source: trunk/doc/src/docbook/appendix/incompatible.xml @ 3495

<?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 3495 2007-06-14 12:36:26Z nicklas $
  
  Copyright (C) Authors contributing to this file.
  
  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 2
  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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330,
  Boston, MA  02111-1307, USA.
-->

<appendix id="appendix.incompatible">
  <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="api_overview.public_api" /> for more
    information about what we mean with the <emphasis>Public API</emphasis>
    and backwards compatible.
  </para>
  
  <note>
    <para>
    There is no history for releases prior to BASE 2.2 because
    we did not actively keep track of them. We believe that if such
    changes exists, they are minor and does not affect many plug-ins
    since in those days very few 3rd-party plug-ins existed.
    </para>
  </note>
  
  <sect1 id="appendix.incompatible.2.4">
    <title>BASE 2.4 release</title>
    
    <bridgehead>Plugin API</bridgehead>
    <para>
      The <methodname>InteractivePlugin.isInContext()</methodname>
      method may now throw exceptions to indicate error-level
      messages. Messages that are returned by the method are
      considered as a warning message and are by default no longer
      shown to the users. 
      See <xref linkend="plugin_developer.api.interfaces.interactive" />
      and <xref linkend="webclient.configuration.preferences.plugins" />.
    </para>
    
    <bridgehead>JEP parser</bridgehead>
    <para>
      The <methodname>Jep.nodeToExpression()</methodname>
      and <methodname>Jep.nodeToString()</methodname> methods
      return <constant>NULL</constant> if they find an unqouted
      <constant>NULL</constant> string in the expression. This
      allows JEP to convert expressions like <code>ch(1) == NULL</code>
      into a Query API expression testing for null. To get the
      old behaviour use <code>ch(1) == 'NULL'</code>.
    </para>
  </sect1>
  
  <sect1 id="appendix.incompatible.2.3">
    <title>BASE 2.3 release</title>
    
    <bridgehead>FlatFileParser</bridgehead>
    <para>
      The <methodname>hasMoreData()</methodname> method has changed the 
      order of checks made to determine the line type. The checks are
      now made in the following order:
      
      <orderedlist>
      <listitem>
        <para>
        Check if the line should be ignored.
        </para>
      </listitem>
      <listitem>
        <para>
        Check if the line is a data footer.
        </para>
      </listitem>
      <listitem>
        <para>
        Check if the line is the start of a new section.
        </para>
      </listitem>
      <listitem>
        <para>
        Check if the line is a data line.
        </para>
      </listitem>
      </orderedlist>
      The data line check has been moved to the last since it was difficult
      to create settings that made sure section and data footer lines where
      matched correctly.
    </para>

    <bridgehead>BASE 1 Plug-in executer</bridgehead>
    
    <para>
      Changed to store information about plug-in parameters as XML in the
      database instead of in the orignal BASE 1 plug-in definition file.
      Existing BASE 1 plug-ins must be re-configured before they can be 
      used. To do this:
    </para>
    
    <orderedlist>
    <listitem>
      <para>
      Go to 
      <menuchoice>
        <guimenu>Administrate</guimenu>
        <guisubmenu>Plugins</guisubmenu>
        <guimenuitem>Configurations</guimenuitem>
      </menuchoice>
      </para>
    </listitem>
    <listitem>
      <para>
      Step through the configuration wizard for all BASE 1 plug-in
      configurations. You do not need to change any parameters. 
      Just click on the <guibutton>Next</guibutton> button
      until the configuration is complete.
      </para>
    </listitem>
    </orderedlist>
  </sect1>

  <sect1 id="appendix.incompatible.2.2">
    <title>BASE 2.2 release</title>
    
    <bridgehead>BASE 1 Plug-in executer</bridgehead>
    
    <para>
      No longer provides a default mapping between BASE 1 and BASE 2
      raw data columns. To solve this add a <guilabel>Formula</guilabel>
      item with the same name as the BASE 1 column name and an expression
      that picks the BASE 2 raw data property. For example:
    </para>
    
<literallayout>
<guilabel>Name</guilabel>          BCh1Mean
<guilabel>Type</guilabel>          Column expression
<guilabel>Raw data type</guilabel> GenePix
<guilabel>Channels</guilabel>      2
<guilabel>Expressions</guilabel>   1: raw('ch1BgMean')
</literallayout>

  </sect1>

</appendix>