source: trunk/doc/src/docbook/appendix/update_warnings.xml @ 6600

Last change on this file since 6600 was 6600, checked in by Nicklas Nordborg, 9 years ago

Merge BASE 3.3.3 to the trunk.

There is a test failure in "TestFile?" for the https file. I guess this due to updates to the Http client library in #1809 and that it existed already in BASE 3.3.2 when the urls changed due to server move.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 11.1 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: update_warnings.xml 6600 2014-11-17 07:41:18Z 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.update_warnings">
28  <?dbhtml filename="updatewarnings.html" ?>
29  <title>Things to consider when updating an existing BASE installation</title>
30  <para>
31    This document is a list of things that may have to be considered
32    when updating a BASE installation to a newer version. The <xref 
33    linkend="installation.upgrade" /> section only include the most
34    recent information that is needed for updating the previous BASE version
35    to the current version.
36  </para>
38  <sect1 id="appendix.update_warnings.3.4">
39    <title>BASE 3.4</title>
41    <bridgehead>Updating from BASE 2.17 is no longer possible</bridgehead>
42    <para>
43      If you are still running an BASE 2.17 (or earlier) BASE version
44      and want to update to BASE 3.4 you must first update to BASE 3.3
45      or earlier.
46    </para>
48    <bridgehead>Web services support has been removed</bridgehead>
49    <para>
50      As announced earlier web services support has been removed in BASE 3.4.
51      If anyone require web services support or similar we recommend using the BASE
52      extensions mechanism to implement exactly what is needed for that project and
53      we also beleive that a simplier API such as JSON is preferable.
54    </para>
56    <bridgehead>PostgreSQL users should change db.dialect</bridgehead>
57    <para>
58      In <filename>base.config</filename> there is a <constant>db.config</constant>
59      setting. Servers running with PostgreSQL as the database should change the
60      dialect to <classname>org.hibernate.dialect.PostgreSQL9Dialect</classname>
61      since the <classname>org.hibernate.dialect.PostgreSQLDialect</classname> has
62      been deprecated.
63    </para>
65  </sect1>
67  <sect1 id="appendix.update_warnings.3.3.3">
68    <title>BASE 3.3.3</title>
70    <bridgehead>Remaining quantity</bridgehead>
71    <para>
72      A bug that affected remaining quantity calculations for
73      biomaterial item has been fixed. Existing items may have been
74      saved with incorrect remaining quantity and must be fixed.
75      After installing the BASE 3.3.3 update, the existing
76      remaining quantity values are fix by running a special script.
77      Change directory to <filename class="directory">&lt;base-dir&gt;/bin/</filename> 
78      and issue
80./ remaining_quantity -u &lt;root login&gt; -p &lt;root pwd&gt;
82    </para>
84  </sect1>
86  <sect1 id="appendix.update_warnings.3.3">
87    <title>BASE 3.3</title>
89    <bridgehead>Content security policy</bridgehead>
90    <para>
91      The BASE web client now set a rather strict <emphasis>Content
92      Security Policy</emphasis> that prevent browsers from executing
93      code (including JavaScript) that is considered unsafe. Some extensions
94      may cease to work due to this. Go to
95      <menuchoice>
96        <guimenu>Administrate</guimenu>
97        <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
98        <guimenuitem>Overview</guimenuitem>
99      </menuchoice> 
100      (after upgrading) to see if there are any warnings about this.
101      Read more in <xref linkend="appendix.web.xml.csp-filter" />
102      for information about how to relax the policy.
103    </para>
105    <bridgehead>Java SE 7 is required</bridgehead>
106    <para>
107      BASE now require <ulink url="">Java SE 7</ulink>.
108      Servers with Java SE 6 or older should be updated to Java SE 7 before installing BASE 3.3.
109    </para>
111    <bridgehead>Tomcat 7 is required</bridgehead>
112    <para>
113      BASE now require <ulink url="">Tomcat 7</ulink>.
114      Servers with Tomcat 6 or older should be updated to Tomcat 7 before installing BASE 3.3.
115    </para>
117    <bridgehead>Web services support has been deprecated</bridgehead>
118    <para>
119      The current implementation is most likely not very useful and has limited
120      support for accessing information in BASE. Therefore it has been decided to
121      remove the web services support in BASE 3.4. If anyone require web services
122      support or similar we recommend using the BASE extensions mechanism to implement
123      exactly what is needed for that project and we also beleive that a simplier
124      API such as JSON is preferable.
125    </para>
127  </sect1>
129  <sect1 id="appendix.update_warnings.3.2">
130    <title>BASE 3.2</title>
132    <bridgehead>Custom logging implementations must be updated</bridgehead>
133    <para>
134      The plug-in functionality for custom logging has been converted
135      to an extension point. The default database logging will continue
136      to function, but custom logging implementations must be converted
137      to an extension. See <xref linkend="appendix.incompatible.3.2" /> and
138      <xref linkend="extensions_developer.logging" /> for more information.
139    </para>
141  </sect1>
143  <sect1 id="appendix.update_warnings.3.0">
144    <title>BASE 3.0</title>
146    <note>
147      <title>Upgrading to BASE 3 is possible from BASE 2.17 only</title>
148      <para>
149        If your BASE is an older 2.x version you'll need to upgrade
150        to BASE 2.17 before an upgrade to BASE 3 is possible. Also note
151        that since BASE 3.3 we no longer actively test the upgrade
152        script. If upgrading doesn't work for a particular BASE 3.x version
153        (where x &gt; 2) please try to upgrade to BASE 3.2 first and then
154        from BASE 3.2 to BASE 3.x.
155      </para>
156    </note>
158    <warning>
159      <title>Make sure that you have a recent backup of the BASE 2.17 database</title>
160      <para>
161        Before starting the upgrade from BASE 2.17 to BASE 3 ensure that you
162        have a recent backup. If the upgrade fails you must restore the
163        2.17 database before you can try again. The upgrade only changes the
164        'static' part of the database, so you do not have to restore the
165        'dynamic' part or the uploaded files.
166      </para>
167    </warning>
169    <bridgehead>Old plug-ins and extensions may not work</bridgehead>
170    <para>
171      The BASE API has changed in several places and it is not certain that
172      plug-ins and extensions developed for BASE 2 works with BASE 3. The
173      upgrade will disable all plug-ins and extensions that are currently installed.
174      Before you upgrade we recommend that you go through all (external) plug-ins
175      and check if there is an updated version. The recommended approach
176      is to first upgrade BASE and then install updated versions of plug-ins
177      and extensions following the instructions in <xref 
178      linkend="plugins.installation"/>.
179    </para>
181    <para>
182      If there is no updated version of a specific plug-in you may try
183      a manual re-installation of the old plug-ins. Follow the instructions
184      in <xref linkend="plugins.installation.manual" />.
185    </para>
187    <para>
188      If there is no updated version and the old plug-in doesn't work with
189      BASE 3, you'll need to decide if you really need the plug-in or if
190      the upgrade should wait until a new version of the plug-in
191      has been released.
192    </para>
194    <bridgehead>Batch item importer changes</bridgehead>
195    <para>
196      There are several changes to batch item importers that may affect
197      current workflows and file templates used for importing data.
198    </para>
200    <itemizedlist>
201      <listitem>
202        <para>
203          Sample and extract importers: The 'pooled' column is no longer used.
204          Instead a 'parent type' column should be used with
205          the parent type as a string value (BIOSOURCE, SAMPLE or EXTRACT).
206          Existing importer configurations and file templates may have to be
207          updated. If no parent type is specified the sample importer assumes
208          a biosource and the extract importer assumes a sample.
209        </para>
210      </listitem>
211      <listitem>
212        <para>
213          Labeled extract importer: This has been deprecated and it is recommended
214          that the <emphasis>Extract importer</emphasis> is used instead.
215          We recommend that existing labeled extract importer configurations are re-created as extract
216          importer configurations. The old labeled extract importer can be
217          re-enabled, but note that the existing configurations still need
218          to be changed due to the 'pooled' column is no longer used.
219        </para>
220      </listitem>
221      <listitem>
222        <para>
223          Hybridization importer: This has been deprecated and we recommend
224          that the <emphasis>Physical bioassay importer</emphasis> is used instead.
225          Existing hybridization importer configurations should be re-created as
226          physical bioassay importer configurations.
227        </para>
228      </listitem>
229      <listitem>
230        <para>
231          Scan importer: This has been deprecated and it is recommended
232          that the <emphasis>Derived bioassay importer</emphasis> is used instead.
233          Existing scan importer configurations should be re-created as derived
234          bioassay importer configurations.
235        </para>
236      </listitem>
237    </itemizedlist>
239    <note>
240      The deprecated importers can be re-enabled by an administrator from the
241      <menuchoice>
242        <guimenu>Administrate</guimenu>
243        <guisubmenu>Plug-ins &amp; extensions</guisubmenu>
244        <guimenuitem>Overview</guimenuitem>
245      </menuchoice> page, but they are
246      lacking features that are available in the new importers so this is not
247      something that we recommend.
248    </note>
250    <bridgehead>MySQL and PostgreSQL versions</bridgehead>
251    <para>
252      We have only tested BASE 3 with PostgreSQL 9.1. If anyone
253      experiences any issues with earlier PostgreSQL versions, we
254      recommend an upgrade to PostgreSQL 9.1. This is a change since
255      BASE 2 which was tested with PostgreSQL 8.4. Even though BASE 3
256      may work with older PostgreSQL versions, we don't have the resources
257      needed to test and provide support for it.
258    </para>
260    <para>
261      We have only tested BASE 3 with MySQL 5.1 (no change since BASE 2).
262      If anyone experiences any issues with earlier (or later) MySQL versions,
263      we recommend an upgrade/downgrade to MySQL 5.1.
264    </para>
266  </sect1>
268  <sect1 id="appendix.update_warnings.2.x">
269    <title>All BASE 2.x releases</title>
271    <para>
272      We only support updating to BASE 3 from BASE 2.17. If you have an older BASE
273      version and wish to update to BASE 3, you first have to upgrade to BASE 2.17.
274      BASE 2.17 can be downloaded from the <ulink url="">BASE
275      download page</ulink>. Documentation for BASE 2.17 is available as part of the
276      download and at <ulink url=""
277      ></ulink>.
278    </para>
280  </sect1>
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