source: trunk/doc/src/docbook/appendix/incompatible.xml @ 6336

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE appendix PUBLIC 
    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" 
    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
<!--
  $Id: incompatible.xml 6336 2013-10-28 11:57:45Z nicklas $
  
  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg
  
  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/
  
  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
  of the License, or (at your option) any later version.
  
  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
  
  You should have received a copy of the GNU General Public License
  along with BASE. If not, see <http://www.gnu.org/licenses/>.
-->

<appendix id="appendix.incompatible">
  <?dbhtml filename="incompatible.html" ?>
  <title>API changes that may affect backwards compatibility</title>
  <para>
    In this document we list all changes to code in the <emphasis>Public API</emphasis>
    that may be backwards incompatible with existing client applications
    and or plug-ins. See <xref linkend="base_api.public" /> for more
    information about what we mean with the <emphasis>Public API</emphasis>
    and backwards compatible.
  </para>
  
  <sect1 id="appendix.incompatible.3.3">
    <title>BASE 3.3 release</title>

    <bridgehead>Biomaterial items are now lazy-loading</bridgehead>
    <para>
      For performance reasons biomaterial items have been changed from
      eager-loading to lazy-loading. This may affect clients and/or plug-ins
      that expect the parent chain of biomaterials to always be fully initialized
      without explicitely having told the BASE core to do so.
    </para>
    
    <bridgehead>Tables can have columns with different sort order</bridgehead>
    <para>
      A new feature has been implemented which allows columns in a table to
      have different sort order. This is implemented by allowing '+' or '-'
      as a prefix to properties returned by the <methodname>ItemContext.getSortProperty()</methodname>
      method. Properties without a prefix still use the global sort order as returned
      by <methodname>ItemContext.getSortDirection()</methodname>.
    </para>
    
    <para>
      Code that is not aware of the prefixes may fail since '+' and '-' are not
      allowed in property names.
    </para>
  </sect1>
  
  <sect1 id="appendix.incompatible.3.2">
    <title>BASE 3.2 release</title>

    <bridgehead>Derived bioassays can now have multiple parents</bridgehead>
    <para>
      Before BASE 3.2 a derived bioassay was restricted to a single parent 
      item. This affects the API and the <methodname>DerivedBioAssay.getParent()</methodname>
      and <methodname>DerivedBioAssay.getPhysicalBioAssays()</methodname> now always
      return null. Existing code should be updated to use <methodname>getPhysicalBioAssays()</methodname>
      and <methodname>getParents()</methodname> (which return <classname>ItemQuery</classname> instances)
      instead. Code that is using queries to filter or sort on parent items must also be
      updated since the association names have changed.
    </para>

    <bridgehead>BASEfile exporter automatically closes the output stream</bridgehead>
    <para>
      The implementation of the BASEfile exporter has been changed to
      automatically close the provided output stream when the export
      is complete. Clients that need the old behavior should call
      <code>BaseFileExporter.setAutoCloseWriters(false)</code> before
      using it.
    </para>

    <bridgehead>Change history logging is now an extension point</bridgehead>
    <para>
      The change history logging has been converted to an extension point.
      The <constant>changelog.factory</constant> setting in <filename>base.config</filename>
      is no longer used. Existing logging implementations should be updated
      to use the extension system. See <xref linkend="extensions_developer.logging" />.
      A temporary solution is to use one of the debugging action factories to 
      define the extension point:
    </para>
    
    <programlisting language="xml">
<![CDATA[
<extension 
   id="id-of-custom-log-manager"
   extends="net.sf.basedb.core.log-manager"
   >
   <about>
      <name>My custom log manager</name>
      <description>
         Temporary solution to allow the old log manager to work with the extension system.
      </description>
   </about>
   <index>1</index>
   <action-factory>
      <factory-class>net.sf.basedb.util.extensions.debug.BeanActionFactory</factory-class>
      <parameters>
         <beanClass>my.custom.LogmangerClass</beanClass>
      </parameters>
   </action-factory>
</extension>
]]>
</programlisting>

  </sect1>
  
  <sect1 id="appendix.incompatible.3.1">
    <title>BASE 3.1 release</title>

    <bridgehead>Web service framework updated to Axis2 1.6</bridgehead>
    <para>
      We have updated the web services framework to Axis2 1.6. Clients
      that use earlier Axis2 versions may not work when connecting to a
      BASE 3.1 server. Unfortunately, clients that use the Axis2 1.6
      framework may have problems connecting to BASE 3.0 servers so it
      may be difficult to implement support for both BASE 3.0 and BASE 3.1
      in a single client application.
    </para>

    <bridgehead>New GUI look and feel</bridgehead>
    <para>
      Taglibs, stylesheets and javscript functions have been changed
      to create a new look and feel. Plug-ins and extensions that uses
      GUI elements from the core BASE installation may need to be updated
      for the best user experience. The changes are too numerous so we can't
      list them here. Please use the developers mailing list if specific
      information is needed or see <ulink url="http://base.thep.lu.se/ticket/1655">ticket
      1655</ulink> for some screenshots and other information.
    </para>
    
    <bridgehead>Per-experiment copy of reporter annotations</bridgehead>
    <para>
      A new feature has been implemented that allows a user to make a
      local copy of reporter annotations for reporters that are used
      in an experiment. The existing API will by default use the local
      copy if one is available. It is possible to use the master reporter
      annotations by invoking certain API methods (for example: 
      <code>DynamicQuery.setUseClonedReporters(false)</code>). Since the copy
      may include only a subset of the available reporter annotations this
      may cause problems for code that is expecting all annotations to be
      available. See <classname docapi="net.sf.basedb.core">ReporterCloneTemplate</classname>
      and <ulink url="http://base.thep.lu.se/ticket/1616">ticket 1616</ulink>
      for more information.
    </para>

    <bridgehead>Annotations can be inherited/pushed from child to parent item</bridgehead>
    <para>
      A new feature has been implemented that allows an item to "push" annotations
      up to it's parent in addition to the normal "inherit to child" method.
      This has been implemented as a change in the <methodname>getAnnotatableParents()</methodname>
      method defined by the <interfacename docapi="net.sf.basedb.core">Annotatable</interfacename>
      interface. This may cause unexpected issues with code that is not prepared to handle
      this situation. Particulary, infinite loops must be avoided when traversing the "parent"
      tree of an item (but this should already be in place since it can already happen due to
      mistakes when creating items). See <ulink url="http://base.thep.lu.se/ticket/1605">ticket 1605</ulink>
      for more information.
    </para>

  </sect1>
  
  
  <sect1 id="appendix.incompatible.3.0">
    <title>BASE 3.0 release</title>

    <para>
      There are a lot incompatible changes between BASE 3 and any of the BASE 2.x
      versions. We do not list list those changes here since we do not expect existing
      plug-ins, extensions or other client application to work with BASE 3 without
      modification. See <xref linkend="migrate_2_3" /> for more information.
    </para>
  </sect1>
  
  <sect1 id="appendix.incompatible.2.x">
    <title>All BASE 2.x releases</title>

    <para>
      The list of changes made in the various BASE 2.x releases can be found
      in the <ulink url="http://base.thep.lu.se/chrome/site/2.17/html/appendix/appendix.incompatible.html"
      >BASE 2.17 documentation</ulink>.
    </para>
    
  </sect1>
  

</appendix>