source: trunk/doc/src/docbook/appendix/incompatible.xml @ 7161

Last change on this file since 7161 was 7161, checked in by Nicklas Nordborg, 6 years ago

References #2011: Check that session id and client id match every time a new page is requested

Added notes in the documentation that this change may affect backwards compatibility.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 16.1 KB
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 7161 2016-05-27 09:26:39Z 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.3.9">
39    <title>BASE 3.9 release</title>
41    <bridgehead id="appendix.incompatible.session-control">Application.getSessionControl()</bridgehead>
42    <para>
43      The <classname docapi="net.sf.basedb.core">Application.getSessionControl()</classname> 
44      method for getting access to an existing session has been deprecated. A new
45      version has been implemented that require that an <emphasis>external client id</emphasis>
46      is specified. This change was needed to avoid sessions leaking between client
47      applications and prevent users to use an application they don't have permission to use.
48    </para>
50    <para>
51      The deprecated method use the client id from the BASE web client. Extensions and
52      other clients that use a different client id are affected and may stop to work
53      until they have been updated to use the new API. For more information see
54      <ulink url="">ticket 2011</ulink>.
55    </para>
57  </sect1>
60  <sect1 id="appendix.incompatible.3.8">
61    <title>BASE 3.8 release</title>
63    <bridgehead id="appendix.incompatible.service-session-control">ServiceSessionControl API</bridgehead>
64    <para>
65      The <classname docapi="net.sf.basedb.core">ServiceSessionControl</classname> API for
66      configuration and building Hibernate <classname>SessionFactory</classname>
67      instances has been changed due the Hibernate 5 upgrade. This change affects
68      extensions that use the API for storing their own data inside the BASE database.
69      Extensions that use this API must be updated or they will not work with BASE 3.8.
70    </para>
72  </sect1>
75  <sect1 id="appendix.incompatible.3.6">
76    <title>BASE 3.6 release</title>
78    <bridgehead id="appendix.incompatible.cloned-annotation">Cloned annotations</bridgehead>
79    <para>
80      A new feature that allows an inherited annotation to be cloned has been implemented.
81      Several methods in <classname docapi="net.sf.basedb.core">AnnotationSet</classname>,
82      <classname docapi="net.sf.basedb.core.snapshot">AnnotationSnapshot</classname> and some
83      other classes has been deprecated and replaced with new methods. Existing code that
84      is not aware of cloned annotations should continue to work, but may experience some
85      inconsistent behaviour in case the cloned values are out-of-sync with the original
86      values.
87    </para>
89    <bridgehead id="appendix.incompatible.experimental-factors">Experimental factors have moved</bridgehead>
90    <para>
91      To allow the owner of an experiment to manage experimental factor values as part
92      of the experiment, the <classname docapi="net.sf.basedb.core">RootRawBioassay</classname>
93      item was introduced. The new item is a one-to-one representation of a <classname 
94      docapi="net.sf.basedb.core">RawBioAssay</classname> inside that experiment.
95      Experimental factor values that are found on existing raw bioassays are copied to the
96      root rawbioassays when updating BASE. Changes made after the update will only
97      affect the root raw bioassays. Existing code that is not aware of root raw bioassays
98      may not find the experimental factor values.
99    </para>
101  </sect1>
103  <sect1 id="appendix.incompatible.3.5">
104    <title>BASE 3.5 release</title>
106    <bridgehead id="appendix.incompatible.itemlists">Biomaterial lists has been replaced with item lists</bridgehead>
107    <para>
108      The <classname docapi="net.sf.basedb.core">BioMaterialList</classname> 
109      class has been removed and replaced with <classname 
110      docapi="net.sf.basedb.core">ItemList</classname>. The API is similar
111      but not exactly the same. In most cases only minor changes are required
112      to make existing code work with the new API.
113    </para>
115    <para>
116      Queries that use the <code>BioMaterial.bioMaterialLists</code> association
117      for joining will no longer work. There is no replacement functionality for
118      joining item lists.
119    </para>
121    <para>
122      All classes in the <code>net.sf.basedb.util.biomaterial</code> package has
123      been deprecated. It is recommended that code that uses any of these classes
124      are updated to use classes in <code>net.sf.basedb.util.listable</code> instead.
125      The API is a bit different, but the new implementations typically performs a
126      lot better so it is worth the work.
127    </para>
129    <para>
130      There are several other minor changes in the API that previously worked with
131      the <code>BioMaterialList</code> class that has been removed and replaced
132      with something else.
133    </para>
135  </sect1>
137  <sect1 id="appendix.incompatible.3.4">
138    <title>BASE 3.4 release</title>
140    <bridgehead>Updated JDOM to 2.0</bridgehead>
141    <para>
142      The JDOM library has been updated to version 2.0 from 1.1. The
143      new version is incompatible with the old version. BASE 3.4 will
144      ship with both versions but JDOM 1.1 will be removed in BASE 3.5
145      and so will all API methods that expose JDOM 1.1 classes.
146      It is recommended that plug-ins and extensions that use JDOM also
147      update to JDOM 2.0.
148    </para>
150    <bridgehead>Updated to Apache HttpClient 4.3.4</bridgehead>
151    <para>
152      The Apache HTTP Client library has been updated to version 4.3.4.
153      The new version has deprecated some classes that are exposed through
154      the BASE API (mainly in <classname docapi="net.sf.basedb.util.ssl">SSLUtil</classname>).
155      As a result we had to deprecate parts of the BASE API, which will
156      be removed in BASE 3.5. It is recommended that plug-ins and
157      extensions that are affected are updated to use the replacement API
158      instead.
159    </para>
161  </sect1>
163  <sect1 id="appendix.incompatible.3.3">
164    <title>BASE 3.3 release</title>
166    <bridgehead>Content security policy</bridgehead>
167    <para>
168      The BASE web client now set a rather strict <emphasis>Content
169      Security Policy</emphasis> that prevent browsers from executing
170      code (including JavaScript) that is considered unsafe. Some extensions
171      may cease to work due to this. Go to
172      <menuchoice>
173        <guimenu>Administrate</guimenu>
174        <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
175        <guimenuitem>Overview</guimenuitem>
176      </menuchoice> 
177      (after upgrading) to see if there are any warnings about this.
178      Read more in <xref linkend="appendix.web.xml.csp-filter" />
179      for information about how to relax the policy.
180    </para>
182    <bridgehead>Re-factored JavaScript API</bridgehead>
183    <para>
184      The BASE web client has undergone a major refactoring with respect to
185      the JavaScript API that is used on the server. A lot of functions have
186      been replaced with new implementations. We have tried to map the old
187      functions to the new ones, but this has not always been possible. Extentions
188      that use the BASE JavaScript API must be tested with BASE 3.3 to find
189      out if they are still working or if modifications are needed.
190    </para>
192    <note>
193      <title>Avoid in-line event handlers and script</title>
194      <para>
195        The main reason for the refactoring is to get rid of all in-line
196        event handlers and script sections since this is a possible entry
197        point for cross-site scripting attacks (see <ulink 
198          url="">ticket 1712</ulink>).
199        Extension developers are encouraged to make the same changes in
200        their applications.
201      </para>
202    </note>
204    <bridgehead>Biomaterial items are now lazy-loading</bridgehead>
205    <para>
206      For performance reasons biomaterial items have been changed from
207      eager-loading to lazy-loading. This may affect clients and/or plug-ins
208      that expect the parent chain of biomaterials to always be fully initialized
209      without explicitely having told the BASE core to do so.
210    </para>
212    <bridgehead>Tables can have columns with different sort order</bridgehead>
213    <para>
214      A new feature has been implemented which allows columns in a table to
215      have different sort order. This is implemented by allowing '+' or '-'
216      as a prefix to properties returned by the <methodname>ItemContext.getSortProperty()</methodname>
217      method. Properties without a prefix still use the global sort order as returned
218      by <methodname>ItemContext.getSortDirection()</methodname>.
219    </para>
221    <para>
222      Code that is not aware of the prefixes may fail since '+' and '-' are not
223      allowed in property names.
224    </para>
226    <bridgehead>External authentication has been converted to an extension point</bridgehead>
227    <para>
228      External authentication plug-ins using the old system are supported through a
229      wrapper extension, but the recommendation is to update those plug-in to the
230      new system. See <xref linkend="extensions_developer.login-manager" /> for more information.
231    </para>
233    <bridgehead>Setting parameters for a job no longer set it to status=WAITING</bridgehead>
234    <para>
235      Added <methodname>Job.setScheduled()</methodname> to switch the state
236      from <constant>UNCONFIGURED</constant> to <constant>WAITING</constant>.
237      A job can't be executed before it has entered the <constant>WAITING</constant>
238      state. The change makes it possible to register a job and some parameters for
239      it and remain in the <constant>UNCONFIGURED</constant> state.
240    </para>
242  </sect1>
244  <sect1 id="appendix.incompatible.3.2">
245    <title>BASE 3.2 release</title>
247    <bridgehead>Derived bioassays can now have multiple parents</bridgehead>
248    <para>
249      Before BASE 3.2 a derived bioassay was restricted to a single parent
250      item. This affects the API and the <methodname>DerivedBioAssay.getParent()</methodname>
251      and <methodname>DerivedBioAssay.getPhysicalBioAssays()</methodname> now always
252      return null. Existing code should be updated to use <methodname>getPhysicalBioAssays()</methodname>
253      and <methodname>getParents()</methodname> (which return <classname>ItemQuery</classname> instances)
254      instead. Code that is using queries to filter or sort on parent items must also be
255      updated since the association names have changed.
256    </para>
258    <bridgehead>BASEfile exporter automatically closes the output stream</bridgehead>
259    <para>
260      The implementation of the BASEfile exporter has been changed to
261      automatically close the provided output stream when the export
262      is complete. Clients that need the old behavior should call
263      <code>BaseFileExporter.setAutoCloseWriters(false)</code> before
264      using it.
265    </para>
267    <bridgehead>Change history logging is now an extension point</bridgehead>
268    <para>
269      The change history logging has been converted to an extension point.
270      The <constant>changelog.factory</constant> setting in <filename>base.config</filename>
271      is no longer used. Existing logging implementations should be updated
272      to use the extension system. See <xref linkend="extensions_developer.logging" />.
273      A temporary solution is to use one of the debugging action factories to
274      define the extension point:
275    </para>
277    <programlisting language="xml">
280   id="id-of-custom-log-manager"
281   extends="net.sf.basedb.core.log-manager"
282   >
283   <about>
284      <name>My custom log manager</name>
285      <description>
286         Temporary solution to allow the old log manager to work with the extension system.
287      </description>
288   </about>
289   <index>1</index>
290   <action-factory>
291      <factory-class>net.sf.basedb.util.extensions.debug.BeanActionFactory</factory-class>
292      <parameters>
293         <beanClass>my.custom.LogmangerClass</beanClass>
294      </parameters>
295   </action-factory>
300  </sect1>
302  <sect1 id="appendix.incompatible.3.1">
303    <title>BASE 3.1 release</title>
305    <bridgehead>Web service framework updated to Axis2 1.6</bridgehead>
306    <para>
307      We have updated the web services framework to Axis2 1.6. Clients
308      that use earlier Axis2 versions may not work when connecting to a
309      BASE 3.1 server. Unfortunately, clients that use the Axis2 1.6
310      framework may have problems connecting to BASE 3.0 servers so it
311      may be difficult to implement support for both BASE 3.0 and BASE 3.1
312      in a single client application.
313    </para>
315    <bridgehead>New GUI look and feel</bridgehead>
316    <para>
317      Taglibs, stylesheets and javscript functions have been changed
318      to create a new look and feel. Plug-ins and extensions that uses
319      GUI elements from the core BASE installation may need to be updated
320      for the best user experience. The changes are too numerous so we can't
321      list them here. Please use the developers mailing list if specific
322      information is needed or see <ulink url="">ticket
323      1655</ulink> for some screenshots and other information.
324    </para>
326    <bridgehead>Per-experiment copy of reporter annotations</bridgehead>
327    <para>
328      A new feature has been implemented that allows a user to make a
329      local copy of reporter annotations for reporters that are used
330      in an experiment. The existing API will by default use the local
331      copy if one is available. It is possible to use the master reporter
332      annotations by invoking certain API methods (for example:
333      <code>DynamicQuery.setUseClonedReporters(false)</code>). Since the copy
334      may include only a subset of the available reporter annotations this
335      may cause problems for code that is expecting all annotations to be
336      available. See <classname docapi="net.sf.basedb.core">ReporterCloneTemplate</classname>
337      and <ulink url="">ticket 1616</ulink>
338      for more information.
339    </para>
341    <bridgehead>Annotations can be inherited/pushed from child to parent item</bridgehead>
342    <para>
343      A new feature has been implemented that allows an item to "push" annotations
344      up to it's parent in addition to the normal "inherit to child" method.
345      This has been implemented as a change in the <methodname>getAnnotatableParents()</methodname>
346      method defined by the <interfacename docapi="net.sf.basedb.core">Annotatable</interfacename>
347      interface. This may cause unexpected issues with code that is not prepared to handle
348      this situation. Particulary, infinite loops must be avoided when traversing the "parent"
349      tree of an item (but this should already be in place since it can already happen due to
350      mistakes when creating items). See <ulink url="">ticket 1605</ulink>
351      for more information.
352    </para>
354  </sect1>
357  <sect1 id="appendix.incompatible.3.0">
358    <title>BASE 3.0 release</title>
360    <para>
361      There are a lot incompatible changes between BASE 3 and any of the BASE 2.x
362      versions. We do not list list those changes here since we do not expect existing
363      plug-ins, extensions or other client application to work with BASE 3 without
364      modification. See <xref linkend="migrate_2_3" /> for more information.
365    </para>
366  </sect1>
368  <sect1 id="appendix.incompatible.2.x">
369    <title>All BASE 2.x releases</title>
371    <para>
372      The list of changes made in the various BASE 2.x releases can be found
373      in the <ulink url=""
374      >BASE 2.17 documentation</ulink>.
375    </para>
377  </sect1>
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