source: trunk/doc/src/docbook/appendix/incompatible.xml @ 6807

Last change on this file since 6807 was 6807, checked in by Nicklas Nordborg, 7 years ago

References #1924, #1927 and #1325. Added information about incompatible changes and things to consider when updgrading to BASE 3.5.

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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">
6  $Id: incompatible.xml 6807 2015-03-26 12:10:52Z nicklas $
8  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg
10  This file is part of BASE - BioArray Software Environment.
11  Available at
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 3
16  of the License, or (at your option) any later version.
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
21  GNU General Public License for more details.
23  You should have received a copy of the GNU General Public License
24  along with BASE. If not, see <>.
27<appendix id="appendix.incompatible">
28  <?dbhtml filename="incompatible.html" ?>
29  <title>API changes that may affect backwards compatibility</title>
30  <para>
31    In this document we list all changes to code in the <emphasis>Public API</emphasis>
32    that may be backwards incompatible with existing client applications
33    and or plug-ins. See <xref linkend="base_api.public" /> for more
34    information about what we mean with the <emphasis>Public API</emphasis>
35    and backwards compatible.
36  </para>
38  <sect1 id="appendix.incompatible.3.5">
39    <title>BASE 3.5 release</title>
41    <bridgehead id="appendix.incompatible.itemlists">Biomaterial lists has been replaced with item lists</bridgehead>
42    <para>
43      The <classname docapi="net.sf.basedb.core">BioMaterialList</classname> 
44      class has been removed and replaced with <classname 
45      docapi="net.sf.basedb.core">ItemList</classname>. The API is similar
46      but not exactly the same. In most cases only minor changes are required
47      to make existing code work with the new API.
48    </para>
50    <para>
51      Queries that use the <code>BioMaterial.bioMaterialLists</code> association
52      for joining will no longer work. There is no replacement functionality for
53      joining item lists.
54    </para>
56    <para>
57      All classes in the <code>net.sf.basedb.util.biomaterial</code> package has
58      been deprecated. It is recommended that code that uses any of these classes
59      are updated to use classes in <code>net.sf.basedb.util.listable</code> instead.
60      The API is a bit different, but the new implementations typically performs a
61      lot better so it is worth the work.
62    </para>
64    <para>
65      There are several other minor changes in the API that previously worked with
66      the <code>BioMaterialList</code> class that has been removed and replaced
67      with something else.
68    </para>
70  </sect1>
72  <sect1 id="appendix.incompatible.3.4">
73    <title>BASE 3.4 release</title>
75    <bridgehead>Updated JDOM to 2.0</bridgehead>
76    <para>
77      The JDOM library has been updated to version 2.0 from 1.1. The
78      new version is incompatible with the old version. BASE 3.4 will
79      ship with both versions but JDOM 1.1 will be removed in BASE 3.5
80      and so will all API methods that expose JDOM 1.1 classes.
81      It is recommended that plug-ins and extensions that use JDOM also
82      update to JDOM 2.0.
83    </para>
85    <bridgehead>Updated to Apache HttpClient 4.3.4</bridgehead>
86    <para>
87      The Apache HTTP Client library has been updated to version 4.3.4.
88      The new version has deprecated some classes that are exposed through
89      the BASE API (mainly in <classname docapi="net.sf.basedb.util.ssl">SSLUtil</classname>).
90      As a result we had to deprecate parts of the BASE API, which will
91      be removed in BASE 3.5. It is recommended that plug-ins and
92      extensions that are affected are updated to use the replacement API
93      instead.
94    </para>
96  </sect1>
98  <sect1 id="appendix.incompatible.3.3">
99    <title>BASE 3.3 release</title>
101    <bridgehead>Content security policy</bridgehead>
102    <para>
103      The BASE web client now set a rather strict <emphasis>Content
104      Security Policy</emphasis> that prevent browsers from executing
105      code (including JavaScript) that is considered unsafe. Some extensions
106      may cease to work due to this. Go to
107      <menuchoice>
108        <guimenu>Administrate</guimenu>
109        <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
110        <guimenuitem>Overview</guimenuitem>
111      </menuchoice> 
112      (after upgrading) to see if there are any warnings about this.
113      Read more in <xref linkend="appendix.web.xml.csp-filter" />
114      for information about how to relax the policy.
115    </para>
117    <bridgehead>Re-factored JavaScript API</bridgehead>
118    <para>
119      The BASE web client has undergone a major refactoring with respect to
120      the JavaScript API that is used on the server. A lot of functions have
121      been replaced with new implementations. We have tried to map the old
122      functions to the new ones, but this has not always been possible. Extentions
123      that use the BASE JavaScript API must be tested with BASE 3.3 to find
124      out if they are still working or if modifications are needed.
125    </para>
127    <note>
128      <title>Avoid in-line event handlers and script</title>
129      <para>
130        The main reason for the refactoring is to get rid of all in-line
131        event handlers and script sections since this is a possible entry
132        point for cross-site scripting attacks (see <ulink 
133          url="">ticket 1712</ulink>).
134        Extension developers are encouraged to make the same changes in
135        their applications.
136      </para>
137    </note>
139    <bridgehead>Biomaterial items are now lazy-loading</bridgehead>
140    <para>
141      For performance reasons biomaterial items have been changed from
142      eager-loading to lazy-loading. This may affect clients and/or plug-ins
143      that expect the parent chain of biomaterials to always be fully initialized
144      without explicitely having told the BASE core to do so.
145    </para>
147    <bridgehead>Tables can have columns with different sort order</bridgehead>
148    <para>
149      A new feature has been implemented which allows columns in a table to
150      have different sort order. This is implemented by allowing '+' or '-'
151      as a prefix to properties returned by the <methodname>ItemContext.getSortProperty()</methodname>
152      method. Properties without a prefix still use the global sort order as returned
153      by <methodname>ItemContext.getSortDirection()</methodname>.
154    </para>
156    <para>
157      Code that is not aware of the prefixes may fail since '+' and '-' are not
158      allowed in property names.
159    </para>
161    <bridgehead>External authentication has been converted to an extension point</bridgehead>
162    <para>
163      External authentication plug-ins using the old system are supported through a
164      wrapper extension, but the recommendation is to update those plug-in to the
165      new system. See <xref linkend="extensions_developer.login-manager" /> for more information.
166    </para>
168    <bridgehead>Setting parameters for a job no longer set it to status=WAITING</bridgehead>
169    <para>
170      Added <methodname>Job.setScheduled()</methodname> to switch the state
171      from <constant>UNCONFIGURED</constant> to <constant>WAITING</constant>.
172      A job can't be executed before it has entered the <constant>WAITING</constant>
173      state. The change makes it possible to register a job and some parameters for
174      it and remain in the <constant>UNCONFIGURED</constant> state.
175    </para>
177  </sect1>
179  <sect1 id="appendix.incompatible.3.2">
180    <title>BASE 3.2 release</title>
182    <bridgehead>Derived bioassays can now have multiple parents</bridgehead>
183    <para>
184      Before BASE 3.2 a derived bioassay was restricted to a single parent
185      item. This affects the API and the <methodname>DerivedBioAssay.getParent()</methodname>
186      and <methodname>DerivedBioAssay.getPhysicalBioAssays()</methodname> now always
187      return null. Existing code should be updated to use <methodname>getPhysicalBioAssays()</methodname>
188      and <methodname>getParents()</methodname> (which return <classname>ItemQuery</classname> instances)
189      instead. Code that is using queries to filter or sort on parent items must also be
190      updated since the association names have changed.
191    </para>
193    <bridgehead>BASEfile exporter automatically closes the output stream</bridgehead>
194    <para>
195      The implementation of the BASEfile exporter has been changed to
196      automatically close the provided output stream when the export
197      is complete. Clients that need the old behavior should call
198      <code>BaseFileExporter.setAutoCloseWriters(false)</code> before
199      using it.
200    </para>
202    <bridgehead>Change history logging is now an extension point</bridgehead>
203    <para>
204      The change history logging has been converted to an extension point.
205      The <constant>changelog.factory</constant> setting in <filename>base.config</filename>
206      is no longer used. Existing logging implementations should be updated
207      to use the extension system. See <xref linkend="extensions_developer.logging" />.
208      A temporary solution is to use one of the debugging action factories to
209      define the extension point:
210    </para>
212    <programlisting language="xml">
215   id="id-of-custom-log-manager"
216   extends="net.sf.basedb.core.log-manager"
217   >
218   <about>
219      <name>My custom log manager</name>
220      <description>
221         Temporary solution to allow the old log manager to work with the extension system.
222      </description>
223   </about>
224   <index>1</index>
225   <action-factory>
226      <factory-class>net.sf.basedb.util.extensions.debug.BeanActionFactory</factory-class>
227      <parameters>
228         <beanClass>my.custom.LogmangerClass</beanClass>
229      </parameters>
230   </action-factory>
235  </sect1>
237  <sect1 id="appendix.incompatible.3.1">
238    <title>BASE 3.1 release</title>
240    <bridgehead>Web service framework updated to Axis2 1.6</bridgehead>
241    <para>
242      We have updated the web services framework to Axis2 1.6. Clients
243      that use earlier Axis2 versions may not work when connecting to a
244      BASE 3.1 server. Unfortunately, clients that use the Axis2 1.6
245      framework may have problems connecting to BASE 3.0 servers so it
246      may be difficult to implement support for both BASE 3.0 and BASE 3.1
247      in a single client application.
248    </para>
250    <bridgehead>New GUI look and feel</bridgehead>
251    <para>
252      Taglibs, stylesheets and javscript functions have been changed
253      to create a new look and feel. Plug-ins and extensions that uses
254      GUI elements from the core BASE installation may need to be updated
255      for the best user experience. The changes are too numerous so we can't
256      list them here. Please use the developers mailing list if specific
257      information is needed or see <ulink url="">ticket
258      1655</ulink> for some screenshots and other information.
259    </para>
261    <bridgehead>Per-experiment copy of reporter annotations</bridgehead>
262    <para>
263      A new feature has been implemented that allows a user to make a
264      local copy of reporter annotations for reporters that are used
265      in an experiment. The existing API will by default use the local
266      copy if one is available. It is possible to use the master reporter
267      annotations by invoking certain API methods (for example:
268      <code>DynamicQuery.setUseClonedReporters(false)</code>). Since the copy
269      may include only a subset of the available reporter annotations this
270      may cause problems for code that is expecting all annotations to be
271      available. See <classname docapi="net.sf.basedb.core">ReporterCloneTemplate</classname>
272      and <ulink url="">ticket 1616</ulink>
273      for more information.
274    </para>
276    <bridgehead>Annotations can be inherited/pushed from child to parent item</bridgehead>
277    <para>
278      A new feature has been implemented that allows an item to "push" annotations
279      up to it's parent in addition to the normal "inherit to child" method.
280      This has been implemented as a change in the <methodname>getAnnotatableParents()</methodname>
281      method defined by the <interfacename docapi="net.sf.basedb.core">Annotatable</interfacename>
282      interface. This may cause unexpected issues with code that is not prepared to handle
283      this situation. Particulary, infinite loops must be avoided when traversing the "parent"
284      tree of an item (but this should already be in place since it can already happen due to
285      mistakes when creating items). See <ulink url="">ticket 1605</ulink>
286      for more information.
287    </para>
289  </sect1>
292  <sect1 id="appendix.incompatible.3.0">
293    <title>BASE 3.0 release</title>
295    <para>
296      There are a lot incompatible changes between BASE 3 and any of the BASE 2.x
297      versions. We do not list list those changes here since we do not expect existing
298      plug-ins, extensions or other client application to work with BASE 3 without
299      modification. See <xref linkend="migrate_2_3" /> for more information.
300    </para>
301  </sect1>
303  <sect1 id="appendix.incompatible.2.x">
304    <title>All BASE 2.x releases</title>
306    <para>
307      The list of changes made in the various BASE 2.x releases can be found
308      in the <ulink url=""
309      >BASE 2.17 documentation</ulink>.
310    </para>
312  </sect1>
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