Changeset 4638

Timestamp:

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

Author:

Nicklas Nordborg

Message:

Fixes #1170: Move old update warnings to an appendix

Location:

trunk/doc/src/docbook

Files:

• admindoc/installation_upgrade.xml (modified) (3 diffs)
• appendix/index.xml (modified) (1 diff)
• appendix/update_warnings.xml (added)

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

@@ -65 +65 @@
     <title>Upgrade instructions</title>
 
-    <important id="useUTF8">
-      <title>BASE 2.9 must use a database that supports UTF-8</title>
+    <important id="installation_upgrade.upgrade.important">
+      <title>Important information for upgrading to the current release</title>
+      <para>
+        This section list some important information that may or may not
+        apply when upgrading from the <emphasis>previous</emphasis> BASE
+        release to the current release (eg. 2.8.x to 2.9.x). If you are 
+        upgrading from a BASE installation that is older (eg. 2.7.x to 2.9.x)
+        you should also read <xref linkend="appendix.update_warnings" />.
+      </para>
+    
+      <bridgehead>BASE 2.9 must use a database that supports UTF-8</bridgehead>
       <para>
         If you are upgrading from BASE 2.8 or lower and your existing
@@ -85 +94 @@
 ]]>
 </programlisting>
-      
+    
       <para>
         The <code>-x</code> option makes the script update the database immediately.
@@ -102 +111 @@
         restore the backup into the new database.
       </para>
+
     </important>
     
-    <important id="lowess_bug">
-      <title>Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1</title>
-      <para>
-      BASE 2.7.2 fixes a serious bug in the LOWESS plug-in shipped
-      as a part of the BASE package. The bug is found in all
-      BASE versions between 2.0 and 2.7.1, and has caused incorrect normalization values to be 
-      calculated. All data that has been normalized with the LOWESS plug-in prior 
-      to BASE 2.7.2 should be considered invalid and needs to be re-normalized with
-      the fixed version. Downstream analysis steps that has used the incorrectly
-      normalized data also needs to be redone. For more information about the bug see 
-      <ulink url="http://base.thep.lu.se/ticket/1077">http://base.thep.lu.se/ticket/1077</ulink>
-      </para>
-      
-      <para>
-      BASE 2.7.2 includes a utility for finding all experiments/bioassay sets that
-      includes data normalized with the LOWESS plug-in. An administrator can use
-      this utility to extract a list of all experiments/bioassay sets that needs to be fixed.
-      The utility can also tag the name of the found experiments/bioassay sets with
-      <code>FIX LOWESS</code> to make it easier to find data that needs to be fixed.
-      </para>
-      
-      <para>
-      The utility can't see any difference between data normalized with the 
-      old version and the fixed version. It will simply report all data that
-      has been normalized with the LOWESS plug-in. Only use the utility a single
-      time right after the upgrade to BASE 2.7.2.
-      </para>
-      
-      <para>
-      The utility is a command line program that should be executed on the BASE
-      application (web) server.
-      </para>
-      
-      <programlisting>
-<![CDATA[
-cd <base-dir>/bin
-./onetimefix.sh lowess_warn -u <login> -p <password> -f
-]]>
-</programlisting>
-      
-      <para>
-        We recommend running the utility as the root user. The <option>-f</option>
-        option is optional. If it is included the found experiments/bioassay sets
-        are tagged with <code>FIX LOWESS</code>, otherwise only a list with the
-        information is generated. 
-      </para>
-      
-    </important>
-
-    <important id="tomcat6">
-      <title>BASE 2.7 requires Tomcat 6 or higher</title>
-      <para>
-        If you are upgrading from older BASE versions to BASE 2.7 or higher
-        you must also make sure that you are running Tomcat 6 or higher.
-        Earlier BASE versions only required Tomcat 5.5. If you are not
-        already running Tomcat 6 you need to upgrade. Other servlet
-        engines may work if they implement the Servlet 2.5 and JSP
-        2.1 specifications.
-      </para>
-    </important>
-
-    <important id="dropindexes">
-      <title>Upgrading from BASE 2.4.3 or lower to 2.4.4 or higher</title>
-      <para>
-        Older releases of BASE 2 used to create indexes for many columns
-        in the dynamic database. The same columns are part of the primary
-        key for the tables so the indexes are not really needed. The 
-        result is very bad performance since the database engine sometimes 
-        get stuck in "index update" mode making the entire server
-        very slow. BASE 2.4.4 no longer creates the indexes. Indexes on
-        existing tables should be dropped to increase the performance.
-        Tests have shown a 50-90% decrease in execution time for some 
-        plug-ins
-        (<ulink url="http://base.thep.lu.se/ticket/294">http://base.thep.lu.se/ticket/294</ulink>). 
-      </para>
-      <para>
-        Removing the indexes is very simple. <emphasis>After the server
-        has been upgraded</emphasis> following the usual instructions below, issue the
-        the following commands:
-      </para>
-    
-      <programlisting>
-cd &lt;basedir&gt;/bin
-./dynamicdb.sh -v -dropindexes
-</programlisting>
-
-      <para>
-        Skip the <option>-dropindexes</option> option to do a dry
-        run without actually deleting the indexes.
-      </para>
-    </important>
-
     <para>
       As always, backup your database before attempting an

trunk/doc/src/docbook/appendix/index.xml

@@ -38 +38 @@
   <include file="other_config.xml" />
   <include file="incompatible.xml" />
+  <include file="update_warnings.xml" />
 </part>