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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE appendix PUBLIC |
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"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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<!-- |
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$Id$ |
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7 |
|
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Copyright (C) 2007 Peter Johansson, Nicklas Nordborg |
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9 |
|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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12 |
|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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jari |
as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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17 |
|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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31 May 07 |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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31 May 07 |
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GNU General Public License for more details. |
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22 |
|
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You should have received a copy of the GNU General Public License |
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11 Sep 08 |
jari |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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25 |
--> |
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|
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<appendix id="appendix.incompatible"> |
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04 Oct 11 |
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<?dbhtml filename="incompatible.html" ?> |
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<title>API changes that may affect backwards compatibility</title> |
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31 May 07 |
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30 |
<para> |
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31 May 07 |
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31 |
In this document we list all changes to code in the <emphasis>Public API</emphasis> |
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31 May 07 |
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32 |
that may be backwards incompatible with existing client applications |
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04 Oct 11 |
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33 |
and or plug-ins. See <xref linkend="base_api.public" /> for more |
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31 May 07 |
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34 |
information about what we mean with the <emphasis>Public API</emphasis> |
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31 May 07 |
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35 |
and backwards compatible. |
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31 May 07 |
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36 |
</para> |
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31 May 07 |
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37 |
|
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22 Feb 19 |
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38 |
<sect1 id="appendix.incompatible.3.15"> |
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22 Feb 19 |
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39 |
<title>BASE 3.15 release</title> |
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22 Feb 19 |
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40 |
|
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22 Feb 19 |
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41 |
<bridgehead id="appendix.incompatible.secondarystorage">Secondary storage support has been removed</bridgehead> |
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22 Feb 19 |
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42 |
<para> |
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22 Feb 19 |
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43 |
API that is related to the secondary storage feature has been removed. For example, |
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11 Mar 19 |
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44 |
in the <classname docapi="net.sf.basedb.core">File</classname> class, <code>getAction()/setAction()</code> |
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22 Feb 19 |
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45 |
has been removed. In the <classname docapi="net.sf.basedb.core">Location</classname> enumeration, |
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22 Feb 19 |
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46 |
<code>SECONDARY</code> has been removed. |
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22 Feb 19 |
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47 |
</para> |
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27 Feb 19 |
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48 |
|
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11 Mar 19 |
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49 |
<bridgehead id="appendix.incompatible.spotimages">Spot images support has been removed</bridgehead> |
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11 Mar 19 |
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50 |
<para> |
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11 Mar 19 |
nicklas |
51 |
API that is related to creating and viewing spot images has been removed. For example, |
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11 Mar 19 |
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52 |
in the <classname docapi="net.sf.basedb.core">RawBioAssay</classname> class, the |
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11 Mar 19 |
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53 |
<code>getSpotImages()</code> method has been removed. The <classname>SpotImages</classname> |
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11 Mar 19 |
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54 |
class has been removed and there are several other minor changes related to this. |
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55 |
There is no replacement. |
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11 Mar 19 |
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56 |
</para> |
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11 Mar 19 |
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57 |
|
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04 Apr 19 |
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58 |
<bridgehead id="appendix.incompatible.deprecated">Some deprecated classes and methods has been removed</bridgehead> |
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04 Apr 19 |
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59 |
<para> |
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04 Apr 19 |
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60 |
Classes and methods that has been deprecated since BASE 3.10 or earlier have been removed. This |
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04 Apr 19 |
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61 |
may affect existing plug-ins and extensions. In most cases there exists a replacement method or |
7681 |
04 Apr 19 |
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62 |
class as indicated in the BASE 3.14 documentation. |
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04 Apr 19 |
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63 |
</para> |
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04 Apr 19 |
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64 |
|
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27 Feb 19 |
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65 |
<bridgehead id="appendix.incompatible.generics">Introduced generic return parameters</bridgehead> |
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27 Feb 19 |
nicklas |
66 |
<para> |
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27 Feb 19 |
nicklas |
67 |
Some API methods with a return type of <classname>Object</classname> have been |
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27 Feb 19 |
nicklas |
68 |
changed to <code><T> T</code> (for example <code>public <T> T getObject(String name)</code> in |
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27 Feb 19 |
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69 |
<classname>ItemContext</classname>) |
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27 Feb 19 |
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70 |
which means that no explicit cast is needed since the compiler can typically infer this from the |
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27 Feb 19 |
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71 |
assignment made by the calling code. Note that this change is binary compatible with existing |
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27 Feb 19 |
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72 |
code, but in some cases it may be source code incompatible. Thus, already compiled code |
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27 Feb 19 |
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should continue to work, but source code may have to modified if compiling against the |
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27 Feb 19 |
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BASE 3.15 API. Here are some examples: |
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27 Feb 19 |
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75 |
</para> |
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27 Feb 19 |
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|
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<programlisting language="java"> |
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27 Feb 19 |
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<![CDATA[ |
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27 Feb 19 |
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// With BASE 3.14 (also works with BASE 3.15) |
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27 Feb 19 |
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80 |
ItemContext cc = ... |
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27 Feb 19 |
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81 |
Hardware hardware = (Hardware)cc.getObject("item"); |
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|
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// With BASE 3.15 |
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27 Feb 19 |
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Hardware hardware = cc.getObject("item"); |
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|
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// This will not compile against BASE 3.15! |
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Set<AnnotatedItem> items = (Set<AnnotatedItem>)cc.getObject("AnnotatedItems"); |
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27 Feb 19 |
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|
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27 Feb 19 |
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// The explict cast must be removed |
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27 Feb 19 |
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Set<AnnotatedItem> items = cc.getObject("AnnotatedItems"); |
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27 Feb 19 |
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91 |
]]> |
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</programlisting> |
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|
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<para> |
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27 Feb 19 |
nicklas |
95 |
Besides the change in the <methodname>ItemContext.getObject()</methodname> method there |
7609 |
27 Feb 19 |
nicklas |
96 |
are several similar changes in the <classname docapi="net.sf.basedb.core">ItemContext</classname> |
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27 Feb 19 |
nicklas |
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class as well as in <classname docapi="net.sf.basedb.core">SessionControl</classname>, |
7610 |
27 Feb 19 |
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98 |
<classname docapi="net.sf.basedb.core">Annotation</classname>, |
7610 |
27 Feb 19 |
nicklas |
99 |
<classname docapi="net.sf.basedb.core">AnnotationType</classname> |
7609 |
27 Feb 19 |
nicklas |
100 |
<classname docapi="net.sf.basedb.clients.web.formatter">FormatterFactory</classname>, |
7609 |
27 Feb 19 |
nicklas |
101 |
<classname docapi="net.sf.basedb.core">ParameterValues</classname> and several other |
7609 |
27 Feb 19 |
nicklas |
102 |
classes. In all cases, it should be relatively simple to update the code that doesn't compile. |
7609 |
27 Feb 19 |
nicklas |
103 |
</para> |
7609 |
27 Feb 19 |
nicklas |
104 |
|
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27 Feb 19 |
nicklas |
105 |
<note> |
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27 Feb 19 |
nicklas |
106 |
<title>Beware of JSP files</title> |
7609 |
27 Feb 19 |
nicklas |
107 |
<para> |
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27 Feb 19 |
nicklas |
108 |
Since this change doesn't affect already compiled code, extensions and plug-ins are |
7609 |
27 Feb 19 |
nicklas |
109 |
typically not affected. The exception is of course JSP files that are part of an |
7609 |
27 Feb 19 |
nicklas |
110 |
extension since they are compiled at runtime by Tomcat. It may be wise to test this |
7609 |
27 Feb 19 |
nicklas |
111 |
before upgrading a live BASE installation to BASE 3.15. |
7609 |
27 Feb 19 |
nicklas |
112 |
</para> |
7609 |
27 Feb 19 |
nicklas |
113 |
</note> |
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22 Feb 19 |
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114 |
</sect1> |
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22 Feb 19 |
nicklas |
115 |
|
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07 Dec 18 |
nicklas |
116 |
<sect1 id="appendix.incompatible.3.14"> |
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07 Dec 18 |
nicklas |
117 |
<title>BASE 3.14 release</title> |
7545 |
07 Dec 18 |
nicklas |
118 |
|
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07 Dec 18 |
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119 |
<bridgehead id="appendix.incompatible.authenticator">The (very) old Authenticator API has been removed</bridgehead> |
7545 |
07 Dec 18 |
nicklas |
120 |
<para> |
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07 Dec 18 |
nicklas |
121 |
The <code>net.sf.basedb.core.authentication.Authenticator</code> |
7545 |
07 Dec 18 |
nicklas |
122 |
interface and other related code that was deprecated in BASE 3.3 |
7545 |
07 Dec 18 |
nicklas |
123 |
has been removed. Systems that still use old authentication code |
7545 |
07 Dec 18 |
nicklas |
124 |
need to replace this with a newer version before updating. |
7545 |
07 Dec 18 |
nicklas |
125 |
</para> |
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07 Dec 18 |
nicklas |
126 |
|
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07 Dec 18 |
nicklas |
127 |
</sect1> |
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07 Dec 18 |
nicklas |
128 |
|
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18 Apr 17 |
nicklas |
129 |
<sect1 id="appendix.incompatible.3.11"> |
7342 |
18 Apr 17 |
nicklas |
130 |
<title>BASE 3.11 release</title> |
7342 |
18 Apr 17 |
nicklas |
131 |
|
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18 Apr 17 |
nicklas |
132 |
<bridgehead id="appendix.incompatible.paused-job">Job.Status.PAUSED</bridgehead> |
7342 |
18 Apr 17 |
nicklas |
133 |
<para> |
7342 |
18 Apr 17 |
nicklas |
134 |
Added the <code>PAUSED</code> option to the <code>Job.Status</code> |
7342 |
18 Apr 17 |
nicklas |
135 |
enumeration. This option is used when a running job has been temporarily paused. |
7342 |
18 Apr 17 |
nicklas |
136 |
Code that uses the job's status to decide what action to take may fail since |
7342 |
18 Apr 17 |
nicklas |
137 |
this is a new option. In most cases, it should be handled in the same way as |
7342 |
18 Apr 17 |
nicklas |
138 |
if the job is <code>WAITING</code>. |
7342 |
18 Apr 17 |
nicklas |
139 |
</para> |
7342 |
18 Apr 17 |
nicklas |
140 |
|
7343 |
18 Apr 17 |
nicklas |
141 |
<bridgehead id="appendix.incompatible.sha-256">SHA-256 fingerprint on file servers</bridgehead> |
7343 |
18 Apr 17 |
nicklas |
142 |
<para> |
7343 |
18 Apr 17 |
nicklas |
143 |
Added support for storing SHA-256 fingerprints on file servers. Code |
7343 |
18 Apr 17 |
nicklas |
144 |
that is expecting the fingerprint to always be a MD5 value may stop |
7343 |
18 Apr 17 |
nicklas |
145 |
to work. A new method <code>FileServer.getFingerprintType()</code> |
7343 |
18 Apr 17 |
nicklas |
146 |
has been added. |
7343 |
18 Apr 17 |
nicklas |
147 |
</para> |
7344 |
18 Apr 17 |
nicklas |
148 |
|
7344 |
18 Apr 17 |
nicklas |
149 |
<bridgehead id="appendix.incompatible.inactive-roles">Inactive roles</bridgehead> |
7344 |
18 Apr 17 |
nicklas |
150 |
<para> |
7344 |
18 Apr 17 |
nicklas |
151 |
A new feature which allows a user to activate and de-activate roles on the |
7344 |
18 Apr 17 |
nicklas |
152 |
fly during a login session has been implemented. This may cause a user to |
7344 |
18 Apr 17 |
nicklas |
153 |
gain or lose permissions at any time. A change of active roles triggers an |
7344 |
18 Apr 17 |
nicklas |
154 |
internal reload of permissions and since there are already other things that |
7344 |
18 Apr 17 |
nicklas |
155 |
do this, it should not cause any problems. The <code>SessionControl.getRoles()</code> |
7344 |
18 Apr 17 |
nicklas |
156 |
method has been deprecated and replaced with <code>SessionControl.getAllRoles()</code>, |
7344 |
18 Apr 17 |
nicklas |
157 |
<code>SessionControl.getActiveRoles()</code> and <code>SessionControl.getInactiveRoles()</code>. |
7344 |
18 Apr 17 |
nicklas |
158 |
</para> |
7343 |
18 Apr 17 |
nicklas |
159 |
|
7342 |
18 Apr 17 |
nicklas |
160 |
</sect1> |
7342 |
18 Apr 17 |
nicklas |
161 |
|
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04 Nov 16 |
nicklas |
162 |
<sect1 id="appendix.incompatible.3.10"> |
7221 |
04 Nov 16 |
nicklas |
163 |
<title>BASE 3.10 release</title> |
7221 |
04 Nov 16 |
nicklas |
164 |
|
7221 |
04 Nov 16 |
nicklas |
165 |
<bridgehead id="appendix.incompatible.annotate-permission">Annotate permission</bridgehead> |
7221 |
04 Nov 16 |
nicklas |
166 |
<para> |
7221 |
04 Nov 16 |
nicklas |
167 |
A new permission level, <code>ANNOTATE</code> has been added to |
7221 |
04 Nov 16 |
nicklas |
168 |
the permission system. Extensions and other clients that are not |
7221 |
04 Nov 16 |
nicklas |
169 |
aware of this permission may think that the user only has |
7221 |
04 Nov 16 |
nicklas |
170 |
<code>READ</code> permission. |
7221 |
04 Nov 16 |
nicklas |
171 |
</para> |
7221 |
04 Nov 16 |
nicklas |
172 |
|
7276 |
24 Jan 17 |
nicklas |
173 |
<bridgehead id="appendix.incompatible.project-annotations">Project-specific annotations</bridgehead> |
7276 |
24 Jan 17 |
nicklas |
174 |
<para> |
7276 |
24 Jan 17 |
nicklas |
175 |
The annotation system has been extended with a new feature: project-specific annotations. |
7276 |
24 Jan 17 |
nicklas |
176 |
Extensions and other code that is not aware of this may experience strange behaviour |
7276 |
24 Jan 17 |
nicklas |
177 |
where annotation values may not change as expected or may change in unexpected ways. |
7276 |
24 Jan 17 |
nicklas |
178 |
For example, trying to change the default value of a project-specific annotation when |
7276 |
24 Jan 17 |
nicklas |
179 |
a project is active causes a new annotation to be created in the background instead |
7276 |
24 Jan 17 |
nicklas |
180 |
of changing the current one. Note that this feature is disabled by default and |
7276 |
24 Jan 17 |
nicklas |
181 |
must be enabled per annotation type. Updating an existing server should be safe |
7276 |
24 Jan 17 |
nicklas |
182 |
and will not affect existing annotations or annotation types. |
7276 |
24 Jan 17 |
nicklas |
183 |
</para> |
7276 |
24 Jan 17 |
nicklas |
184 |
|
7221 |
04 Nov 16 |
nicklas |
185 |
</sect1> |
7221 |
04 Nov 16 |
nicklas |
186 |
|
7161 |
27 May 16 |
nicklas |
187 |
<sect1 id="appendix.incompatible.3.9"> |
7161 |
27 May 16 |
nicklas |
188 |
<title>BASE 3.9 release</title> |
7161 |
27 May 16 |
nicklas |
189 |
|
7161 |
27 May 16 |
nicklas |
190 |
<bridgehead id="appendix.incompatible.session-control">Application.getSessionControl()</bridgehead> |
7161 |
27 May 16 |
nicklas |
191 |
<para> |
7161 |
27 May 16 |
nicklas |
192 |
The <classname docapi="net.sf.basedb.core">Application.getSessionControl()</classname> |
7161 |
27 May 16 |
nicklas |
193 |
method for getting access to an existing session has been deprecated. A new |
7161 |
27 May 16 |
nicklas |
194 |
version has been implemented that require that an <emphasis>external client id</emphasis> |
7161 |
27 May 16 |
nicklas |
195 |
is specified. This change was needed to avoid sessions leaking between client |
7161 |
27 May 16 |
nicklas |
196 |
applications and prevent users to use an application they don't have permission to use. |
7161 |
27 May 16 |
nicklas |
197 |
</para> |
7161 |
27 May 16 |
nicklas |
198 |
|
7161 |
27 May 16 |
nicklas |
199 |
<para> |
7161 |
27 May 16 |
nicklas |
200 |
The deprecated method use the client id from the BASE web client. Extensions and |
7161 |
27 May 16 |
nicklas |
201 |
other clients that use a different client id are affected and may stop to work |
7161 |
27 May 16 |
nicklas |
202 |
until they have been updated to use the new API. For more information see |
7982 |
14 Jun 21 |
nicklas |
203 |
<ulink url="https://base.thep.lu.se/ticket/2011">ticket 2011</ulink>. |
7161 |
27 May 16 |
nicklas |
204 |
</para> |
7161 |
27 May 16 |
nicklas |
205 |
|
7161 |
27 May 16 |
nicklas |
206 |
</sect1> |
7161 |
27 May 16 |
nicklas |
207 |
|
7161 |
27 May 16 |
nicklas |
208 |
|
7079 |
16 Feb 16 |
nicklas |
209 |
<sect1 id="appendix.incompatible.3.8"> |
7079 |
16 Feb 16 |
nicklas |
210 |
<title>BASE 3.8 release</title> |
7079 |
16 Feb 16 |
nicklas |
211 |
|
7079 |
16 Feb 16 |
nicklas |
212 |
<bridgehead id="appendix.incompatible.service-session-control">ServiceSessionControl API</bridgehead> |
7079 |
16 Feb 16 |
nicklas |
213 |
<para> |
7079 |
16 Feb 16 |
nicklas |
214 |
The <classname docapi="net.sf.basedb.core">ServiceSessionControl</classname> API for |
7079 |
16 Feb 16 |
nicklas |
215 |
configuration and building Hibernate <classname>SessionFactory</classname> |
7079 |
16 Feb 16 |
nicklas |
216 |
instances has been changed due the Hibernate 5 upgrade. This change affects |
7079 |
16 Feb 16 |
nicklas |
217 |
extensions that use the API for storing their own data inside the BASE database. |
7079 |
16 Feb 16 |
nicklas |
218 |
Extensions that use this API must be updated or they will not work with BASE 3.8. |
7079 |
16 Feb 16 |
nicklas |
219 |
</para> |
7079 |
16 Feb 16 |
nicklas |
220 |
|
7079 |
16 Feb 16 |
nicklas |
221 |
</sect1> |
7079 |
16 Feb 16 |
nicklas |
222 |
|
7079 |
16 Feb 16 |
nicklas |
223 |
|
6964 |
02 Oct 15 |
nicklas |
224 |
<sect1 id="appendix.incompatible.3.6"> |
6964 |
02 Oct 15 |
nicklas |
225 |
<title>BASE 3.6 release</title> |
6964 |
02 Oct 15 |
nicklas |
226 |
|
6964 |
02 Oct 15 |
nicklas |
227 |
<bridgehead id="appendix.incompatible.cloned-annotation">Cloned annotations</bridgehead> |
6964 |
02 Oct 15 |
nicklas |
228 |
<para> |
6964 |
02 Oct 15 |
nicklas |
229 |
A new feature that allows an inherited annotation to be cloned has been implemented. |
6964 |
02 Oct 15 |
nicklas |
230 |
Several methods in <classname docapi="net.sf.basedb.core">AnnotationSet</classname>, |
6964 |
02 Oct 15 |
nicklas |
231 |
<classname docapi="net.sf.basedb.core.snapshot">AnnotationSnapshot</classname> and some |
6964 |
02 Oct 15 |
nicklas |
232 |
other classes has been deprecated and replaced with new methods. Existing code that |
6964 |
02 Oct 15 |
nicklas |
233 |
is not aware of cloned annotations should continue to work, but may experience some |
6964 |
02 Oct 15 |
nicklas |
234 |
inconsistent behaviour in case the cloned values are out-of-sync with the original |
6964 |
02 Oct 15 |
nicklas |
235 |
values. |
6964 |
02 Oct 15 |
nicklas |
236 |
</para> |
6964 |
02 Oct 15 |
nicklas |
237 |
|
6964 |
02 Oct 15 |
nicklas |
238 |
<bridgehead id="appendix.incompatible.experimental-factors">Experimental factors have moved</bridgehead> |
6964 |
02 Oct 15 |
nicklas |
239 |
<para> |
6964 |
02 Oct 15 |
nicklas |
240 |
To allow the owner of an experiment to manage experimental factor values as part |
6964 |
02 Oct 15 |
nicklas |
241 |
of the experiment, the <classname docapi="net.sf.basedb.core">RootRawBioassay</classname> |
6964 |
02 Oct 15 |
nicklas |
242 |
item was introduced. The new item is a one-to-one representation of a <classname |
6964 |
02 Oct 15 |
nicklas |
243 |
docapi="net.sf.basedb.core">RawBioAssay</classname> inside that experiment. |
6964 |
02 Oct 15 |
nicklas |
244 |
Experimental factor values that are found on existing raw bioassays are copied to the |
6964 |
02 Oct 15 |
nicklas |
245 |
root rawbioassays when updating BASE. Changes made after the update will only |
6964 |
02 Oct 15 |
nicklas |
246 |
affect the root raw bioassays. Existing code that is not aware of root raw bioassays |
6964 |
02 Oct 15 |
nicklas |
247 |
may not find the experimental factor values. |
6964 |
02 Oct 15 |
nicklas |
248 |
</para> |
6964 |
02 Oct 15 |
nicklas |
249 |
|
6964 |
02 Oct 15 |
nicklas |
250 |
</sect1> |
6964 |
02 Oct 15 |
nicklas |
251 |
|
6807 |
26 Mar 15 |
nicklas |
252 |
<sect1 id="appendix.incompatible.3.5"> |
6807 |
26 Mar 15 |
nicklas |
253 |
<title>BASE 3.5 release</title> |
6807 |
26 Mar 15 |
nicklas |
254 |
|
6807 |
26 Mar 15 |
nicklas |
255 |
<bridgehead id="appendix.incompatible.itemlists">Biomaterial lists has been replaced with item lists</bridgehead> |
6807 |
26 Mar 15 |
nicklas |
256 |
<para> |
6807 |
26 Mar 15 |
nicklas |
257 |
The <classname docapi="net.sf.basedb.core">BioMaterialList</classname> |
6807 |
26 Mar 15 |
nicklas |
258 |
class has been removed and replaced with <classname |
6807 |
26 Mar 15 |
nicklas |
259 |
docapi="net.sf.basedb.core">ItemList</classname>. The API is similar |
6807 |
26 Mar 15 |
nicklas |
260 |
but not exactly the same. In most cases only minor changes are required |
6807 |
26 Mar 15 |
nicklas |
261 |
to make existing code work with the new API. |
6807 |
26 Mar 15 |
nicklas |
262 |
</para> |
6807 |
26 Mar 15 |
nicklas |
263 |
|
6807 |
26 Mar 15 |
nicklas |
264 |
<para> |
6807 |
26 Mar 15 |
nicklas |
265 |
Queries that use the <code>BioMaterial.bioMaterialLists</code> association |
6807 |
26 Mar 15 |
nicklas |
266 |
for joining will no longer work. There is no replacement functionality for |
6807 |
26 Mar 15 |
nicklas |
267 |
joining item lists. |
6807 |
26 Mar 15 |
nicklas |
268 |
</para> |
6807 |
26 Mar 15 |
nicklas |
269 |
|
6807 |
26 Mar 15 |
nicklas |
270 |
<para> |
6807 |
26 Mar 15 |
nicklas |
271 |
All classes in the <code>net.sf.basedb.util.biomaterial</code> package has |
6807 |
26 Mar 15 |
nicklas |
272 |
been deprecated. It is recommended that code that uses any of these classes |
6807 |
26 Mar 15 |
nicklas |
273 |
are updated to use classes in <code>net.sf.basedb.util.listable</code> instead. |
6807 |
26 Mar 15 |
nicklas |
274 |
The API is a bit different, but the new implementations typically performs a |
6807 |
26 Mar 15 |
nicklas |
275 |
lot better so it is worth the work. |
6807 |
26 Mar 15 |
nicklas |
276 |
</para> |
6807 |
26 Mar 15 |
nicklas |
277 |
|
6807 |
26 Mar 15 |
nicklas |
278 |
<para> |
6807 |
26 Mar 15 |
nicklas |
279 |
There are several other minor changes in the API that previously worked with |
6807 |
26 Mar 15 |
nicklas |
280 |
the <code>BioMaterialList</code> class that has been removed and replaced |
6807 |
26 Mar 15 |
nicklas |
281 |
with something else. |
6807 |
26 Mar 15 |
nicklas |
282 |
</para> |
6807 |
26 Mar 15 |
nicklas |
283 |
|
6807 |
26 Mar 15 |
nicklas |
284 |
</sect1> |
6807 |
26 Mar 15 |
nicklas |
285 |
|
6480 |
12 Jun 14 |
nicklas |
286 |
<sect1 id="appendix.incompatible.3.4"> |
6480 |
12 Jun 14 |
nicklas |
287 |
<title>BASE 3.4 release</title> |
6480 |
12 Jun 14 |
nicklas |
288 |
|
6480 |
12 Jun 14 |
nicklas |
289 |
<bridgehead>Updated JDOM to 2.0</bridgehead> |
6480 |
12 Jun 14 |
nicklas |
290 |
<para> |
6480 |
12 Jun 14 |
nicklas |
291 |
The JDOM library has been updated to version 2.0 from 1.1. The |
6480 |
12 Jun 14 |
nicklas |
292 |
new version is incompatible with the old version. BASE 3.4 will |
6480 |
12 Jun 14 |
nicklas |
293 |
ship with both versions but JDOM 1.1 will be removed in BASE 3.5 |
6480 |
12 Jun 14 |
nicklas |
294 |
and so will all API methods that expose JDOM 1.1 classes. |
6480 |
12 Jun 14 |
nicklas |
295 |
It is recommended that plug-ins and extensions that use JDOM also |
6480 |
12 Jun 14 |
nicklas |
296 |
update to JDOM 2.0. |
6480 |
12 Jun 14 |
nicklas |
297 |
</para> |
6480 |
12 Jun 14 |
nicklas |
298 |
|
6480 |
12 Jun 14 |
nicklas |
299 |
<bridgehead>Updated to Apache HttpClient 4.3.4</bridgehead> |
6480 |
12 Jun 14 |
nicklas |
300 |
<para> |
6480 |
12 Jun 14 |
nicklas |
301 |
The Apache HTTP Client library has been updated to version 4.3.4. |
6480 |
12 Jun 14 |
nicklas |
302 |
The new version has deprecated some classes that are exposed through |
6480 |
12 Jun 14 |
nicklas |
303 |
the BASE API (mainly in <classname docapi="net.sf.basedb.util.ssl">SSLUtil</classname>). |
6480 |
12 Jun 14 |
nicklas |
304 |
As a result we had to deprecate parts of the BASE API, which will |
6480 |
12 Jun 14 |
nicklas |
305 |
be removed in BASE 3.5. It is recommended that plug-ins and |
6480 |
12 Jun 14 |
nicklas |
306 |
extensions that are affected are updated to use the replacement API |
6480 |
12 Jun 14 |
nicklas |
307 |
instead. |
6480 |
12 Jun 14 |
nicklas |
308 |
</para> |
6480 |
12 Jun 14 |
nicklas |
309 |
|
6480 |
12 Jun 14 |
nicklas |
310 |
</sect1> |
6480 |
12 Jun 14 |
nicklas |
311 |
|
6281 |
27 May 13 |
nicklas |
312 |
<sect1 id="appendix.incompatible.3.3"> |
6281 |
27 May 13 |
nicklas |
313 |
<title>BASE 3.3 release</title> |
6410 |
31 Jan 14 |
nicklas |
314 |
|
6410 |
31 Jan 14 |
nicklas |
315 |
<bridgehead>Content security policy</bridgehead> |
6410 |
31 Jan 14 |
nicklas |
316 |
<para> |
6410 |
31 Jan 14 |
nicklas |
317 |
The BASE web client now set a rather strict <emphasis>Content |
6410 |
31 Jan 14 |
nicklas |
318 |
Security Policy</emphasis> that prevent browsers from executing |
6410 |
31 Jan 14 |
nicklas |
319 |
code (including JavaScript) that is considered unsafe. Some extensions |
6410 |
31 Jan 14 |
nicklas |
320 |
may cease to work due to this. Go to |
6410 |
31 Jan 14 |
nicklas |
321 |
<menuchoice> |
6410 |
31 Jan 14 |
nicklas |
322 |
<guimenu>Administrate</guimenu> |
6410 |
31 Jan 14 |
nicklas |
323 |
<guimenuitem>Plug-ins & extensions</guimenuitem> |
6410 |
31 Jan 14 |
nicklas |
324 |
<guimenuitem>Overview</guimenuitem> |
6410 |
31 Jan 14 |
nicklas |
325 |
</menuchoice> |
6410 |
31 Jan 14 |
nicklas |
326 |
(after upgrading) to see if there are any warnings about this. |
6410 |
31 Jan 14 |
nicklas |
327 |
Read more in <xref linkend="appendix.web.xml.csp-filter" /> |
6410 |
31 Jan 14 |
nicklas |
328 |
for information about how to relax the policy. |
6410 |
31 Jan 14 |
nicklas |
329 |
</para> |
6281 |
27 May 13 |
nicklas |
330 |
|
6403 |
29 Jan 14 |
nicklas |
331 |
<bridgehead>Re-factored JavaScript API</bridgehead> |
6403 |
29 Jan 14 |
nicklas |
332 |
<para> |
6403 |
29 Jan 14 |
nicklas |
333 |
The BASE web client has undergone a major refactoring with respect to |
6403 |
29 Jan 14 |
nicklas |
334 |
the JavaScript API that is used on the server. A lot of functions have |
6403 |
29 Jan 14 |
nicklas |
335 |
been replaced with new implementations. We have tried to map the old |
6403 |
29 Jan 14 |
nicklas |
336 |
functions to the new ones, but this has not always been possible. Extentions |
6403 |
29 Jan 14 |
nicklas |
337 |
that use the BASE JavaScript API must be tested with BASE 3.3 to find |
6403 |
29 Jan 14 |
nicklas |
338 |
out if they are still working or if modifications are needed. |
6403 |
29 Jan 14 |
nicklas |
339 |
</para> |
6403 |
29 Jan 14 |
nicklas |
340 |
|
6403 |
29 Jan 14 |
nicklas |
341 |
<note> |
6403 |
29 Jan 14 |
nicklas |
342 |
<title>Avoid in-line event handlers and script</title> |
6403 |
29 Jan 14 |
nicklas |
343 |
<para> |
6403 |
29 Jan 14 |
nicklas |
344 |
The main reason for the refactoring is to get rid of all in-line |
6403 |
29 Jan 14 |
nicklas |
345 |
event handlers and script sections since this is a possible entry |
6403 |
29 Jan 14 |
nicklas |
346 |
point for cross-site scripting attacks (see <ulink |
7982 |
14 Jun 21 |
nicklas |
347 |
url="https://base.thep.lu.se/ticket/1712">ticket 1712</ulink>). |
6403 |
29 Jan 14 |
nicklas |
348 |
Extension developers are encouraged to make the same changes in |
6403 |
29 Jan 14 |
nicklas |
349 |
their applications. |
6403 |
29 Jan 14 |
nicklas |
350 |
</para> |
6403 |
29 Jan 14 |
nicklas |
351 |
</note> |
6403 |
29 Jan 14 |
nicklas |
352 |
|
6281 |
27 May 13 |
nicklas |
353 |
<bridgehead>Biomaterial items are now lazy-loading</bridgehead> |
6281 |
27 May 13 |
nicklas |
354 |
<para> |
6281 |
27 May 13 |
nicklas |
355 |
For performance reasons biomaterial items have been changed from |
6281 |
27 May 13 |
nicklas |
356 |
eager-loading to lazy-loading. This may affect clients and/or plug-ins |
6281 |
27 May 13 |
nicklas |
357 |
that expect the parent chain of biomaterials to always be fully initialized |
6281 |
27 May 13 |
nicklas |
358 |
without explicitely having told the BASE core to do so. |
6281 |
27 May 13 |
nicklas |
359 |
</para> |
6336 |
28 Oct 13 |
nicklas |
360 |
|
6336 |
28 Oct 13 |
nicklas |
361 |
<bridgehead>Tables can have columns with different sort order</bridgehead> |
6336 |
28 Oct 13 |
nicklas |
362 |
<para> |
6336 |
28 Oct 13 |
nicklas |
363 |
A new feature has been implemented which allows columns in a table to |
6336 |
28 Oct 13 |
nicklas |
364 |
have different sort order. This is implemented by allowing '+' or '-' |
6336 |
28 Oct 13 |
nicklas |
365 |
as a prefix to properties returned by the <methodname>ItemContext.getSortProperty()</methodname> |
6336 |
28 Oct 13 |
nicklas |
366 |
method. Properties without a prefix still use the global sort order as returned |
6336 |
28 Oct 13 |
nicklas |
367 |
by <methodname>ItemContext.getSortDirection()</methodname>. |
6336 |
28 Oct 13 |
nicklas |
368 |
</para> |
6336 |
28 Oct 13 |
nicklas |
369 |
|
6336 |
28 Oct 13 |
nicklas |
370 |
<para> |
6336 |
28 Oct 13 |
nicklas |
371 |
Code that is not aware of the prefixes may fail since '+' and '-' are not |
6336 |
28 Oct 13 |
nicklas |
372 |
allowed in property names. |
6336 |
28 Oct 13 |
nicklas |
373 |
</para> |
6429 |
10 Mar 14 |
nicklas |
374 |
|
6429 |
10 Mar 14 |
nicklas |
375 |
<bridgehead>External authentication has been converted to an extension point</bridgehead> |
6429 |
10 Mar 14 |
nicklas |
376 |
<para> |
6429 |
10 Mar 14 |
nicklas |
377 |
External authentication plug-ins using the old system are supported through a |
6429 |
10 Mar 14 |
nicklas |
378 |
wrapper extension, but the recommendation is to update those plug-in to the |
6429 |
10 Mar 14 |
nicklas |
379 |
new system. See <xref linkend="extensions_developer.login-manager" /> for more information. |
6429 |
10 Mar 14 |
nicklas |
380 |
</para> |
6429 |
10 Mar 14 |
nicklas |
381 |
|
6433 |
14 Mar 14 |
nicklas |
382 |
<bridgehead>Setting parameters for a job no longer set it to status=WAITING</bridgehead> |
6433 |
14 Mar 14 |
nicklas |
383 |
<para> |
6433 |
14 Mar 14 |
nicklas |
384 |
Added <methodname>Job.setScheduled()</methodname> to switch the state |
6433 |
14 Mar 14 |
nicklas |
385 |
from <constant>UNCONFIGURED</constant> to <constant>WAITING</constant>. |
6433 |
14 Mar 14 |
nicklas |
386 |
A job can't be executed before it has entered the <constant>WAITING</constant> |
6433 |
14 Mar 14 |
nicklas |
387 |
state. The change makes it possible to register a job and some parameters for |
6433 |
14 Mar 14 |
nicklas |
388 |
it and remain in the <constant>UNCONFIGURED</constant> state. |
6433 |
14 Mar 14 |
nicklas |
389 |
</para> |
6433 |
14 Mar 14 |
nicklas |
390 |
|
6281 |
27 May 13 |
nicklas |
391 |
</sect1> |
6281 |
27 May 13 |
nicklas |
392 |
|
6077 |
03 Aug 12 |
nicklas |
393 |
<sect1 id="appendix.incompatible.3.2"> |
6077 |
03 Aug 12 |
nicklas |
394 |
<title>BASE 3.2 release</title> |
6077 |
03 Aug 12 |
nicklas |
395 |
|
6102 |
04 Sep 12 |
nicklas |
396 |
<bridgehead>Derived bioassays can now have multiple parents</bridgehead> |
6102 |
04 Sep 12 |
nicklas |
397 |
<para> |
6102 |
04 Sep 12 |
nicklas |
398 |
Before BASE 3.2 a derived bioassay was restricted to a single parent |
6102 |
04 Sep 12 |
nicklas |
399 |
item. This affects the API and the <methodname>DerivedBioAssay.getParent()</methodname> |
6102 |
04 Sep 12 |
nicklas |
400 |
and <methodname>DerivedBioAssay.getPhysicalBioAssays()</methodname> now always |
6102 |
04 Sep 12 |
nicklas |
401 |
return null. Existing code should be updated to use <methodname>getPhysicalBioAssays()</methodname> |
6102 |
04 Sep 12 |
nicklas |
402 |
and <methodname>getParents()</methodname> (which return <classname>ItemQuery</classname> instances) |
6102 |
04 Sep 12 |
nicklas |
403 |
instead. Code that is using queries to filter or sort on parent items must also be |
6102 |
04 Sep 12 |
nicklas |
404 |
updated since the association names have changed. |
6102 |
04 Sep 12 |
nicklas |
405 |
</para> |
6102 |
04 Sep 12 |
nicklas |
406 |
|
6077 |
03 Aug 12 |
nicklas |
407 |
<bridgehead>BASEfile exporter automatically closes the output stream</bridgehead> |
6077 |
03 Aug 12 |
nicklas |
408 |
<para> |
6077 |
03 Aug 12 |
nicklas |
409 |
The implementation of the BASEfile exporter has been changed to |
6077 |
03 Aug 12 |
nicklas |
410 |
automatically close the provided output stream when the export |
6077 |
03 Aug 12 |
nicklas |
411 |
is complete. Clients that need the old behavior should call |
6077 |
03 Aug 12 |
nicklas |
412 |
<code>BaseFileExporter.setAutoCloseWriters(false)</code> before |
6077 |
03 Aug 12 |
nicklas |
413 |
using it. |
6077 |
03 Aug 12 |
nicklas |
414 |
</para> |
6080 |
07 Aug 12 |
nicklas |
415 |
|
6080 |
07 Aug 12 |
nicklas |
416 |
<bridgehead>Change history logging is now an extension point</bridgehead> |
6080 |
07 Aug 12 |
nicklas |
417 |
<para> |
6080 |
07 Aug 12 |
nicklas |
418 |
The change history logging has been converted to an extension point. |
6080 |
07 Aug 12 |
nicklas |
419 |
The <constant>changelog.factory</constant> setting in <filename>base.config</filename> |
6080 |
07 Aug 12 |
nicklas |
420 |
is no longer used. Existing logging implementations should be updated |
6080 |
07 Aug 12 |
nicklas |
421 |
to use the extension system. See <xref linkend="extensions_developer.logging" />. |
6080 |
07 Aug 12 |
nicklas |
422 |
A temporary solution is to use one of the debugging action factories to |
6080 |
07 Aug 12 |
nicklas |
423 |
define the extension point: |
6080 |
07 Aug 12 |
nicklas |
424 |
</para> |
6080 |
07 Aug 12 |
nicklas |
425 |
|
6080 |
07 Aug 12 |
nicklas |
426 |
<programlisting language="xml"> |
6080 |
07 Aug 12 |
nicklas |
427 |
<![CDATA[ |
6080 |
07 Aug 12 |
nicklas |
428 |
<extension |
6080 |
07 Aug 12 |
nicklas |
429 |
id="id-of-custom-log-manager" |
6080 |
07 Aug 12 |
nicklas |
430 |
extends="net.sf.basedb.core.log-manager" |
6080 |
07 Aug 12 |
nicklas |
431 |
> |
6080 |
07 Aug 12 |
nicklas |
432 |
<about> |
6080 |
07 Aug 12 |
nicklas |
433 |
<name>My custom log manager</name> |
6080 |
07 Aug 12 |
nicklas |
434 |
<description> |
6080 |
07 Aug 12 |
nicklas |
435 |
Temporary solution to allow the old log manager to work with the extension system. |
6080 |
07 Aug 12 |
nicklas |
436 |
</description> |
6080 |
07 Aug 12 |
nicklas |
437 |
</about> |
6080 |
07 Aug 12 |
nicklas |
438 |
<index>1</index> |
6080 |
07 Aug 12 |
nicklas |
439 |
<action-factory> |
6080 |
07 Aug 12 |
nicklas |
440 |
<factory-class>net.sf.basedb.util.extensions.debug.BeanActionFactory</factory-class> |
6080 |
07 Aug 12 |
nicklas |
441 |
<parameters> |
6080 |
07 Aug 12 |
nicklas |
442 |
<beanClass>my.custom.LogmangerClass</beanClass> |
6080 |
07 Aug 12 |
nicklas |
443 |
</parameters> |
6080 |
07 Aug 12 |
nicklas |
444 |
</action-factory> |
6080 |
07 Aug 12 |
nicklas |
445 |
</extension> |
6080 |
07 Aug 12 |
nicklas |
446 |
]]> |
6080 |
07 Aug 12 |
nicklas |
447 |
</programlisting> |
6080 |
07 Aug 12 |
nicklas |
448 |
|
6077 |
03 Aug 12 |
nicklas |
449 |
</sect1> |
6077 |
03 Aug 12 |
nicklas |
450 |
|
5874 |
11 Nov 11 |
nicklas |
451 |
<sect1 id="appendix.incompatible.3.1"> |
5874 |
11 Nov 11 |
nicklas |
452 |
<title>BASE 3.1 release</title> |
5874 |
11 Nov 11 |
nicklas |
453 |
|
5874 |
11 Nov 11 |
nicklas |
454 |
<bridgehead>Web service framework updated to Axis2 1.6</bridgehead> |
5874 |
11 Nov 11 |
nicklas |
455 |
<para> |
5874 |
11 Nov 11 |
nicklas |
456 |
We have updated the web services framework to Axis2 1.6. Clients |
5874 |
11 Nov 11 |
nicklas |
457 |
that use earlier Axis2 versions may not work when connecting to a |
5874 |
11 Nov 11 |
nicklas |
458 |
BASE 3.1 server. Unfortunately, clients that use the Axis2 1.6 |
5874 |
11 Nov 11 |
nicklas |
459 |
framework may have problems connecting to BASE 3.0 servers so it |
5874 |
11 Nov 11 |
nicklas |
460 |
may be difficult to implement support for both BASE 3.0 and BASE 3.1 |
5874 |
11 Nov 11 |
nicklas |
461 |
in a single client application. |
5874 |
11 Nov 11 |
nicklas |
462 |
</para> |
5968 |
16 Feb 12 |
nicklas |
463 |
|
5968 |
16 Feb 12 |
nicklas |
464 |
<bridgehead>New GUI look and feel</bridgehead> |
5968 |
16 Feb 12 |
nicklas |
465 |
<para> |
5968 |
16 Feb 12 |
nicklas |
466 |
Taglibs, stylesheets and javscript functions have been changed |
5968 |
16 Feb 12 |
nicklas |
467 |
to create a new look and feel. Plug-ins and extensions that uses |
5968 |
16 Feb 12 |
nicklas |
468 |
GUI elements from the core BASE installation may need to be updated |
5968 |
16 Feb 12 |
nicklas |
469 |
for the best user experience. The changes are too numerous so we can't |
5968 |
16 Feb 12 |
nicklas |
470 |
list them here. Please use the developers mailing list if specific |
7982 |
14 Jun 21 |
nicklas |
471 |
information is needed or see <ulink url="https://base.thep.lu.se/ticket/1655">ticket |
5968 |
16 Feb 12 |
nicklas |
472 |
1655</ulink> for some screenshots and other information. |
5968 |
16 Feb 12 |
nicklas |
473 |
</para> |
5969 |
16 Feb 12 |
nicklas |
474 |
|
5969 |
16 Feb 12 |
nicklas |
475 |
<bridgehead>Per-experiment copy of reporter annotations</bridgehead> |
5969 |
16 Feb 12 |
nicklas |
476 |
<para> |
5969 |
16 Feb 12 |
nicklas |
477 |
A new feature has been implemented that allows a user to make a |
5969 |
16 Feb 12 |
nicklas |
478 |
local copy of reporter annotations for reporters that are used |
5969 |
16 Feb 12 |
nicklas |
479 |
in an experiment. The existing API will by default use the local |
5969 |
16 Feb 12 |
nicklas |
480 |
copy if one is available. It is possible to use the master reporter |
5969 |
16 Feb 12 |
nicklas |
481 |
annotations by invoking certain API methods (for example: |
5969 |
16 Feb 12 |
nicklas |
482 |
<code>DynamicQuery.setUseClonedReporters(false)</code>). Since the copy |
5969 |
16 Feb 12 |
nicklas |
483 |
may include only a subset of the available reporter annotations this |
5969 |
16 Feb 12 |
nicklas |
484 |
may cause problems for code that is expecting all annotations to be |
5969 |
16 Feb 12 |
nicklas |
485 |
available. See <classname docapi="net.sf.basedb.core">ReporterCloneTemplate</classname> |
7982 |
14 Jun 21 |
nicklas |
486 |
and <ulink url="https://base.thep.lu.se/ticket/1616">ticket 1616</ulink> |
5969 |
16 Feb 12 |
nicklas |
487 |
for more information. |
5969 |
16 Feb 12 |
nicklas |
488 |
</para> |
5968 |
16 Feb 12 |
nicklas |
489 |
|
5983 |
23 Feb 12 |
nicklas |
490 |
<bridgehead>Annotations can be inherited/pushed from child to parent item</bridgehead> |
5983 |
23 Feb 12 |
nicklas |
491 |
<para> |
5983 |
23 Feb 12 |
nicklas |
492 |
A new feature has been implemented that allows an item to "push" annotations |
5983 |
23 Feb 12 |
nicklas |
493 |
up to it's parent in addition to the normal "inherit to child" method. |
5983 |
23 Feb 12 |
nicklas |
494 |
This has been implemented as a change in the <methodname>getAnnotatableParents()</methodname> |
5983 |
23 Feb 12 |
nicklas |
495 |
method defined by the <interfacename docapi="net.sf.basedb.core">Annotatable</interfacename> |
5983 |
23 Feb 12 |
nicklas |
496 |
interface. This may cause unexpected issues with code that is not prepared to handle |
5983 |
23 Feb 12 |
nicklas |
497 |
this situation. Particulary, infinite loops must be avoided when traversing the "parent" |
5983 |
23 Feb 12 |
nicklas |
498 |
tree of an item (but this should already be in place since it can already happen due to |
7982 |
14 Jun 21 |
nicklas |
499 |
mistakes when creating items). See <ulink url="https://base.thep.lu.se/ticket/1605">ticket 1605</ulink> |
5983 |
23 Feb 12 |
nicklas |
500 |
for more information. |
5983 |
23 Feb 12 |
nicklas |
501 |
</para> |
5983 |
23 Feb 12 |
nicklas |
502 |
|
5874 |
11 Nov 11 |
nicklas |
503 |
</sect1> |
5874 |
11 Nov 11 |
nicklas |
504 |
|
5874 |
11 Nov 11 |
nicklas |
505 |
|
5677 |
29 Jun 11 |
nicklas |
506 |
<sect1 id="appendix.incompatible.3.0"> |
5677 |
29 Jun 11 |
nicklas |
507 |
<title>BASE 3.0 release</title> |
5560 |
31 Jan 11 |
nicklas |
508 |
|
5560 |
31 Jan 11 |
nicklas |
509 |
<para> |
5677 |
29 Jun 11 |
nicklas |
510 |
There are a lot incompatible changes between BASE 3 and any of the BASE 2.x |
5677 |
29 Jun 11 |
nicklas |
511 |
versions. We do not list list those changes here since we do not expect existing |
5677 |
29 Jun 11 |
nicklas |
512 |
plug-ins, extensions or other client application to work with BASE 3 without |
5677 |
29 Jun 11 |
nicklas |
513 |
modification. See <xref linkend="migrate_2_3" /> for more information. |
5560 |
31 Jan 11 |
nicklas |
514 |
</para> |
5560 |
31 Jan 11 |
nicklas |
515 |
</sect1> |
3415 |
31 May 07 |
nicklas |
516 |
|
5677 |
29 Jun 11 |
nicklas |
517 |
<sect1 id="appendix.incompatible.2.x"> |
5677 |
29 Jun 11 |
nicklas |
518 |
<title>All BASE 2.x releases</title> |
5325 |
29 Apr 10 |
nicklas |
519 |
|
5325 |
29 Apr 10 |
nicklas |
520 |
<para> |
5677 |
29 Jun 11 |
nicklas |
521 |
The list of changes made in the various BASE 2.x releases can be found |
7982 |
14 Jun 21 |
nicklas |
522 |
in the <ulink url="https://base.thep.lu.se/chrome/site/2.17/html/appendix/appendix.incompatible.html" |
5677 |
29 Jun 11 |
nicklas |
523 |
>BASE 2.17 documentation</ulink>. |
5325 |
29 Apr 10 |
nicklas |
524 |
</para> |
5325 |
29 Apr 10 |
nicklas |
525 |
|
5325 |
29 Apr 10 |
nicklas |
526 |
</sect1> |
5325 |
29 Apr 10 |
nicklas |
527 |
|
5204 |
16 Dec 09 |
nicklas |
528 |
|
3415 |
31 May 07 |
nicklas |
529 |
</appendix> |
3415 |
31 May 07 |
nicklas |
530 |
|