Changeset 4638

Nov 17, 2008, 1:02:41 PM (15 years ago)
Nicklas Nordborg

Fixes #1170: Move old update warnings to an appendix

1 added
2 edited


  • trunk/doc/src/docbook/admindoc/installation_upgrade.xml

    r4637 r4638  
    6565    <title>Upgrade instructions</title>
    67     <important id="useUTF8">
    68       <title>BASE 2.9 must use a database that supports UTF-8</title>
     67    <important id="installation_upgrade.upgrade.important">
     68      <title>Important information for upgrading to the current release</title>
     69      <para>
     70        This section list some important information that may or may not
     71        apply when upgrading from the <emphasis>previous</emphasis> BASE
     72        release to the current release (eg. 2.8.x to 2.9.x). If you are
     73        upgrading from a BASE installation that is older (eg. 2.7.x to 2.9.x)
     74        you should also read <xref linkend="appendix.update_warnings" />.
     75      </para>
     77      <bridgehead>BASE 2.9 must use a database that supports UTF-8</bridgehead>
    6978      <para>
    7079        If you are upgrading from BASE 2.8 or lower and your existing
    8897      <para>
    8998        The <code>-x</code> option makes the script update the database immediately.
    102111        restore the backup into the new database.
    103112      </para>
    104114    </important>
    106     <important id="lowess_bug">
    107       <title>Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1</title>
    108       <para>
    109       BASE 2.7.2 fixes a serious bug in the LOWESS plug-in shipped
    110       as a part of the BASE package. The bug is found in all
    111       BASE versions between 2.0 and 2.7.1, and has caused incorrect normalization values to be
    112       calculated. All data that has been normalized with the LOWESS plug-in prior
    113       to BASE 2.7.2 should be considered invalid and needs to be re-normalized with
    114       the fixed version. Downstream analysis steps that has used the incorrectly
    115       normalized data also needs to be redone. For more information about the bug see
    116       <ulink url=""></ulink>
    117       </para>
    119       <para>
    120       BASE 2.7.2 includes a utility for finding all experiments/bioassay sets that
    121       includes data normalized with the LOWESS plug-in. An administrator can use
    122       this utility to extract a list of all experiments/bioassay sets that needs to be fixed.
    123       The utility can also tag the name of the found experiments/bioassay sets with
    124       <code>FIX LOWESS</code> to make it easier to find data that needs to be fixed.
    125       </para>
    127       <para>
    128       The utility can't see any difference between data normalized with the
    129       old version and the fixed version. It will simply report all data that
    130       has been normalized with the LOWESS plug-in. Only use the utility a single
    131       time right after the upgrade to BASE 2.7.2.
    132       </para>
    134       <para>
    135       The utility is a command line program that should be executed on the BASE
    136       application (web) server.
    137       </para>
    139       <programlisting>
    140 <![CDATA[
    141 cd <base-dir>/bin
    142 ./ lowess_warn -u <login> -p <password> -f
    143 ]]>
    144 </programlisting>
    146       <para>
    147         We recommend running the utility as the root user. The <option>-f</option>
    148         option is optional. If it is included the found experiments/bioassay sets
    149         are tagged with <code>FIX LOWESS</code>, otherwise only a list with the
    150         information is generated.
    151       </para>
    153     </important>
    155     <important id="tomcat6">
    156       <title>BASE 2.7 requires Tomcat 6 or higher</title>
    157       <para>
    158         If you are upgrading from older BASE versions to BASE 2.7 or higher
    159         you must also make sure that you are running Tomcat 6 or higher.
    160         Earlier BASE versions only required Tomcat 5.5. If you are not
    161         already running Tomcat 6 you need to upgrade. Other servlet
    162         engines may work if they implement the Servlet 2.5 and JSP
    163         2.1 specifications.
    164       </para>
    165     </important>
    167     <important id="dropindexes">
    168       <title>Upgrading from BASE 2.4.3 or lower to 2.4.4 or higher</title>
    169       <para>
    170         Older releases of BASE 2 used to create indexes for many columns
    171         in the dynamic database. The same columns are part of the primary
    172         key for the tables so the indexes are not really needed. The
    173         result is very bad performance since the database engine sometimes
    174         get stuck in "index update" mode making the entire server
    175         very slow. BASE 2.4.4 no longer creates the indexes. Indexes on
    176         existing tables should be dropped to increase the performance.
    177         Tests have shown a 50-90% decrease in execution time for some
    178         plug-ins
    179         (<ulink url=""></ulink>).
    180       </para>
    181       <para>
    182         Removing the indexes is very simple. <emphasis>After the server
    183         has been upgraded</emphasis> following the usual instructions below, issue the
    184         the following commands:
    185       </para>
    187       <programlisting>
    188 cd &lt;basedir&gt;/bin
    189 ./ -v -dropindexes
    190 </programlisting>
    192       <para>
    193         Skip the <option>-dropindexes</option> option to do a dry
    194         run without actually deleting the indexes.
    195       </para>
    196     </important>
    198116    <para>
    199117      As always, backup your database before attempting an
  • trunk/doc/src/docbook/appendix/index.xml

    r4509 r4638  
    3838  <include file="other_config.xml" />
    3939  <include file="incompatible.xml" />
     40  <include file="update_warnings.xml" />
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