type
+    @return The validated value which may have been converted to the
+      default unit
     @throws InvalidDataException If the value object can not be used.
-  */
-  public void validateAnnotationValue(Object value)
+    @since 2.11
+  */
+  public Object validateAnnotationValue(Object value, Unit unit)
     throws InvalidDataException
   {
     if (value == null) throw new InvalidUseOfNullException("value");
     Type valueType = getValueType();
+    
+    if (supportUnits() && unit != null && value instanceof Number)
+    {
+      Unit defaultUnit = getDefaultUnit();
+      value = valueType.convertNumber(
+          defaultUnit.fromOther(((Number)value).doubleValue(), unit));
+    }
     valueType.validate(value);
+    
     if (valueType == Type.INT)
     {
@@ -1361 +1393 @@
       }
     }
+    return value;
   }
   

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

@@ -64 +64 @@
 import net.sf.basedb.core.StringTooLongException;
 import net.sf.basedb.core.Type;
+import net.sf.basedb.core.Unit;
 import net.sf.basedb.core.Version;
 import net.sf.basedb.core.plugin.About;
@@ -88 +89 @@
 import net.sf.basedb.util.parser.Mapper;
 import net.sf.basedb.util.parser.FlatFileParser.Data;
+import net.sf.basedb.util.units.UnitCache;
+import net.sf.basedb.util.units.UnitUtil;
 
 /**
@@ -345 +348 @@
       permissions.add(new Permissions(Item.FILE, null, EnumSet.of(Permission.READ)));
       permissions.add(new Permissions(Item.ANNOTATIONTYPE, null, EnumSet.of(Permission.READ)));
-      
+      permissions.add(new Permissions(Item.UNIT, EnumSet.of(Permission.READ), null));
+      permissions.add(new Permissions(Item.QUANTITY, EnumSet.of(Permission.READ), null));
       for (GuiContext ctx : getGuiContexts())
       {
@@ -591 +595 @@
   private List<String> columnHeaders;
   private DbControl dc;
+  private UnitCache unitCache;
   private FlatFileParser ffp;
   private NumberFormat numberFormat;
@@ -694 +699 @@
   {
     this.dc = sc.newDbControl();
+    this.unitCache = new UnitCache(dc);
     
     // Mapper to get name or external ID
@@ -786 +792 @@
 
         Object annotationValue = null;
+        Unit unit = null;
+        Unit defaultUnit = at.getDefaultUnit();
         try
         {
@@ -794 +802 @@
             if (enumValue != null) sValue = enumValue;
           }
-          annotationValue = at.getValueType().parseString(sValue, numberFormat, false);
+          if (at.supportUnits())
+          {
+            // Check if the value is followed by a unit
+            String[] valueAndUnit = UnitUtil.splitValueWithUnit(sValue);
+            if (valueAndUnit != null)
+            {
+              String unitSymbol = valueAndUnit[1];
+              if (unitSymbol != null)
+              {
+                // Yes.. there is a unit, look it up
+                unit = unitCache.findUnit(at.getQuantity(), unitSymbol);
+                if (unit == null)
+                {
+                  // The unit doesn't exists
+                  throw new NumberFormatException("Unknown unit for value: " + sValue);
+                }
+              }
+              else
+              {
+                // No unit specified, use the default unit
+                unit = at.getDefaultUnit();
+              }
+              sValue = valueAndUnit[0];
+            }
+          }
+          if (unit != null)
+          {
+            annotationValue = Type.DOUBLE.parseString(sValue, numberFormat, false);
+          }
+          else
+          {
+            annotationValue = at.getValueType().parseString(sValue, numberFormat, false);
+          }
           if (annotationValue != null)
           {
-            at.validateAnnotationValue(annotationValue);
+            at.validateAnnotationValue(annotationValue, unit);
           }
           for (NewAnnotations item : items)
           {
             // Add annotation value to the cache
-            item.addValue(at, annotationValue);
+            item.addValue(at, annotationValue, unit);
           }
         }
@@ -1177 +1217 @@
   }
   
+  private static class AnnotationValue
+  {
+    final Object value;
+    final Unit unit;
+    AnnotationValue(Object value, Unit unit)
+    {
+      this.value = value;
+      this.unit = unit;
+    }
+  }
+  
   /**
     Internal cache for storing annotation values from the file 
@@ -1185 +1236 @@
   {
     private final Annotatable item;
-    private final Map<AnnotationType, List<Object>> values;
+    private final Map<AnnotationType, List<AnnotationValue>> values;
     private int numAnnotations;
     private int numSet;
@@ -1198 +1249 @@
     {
       this.item = item;
-      this.values = new HashMap<AnnotationType, List<Object>>();
+      this.values = new HashMap<AnnotationType, List<AnnotationValue>>();
       this.numAnnotations = 0;
     }
@@ -1206 +1257 @@
       error before calling this method.
     */
-    void addValue(AnnotationType at, Object value)
-    {
-      List<Object> listOfValues = values.get(at);
+    void addValue(AnnotationType at, Object value, Unit unit)
+    {
+      List<AnnotationValue> listOfValues = values.get(at);
       if (listOfValues == null)
       {
-        listOfValues = new LinkedList<Object>();
+        listOfValues = new LinkedList<AnnotationValue>();
         values.put(at, listOfValues);
       }
       if (value != null) 
       {
-        listOfValues.add(value);
+        listOfValues.add(new AnnotationValue(value, unit));
         numAnnotations++;
       }
@@ -1244 +1295 @@
       int numAnnotations = 0;
       AnnotationSet as = item.getAnnotationSet();
-      for (Map.Entry<AnnotationType, List<Object>> entry : values.entrySet())
+      for (Map.Entry<AnnotationType, List<AnnotationValue>> entry : values.entrySet())
       {
         AnnotationType at = entry.getKey();
-        List<Object> newValues = entry.getValue();
+        List<AnnotationValue> newValues = entry.getValue();
         int size = newValues.size();
         int multiplicity = at.getMultiplicity();
         boolean hasAnnotation = as.hasAnnotation(at);
         boolean merge = addToUnlimited && hasAnnotation && multiplicity == 0;
-        boolean tooManyValues = multiplicity > 0 && newValues.size() > multiplicity;
+        boolean tooManyValues = multiplicity > 0 && size > multiplicity;
         if (size == 0)
         {
@@ -1268 +1319 @@
             {
               Annotation a = as.getAnnotation(at);
-              if (merge) newValues.addAll(0, a.getValues());
-              a.setValues(newValues);
+              List<Object> theValues = new ArrayList<Object>(newValues.size());
+              // Make sure all annotation values are converted to the same unit
+              final Unit unit = merge ? a.getUnit() : newValues.get(0).unit;
+              if (merge)
+              {
+                theValues.addAll(a.getValues(unit));
+              }
+              for (AnnotationValue value : newValues)
+              {
+                Object theValue = value.value;
+                if (unit != null && !unit.equals(value.unit)) 
+                {
+                  theValue = unit.fromOther(((Number)value.value).doubleValue(), value.unit);
+                }
+                theValues.add(theValue);
+              }
+              a.setValues(theValues, unit);
               numSet += size;
               if (hasAnnotation && !merge) numReplaced += size;

trunk/src/test/TestAnnotationFlatFileImporter.java

@@ -33 +33 @@
 import net.sf.basedb.core.PluginParameter;
 import net.sf.basedb.core.PluginResponse;
+import net.sf.basedb.core.Quantity;
 import net.sf.basedb.core.RequestInformation;
+import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.Type;
 import net.sf.basedb.core.plugin.GuiContext;
@@ -56 +58 @@
     // Create annotation types, samples and upload file
     
-    int timeId = TestAnnotationType.test_create("Time (hours)", Type.INT, 0, null, 25, Item.SAMPLE, 1, null, false);
+    int timeQuantityId = SystemItems.getId(Quantity.TIME);
+    int hoursId = TestUnit.test_load_by_symbol(timeQuantityId, "h");
+    
+    int timeId = TestAnnotationType.test_create("Time (hours)", Type.INT, hoursId, 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);
@@ -69 +74 @@
     int sampleDup2 = TestSample.test_create(0, "Sample dup", false);
     
-    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");
@@ -87 +91 @@
     TestAnnotation.test_list_annotations(Item.SAMPLE, sample2, 2);
     TestAnnotation.test_list_annotations(Item.SAMPLE, sample3, 2);
-    TestAnnotation.test_list_annotations(Item.SAMPLE, sample4, 1);
+    TestAnnotation.test_list_annotations(Item.SAMPLE, sample4, 2);
     TestAnnotation.test_list_annotations(Item.SAMPLE, sampleDup1, 4);
     TestAnnotation.test_list_annotations(Item.SAMPLE, sampleDup2, 4);

trunk/src/test/data/test.annotation.import.txt

@@ -12 +12 @@
 # Test: item not found
 NoSample  0 0 alfa  Good  Very good
-# Test: remove annotations; add value to existing
-Sample #4         A comment from file
+# Test: remove annotations; add value to existing; value with unit (120min=2h)
+Sample #4 120min        A comment from file