source: trunk/doc/src/docbook/appendix/base.config.xml @ 5071

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE appendix PUBLIC 
    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" 
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<!--
  $Id: base.config.xml 5071 2009-08-21 06:17:57Z nicklas $
  
  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Martin Svensson
  
  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
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  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
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-->

<appendix id="appendix.base.config">
  
  <title>base.config reference</title>

  <para>
    The <filename>base.config</filename> file is the main configuration file
    for BASE. It is located in the <filename>&lt;basedir&gt;/www/WEB-INF/classes</filename>
    directory.
  </para>
  
  <simplesect id="appendix.base.config.dbdriver">
    <title>Database driver section</title>
    
    <para>
      This section has parameters needed for the database connection, such
      as the database dialect, username and password.
    </para>
    
    <variablelist>
    <varlistentry>
      <term><property>db.dialect</property></term>
      <listitem>
        <para>
          The Hibernate dialect to use when generating SQL commands to the database. 
          Use:
          <itemizedlist>
          <listitem>
            <userinput>org.hibernate.dialect.MySQLInnoDBDialect</userinput> 
            for MySQL
          </listitem>
          <listitem>
            <userinput>org.hibernate.dialect.PostgreSQLDialect</userinput> 
            for PostgreSQL
          </listitem>
          </itemizedlist> 
          Other dialects may work but are not supported.
        </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>db.driver</property></term>
      <listitem>
        <para>
          The JDBC driver to use when connecting to the database. Use:
          <itemizedlist>
          <listitem>
            <userinput>com.mysql.jdbc.Driver</userinput> 
            for MySQL
          </listitem>
          <listitem>
            <userinput>org.postgresql.Driver</userinput> 
            for PostgreSQL
          </listitem>
          </itemizedlist> 
          Other JDBC drivers may work but are not supported.
        </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>db.url</property></term>
      <listitem>
        <para>
          The connection URL that locates the BASE database. The exact syntax 
          of the string depends on the JDBC driver. Here are two examples which 
          leaves all other settings to their defaults:
          <itemizedlist>
          <listitem>
            <userinput>jdbc:mysql://localhost/base2</userinput> 
            for MySQL
          </listitem>
          <listitem>
            <userinput>jdbc:postgresql:base2</userinput> 
            for PostgreSQL
          </listitem>
          </itemizedlist>
          
          You can get more information about the parameters that are supported on the 
          connection URL by reading the documentation from 
          <ulink url="http://dev.mysql.com/doc/refman/5.0/en/connector-j-reference-configuration-properties.html"
            >MySQL</ulink> and 
          <ulink url="http://jdbc.postgresql.org/documentation/81/connect.html"
            >PostgreSQL</ulink>.
            
            
          <note>
            <para>
            For MySQL we recommend that you set the character encoding to UTF-8
            and enable the server-side cursors feature. The latter option will 
            reduce memory usage since the JDBC driver does not have to
            load all data into memory. The value below should go into one line
            <userinput>
            jdbc:mysql://localhost/base2?characterEncoding=UTF-8&amp;
              useCursorFetch=true&amp;defaultFetchSize=100&amp;useServerPrepStmts=true
            </userinput>
            </para>
            
            <para>
            Some MySQL versions (for example, 5.0.27) contains a bug that causes some 
            queries to fail if <userinput>useCursorFetch=true</userinput>. If you experience
            this problem, you have to set it to false. For more information
            see <ulink url="http://base.thep.lu.se/ticket/509">http://base.thep.lu.se/ticket/509</ulink>.
            </para>
          </note>
            
        </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>db.dynamic.catalog</property></term>
      <listitem>
        <para>
        The name of the catalog where the dynamic database used to store
        analysed data is located. If not specified the same catalog as the regular 
        database is used. The exact meaning of catalog depends on the actual database. 
        For MySQL the catalog is the name of the database so this value is simply the 
        name of the dynamic database. PostgreSQL does not support connecting to multiple 
        databases with the same connection so this should have the same value as the 
        database in the <property>db.url</property> setting.
        </para>
      </listitem>
    </varlistentry>

    <varlistentry>
      <term><property>db.dynamic.schema</property></term>
      <listitem>
        <para>
        The name of the schema where the dynamic database used to store
        analysed data is located. MySQL does not have schemas so this value should 
        be left empty. PostgreSQL supports schemas and we recommend that the dynamic 
        part is created in it's own schema to avoid mixing the dynamic tables with
        the regular ones.
        </para>
      </listitem>
    </varlistentry>

    <varlistentry>
      <term><property>db.username</property></term>
      <listitem>
        <para>
        The username to connect to the database. The user should have full permission 
        to both the regular and the dynamic database.
        </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>db.password</property></term>
      <listitem>
        <para>
         The password for the user.
         </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>db.batch-size</property></term>
      <listitem>
        <para>
        The batch size to use when inserting/updating items with the Batch API. 
        A higher value requires more memory, a lower value degrades performance
        since the number of database connections increases. The default value is 
        50.
        </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>db.queries</property></term>
      <listitem>
        <para>
        The location of an XML file which contains database-specific 
        queries overriding those that does not work from the 
        <filename>/common-queries.xml</filename> file. Use:
        
        <itemizedlist>
          <listitem><userinput>/mysql-queries.xml</userinput> for MySQL</listitem>
          <listitem><userinput>/postgres-queries.xml</userinput> for PostgreSQL</listitem>
        </itemizedlist>
          See also <xref linkend="appendix.otherconfig.sql" />.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>db.extended-properties</property></term>
      <listitem>
        <para>
        The location of an XML file describing the extended properties for extendable 
        item types, ie. the reporters. The default value is <userinput>/extended-properties.xml</userinput>.
        See <xref linkend="appendix.extendedproperties" /> for more information
        about extended properties.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>db.raw-data-types</property></term>
      <listitem>
        <para>
        The location of an XML file describing all raw data types and their properties. 
        The default value is <userinput>/raw-data-types.xml</userinput>.
        See <xref linkend="appendix.rawdatatypes" /> for more information
        about raw data types.
          </para>
      </listitem>
    </varlistentry>

    <varlistentry>
      <term><property>db.cleanup.interval</property></term>
      <listitem>
        <para>
        Interval in hours between database cleanups. Set this to
        0 to disable (recommened for job agents). The default value 
        is 24.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>export.max.items</property></term>
      <listitem>
        <para>
        The maximum number of items the export function should try to load in a single 
        query. This setting exists because MySQL prior to 5.0.2 does not support scrollable 
        result sets, but loads all data into memory. This will result in out of memory 
        exception if exporting too many items at the same time. PostgreSQL does not have 
        this problem. Use:
        
        <itemizedlist>
        <listitem><para>0 for PostgreSQL</para></listitem>
        <listitem>
          <para>
            0 for MySQL version 5.0.2 or above.
            Requires that <userinput>useCursorFetch=true</userinput> is specified in 
            the connection url and  that <userinput>defaultFetchSize=xxx</userinput>
            is set to a value &gt; 0.
          </para>
        </listitem>
        <listitem>
          <para>
            As large as possible value for other MySQL versions. 
            A low value results in more queries and slower performance when 
            exporting data.
          </para>
        </listitem>
        </itemizedlist>
        </para>
      </listitem>
    </varlistentry>
    </variablelist>
    
  </simplesect>
  
  <simplesect id="appendix.base.config.authentication">
    <title>Authentication section</title>
    <para>
      This section describes parameters that are needed if you are
      going to use external authentication. If you let BASE handle this
      you will not have to bother about these settings. See
      <xref linkend="plugin_developer.other.authentication"/> for more information about 
      external authentication.
    </para>
    
    <variablelist>
    <varlistentry>
      <term><property>auth.driver</property></term>
      <listitem>
        <para>
        The class name of the plug-in that acts as the authentication driver. 
        BASE ships with a simple plug-in that checks if a user has a valid email 
        account on a POP3 server. It is not enabled by default. The class name 
        of that plug-in is <classname docapi="net.sf.basedb.core.authentication">net.sf.basedb.core.authentication.POP3Authenticator</classname>. 
        If no class is specified internal authentication is used.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>auth.init</property></term>
      <listitem>
        <para>
        Initialisation parameters sent to the plug-in when calling the 
        <methodname>init()</methodname> method. The syntax and meaning of this 
        string depends on the plug-in. For the <classname docapi="net.sf.basedb.core.authentication">POP3Authenticator</classname> 
        this is simply the name or IP-address of the mail server.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>auth.synchronize</property></term>
      <listitem>
        <para>
        If this setting is 1 or TRUE, BASE will synchronize the extra 
        information (name, address, email, etc.) sent by the authentication driver 
        when a user logs in to BASE. This setting is ignored if the driver does not 
        support extra information.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>auth.cachepasswords</property></term>
      <listitem>
        <para>
        If passwords should be cached by BASE or not. If the passwords are 
        cached a user may login to BASE even if the external authentication 
        server is down. The cached passwords are only used if the external
        authentication does not answer properly.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>auth.daystocache</property></term>
      <listitem>
        <para>
        How many days a cached password is valid if caching is enabled. A value of
        0 caches the passwords forever.
          </para>
      </listitem>
    </varlistentry>
    </variablelist>
  </simplesect>
  
  <simplesect id="appendix.base.config.jobqueue">
    <title>Internal job queue section</title>
    
    <para>
      This section contains setting that control the internal job queue.
      The internal job queue is a simple queue that executes jobs more or
      less in the order they were added to the queue. To make sure long-running
      jobs do not block the queue, there are four slots that uses the
      expected execution time to decide if a job should be allowed to execute 
      or not.
    </para>
    
    <variablelist>
    <varlistentry>
      <term><property>jobqueue.internal.enabled</property></term>
      <listitem>
        <para>
         If <userinput>0</userinput> or <userinput>FALSE</userinput> the internal 
         job queue will be disabled.
         </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>jobqueue.internal.runallplugins</property></term>
      <listitem>
        <para>
         If <userinput>1</userinput> or <userinput>TRUE</userinput> the internal 
         job queue will ignore the <property>useInternalJobQueue</property>
         flag specified on plug-ins. If <userinput>0</userinput> or <userinput>FALSE</userinput>
         the internal job queue will only execute plug-ins which has
         <property>useInternalJobQueue=true</property>
         </para>
      </listitem>
    </varlistentry>

    <varlistentry>
      <term><property>jobqueue.internal.signalreceiver.class</property></term>
      <listitem>
        <para>
         A class implementing the <interfacename docapi="net.sf.basedb.core.signal"
         >SignalReceiver</interfacename>
         interface. The class must have a public no-argument constructor. If
         no value is specified the default setting is:
         <classname docapi="net.sf.basedb.core.signal"
         >net.sf.basedb.core.signal.LocalSignalReceiver</classname>.
         </para>
         <para>
         Change to <classname docapi="net.sf.basedb.core.signal"
         >net.sf.basedb.core.signal.SocketSignalReceiver</classname>
         if the internal job queue must be able to receive signals from outside
         this JVM.
         </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>jobqueue.internal.signalreceiver.init</property></term>
      <listitem>
        <para>
        Initialisation string sent to <methodname>SignalReceiver.init()</methodname>.
        The syntax and meaning of the string depends on the actual implementation
        that is used. Please see the Javadoc for more information.
         </para>
      </listitem>
    </varlistentry>

    <varlistentry>
      <term><property>jobqueue.internal.checkinterval</property></term>
      <listitem>
        <para>
         The number of seconds between checks to the database for jobs 
         that are waiting for execution.
         </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>jobqueue.internal.shortest.threads</property></term>
      <term><property>jobqueue.internal.short.threads</property></term>
      <term><property>jobqueue.internal.medium.threads</property></term>
      <term><property>jobqueue.internal.long.threads</property></term>
      <listitem>
        <para>
        Maximum number of threads to reserve for jobs with a given expected
        execution time. A job with a short execution time may use a thread
        from one of the slots with longer execution time. When all threads
        are in use, new jobs will have to wait until an executing job
        has finished.
        </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>jobqueue.internal.shortest.threadpriority</property></term>
      <term><property>jobqueue.internal.short.threadpriority</property></term>
      <term><property>jobqueue.internal.medium.threadpriority</property></term>
      <term><property>jobqueue.internal.long.threadpriority</property></term>
      <listitem>
        <para>
        The priority to give to jobs. The priority is a value between 1 and 10. 
        See <ulink url="http://java.sun.com/javase/6/docs/api/java/lang/Thread.html"
        >http://java.sun.com/javase/6/docs/api/java/lang/Thread.html</ulink> 
        for more information about thread priorities.
        </para>
      </listitem>
    </varlistentry>
    </variablelist>

  </simplesect>

  <simplesect id="appendix.base.config.jobagent">
    <title>Job agent section</title>
    
    <para>
      This section contains settings that BASE uses when communicating
      with external job agents. See <xref linkend="installation_upgrade.jobagents"/> 
      for more information about job agents.
    </para>
    
    <variablelist>
    <varlistentry>
      <term><property>agent.maxage</property></term>
      <listitem>
        <para>
        Number of seconds to keep job agent information in the internal cache. 
        The information includes, CPU and memory usage and the status of executing 
        jobs. This setting controls how long the information is kept in the cache 
        before a new request is made to the job agent. The default value is 60 seconds.
          </para>
      </listitem>
    </varlistentry>

    <varlistentry>
      <term><property>agent.connection.timeout</property></term>
      <listitem>
        <para>
        The timeout in milliseconds to wait for a response from a job agent 
        when sending a request to it. The default timeout is 1000 milliseconds. 
        This should be more than enough if the job agent is on the internal 
        network, but may have to be increased if it is located somewhere else.
          </para>
      </listitem>
    </varlistentry>

    </variablelist>
    
  </simplesect>

  <simplesect id="appendix.base.config.secondary">
    <title>Secondary storage controller</title>
    
    <para>
      This section contains settings for the secondary storage controller. See
      <xref linkend="plugin_developer.other.secondary"/> for more
      information about secondary storage.
    </para>
    
    <variablelist>
    <varlistentry>
      <term><property>secondary.storage.driver</property></term>
      <listitem>
        <para>
        The class name of the plug-in that acts as the secondary storage controller. 
        BASE ships with a simple plug-in that just moves files to another directory, 
        but it is not enabled by default. The class name of that plug-in is 
        <classname docapi="net.sf.basedb.core">net.sf.basedb.core.InternalStorageController</classname>. 
        If no class is specified the secondary storage feature is disabled.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>secondary.storage.init</property></term>
      <listitem>
        <para>
        Initialisation parameters sent to the plug-in when calling the 
        <methodname>init()</methodname> method. The syntax and meaning of this 
        string depends on the plug-in. For the internal controller this is simply 
        the path to the secondary directory.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>secondary.storage.interval</property></term>
      <listitem>
        <para>
        Interval in seconds between each execution of the secondary storage 
        controller plug-in. It must be a value greater than zero or the secondary 
        storage feature will be disabled.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>secondary.storage.time</property></term>
      <listitem>
        <para>
        Time-point values specifying the time(s) of day that the secondary storage controller 
        should be executed. If present, this setting overrides the 
        <property>secondary.storage.interval</property> setting. 
        Time-point values are given as comma-separated list of two-digit, 24-based hour 
        and two-digit minute values. For example: <userinput>03:10,09:00,23:59</userinput>.
          </para>
      </listitem>
    </varlistentry>
    </variablelist>
    
  </simplesect>
  
  <simplesect id="appendix.base.config.log">
    <title>Change history logging section</title>
    
    <para>
      This section contains settings for logging the change history
      of items.
    </para>
    
    <variablelist>
    <varlistentry>
      <term><property>changelog.factory</property></term>
      <listitem>
        <para>
        The factory class that controls the entire logging system. The 
        factory has control of what should be logged, were it should
        be logged, etc. BASE ships with one factory implementation
        <classname docapi="net.sf.basedb.core.log.db">DbLogManagerFactory</classname>
        which logs changes into tables in the database. The server admin
        may choose a different implementation provided that it implements
        the <interfacename docapi="net.sf.basedb.core.log">LogManagerFactory</interfacename>
        interface. See <xref linkend="plugin_developer.other.logging" />.
        If no factory is specified, logging is disabled. 
          </para>
      </listitem>
    </varlistentry>
    <varlistentry>
      <term><property>changelog.show-in-web</property></term>
      <listitem>
        <para>
        A boolean value that specifies if the <guilabel>Change history</guilabel>
        tab should be visible in the web interface or not. The change history
        tab will show log information that has been stored in the database
        and it doesn't make sense to show this tab unless the 
        <classname docapi="net.sf.basedb.core.log.db">DbLogManagerFactory</classname>
        is used.
          </para>
          
          <note>
            <para>
            By default, only users that are members of the 
            <guilabel>Administrator</guilabel> role have permission to 
            view the change history. To give other users the same permission,
            add the <guilabel>Change history</guilabel> permission to
            the appropriate role(s).
            </para>
          </note>
      </listitem>
    </varlistentry>
    <varlistentry>
      <term><property>changelog.dblogger.detailed-properties</property></term>
      <listitem>
        <para>
        A boolean value that specifies the amount of information 
        that should be logged. If set, the log will contain information 
        about which properties that was modified on each item, 
        otherwise only the type of change (create, update, delete) is
        logged.
        </para>
      </listitem>
    </varlistentry>
    </variablelist>
    
  </simplesect>
  
  <simplesect id="appendix.base.config.secondary.other">
    <title>Other settings</title>
    
    <variablelist>
    <varlistentry>
      <term><property>userfiles</property></term>
      <listitem>
        <para>
        The path to the directory where uploaded and generated files should 
        be stored. This is the primary file storage. See <xref linkend="appendix.base.config.secondary" /> 
        for information about how to configure the secondary storage. Files are not 
        stored in the same directory structure or with the same names as in 
        the BASE file system. The internal structure may contain sub-directories.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>permission.timeout</property></term>
      <listitem>
        <para>
        Number of minutes to cache a logged in user's permissions before 
        reloading them. The default value is 10. This setting affect how 
        quickly a changed permission propagate to a logged in user. Permissions 
        are always reloaded when a user logs in.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>cache.timeout</property></term>
      <listitem>
        <para>
        Number of minutes to keep user sessions in the internal cache 
        before the user is automatically logged out. The timeout is counted 
        from the last access made from the user.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>cache.static.disabled</property></term>
      <listitem>
        <para>
        If the static cache should be enabled or disabled. It is enabled by
        default. Disabling the static cache may reduce performance in some
        cases. The static cache is used to cache processed information,
        for example images, so that the database doesn't have to be queried
        on every request.
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>cache.static.max-age</property></term>
      <listitem>
        <para>
        The maximum age in days of files in the static cache. Files that 
        hasn't been accessed (read or written) in the specified amount
        of time are deleted. 
          </para>
      </listitem>
    </varlistentry>
    
    <varlistentry>
      <term><property>helptext.update</property></term>
      <listitem>
        <para>
          Defines if already existing helptexts in BASE should be overwritten when
          updating the program,
          <xref linkend="installation_upgrade.upgrade" />
          <itemizedlist>
            <listitem>
              <simpara>
                <userinput>true</userinput>
                will overwrite existing helptexts.
              </simpara>
            </listitem>
            <listitem>
              <simpara>
                <userinput>false</userinput>
                will leave the existing helptexts in database unchanged and only
                insert new helptexts.
              </simpara>
            </listitem>
          </itemizedlist>
        </para>
      </listitem>
    </varlistentry>
    <varlistentry>
      <term><property>plugins.autounload</property></term>
      <listitem>
        <para>
          Enable this setting to let BASE detect if a plug-in JAR file is changed
          and automatically load and use the new code instead of the old code.
          This setting is useful for plug-in developers since they don't have to
          restart the web server each time the plug-in is recompiled.
          <itemizedlist>
            <listitem>
              <simpara>
                <userinput>true,yes,1</userinput>
                to enable
              </simpara>
            </listitem>
            <listitem>
              <simpara>
                <userinput>false,no,0</userinput>
                to disable (default if no value is specified)
              </simpara>
            </listitem>
          </itemizedlist>
        </para>
      </listitem>
    </varlistentry>
    <varlistentry>
      <term><property>plugins.dir</property></term>
      <listitem>
        <para>
          The path to the directory where jar-files for external plugins should be located
          if they should be used with the auto-installer. All new plugins found in this directory, 
          or in any of it's sub-directories, can be selected for installation, see
          <xref linkend="plugins.installation" />. 
          The plugging auto-installer will not be available if this property isn't defined. 
        </para>

        <para>
          Another benefit is that all plug-ins inside this directory are registered
          with relative paths. This means that there is a lot less hassle when 
          using job agents to run plug-ins. Just change this setting for the job
          agent installation and all plug-ins will work. For plug-ins that are outside
          of this directory you may have to manually register the path if it is different from
          the main path. It will also be a lot easier if you plan to move all plug-ins to
          a different directory. Just move the JAR files and change this setting. There is
          no need to change the paths for each plug-in in the database.
        </para>
            
      </listitem>
    </varlistentry>
    </variablelist>
  </simplesect>

</appendix>