Changeset 6081


Ignore:
Timestamp:
Aug 8, 2012, 10:02:14 AM (9 years ago)
Author:
Nicklas Nordborg
Message:

References #1601: Convert logging plug-in system to an extension point

Added a note in the upgrade instructions about this change and how it affects custom logging implementations.

Location:
trunk
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/config/dist/base.config

    r5895 r6081  
    144144# =========================
    145145
    146 # Class name of the changelog factory; leave empty to disable the changelog
    147 # changelog.factory = net.sf.basedb.core.log.db.DbLogManagerFactory
     146# Change history for items can be logged with the help of extensions.
     147# BASE ships with a built-in extension that log changes to the database.
     148# This is disabled by default, but can be enabled through the web
     149# interface: Adminstrate -> Plug-ins & extensions -> Overview
    148150
    149151# If the "Change history" tab should be visible in the web interface
  • trunk/doc/src/docbook/admin/installation.xml

    r6072 r6081  
    4545
    4646    <important id="installation.upgrade.important">
    47       <title>Important information for upgrading from BASE 2.17 to BASE 3.0</title>
    48      
    49       <bridgehead>Upgrading is supported from BASE 2.17 only</bridgehead>
     47      <title>Important information for upgrading to the current release</title>
    5048      <para>
    51         If your BASE is an older 2.x version you'll need to upgrade
    52         to BASE 2.17 before an upgrade to BASE 3.0 is possible.
    53       </para>
    54 
    55       <warning>
    56         <title>Make sure that you have a recent backup of the BASE 2.17 database</title>
    57         <para>
    58           Before starting the upgrade from BASE 2.17 to BASE 3 ensure that you
    59           have a recent backup. If the upgrade fails you must restore the
    60           2.17 database before you can try again. The upgrade only changes the
    61           'static' part of the database, so you do not have to restore the
    62           'dynamic' part or the uploaded files.
    63         </para>
    64       </warning>
    65 
    66       <bridgehead>Old plug-ins and extensions may not work</bridgehead>
    67       <para>
    68         The BASE API has changed in several places and it is not certain that
    69         plug-ins and extensions developed for BASE 2 works with BASE 3. The
    70         upgrade will disable all plug-ins and extensions that are currently installed.
    71         Before you upgrade we recommend that you go through all (external) plug-ins
    72         and check if there is an updated version. The recommended approach
    73         is to first upgrade BASE and then install updated versions of plug-ins
    74         and extensions following the instructions in <xref
    75         linkend="plugins.installation"/>.
     49        This section list some important information that may or may not
     50        apply when upgrading from the <emphasis>previous</emphasis> BASE
     51        release to the current release (eg. 3.1.x to 3.2.x). If you are
     52        upgrading from a BASE installation that is older (eg. 2.x or 3.0.x to
     53        3.2.x) you should also read <xref linkend="appendix.update_warnings" />.
    7654      </para>
    7755     
     56      <bridgehead>Custom logging implementations must be updated</bridgehead>
    7857      <para>
    79         If there is no updated version of a specific plug-in you may try
    80         a manual re-installation of the old plug-ins. Follow the instructions
    81         in <xref linkend="plugins.installation.manual" />.
     58        The plug-in functionality for custom logging has been converted
     59        to an extension point. The default database logging will continue
     60        to function, but custom logging implementations must be converted
     61        to an extension. See <xref linkend="appendix.incompatible.3.2" /> and
     62        <xref linkend="extensions_developer.logging" /> for more information.
    8263      </para>
    83      
    84       <para>
    85         If there is no updated version and the old plug-in doesn't work with
    86         BASE 3, you'll need to decide if you really need the plug-in or if
    87         the upgrade should wait until a new version of the plug-in
    88         has been released.
    89       </para>
    90      
    91       <bridgehead>Batch item importer changes</bridgehead>
    92       <para>
    93         There are several changes to batch item importers that may affect
    94         current workflows and file templates used for importing data.
    95       </para>
    96      
    97       <itemizedlist>
    98         <listitem>
    99           <para>
    100             Sample and extract importers: The 'pooled' column is no longer used.
    101             Instead a 'parent type' column should be used with
    102             the parent type as a string value (BIOSOURCE, SAMPLE or EXTRACT).
    103             Existing importer configurations and file templates may have to be
    104             updated. If no parent type is specified the sample importer assumes
    105             a biosource and the extract importer assumes a sample.
    106           </para>
    107         </listitem>
    108         <listitem>
    109           <para>
    110             Labeled extract importer: This has been deprecated and it is recommended
    111             that the <emphasis>Extract importer</emphasis> is used instead.
    112             We recommend that existing labeled extract importer configurations are re-created as extract
    113             importer configurations. The old labeled extract importer can be
    114             re-enabled, but note that the existing configurations still need
    115             to be changed due to the 'pooled' column is no longer used.
    116           </para>
    117         </listitem>
    118         <listitem>
    119           <para>
    120             Hybridization importer: This has been deprecated and we recommend
    121             that the <emphasis>Physical bioassay importer</emphasis> is used instead.
    122             Existing hybridization importer configurations should be re-created as
    123             physical bioassay importer configurations.
    124           </para>
    125         </listitem>
    126         <listitem>
    127           <para>
    128             Scan importer: This has been deprecated and it is recommended
    129             that the <emphasis>Derived bioassay importer</emphasis> is used instead.
    130             Existing scan importer configurations should be re-created as derived
    131             bioassay importer configurations.
    132           </para>
    133         </listitem>
    134       </itemizedlist>
    135      
    136       <note>
    137         The deprecated importers can be re-enabled by an administrator from the
    138         <menuchoice>
    139           <guimenu>Administrate</guimenu>
    140           <guisubmenu>Plug-ins &amp; extensions</guisubmenu>
    141           <guimenuitem>Overview</guimenuitem>
    142         </menuchoice> page, but they are
    143         lacking features that are available in the new importers so this is not
    144         something that we recommend.
    145       </note>
    146      
    147       <bridgehead>MySQL and PostgreSQL versions</bridgehead>
    148       <para>
    149         We have only tested BASE 3 with PostgreSQL 9.1. If anyone
    150         experiences any issues with earlier PostgreSQL versions, we
    151         recommend an upgrade to PostgreSQL 9.1. This is a change since
    152         BASE 2 which was tested with PostgreSQL 8.4. Even though BASE 3
    153         may work with older PostgreSQL versions, we don't have the resources
    154         needed to test and provide support for it.
    155       </para>
    156      
    157       <para>
    158         We have only tested BASE 3 with MySQL 5.1 (no change since BASE 2).
    159         If anyone experiences any issues with earlier (or later) MySQL versions,
    160         we recommend an upgrade/downgrade to MySQL 5.1.
    161       </para>
    162      
     64
    16365    </important>
    16466   
  • trunk/doc/src/docbook/appendix/update_warnings.xml

    r5782 r6081  
    3636  </para>
    3737 
     38  <sect1 id="appendix.update_warnings.3.2">
     39    <title>BASE 3.2</title>
     40 
     41    <bridgehead>Custom logging implementations must be updated</bridgehead>
     42    <para>
     43      The plug-in functionality for custom logging has been converted
     44      to an extension point. The default database logging will continue
     45      to function, but custom logging implementations must be converted
     46      to an extension. See <xref linkend="appendix.incompatible.3.2" /> and
     47      <xref linkend="extensions_developer.logging" /> for more information.
     48    </para>
     49 
     50  </sect1>
     51 
     52  <sect1 id="appendix.update_warnings.3.0">
     53    <title>BASE 3.0</title>
     54   
     55    <note>
     56      <title>Upgrading to BASE 3.0 is supported from BASE 2.17 only</title>
     57      <para>
     58        If your BASE is an older 2.x version you'll need to upgrade
     59        to BASE 2.17 before an upgrade to BASE 3.0 is possible.
     60      </para>
     61    </note>
     62
     63    <warning>
     64      <title>Make sure that you have a recent backup of the BASE 2.17 database</title>
     65      <para>
     66        Before starting the upgrade from BASE 2.17 to BASE 3 ensure that you
     67        have a recent backup. If the upgrade fails you must restore the
     68        2.17 database before you can try again. The upgrade only changes the
     69        'static' part of the database, so you do not have to restore the
     70        'dynamic' part or the uploaded files.
     71      </para>
     72    </warning>
     73
     74    <bridgehead>Old plug-ins and extensions may not work</bridgehead>
     75    <para>
     76      The BASE API has changed in several places and it is not certain that
     77      plug-ins and extensions developed for BASE 2 works with BASE 3. The
     78      upgrade will disable all plug-ins and extensions that are currently installed.
     79      Before you upgrade we recommend that you go through all (external) plug-ins
     80      and check if there is an updated version. The recommended approach
     81      is to first upgrade BASE and then install updated versions of plug-ins
     82      and extensions following the instructions in <xref
     83      linkend="plugins.installation"/>.
     84    </para>
     85   
     86    <para>
     87      If there is no updated version of a specific plug-in you may try
     88      a manual re-installation of the old plug-ins. Follow the instructions
     89      in <xref linkend="plugins.installation.manual" />.
     90    </para>
     91   
     92    <para>
     93      If there is no updated version and the old plug-in doesn't work with
     94      BASE 3, you'll need to decide if you really need the plug-in or if
     95      the upgrade should wait until a new version of the plug-in
     96      has been released.
     97    </para>
     98   
     99    <bridgehead>Batch item importer changes</bridgehead>
     100    <para>
     101      There are several changes to batch item importers that may affect
     102      current workflows and file templates used for importing data.
     103    </para>
     104   
     105    <itemizedlist>
     106      <listitem>
     107        <para>
     108          Sample and extract importers: The 'pooled' column is no longer used.
     109          Instead a 'parent type' column should be used with
     110          the parent type as a string value (BIOSOURCE, SAMPLE or EXTRACT).
     111          Existing importer configurations and file templates may have to be
     112          updated. If no parent type is specified the sample importer assumes
     113          a biosource and the extract importer assumes a sample.
     114        </para>
     115      </listitem>
     116      <listitem>
     117        <para>
     118          Labeled extract importer: This has been deprecated and it is recommended
     119          that the <emphasis>Extract importer</emphasis> is used instead.
     120          We recommend that existing labeled extract importer configurations are re-created as extract
     121          importer configurations. The old labeled extract importer can be
     122          re-enabled, but note that the existing configurations still need
     123          to be changed due to the 'pooled' column is no longer used.
     124        </para>
     125      </listitem>
     126      <listitem>
     127        <para>
     128          Hybridization importer: This has been deprecated and we recommend
     129          that the <emphasis>Physical bioassay importer</emphasis> is used instead.
     130          Existing hybridization importer configurations should be re-created as
     131          physical bioassay importer configurations.
     132        </para>
     133      </listitem>
     134      <listitem>
     135        <para>
     136          Scan importer: This has been deprecated and it is recommended
     137          that the <emphasis>Derived bioassay importer</emphasis> is used instead.
     138          Existing scan importer configurations should be re-created as derived
     139          bioassay importer configurations.
     140        </para>
     141      </listitem>
     142    </itemizedlist>
     143   
     144    <note>
     145      The deprecated importers can be re-enabled by an administrator from the
     146      <menuchoice>
     147        <guimenu>Administrate</guimenu>
     148        <guisubmenu>Plug-ins &amp; extensions</guisubmenu>
     149        <guimenuitem>Overview</guimenuitem>
     150      </menuchoice> page, but they are
     151      lacking features that are available in the new importers so this is not
     152      something that we recommend.
     153    </note>
     154   
     155    <bridgehead>MySQL and PostgreSQL versions</bridgehead>
     156    <para>
     157      We have only tested BASE 3 with PostgreSQL 9.1. If anyone
     158      experiences any issues with earlier PostgreSQL versions, we
     159      recommend an upgrade to PostgreSQL 9.1. This is a change since
     160      BASE 2 which was tested with PostgreSQL 8.4. Even though BASE 3
     161      may work with older PostgreSQL versions, we don't have the resources
     162      needed to test and provide support for it.
     163    </para>
     164   
     165    <para>
     166      We have only tested BASE 3 with MySQL 5.1 (no change since BASE 2).
     167      If anyone experiences any issues with earlier (or later) MySQL versions,
     168      we recommend an upgrade/downgrade to MySQL 5.1.
     169    </para>
     170 
     171  </sect1>
     172 
    38173  <sect1 id="appendix.update_warnings.2.x">
    39174    <title>All BASE 2.x releases</title>
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