Changeset 5704 for trunk/doc/src/docbook/developerdoc/migrate_2_3.xml

Timestamp:

Aug 22, 2011, 9:21:20 AM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1603: Developers migration guide

Updated the migration guide to make it up to date with the latest development.

File:

• trunk/doc/src/docbook/developerdoc/migrate_2_3.xml (modified) (3 diffs)

trunk/doc/src/docbook/developerdoc/migrate_2_3.xml

@@ -47 +47 @@
       simple replacment API that can be used instead. Since the deprecated API 
       has been removed in BASE 3 so has the instructions. You'll need to check 
-      with the BASE 2.17 documentation which is located at 
-      <ulink url="http://base.thep.lu.se/chrome/site/2.17">http://base.thep.lu.se/chrome/site/2.17</ulink>.
-    </para>
+      with the BASE 2.17 documentation which is located at:
+    </para>
+    
+    <itemizedlist>
+      <listitem>
+        <para><ulink url="http://base.thep.lu.se/chrome/site/2.17/html/index.html">http://base.thep.lu.se/chrome/site/2.17/html/index.html</ulink>:
+        User manual.
+        </para>
+      </listitem>
+      <listitem>
+        <para><ulink url="http://base.thep.lu.se/chrome/site/2.17/api/index.html">http://base.thep.lu.se/chrome/site/2.17/api/index.html</ulink>:
+        API documentation.
+        </para>
+      </listitem>
+    
+    </itemizedlist>
+    
     <para>
       Do not proceed until you are sure that your code is not using any
@@ -115 +129 @@
         <para>
           <classname>Label</classname> has been replaced with <classname docapi="net.sf.basedb.core">Tag</classname>.
-          <classname>LabeledExtract</classname> has been merged into <classname 
+          <classname>LabeledExtract</classname> has been merged with <classname 
           docapi="net.sf.basedb.core">Extract</classname>. <classname>Hybridization</classname> has been 
           replaced with <classname docapi="net.sf.basedb.core">PhysicalBioAssay</classname>. 
           <classname>Scan</classname> and <classname>Image</classname> has been replaced with
-          <classname docapi="net.sf.basedb.core">BioAssayEvent</classname>,
-          <classname docapi="net.sf.basedb.core">DerivedBioAssaySet</classname> and
-          <classname docapi="net.sf.basedb.core">DerivedBioAssay</classname>.
+          <classname docapi="net.sf.basedb.core">DerivedBioAssay</classname>. The API for linking
+          parent/child biomaterial has been changed. The <property>pooled</property> property
+          of biomaterials has been removed.
           The changes are driven by the support for sequencing experiments. The new items are
           using the new subtype feature. For example, a hybridization in BASE 2 has been
@@ -185 +199 @@
         </para>
       </listitem>
+      
+      <listitem>
+        <para>
+          All plug-ins and extensions are required to be installed in the directory specified by 
+          <code>plugins.dir</code> setting in the <filename>base.config</filename> file. Sub-directories
+          are <emphasis>not</emphasis> searched any longer.
+          This is usually not something that you need to worry about as a developer except that
+          you should make sure the installation instruction are up to date. See <ulink 
+          url="http://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation 
+          procedure for plug-ins, extensions and more...)</ulink> for more information.
+        </para>
+      </listitem>
+      
+      <listitem>
+        <para>
+          Plug-ins/extensions that depend on 3-rd party JAR files are now recommended to include
+          those JAR file inside the <filename>META-INF/lib</filename> directory in the plug-in
+          JAR file. The <property>Class-Path</property> attribute in <filename>META-INF/MANIFEST.MF</filename>
+          must still be set. See <xref linkend="plugin_developer.organize"/> and <ulink 
+          url="http://base.thep.lu.se/ticket/1594">ticket #1594 (JarClassLoader support for JARs within JARs)</ulink>.
+        </para>
+      </listitem>
+      
     </itemizedlist>
     
-    <para>
-      Another change is that plug-ins and extensions are 
-      required to be installed in the directory specified by <code>plugins.dir</code>
-      setting in the <filename>base.config</filename> file. This is usually not something that
-      you need to worry about as a developer. See <ulink 
-      url="http://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation 
-      procedure for plug-ins, extensions and more...)</ulink> for more information.
-    </para>
-    
   </sect1>