source: trunk/doc/src/docbook/appendix/incompatible.xml @ 7545

Last change on this file since 7545 was 7545, checked in by Nicklas Nordborg, 3 years ago

References #2131: Add support for installing multiple authentication managers

Added note to the update information about the changes.

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File size: 19.3 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 7545 2018-12-07 07:07:20Z 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.3.14">
39    <title>BASE 3.14 release</title>
41    <bridgehead id="appendix.incompatible.authenticator">The (very) old Authenticator API has been removed</bridgehead>
42    <para>
43      The <code>net.sf.basedb.core.authentication.Authenticator</code>
44      interface and other related code that was deprecated in BASE 3.3
45      has been removed. Systems that still use old authentication code
46      need to replace this with a newer version before updating.
47    </para>
49  </sect1>
51  <sect1 id="appendix.incompatible.3.11">
52    <title>BASE 3.11 release</title>
54    <bridgehead id="appendix.incompatible.paused-job">Job.Status.PAUSED</bridgehead>
55    <para>
56      Added the <code>PAUSED</code> option to the <code>Job.Status</code>
57      enumeration. This option is used when a running job has been temporarily paused.
58      Code that uses the job's status to decide what action to take may fail since
59      this is a new option. In most cases, it should be handled in the same way as
60      if the job is <code>WAITING</code>.
61    </para>
63    <bridgehead id="appendix.incompatible.sha-256">SHA-256 fingerprint on file servers</bridgehead>
64    <para>
65      Added support for storing SHA-256 fingerprints on file servers. Code
66      that is expecting the fingerprint to always be a MD5 value may stop
67      to work. A new method <code>FileServer.getFingerprintType()</code>
68      has been added.
69    </para>
71    <bridgehead id="appendix.incompatible.inactive-roles">Inactive roles</bridgehead>
72    <para>
73      A new feature which allows a user to activate and de-activate roles on the
74      fly during a login session has been implemented. This may cause a user to
75      gain or lose permissions at any time. A change of active roles triggers an
76      internal reload of permissions and since there are already other things that
77      do this, it should not cause any problems. The <code>SessionControl.getRoles()</code>
78      method has been deprecated and replaced with <code>SessionControl.getAllRoles()</code>,
79      <code>SessionControl.getActiveRoles()</code> and <code>SessionControl.getInactiveRoles()</code>.
80    </para>
82  </sect1>
84  <sect1 id="appendix.incompatible.3.10">
85    <title>BASE 3.10 release</title>
87    <bridgehead id="appendix.incompatible.annotate-permission">Annotate permission</bridgehead>
88    <para>
89      A new permission level, <code>ANNOTATE</code> has been added to
90      the permission system. Extensions and other clients that are not
91      aware of this permission may think that the user only has
92      <code>READ</code> permission.
93    </para>
95    <bridgehead id="appendix.incompatible.project-annotations">Project-specific annotations</bridgehead>
96    <para>
97      The annotation system has been extended with a new feature: project-specific annotations.
98      Extensions and other code that is not aware of this may experience strange behaviour
99      where annotation values may not change as expected or may change in unexpected ways.
100      For example, trying to change the default value of a project-specific annotation when
101      a project is active causes a new annotation to be created in the background instead
102      of changing the current one. Note that this feature is disabled by default and
103      must be enabled per annotation type. Updating an existing server should be safe
104      and will not affect existing annotations or annotation types.
105    </para>
107  </sect1>
109  <sect1 id="appendix.incompatible.3.9">
110    <title>BASE 3.9 release</title>
112    <bridgehead id="appendix.incompatible.session-control">Application.getSessionControl()</bridgehead>
113    <para>
114      The <classname docapi="net.sf.basedb.core">Application.getSessionControl()</classname> 
115      method for getting access to an existing session has been deprecated. A new
116      version has been implemented that require that an <emphasis>external client id</emphasis>
117      is specified. This change was needed to avoid sessions leaking between client
118      applications and prevent users to use an application they don't have permission to use.
119    </para>
121    <para>
122      The deprecated method use the client id from the BASE web client. Extensions and
123      other clients that use a different client id are affected and may stop to work
124      until they have been updated to use the new API. For more information see
125      <ulink url="">ticket 2011</ulink>.
126    </para>
128  </sect1>
131  <sect1 id="appendix.incompatible.3.8">
132    <title>BASE 3.8 release</title>
134    <bridgehead id="appendix.incompatible.service-session-control">ServiceSessionControl API</bridgehead>
135    <para>
136      The <classname docapi="net.sf.basedb.core">ServiceSessionControl</classname> API for
137      configuration and building Hibernate <classname>SessionFactory</classname>
138      instances has been changed due the Hibernate 5 upgrade. This change affects
139      extensions that use the API for storing their own data inside the BASE database.
140      Extensions that use this API must be updated or they will not work with BASE 3.8.
141    </para>
143  </sect1>
146  <sect1 id="appendix.incompatible.3.6">
147    <title>BASE 3.6 release</title>
149    <bridgehead id="appendix.incompatible.cloned-annotation">Cloned annotations</bridgehead>
150    <para>
151      A new feature that allows an inherited annotation to be cloned has been implemented.
152      Several methods in <classname docapi="net.sf.basedb.core">AnnotationSet</classname>,
153      <classname docapi="net.sf.basedb.core.snapshot">AnnotationSnapshot</classname> and some
154      other classes has been deprecated and replaced with new methods. Existing code that
155      is not aware of cloned annotations should continue to work, but may experience some
156      inconsistent behaviour in case the cloned values are out-of-sync with the original
157      values.
158    </para>
160    <bridgehead id="appendix.incompatible.experimental-factors">Experimental factors have moved</bridgehead>
161    <para>
162      To allow the owner of an experiment to manage experimental factor values as part
163      of the experiment, the <classname docapi="net.sf.basedb.core">RootRawBioassay</classname>
164      item was introduced. The new item is a one-to-one representation of a <classname 
165      docapi="net.sf.basedb.core">RawBioAssay</classname> inside that experiment.
166      Experimental factor values that are found on existing raw bioassays are copied to the
167      root rawbioassays when updating BASE. Changes made after the update will only
168      affect the root raw bioassays. Existing code that is not aware of root raw bioassays
169      may not find the experimental factor values.
170    </para>
172  </sect1>
174  <sect1 id="appendix.incompatible.3.5">
175    <title>BASE 3.5 release</title>
177    <bridgehead id="appendix.incompatible.itemlists">Biomaterial lists has been replaced with item lists</bridgehead>
178    <para>
179      The <classname docapi="net.sf.basedb.core">BioMaterialList</classname> 
180      class has been removed and replaced with <classname 
181      docapi="net.sf.basedb.core">ItemList</classname>. The API is similar
182      but not exactly the same. In most cases only minor changes are required
183      to make existing code work with the new API.
184    </para>
186    <para>
187      Queries that use the <code>BioMaterial.bioMaterialLists</code> association
188      for joining will no longer work. There is no replacement functionality for
189      joining item lists.
190    </para>
192    <para>
193      All classes in the <code>net.sf.basedb.util.biomaterial</code> package has
194      been deprecated. It is recommended that code that uses any of these classes
195      are updated to use classes in <code>net.sf.basedb.util.listable</code> instead.
196      The API is a bit different, but the new implementations typically performs a
197      lot better so it is worth the work.
198    </para>
200    <para>
201      There are several other minor changes in the API that previously worked with
202      the <code>BioMaterialList</code> class that has been removed and replaced
203      with something else.
204    </para>
206  </sect1>
208  <sect1 id="appendix.incompatible.3.4">
209    <title>BASE 3.4 release</title>
211    <bridgehead>Updated JDOM to 2.0</bridgehead>
212    <para>
213      The JDOM library has been updated to version 2.0 from 1.1. The
214      new version is incompatible with the old version. BASE 3.4 will
215      ship with both versions but JDOM 1.1 will be removed in BASE 3.5
216      and so will all API methods that expose JDOM 1.1 classes.
217      It is recommended that plug-ins and extensions that use JDOM also
218      update to JDOM 2.0.
219    </para>
221    <bridgehead>Updated to Apache HttpClient 4.3.4</bridgehead>
222    <para>
223      The Apache HTTP Client library has been updated to version 4.3.4.
224      The new version has deprecated some classes that are exposed through
225      the BASE API (mainly in <classname docapi="net.sf.basedb.util.ssl">SSLUtil</classname>).
226      As a result we had to deprecate parts of the BASE API, which will
227      be removed in BASE 3.5. It is recommended that plug-ins and
228      extensions that are affected are updated to use the replacement API
229      instead.
230    </para>
232  </sect1>
234  <sect1 id="appendix.incompatible.3.3">
235    <title>BASE 3.3 release</title>
237    <bridgehead>Content security policy</bridgehead>
238    <para>
239      The BASE web client now set a rather strict <emphasis>Content
240      Security Policy</emphasis> that prevent browsers from executing
241      code (including JavaScript) that is considered unsafe. Some extensions
242      may cease to work due to this. Go to
243      <menuchoice>
244        <guimenu>Administrate</guimenu>
245        <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
246        <guimenuitem>Overview</guimenuitem>
247      </menuchoice> 
248      (after upgrading) to see if there are any warnings about this.
249      Read more in <xref linkend="appendix.web.xml.csp-filter" />
250      for information about how to relax the policy.
251    </para>
253    <bridgehead>Re-factored JavaScript API</bridgehead>
254    <para>
255      The BASE web client has undergone a major refactoring with respect to
256      the JavaScript API that is used on the server. A lot of functions have
257      been replaced with new implementations. We have tried to map the old
258      functions to the new ones, but this has not always been possible. Extentions
259      that use the BASE JavaScript API must be tested with BASE 3.3 to find
260      out if they are still working or if modifications are needed.
261    </para>
263    <note>
264      <title>Avoid in-line event handlers and script</title>
265      <para>
266        The main reason for the refactoring is to get rid of all in-line
267        event handlers and script sections since this is a possible entry
268        point for cross-site scripting attacks (see <ulink 
269          url="">ticket 1712</ulink>).
270        Extension developers are encouraged to make the same changes in
271        their applications.
272      </para>
273    </note>
275    <bridgehead>Biomaterial items are now lazy-loading</bridgehead>
276    <para>
277      For performance reasons biomaterial items have been changed from
278      eager-loading to lazy-loading. This may affect clients and/or plug-ins
279      that expect the parent chain of biomaterials to always be fully initialized
280      without explicitely having told the BASE core to do so.
281    </para>
283    <bridgehead>Tables can have columns with different sort order</bridgehead>
284    <para>
285      A new feature has been implemented which allows columns in a table to
286      have different sort order. This is implemented by allowing '+' or '-'
287      as a prefix to properties returned by the <methodname>ItemContext.getSortProperty()</methodname>
288      method. Properties without a prefix still use the global sort order as returned
289      by <methodname>ItemContext.getSortDirection()</methodname>.
290    </para>
292    <para>
293      Code that is not aware of the prefixes may fail since '+' and '-' are not
294      allowed in property names.
295    </para>
297    <bridgehead>External authentication has been converted to an extension point</bridgehead>
298    <para>
299      External authentication plug-ins using the old system are supported through a
300      wrapper extension, but the recommendation is to update those plug-in to the
301      new system. See <xref linkend="extensions_developer.login-manager" /> for more information.
302    </para>
304    <bridgehead>Setting parameters for a job no longer set it to status=WAITING</bridgehead>
305    <para>
306      Added <methodname>Job.setScheduled()</methodname> to switch the state
307      from <constant>UNCONFIGURED</constant> to <constant>WAITING</constant>.
308      A job can't be executed before it has entered the <constant>WAITING</constant>
309      state. The change makes it possible to register a job and some parameters for
310      it and remain in the <constant>UNCONFIGURED</constant> state.
311    </para>
313  </sect1>
315  <sect1 id="appendix.incompatible.3.2">
316    <title>BASE 3.2 release</title>
318    <bridgehead>Derived bioassays can now have multiple parents</bridgehead>
319    <para>
320      Before BASE 3.2 a derived bioassay was restricted to a single parent
321      item. This affects the API and the <methodname>DerivedBioAssay.getParent()</methodname>
322      and <methodname>DerivedBioAssay.getPhysicalBioAssays()</methodname> now always
323      return null. Existing code should be updated to use <methodname>getPhysicalBioAssays()</methodname>
324      and <methodname>getParents()</methodname> (which return <classname>ItemQuery</classname> instances)
325      instead. Code that is using queries to filter or sort on parent items must also be
326      updated since the association names have changed.
327    </para>
329    <bridgehead>BASEfile exporter automatically closes the output stream</bridgehead>
330    <para>
331      The implementation of the BASEfile exporter has been changed to
332      automatically close the provided output stream when the export
333      is complete. Clients that need the old behavior should call
334      <code>BaseFileExporter.setAutoCloseWriters(false)</code> before
335      using it.
336    </para>
338    <bridgehead>Change history logging is now an extension point</bridgehead>
339    <para>
340      The change history logging has been converted to an extension point.
341      The <constant>changelog.factory</constant> setting in <filename>base.config</filename>
342      is no longer used. Existing logging implementations should be updated
343      to use the extension system. See <xref linkend="extensions_developer.logging" />.
344      A temporary solution is to use one of the debugging action factories to
345      define the extension point:
346    </para>
348    <programlisting language="xml">
351   id="id-of-custom-log-manager"
352   extends="net.sf.basedb.core.log-manager"
353   >
354   <about>
355      <name>My custom log manager</name>
356      <description>
357         Temporary solution to allow the old log manager to work with the extension system.
358      </description>
359   </about>
360   <index>1</index>
361   <action-factory>
362      <factory-class>net.sf.basedb.util.extensions.debug.BeanActionFactory</factory-class>
363      <parameters>
364         <beanClass>my.custom.LogmangerClass</beanClass>
365      </parameters>
366   </action-factory>
371  </sect1>
373  <sect1 id="appendix.incompatible.3.1">
374    <title>BASE 3.1 release</title>
376    <bridgehead>Web service framework updated to Axis2 1.6</bridgehead>
377    <para>
378      We have updated the web services framework to Axis2 1.6. Clients
379      that use earlier Axis2 versions may not work when connecting to a
380      BASE 3.1 server. Unfortunately, clients that use the Axis2 1.6
381      framework may have problems connecting to BASE 3.0 servers so it
382      may be difficult to implement support for both BASE 3.0 and BASE 3.1
383      in a single client application.
384    </para>
386    <bridgehead>New GUI look and feel</bridgehead>
387    <para>
388      Taglibs, stylesheets and javscript functions have been changed
389      to create a new look and feel. Plug-ins and extensions that uses
390      GUI elements from the core BASE installation may need to be updated
391      for the best user experience. The changes are too numerous so we can't
392      list them here. Please use the developers mailing list if specific
393      information is needed or see <ulink url="">ticket
394      1655</ulink> for some screenshots and other information.
395    </para>
397    <bridgehead>Per-experiment copy of reporter annotations</bridgehead>
398    <para>
399      A new feature has been implemented that allows a user to make a
400      local copy of reporter annotations for reporters that are used
401      in an experiment. The existing API will by default use the local
402      copy if one is available. It is possible to use the master reporter
403      annotations by invoking certain API methods (for example:
404      <code>DynamicQuery.setUseClonedReporters(false)</code>). Since the copy
405      may include only a subset of the available reporter annotations this
406      may cause problems for code that is expecting all annotations to be
407      available. See <classname docapi="net.sf.basedb.core">ReporterCloneTemplate</classname>
408      and <ulink url="">ticket 1616</ulink>
409      for more information.
410    </para>
412    <bridgehead>Annotations can be inherited/pushed from child to parent item</bridgehead>
413    <para>
414      A new feature has been implemented that allows an item to "push" annotations
415      up to it's parent in addition to the normal "inherit to child" method.
416      This has been implemented as a change in the <methodname>getAnnotatableParents()</methodname>
417      method defined by the <interfacename docapi="net.sf.basedb.core">Annotatable</interfacename>
418      interface. This may cause unexpected issues with code that is not prepared to handle
419      this situation. Particulary, infinite loops must be avoided when traversing the "parent"
420      tree of an item (but this should already be in place since it can already happen due to
421      mistakes when creating items). See <ulink url="">ticket 1605</ulink>
422      for more information.
423    </para>
425  </sect1>
428  <sect1 id="appendix.incompatible.3.0">
429    <title>BASE 3.0 release</title>
431    <para>
432      There are a lot incompatible changes between BASE 3 and any of the BASE 2.x
433      versions. We do not list list those changes here since we do not expect existing
434      plug-ins, extensions or other client application to work with BASE 3 without
435      modification. See <xref linkend="migrate_2_3" /> for more information.
436    </para>
437  </sect1>
439  <sect1 id="appendix.incompatible.2.x">
440    <title>All BASE 2.x releases</title>
442    <para>
443      The list of changes made in the various BASE 2.x releases can be found
444      in the <ulink url=""
445      >BASE 2.17 documentation</ulink>.
446    </para>
448  </sect1>
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