Changeset 4108

Timestamp:

Jan 30, 2008, 11:13:22 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

References #894: Support for array designs with other feature identification methods than coordinates

Do not verify the reporter if null is passed as external ID. Pick the reporter automatically from the array design instead.

File:

• trunk/src/core/net/sf/basedb/core/RawDataBatcher.java (modified) (2 diffs)

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

@@ -384 +384 @@
 
   /**
+    @deprecated Use {@link #insert(RawData, String, String)} instead
+  */
+  public void insert(RawData data, String externalReporterId)
+    throws BaseException
+  {
+    doInsert(data, externalReporterId, null, externalReporterId != null);
+  }
+
+  /**
     Insert a raw data spot and verify the external id of the 
-    reporter. The external id is only verified if the raw bioassay
-    is connected to an array design with features. The external id
+    reporter. The external id is only verified if it is not null and
+    the raw bioassay is connected to an array design with features. The external id
     is verified to match the external id of the reporter attached to
-    feature of the spot's position. If you use this method you don't have
+    feature of the spot's position. If the raw bioassay isn't connected to an
+    array design, the batcher will automatically try to load the reporter
+    with the given external ID. If you use this method you don't have
     the set the reporter with the {@link RawData#setReporter(ReporterData)}
     method.
+    <p>
+    The <code>externalFeatureId</code> is only needed if the 
+    {@link FeatureIdentificationMethod#FEATURE_ID} identification method is used.
+    The other methods will use properties on the <code>RawData</code>
+    object (postion or the coordinates) to find the feature. Feature
+    identification is of course needed when the raw bioassay is connected
+    to an array design but is also used when there is no array design to
+    validate that duplicate spots are not inserted.
     
     @param data The raw data to insert
     @param externalReporterId The external id of the reporter expected to
-      be found at the feature of this spot
-    @throws BaseException If the insertion failed. 
-    @deprecated
-  */
-  public void insert(RawData data, String externalReporterId)
-    throws BaseException
-  {
-    doInsert(data, externalReporterId, null, true);
-  }
-
+      be found at the feature of this spot, or null to use the reporter
+      attached to the feature
+    @param externalFeatureId The feature ID of the feature if the
+      {@link FeatureIdentificationMethod#FEATURE_ID} identification method is used
+    @throws BaseException If the insertion failed
+    @since 2.6
+  */
   public void insert(RawData data, String externalReporterId, String externalFeatureId)
   {
-    doInsert(data, externalReporterId, externalFeatureId, true);
+    doInsert(data, externalReporterId, externalFeatureId, externalReporterId != null);
   }
   
@@ -412 +428 @@
     Do the actual insert.
   */
-  void doInsert(RawData data, String externalReporterId, String externalFeatureId, boolean validateReporterId)
+  private void doInsert(RawData data, String externalReporterId, String externalFeatureId, boolean validateReporterId)
     throws BaseException
   {