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

Last change on this file since 3495 was 3495, checked in by Nicklas Nordborg, 16 years ago

References #625. Major features are now in place. It's a bit tricky to update the isInContext
method on all plug-ins. I need more testing time to verify that all works before I close the
ticket.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 5.2 KB
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE appendix PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: incompatible.xml 3495 2007-06-14 12:36:26Z nicklas $
7 
8  Copyright (C) Authors contributing to this file.
9 
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
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13  BASE is free software; you can redistribute it and/or
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15  as published by the Free Software Foundation; either version 2
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18  BASE is distributed in the hope that it will be useful,
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20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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27-->
28
29<appendix id="appendix.incompatible">
30  <title>API changes that may affect backwards compatibility</title>
31  <para>
32    In this document we list all changes to code in the <emphasis>Public API</emphasis>
33    that may be backwards incompatible with existing client applications
34    and or plug-ins. See <xref linkend="api_overview.public_api" /> for more
35    information about what we mean with the <emphasis>Public API</emphasis>
36    and backwards compatible.
37  </para>
38 
39  <note>
40    <para>
41    There is no history for releases prior to BASE 2.2 because
42    we did not actively keep track of them. We believe that if such
43    changes exists, they are minor and does not affect many plug-ins
44    since in those days very few 3rd-party plug-ins existed.
45    </para>
46  </note>
47 
48  <sect1 id="appendix.incompatible.2.4">
49    <title>BASE 2.4 release</title>
50   
51    <bridgehead>Plugin API</bridgehead>
52    <para>
53      The <methodname>InteractivePlugin.isInContext()</methodname>
54      method may now throw exceptions to indicate error-level
55      messages. Messages that are returned by the method are
56      considered as a warning message and are by default no longer
57      shown to the users.
58      See <xref linkend="plugin_developer.api.interfaces.interactive" />
59      and <xref linkend="webclient.configuration.preferences.plugins" />.
60    </para>
61   
62    <bridgehead>JEP parser</bridgehead>
63    <para>
64      The <methodname>Jep.nodeToExpression()</methodname>
65      and <methodname>Jep.nodeToString()</methodname> methods
66      return <constant>NULL</constant> if they find an unqouted
67      <constant>NULL</constant> string in the expression. This
68      allows JEP to convert expressions like <code>ch(1) == NULL</code>
69      into a Query API expression testing for null. To get the
70      old behaviour use <code>ch(1) == 'NULL'</code>.
71    </para>
72  </sect1>
73 
74  <sect1 id="appendix.incompatible.2.3">
75    <title>BASE 2.3 release</title>
76   
77    <bridgehead>FlatFileParser</bridgehead>
78    <para>
79      The <methodname>hasMoreData()</methodname> method has changed the
80      order of checks made to determine the line type. The checks are
81      now made in the following order:
82     
83      <orderedlist>
84      <listitem>
85        <para>
86        Check if the line should be ignored.
87        </para>
88      </listitem>
89      <listitem>
90        <para>
91        Check if the line is a data footer.
92        </para>
93      </listitem>
94      <listitem>
95        <para>
96        Check if the line is the start of a new section.
97        </para>
98      </listitem>
99      <listitem>
100        <para>
101        Check if the line is a data line.
102        </para>
103      </listitem>
104      </orderedlist>
105      The data line check has been moved to the last since it was difficult
106      to create settings that made sure section and data footer lines where
107      matched correctly.
108    </para>
109
110    <bridgehead>BASE 1 Plug-in executer</bridgehead>
111   
112    <para>
113      Changed to store information about plug-in parameters as XML in the
114      database instead of in the orignal BASE 1 plug-in definition file.
115      Existing BASE 1 plug-ins must be re-configured before they can be
116      used. To do this:
117    </para>
118   
119    <orderedlist>
120    <listitem>
121      <para>
122      Go to
123      <menuchoice>
124        <guimenu>Administrate</guimenu>
125        <guisubmenu>Plugins</guisubmenu>
126        <guimenuitem>Configurations</guimenuitem>
127      </menuchoice>
128      </para>
129    </listitem>
130    <listitem>
131      <para>
132      Step through the configuration wizard for all BASE 1 plug-in
133      configurations. You do not need to change any parameters.
134      Just click on the <guibutton>Next</guibutton> button
135      until the configuration is complete.
136      </para>
137    </listitem>
138    </orderedlist>
139  </sect1>
140
141  <sect1 id="appendix.incompatible.2.2">
142    <title>BASE 2.2 release</title>
143   
144    <bridgehead>BASE 1 Plug-in executer</bridgehead>
145   
146    <para>
147      No longer provides a default mapping between BASE 1 and BASE 2
148      raw data columns. To solve this add a <guilabel>Formula</guilabel>
149      item with the same name as the BASE 1 column name and an expression
150      that picks the BASE 2 raw data property. For example:
151    </para>
152   
153<literallayout>
154<guilabel>Name</guilabel>          BCh1Mean
155<guilabel>Type</guilabel>          Column expression
156<guilabel>Raw data type</guilabel> GenePix
157<guilabel>Channels</guilabel>      2
158<guilabel>Expressions</guilabel>   1: raw('ch1BgMean')
159</literallayout>
160
161  </sect1>
162
163</appendix>
164
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