source: trunk/doc/src/docbook/appendix/incompatible.xml @ 7344

Last change on this file since 7344 was 7344, checked in by Nicklas Nordborg, 5 years ago

References #2043: Activating/deactivating roles on the fly in a login session

Added note about this in the documentation about incompatible API changes.

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File size: 18.9 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 7344 2017-04-18 13:11:50Z 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.3.11">
39    <title>BASE 3.11 release</title>
41    <bridgehead id="appendix.incompatible.paused-job">Job.Status.PAUSED</bridgehead>
42    <para>
43      Added the <code>PAUSED</code> option to the <code>Job.Status</code>
44      enumeration. This option is used when a running job has been temporarily paused.
45      Code that uses the job's status to decide what action to take may fail since
46      this is a new option. In most cases, it should be handled in the same way as
47      if the job is <code>WAITING</code>.
48    </para>
50    <bridgehead id="appendix.incompatible.sha-256">SHA-256 fingerprint on file servers</bridgehead>
51    <para>
52      Added support for storing SHA-256 fingerprints on file servers. Code
53      that is expecting the fingerprint to always be a MD5 value may stop
54      to work. A new method <code>FileServer.getFingerprintType()</code>
55      has been added.
56    </para>
58    <bridgehead id="appendix.incompatible.inactive-roles">Inactive roles</bridgehead>
59    <para>
60      A new feature which allows a user to activate and de-activate roles on the
61      fly during a login session has been implemented. This may cause a user to
62      gain or lose permissions at any time. A change of active roles triggers an
63      internal reload of permissions and since there are already other things that
64      do this, it should not cause any problems. The <code>SessionControl.getRoles()</code>
65      method has been deprecated and replaced with <code>SessionControl.getAllRoles()</code>,
66      <code>SessionControl.getActiveRoles()</code> and <code>SessionControl.getInactiveRoles()</code>.
67    </para>
69  </sect1>
71  <sect1 id="appendix.incompatible.3.10">
72    <title>BASE 3.10 release</title>
74    <bridgehead id="appendix.incompatible.annotate-permission">Annotate permission</bridgehead>
75    <para>
76      A new permission level, <code>ANNOTATE</code> has been added to
77      the permission system. Extensions and other clients that are not
78      aware of this permission may think that the user only has
79      <code>READ</code> permission.
80    </para>
82    <bridgehead id="appendix.incompatible.project-annotations">Project-specific annotations</bridgehead>
83    <para>
84      The annotation system has been extended with a new feature: project-specific annotations.
85      Extensions and other code that is not aware of this may experience strange behaviour
86      where annotation values may not change as expected or may change in unexpected ways.
87      For example, trying to change the default value of a project-specific annotation when
88      a project is active causes a new annotation to be created in the background instead
89      of changing the current one. Note that this feature is disabled by default and
90      must be enabled per annotation type. Updating an existing server should be safe
91      and will not affect existing annotations or annotation types.
92    </para>
94  </sect1>
96  <sect1 id="appendix.incompatible.3.9">
97    <title>BASE 3.9 release</title>
99    <bridgehead id="appendix.incompatible.session-control">Application.getSessionControl()</bridgehead>
100    <para>
101      The <classname docapi="net.sf.basedb.core">Application.getSessionControl()</classname> 
102      method for getting access to an existing session has been deprecated. A new
103      version has been implemented that require that an <emphasis>external client id</emphasis>
104      is specified. This change was needed to avoid sessions leaking between client
105      applications and prevent users to use an application they don't have permission to use.
106    </para>
108    <para>
109      The deprecated method use the client id from the BASE web client. Extensions and
110      other clients that use a different client id are affected and may stop to work
111      until they have been updated to use the new API. For more information see
112      <ulink url="">ticket 2011</ulink>.
113    </para>
115  </sect1>
118  <sect1 id="appendix.incompatible.3.8">
119    <title>BASE 3.8 release</title>
121    <bridgehead id="appendix.incompatible.service-session-control">ServiceSessionControl API</bridgehead>
122    <para>
123      The <classname docapi="net.sf.basedb.core">ServiceSessionControl</classname> API for
124      configuration and building Hibernate <classname>SessionFactory</classname>
125      instances has been changed due the Hibernate 5 upgrade. This change affects
126      extensions that use the API for storing their own data inside the BASE database.
127      Extensions that use this API must be updated or they will not work with BASE 3.8.
128    </para>
130  </sect1>
133  <sect1 id="appendix.incompatible.3.6">
134    <title>BASE 3.6 release</title>
136    <bridgehead id="appendix.incompatible.cloned-annotation">Cloned annotations</bridgehead>
137    <para>
138      A new feature that allows an inherited annotation to be cloned has been implemented.
139      Several methods in <classname docapi="net.sf.basedb.core">AnnotationSet</classname>,
140      <classname docapi="net.sf.basedb.core.snapshot">AnnotationSnapshot</classname> and some
141      other classes has been deprecated and replaced with new methods. Existing code that
142      is not aware of cloned annotations should continue to work, but may experience some
143      inconsistent behaviour in case the cloned values are out-of-sync with the original
144      values.
145    </para>
147    <bridgehead id="appendix.incompatible.experimental-factors">Experimental factors have moved</bridgehead>
148    <para>
149      To allow the owner of an experiment to manage experimental factor values as part
150      of the experiment, the <classname docapi="net.sf.basedb.core">RootRawBioassay</classname>
151      item was introduced. The new item is a one-to-one representation of a <classname 
152      docapi="net.sf.basedb.core">RawBioAssay</classname> inside that experiment.
153      Experimental factor values that are found on existing raw bioassays are copied to the
154      root rawbioassays when updating BASE. Changes made after the update will only
155      affect the root raw bioassays. Existing code that is not aware of root raw bioassays
156      may not find the experimental factor values.
157    </para>
159  </sect1>
161  <sect1 id="appendix.incompatible.3.5">
162    <title>BASE 3.5 release</title>
164    <bridgehead id="appendix.incompatible.itemlists">Biomaterial lists has been replaced with item lists</bridgehead>
165    <para>
166      The <classname docapi="net.sf.basedb.core">BioMaterialList</classname> 
167      class has been removed and replaced with <classname 
168      docapi="net.sf.basedb.core">ItemList</classname>. The API is similar
169      but not exactly the same. In most cases only minor changes are required
170      to make existing code work with the new API.
171    </para>
173    <para>
174      Queries that use the <code>BioMaterial.bioMaterialLists</code> association
175      for joining will no longer work. There is no replacement functionality for
176      joining item lists.
177    </para>
179    <para>
180      All classes in the <code>net.sf.basedb.util.biomaterial</code> package has
181      been deprecated. It is recommended that code that uses any of these classes
182      are updated to use classes in <code>net.sf.basedb.util.listable</code> instead.
183      The API is a bit different, but the new implementations typically performs a
184      lot better so it is worth the work.
185    </para>
187    <para>
188      There are several other minor changes in the API that previously worked with
189      the <code>BioMaterialList</code> class that has been removed and replaced
190      with something else.
191    </para>
193  </sect1>
195  <sect1 id="appendix.incompatible.3.4">
196    <title>BASE 3.4 release</title>
198    <bridgehead>Updated JDOM to 2.0</bridgehead>
199    <para>
200      The JDOM library has been updated to version 2.0 from 1.1. The
201      new version is incompatible with the old version. BASE 3.4 will
202      ship with both versions but JDOM 1.1 will be removed in BASE 3.5
203      and so will all API methods that expose JDOM 1.1 classes.
204      It is recommended that plug-ins and extensions that use JDOM also
205      update to JDOM 2.0.
206    </para>
208    <bridgehead>Updated to Apache HttpClient 4.3.4</bridgehead>
209    <para>
210      The Apache HTTP Client library has been updated to version 4.3.4.
211      The new version has deprecated some classes that are exposed through
212      the BASE API (mainly in <classname docapi="net.sf.basedb.util.ssl">SSLUtil</classname>).
213      As a result we had to deprecate parts of the BASE API, which will
214      be removed in BASE 3.5. It is recommended that plug-ins and
215      extensions that are affected are updated to use the replacement API
216      instead.
217    </para>
219  </sect1>
221  <sect1 id="appendix.incompatible.3.3">
222    <title>BASE 3.3 release</title>
224    <bridgehead>Content security policy</bridgehead>
225    <para>
226      The BASE web client now set a rather strict <emphasis>Content
227      Security Policy</emphasis> that prevent browsers from executing
228      code (including JavaScript) that is considered unsafe. Some extensions
229      may cease to work due to this. Go to
230      <menuchoice>
231        <guimenu>Administrate</guimenu>
232        <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
233        <guimenuitem>Overview</guimenuitem>
234      </menuchoice> 
235      (after upgrading) to see if there are any warnings about this.
236      Read more in <xref linkend="appendix.web.xml.csp-filter" />
237      for information about how to relax the policy.
238    </para>
240    <bridgehead>Re-factored JavaScript API</bridgehead>
241    <para>
242      The BASE web client has undergone a major refactoring with respect to
243      the JavaScript API that is used on the server. A lot of functions have
244      been replaced with new implementations. We have tried to map the old
245      functions to the new ones, but this has not always been possible. Extentions
246      that use the BASE JavaScript API must be tested with BASE 3.3 to find
247      out if they are still working or if modifications are needed.
248    </para>
250    <note>
251      <title>Avoid in-line event handlers and script</title>
252      <para>
253        The main reason for the refactoring is to get rid of all in-line
254        event handlers and script sections since this is a possible entry
255        point for cross-site scripting attacks (see <ulink 
256          url="">ticket 1712</ulink>).
257        Extension developers are encouraged to make the same changes in
258        their applications.
259      </para>
260    </note>
262    <bridgehead>Biomaterial items are now lazy-loading</bridgehead>
263    <para>
264      For performance reasons biomaterial items have been changed from
265      eager-loading to lazy-loading. This may affect clients and/or plug-ins
266      that expect the parent chain of biomaterials to always be fully initialized
267      without explicitely having told the BASE core to do so.
268    </para>
270    <bridgehead>Tables can have columns with different sort order</bridgehead>
271    <para>
272      A new feature has been implemented which allows columns in a table to
273      have different sort order. This is implemented by allowing '+' or '-'
274      as a prefix to properties returned by the <methodname>ItemContext.getSortProperty()</methodname>
275      method. Properties without a prefix still use the global sort order as returned
276      by <methodname>ItemContext.getSortDirection()</methodname>.
277    </para>
279    <para>
280      Code that is not aware of the prefixes may fail since '+' and '-' are not
281      allowed in property names.
282    </para>
284    <bridgehead>External authentication has been converted to an extension point</bridgehead>
285    <para>
286      External authentication plug-ins using the old system are supported through a
287      wrapper extension, but the recommendation is to update those plug-in to the
288      new system. See <xref linkend="extensions_developer.login-manager" /> for more information.
289    </para>
291    <bridgehead>Setting parameters for a job no longer set it to status=WAITING</bridgehead>
292    <para>
293      Added <methodname>Job.setScheduled()</methodname> to switch the state
294      from <constant>UNCONFIGURED</constant> to <constant>WAITING</constant>.
295      A job can't be executed before it has entered the <constant>WAITING</constant>
296      state. The change makes it possible to register a job and some parameters for
297      it and remain in the <constant>UNCONFIGURED</constant> state.
298    </para>
300  </sect1>
302  <sect1 id="appendix.incompatible.3.2">
303    <title>BASE 3.2 release</title>
305    <bridgehead>Derived bioassays can now have multiple parents</bridgehead>
306    <para>
307      Before BASE 3.2 a derived bioassay was restricted to a single parent
308      item. This affects the API and the <methodname>DerivedBioAssay.getParent()</methodname>
309      and <methodname>DerivedBioAssay.getPhysicalBioAssays()</methodname> now always
310      return null. Existing code should be updated to use <methodname>getPhysicalBioAssays()</methodname>
311      and <methodname>getParents()</methodname> (which return <classname>ItemQuery</classname> instances)
312      instead. Code that is using queries to filter or sort on parent items must also be
313      updated since the association names have changed.
314    </para>
316    <bridgehead>BASEfile exporter automatically closes the output stream</bridgehead>
317    <para>
318      The implementation of the BASEfile exporter has been changed to
319      automatically close the provided output stream when the export
320      is complete. Clients that need the old behavior should call
321      <code>BaseFileExporter.setAutoCloseWriters(false)</code> before
322      using it.
323    </para>
325    <bridgehead>Change history logging is now an extension point</bridgehead>
326    <para>
327      The change history logging has been converted to an extension point.
328      The <constant>changelog.factory</constant> setting in <filename>base.config</filename>
329      is no longer used. Existing logging implementations should be updated
330      to use the extension system. See <xref linkend="extensions_developer.logging" />.
331      A temporary solution is to use one of the debugging action factories to
332      define the extension point:
333    </para>
335    <programlisting language="xml">
338   id="id-of-custom-log-manager"
339   extends="net.sf.basedb.core.log-manager"
340   >
341   <about>
342      <name>My custom log manager</name>
343      <description>
344         Temporary solution to allow the old log manager to work with the extension system.
345      </description>
346   </about>
347   <index>1</index>
348   <action-factory>
349      <factory-class>net.sf.basedb.util.extensions.debug.BeanActionFactory</factory-class>
350      <parameters>
351         <beanClass>my.custom.LogmangerClass</beanClass>
352      </parameters>
353   </action-factory>
358  </sect1>
360  <sect1 id="appendix.incompatible.3.1">
361    <title>BASE 3.1 release</title>
363    <bridgehead>Web service framework updated to Axis2 1.6</bridgehead>
364    <para>
365      We have updated the web services framework to Axis2 1.6. Clients
366      that use earlier Axis2 versions may not work when connecting to a
367      BASE 3.1 server. Unfortunately, clients that use the Axis2 1.6
368      framework may have problems connecting to BASE 3.0 servers so it
369      may be difficult to implement support for both BASE 3.0 and BASE 3.1
370      in a single client application.
371    </para>
373    <bridgehead>New GUI look and feel</bridgehead>
374    <para>
375      Taglibs, stylesheets and javscript functions have been changed
376      to create a new look and feel. Plug-ins and extensions that uses
377      GUI elements from the core BASE installation may need to be updated
378      for the best user experience. The changes are too numerous so we can't
379      list them here. Please use the developers mailing list if specific
380      information is needed or see <ulink url="">ticket
381      1655</ulink> for some screenshots and other information.
382    </para>
384    <bridgehead>Per-experiment copy of reporter annotations</bridgehead>
385    <para>
386      A new feature has been implemented that allows a user to make a
387      local copy of reporter annotations for reporters that are used
388      in an experiment. The existing API will by default use the local
389      copy if one is available. It is possible to use the master reporter
390      annotations by invoking certain API methods (for example:
391      <code>DynamicQuery.setUseClonedReporters(false)</code>). Since the copy
392      may include only a subset of the available reporter annotations this
393      may cause problems for code that is expecting all annotations to be
394      available. See <classname docapi="net.sf.basedb.core">ReporterCloneTemplate</classname>
395      and <ulink url="">ticket 1616</ulink>
396      for more information.
397    </para>
399    <bridgehead>Annotations can be inherited/pushed from child to parent item</bridgehead>
400    <para>
401      A new feature has been implemented that allows an item to "push" annotations
402      up to it's parent in addition to the normal "inherit to child" method.
403      This has been implemented as a change in the <methodname>getAnnotatableParents()</methodname>
404      method defined by the <interfacename docapi="net.sf.basedb.core">Annotatable</interfacename>
405      interface. This may cause unexpected issues with code that is not prepared to handle
406      this situation. Particulary, infinite loops must be avoided when traversing the "parent"
407      tree of an item (but this should already be in place since it can already happen due to
408      mistakes when creating items). See <ulink url="">ticket 1605</ulink>
409      for more information.
410    </para>
412  </sect1>
415  <sect1 id="appendix.incompatible.3.0">
416    <title>BASE 3.0 release</title>
418    <para>
419      There are a lot incompatible changes between BASE 3 and any of the BASE 2.x
420      versions. We do not list list those changes here since we do not expect existing
421      plug-ins, extensions or other client application to work with BASE 3 without
422      modification. See <xref linkend="migrate_2_3" /> for more information.
423    </para>
424  </sect1>
426  <sect1 id="appendix.incompatible.2.x">
427    <title>All BASE 2.x releases</title>
429    <para>
430      The list of changes made in the various BASE 2.x releases can be found
431      in the <ulink url=""
432      >BASE 2.17 documentation</ulink>.
433    </para>
435  </sect1>
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