Changeset 5830


Ignore:
Timestamp:
Oct 27, 2011, 9:13:21 AM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

Some final updates to the upgrade and migration instructions. Removed screenshots that are no longer used in the documentation. Some minor fixes in UML diagrams.

Location:
trunk/doc
Files:
1 added
5 deleted
8 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/admin/installation.xml

    r5801 r5830  
    4545
    4646    <important id="installation.upgrade.important">
    47       <title>Important information for upgrading from BASE 2.17 to BASE 3.0-beta</title>
     47      <title>Important information for upgrading from BASE 2.17 to BASE 3.0</title>
    4848     
    49       <bridgehead>Do not use on a production server!</bridgehead>
     49      <bridgehead>Upgrading is supported from BASE 2.17 only</bridgehead>
    5050      <para>
    51         The update has not been tested enough to consider this a safe option.
    52         The update may cause loss of data. Even if the update works, it is not
    53         certain that the 3.0-beta version can be updated to the 3.0-final
    54         version. Before updating make sure that you have a backup of your
    55         BASE 2.17 database.
    56       </para>
    57 
    58       <bridgehead>Updating is supported from BASE 2.17 only</bridgehead>
    59       <para>
    60         If your BASE is an older version you'll first need to update
    61         to BASE 2.17.
     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.
    6253      </para>
    6354
     
    6657        The BASE API has changed in several places and it is not certain that
    6758        plug-ins and extensions developed for BASE 2 works with BASE 3. The
    68         update will disable all plug-ins and extensions that are currently installed.
    69         Before you update we recommend that you go through all (external) plug-ins
     59        upgrade will disable all plug-ins and extensions that are currently installed.
     60        Before you upgrade we recommend that you go through all (external) plug-ins
    7061        and check if there is an updated version. The recommended approach
    71         is to first update BASE and then install updated versions of plug-ins
     62        is to first upgrade BASE and then install updated versions of plug-ins
    7263        and extensions following the instructions in <xref
    7364        linkend="plugins.installation"/>.
     
    8071      </para>
    8172     
     73      <para>
     74        If there is no updated version and the old plug-in doesn't work with
     75        BASE 3, you'll need to decide if you really need the plug-in or if
     76        the upgrade should wait until a new version of the plug-in
     77        has been released.
     78      </para>
     79     
    8280      <bridgehead>Batch item importer changes</bridgehead>
    8381      <para>
     
    8987        <listitem>
    9088          <para>
    91             Sample and extract importer: The 'pooled' column is no longer used.
    92             Instead a 'parent type' column should be used which should contain
     89            Sample and extract importers: The 'pooled' column is no longer used.
     90            Instead a 'parent type' column should be used with
    9391            the parent type as a string value (BIOSOURCE, SAMPLE or EXTRACT).
    94             Existing importer configurations and file templates may have to be updated.
     92            Existing importer configurations and file templates may have to be
     93            updated. If no parent type is specified the sample importer assumes
     94            a biosource and the extract importer assumes a sample.
    9595          </para>
    9696        </listitem>
     
    9898          <para>
    9999            Labeled extract importer: This has been deprecated and it is recommended
    100             that the Extract importer is used instead. Existing labeled extract importer
    101             configurations should be re-created as extract importer configurations.
    102           </para>
    103         </listitem>
    104         <listitem>
    105           <para>
    106             Hybridization importer: This has been deprecated and it is recommended
    107             that the Physical bioassay importer is used instead. Existing hybridization
    108             importer configurations should be re-created as physical bioassay importer
    109             configurations.
     100            that the <emphasis>Extract importer</emphasis> is used instead.
     101            We recommend that existing labeled extract importer configurations are re-created as extract
     102            importer configurations. The old labeled extract importer can be
     103            re-enabled, but note that the existing configurations still need
     104            to be changed due to the 'pooled' column is no longer used.
     105          </para>
     106        </listitem>
     107        <listitem>
     108          <para>
     109            Hybridization importer: This has been deprecated and we recommend
     110            that the <emphasis>Physical bioassay importer</emphasis> is used instead.
     111            Existing hybridization importer configurations should be re-created as
     112            physical bioassay importer configurations.
    110113          </para>
    111114        </listitem>
     
    113116          <para>
    114117            Scan importer: This has been deprecated and it is recommended
    115             that the Derived bioassay importer is used instead. Existing scan
    116             importer configurations should be re-created as derived bioassay
    117             importer configurations.
     118            that the <emphasis>Derived bioassay importer</emphasis> is used instead.
     119            Existing scan importer configurations should be re-created as derived
     120            bioassay importer configurations.
    118121          </para>
    119122        </listitem>
     
    121124     
    122125      <note>
    123         The deprecated importers can be re-enabled by an administrator, but they are
     126        The deprecated importers can be re-enabled by an administrator from the
     127        <menuchoice>
     128          <guimenu>Administrate</guimenu>
     129          <guisubmenu>Plug-ins &amp; extensions</guisubmenu>
     130          <guimenuitem>Overview</guimenuitem>
     131        </menuchoice> page, but they are
    124132        lacking features that are available in the new importers so this is not
    125133        something that we recommend.
  • trunk/doc/src/docbook/admin/plugins.xml

    r5801 r5830  
    239239     
    240240      <para>
    241         To perform a manual installation, go to <menuchoice>
     241        To perform a manual installation the plug-in's JAR file must be
     242        located in the the directory specified by the <constant>plugins.dir</constant>
     243        setting in <filename>base.config</filename>. Subdirectories are not
     244        allowed. This is a change since BASE 2 were plug-ins could be installed
     245        almost anywhere. When the JAR file is in place, go to
     246        <menuchoice>
    242247        <guimenu>Administrate</guimenu>
    243248        <guisubmenu>Plug-ins &amp; extensions</guisubmenu>
  • trunk/doc/src/docbook/developer/migrate_2_3.xml

    r5827 r5830  
    273273        The information that was in
    274274        <filename>META-INF/base-plugins.xml</filename>, should be moved to
    275         <filename>META-INF/extensions.xml</filename>. The XML syntax in the new file is different
    276         from the old file. See <xref linkend="plugin_developer.organize.autoinstallcompatible" />
     275        <filename>META-INF/extensions.xml</filename>. The XML syntax in the new
     276        file is different from the old file. You'll also need to put
     277        the information was returned by the <methodname>Plugin.getAbout()</methodname>
     278        method in this file. See <xref
     279        linkend="plugin_developer.organize.autoinstallcompatible" />
    277280        for more information.
    278281        </para>
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