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

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE appendix PUBLIC 
    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" 
    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
<!--
  $Id: update_warnings.xml 6600 2014-11-17 07:41:18Z nicklas $
  
  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg
  
  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/
  
  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
  of the License, or (at your option) any later version.
  
  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
  
  You should have received a copy of the GNU General Public License
  along with BASE. If not, see <http://www.gnu.org/licenses/>.
-->

<appendix id="appendix.update_warnings">
  <?dbhtml filename="updatewarnings.html" ?>
  <title>Things to consider when updating an existing BASE installation</title>
  <para>
    This document is a list of things that may have to be considered 
    when updating a BASE installation to a newer version. The <xref 
    linkend="installation.upgrade" /> section only include the most 
    recent information that is needed for updating the previous BASE version
    to the current version.
  </para>
  
  <sect1 id="appendix.update_warnings.3.4">
    <title>BASE 3.4</title>
    
    <bridgehead>Updating from BASE 2.17 is no longer possible</bridgehead>
    <para>
      If you are still running an BASE 2.17 (or earlier) BASE version
      and want to update to BASE 3.4 you must first update to BASE 3.3
      or earlier.
    </para>
    
    <bridgehead>Web services support has been removed</bridgehead>
    <para>
      As announced earlier web services support has been removed in BASE 3.4.
      If anyone require web services support or similar we recommend using the BASE 
      extensions mechanism to implement exactly what is needed for that project and 
      we also beleive that a simplier API such as JSON is preferable.
    </para>
    
    <bridgehead>PostgreSQL users should change db.dialect</bridgehead>
    <para>
      In <filename>base.config</filename> there is a <constant>db.config</constant>
      setting. Servers running with PostgreSQL as the database should change the
      dialect to <classname>org.hibernate.dialect.PostgreSQL9Dialect</classname>
      since the <classname>org.hibernate.dialect.PostgreSQLDialect</classname> has
      been deprecated.
    </para>
    
  </sect1>

  <sect1 id="appendix.update_warnings.3.3.3">
    <title>BASE 3.3.3</title>
  
    <bridgehead>Remaining quantity</bridgehead>
    <para>
      A bug that affected remaining quantity calculations for 
      biomaterial item has been fixed. Existing items may have been
      saved with incorrect remaining quantity and must be fixed.
      After installing the BASE 3.3.3 update, the existing
      remaining quantity values are fix by running a special script.
      Change directory to <filename class="directory">&lt;base-dir&gt;/bin/</filename> 
      and issue
<programlisting>
./onetimefix.sh remaining_quantity -u &lt;root login&gt; -p &lt;root pwd&gt;
</programlisting>
    </para>
    
  </sect1>
  
  <sect1 id="appendix.update_warnings.3.3">
    <title>BASE 3.3</title>

    <bridgehead>Content security policy</bridgehead>
    <para>
      The BASE web client now set a rather strict <emphasis>Content 
      Security Policy</emphasis> that prevent browsers from executing
      code (including JavaScript) that is considered unsafe. Some extensions
      may cease to work due to this. Go to
      <menuchoice>
        <guimenu>Administrate</guimenu>
        <guimenuitem>Plug-ins &amp; extensions</guimenuitem>
        <guimenuitem>Overview</guimenuitem>
      </menuchoice> 
      (after upgrading) to see if there are any warnings about this.
      Read more in <xref linkend="appendix.web.xml.csp-filter" />
      for information about how to relax the policy.
    </para>

    <bridgehead>Java SE 7 is required</bridgehead>
    <para>
      BASE now require <ulink url="http://www.oracle.com/technetwork/java/javase/downloads/index.html">Java SE 7</ulink>. 
      Servers with Java SE 6 or older should be updated to Java SE 7 before installing BASE 3.3.
    </para>

    <bridgehead>Tomcat 7 is required</bridgehead>
    <para>
      BASE now require <ulink url="http://tomcat.apache.org/download-70.cgi">Tomcat 7</ulink>.
      Servers with Tomcat 6 or older should be updated to Tomcat 7 before installing BASE 3.3.
    </para>
    
    <bridgehead>Web services support has been deprecated</bridgehead>
    <para>
      The current implementation is most likely not very useful and has limited
      support for accessing information in BASE. Therefore it has been decided to
      remove the web services support in BASE 3.4. If anyone require web services
      support or similar we recommend using the BASE extensions mechanism to implement
      exactly what is needed for that project and we also beleive that a simplier
      API such as JSON is preferable.
    </para>

  </sect1>
  
  <sect1 id="appendix.update_warnings.3.2">
    <title>BASE 3.2</title>
  
    <bridgehead>Custom logging implementations must be updated</bridgehead>
    <para>
      The plug-in functionality for custom logging has been converted
      to an extension point. The default database logging will continue
      to function, but custom logging implementations must be converted
      to an extension. See <xref linkend="appendix.incompatible.3.2" /> and 
      <xref linkend="extensions_developer.logging" /> for more information.
    </para>
  
  </sect1>
  
  <sect1 id="appendix.update_warnings.3.0">
    <title>BASE 3.0</title>
    
    <note>
      <title>Upgrading to BASE 3 is possible from BASE 2.17 only</title>
      <para>
        If your BASE is an older 2.x version you'll need to upgrade
        to BASE 2.17 before an upgrade to BASE 3 is possible. Also note
        that since BASE 3.3 we no longer actively test the upgrade
        script. If upgrading doesn't work for a particular BASE 3.x version 
        (where x &gt; 2) please try to upgrade to BASE 3.2 first and then 
        from BASE 3.2 to BASE 3.x.
      </para>
    </note>

    <warning>
      <title>Make sure that you have a recent backup of the BASE 2.17 database</title>
      <para>
        Before starting the upgrade from BASE 2.17 to BASE 3 ensure that you
        have a recent backup. If the upgrade fails you must restore the 
        2.17 database before you can try again. The upgrade only changes the
        'static' part of the database, so you do not have to restore the
        'dynamic' part or the uploaded files.
      </para>
    </warning>

    <bridgehead>Old plug-ins and extensions may not work</bridgehead>
    <para>
      The BASE API has changed in several places and it is not certain that
      plug-ins and extensions developed for BASE 2 works with BASE 3. The
      upgrade will disable all plug-ins and extensions that are currently installed.
      Before you upgrade we recommend that you go through all (external) plug-ins
      and check if there is an updated version. The recommended approach
      is to first upgrade BASE and then install updated versions of plug-ins
      and extensions following the instructions in <xref 
      linkend="plugins.installation"/>.
    </para>
    
    <para>
      If there is no updated version of a specific plug-in you may try 
      a manual re-installation of the old plug-ins. Follow the instructions
      in <xref linkend="plugins.installation.manual" />.
    </para>
    
    <para>
      If there is no updated version and the old plug-in doesn't work with
      BASE 3, you'll need to decide if you really need the plug-in or if
      the upgrade should wait until a new version of the plug-in 
      has been released.
    </para>
    
    <bridgehead>Batch item importer changes</bridgehead>
    <para>
      There are several changes to batch item importers that may affect
      current workflows and file templates used for importing data.
    </para>
    
    <itemizedlist>
      <listitem>
        <para>
          Sample and extract importers: The 'pooled' column is no longer used.
          Instead a 'parent type' column should be used with
          the parent type as a string value (BIOSOURCE, SAMPLE or EXTRACT). 
          Existing importer configurations and file templates may have to be 
          updated. If no parent type is specified the sample importer assumes
          a biosource and the extract importer assumes a sample.
        </para>
      </listitem>
      <listitem>
        <para>
          Labeled extract importer: This has been deprecated and it is recommended
          that the <emphasis>Extract importer</emphasis> is used instead. 
          We recommend that existing labeled extract importer configurations are re-created as extract 
          importer configurations. The old labeled extract importer can be 
          re-enabled, but note that the existing configurations still need
          to be changed due to the 'pooled' column is no longer used.
        </para>
      </listitem>
      <listitem>
        <para>
          Hybridization importer: This has been deprecated and we recommend
          that the <emphasis>Physical bioassay importer</emphasis> is used instead. 
          Existing hybridization importer configurations should be re-created as 
          physical bioassay importer configurations. 
        </para>
      </listitem>
      <listitem>
        <para>
          Scan importer: This has been deprecated and it is recommended
          that the <emphasis>Derived bioassay importer</emphasis> is used instead. 
          Existing scan importer configurations should be re-created as derived 
          bioassay importer configurations.
        </para>
      </listitem>
    </itemizedlist>
    
    <note>
      The deprecated importers can be re-enabled by an administrator from the 
      <menuchoice>
        <guimenu>Administrate</guimenu>
        <guisubmenu>Plug-ins &amp; extensions</guisubmenu>
        <guimenuitem>Overview</guimenuitem>
      </menuchoice> page, but they are
      lacking features that are available in the new importers so this is not
      something that we recommend.
    </note>
    
    <bridgehead>MySQL and PostgreSQL versions</bridgehead>
    <para>
      We have only tested BASE 3 with PostgreSQL 9.1. If anyone
      experiences any issues with earlier PostgreSQL versions, we 
      recommend an upgrade to PostgreSQL 9.1. This is a change since
      BASE 2 which was tested with PostgreSQL 8.4. Even though BASE 3 
      may work with older PostgreSQL versions, we don't have the resources 
      needed to test and provide support for it.
    </para>
    
    <para>
      We have only tested BASE 3 with MySQL 5.1 (no change since BASE 2). 
      If anyone experiences any issues with earlier (or later) MySQL versions, 
      we recommend an upgrade/downgrade to MySQL 5.1.
    </para>
  
  </sect1>
  
  <sect1 id="appendix.update_warnings.2.x">
    <title>All BASE 2.x releases</title>
    
    <para>
      We only support updating to BASE 3 from BASE 2.17. If you have an older BASE
      version and wish to update to BASE 3, you first have to upgrade to BASE 2.17.
      BASE 2.17 can be downloaded from the <ulink url="http://base.thep.lu.se/wiki/DownloadPage">BASE 
      download page</ulink>. Documentation for BASE 2.17 is available as part of the
      download and at <ulink url="http://base.thep.lu.se/chrome/site/2.17/html/index.html"
      >http://base.thep.lu.se/chrome/site/2.17/html/index.html</ulink>.
    </para>

  </sect1>
  
</appendix>