Changeset 6964

Timestamp:

Oct 2, 2015, 8:43:20 AM (6 years ago)

Author:

Nicklas Nordborg

Message:

References #1941: Store experimental factor values as part experiments

Adding notes about incompatible API changes.

File:

• trunk/doc/src/docbook/appendix/incompatible.xml (modified) (1 diff)

trunk/doc/src/docbook/appendix/incompatible.xml

@@ -35 +35 @@
     and backwards compatible.
   </para>
+  
+  <sect1 id="appendix.incompatible.3.6">
+    <title>BASE 3.6 release</title>
+    
+    <bridgehead id="appendix.incompatible.cloned-annotation">Cloned annotations</bridgehead>
+    <para>
+      A new feature that allows an inherited annotation to be cloned has been implemented.
+      Several methods in <classname docapi="net.sf.basedb.core">AnnotationSet</classname>,
+      <classname docapi="net.sf.basedb.core.snapshot">AnnotationSnapshot</classname> and some 
+      other classes has been deprecated and replaced with new methods. Existing code that
+      is not aware of cloned annotations should continue to work, but may experience some
+      inconsistent behaviour in case the cloned values are out-of-sync with the original
+      values.
+    </para>
+
+    <bridgehead id="appendix.incompatible.experimental-factors">Experimental factors have moved</bridgehead>
+    <para>
+      To allow the owner of an experiment to manage experimental factor values as part
+      of the experiment, the <classname docapi="net.sf.basedb.core">RootRawBioassay</classname>
+      item was introduced. The new item is a one-to-one representation of a <classname 
+      docapi="net.sf.basedb.core">RawBioAssay</classname> inside that experiment.
+      Experimental factor values that are found on existing raw bioassays are copied to the
+      root rawbioassays when updating BASE. Changes made after the update will only
+      affect the root raw bioassays. Existing code that is not aware of root raw bioassays
+      may not find the experimental factor values.
+    </para>
+    
+  </sect1>
   
   <sect1 id="appendix.incompatible.3.5">