Changeset 5738


Ignore:
Timestamp:
Sep 15, 2011, 8:53:11 AM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

Re-orgarnized file/directory structure of documentation to make the paths a little bit shorter.

Location:
trunk
Files:
2 deleted
38 edited
2 copied
4 moved

Legend:

Unmodified
Added
Removed
  • trunk/build.xml

    r5737 r5738  
    12861286    <mkdir dir="${docbook.html.out}" />
    12871287    <!--Create subdirectories to store the chunked files in-->
    1288     <mkdir dir="${docbook.html.out}/admindoc"/>
    1289     <mkdir dir="${docbook.html.out}/admindoc/user_administration"/>
    1290     <mkdir dir="${docbook.html.out}/admindoc/installation_upgrade"/>
    1291     <mkdir dir="${docbook.html.out}/admindoc/plugins"/>
    1292     <mkdir dir="${docbook.html.out}/admindoc/extensions"/>
    1293     <mkdir dir="${docbook.html.out}/admindoc/coreplugin_configuration"/>
    1294     <mkdir dir="${docbook.html.out}/developerdoc"/>
    1295     <mkdir dir="${docbook.html.out}/developerdoc/migrate_2_3"/>
    1296     <mkdir dir="${docbook.html.out}/developerdoc/api"/>
    1297     <mkdir dir="${docbook.html.out}/developerdoc/develop_overview"/>
    1298     <mkdir dir="${docbook.html.out}/developerdoc/extensions"/>
    1299     <mkdir dir="${docbook.html.out}/developerdoc/core_ref"/>
    1300     <mkdir dir="${docbook.html.out}/developerdoc/javadoc"/>
    1301     <mkdir dir="${docbook.html.out}/developerdoc/plugin_developer"/>
    1302     <mkdir dir="${docbook.html.out}/developerdoc/webservices"/>
    1303     <mkdir dir="${docbook.html.out}/developerdoc/write_doc"/>
    1304     <mkdir dir="${docbook.html.out}/overviewdoc"/>
    1305     <mkdir dir="${docbook.html.out}/overviewdoc/features"/>
    1306     <mkdir dir="${docbook.html.out}/overviewdoc/overview"/>
    1307     <mkdir dir="${docbook.html.out}/overviewdoc/resources"/>
    1308     <mkdir dir="${docbook.html.out}/overviewdoc/why_base"/>
    1309     <mkdir dir="${docbook.html.out}/userdoc"/>
    1310     <mkdir dir="${docbook.html.out}/userdoc/about"/>
    1311     <mkdir dir="${docbook.html.out}/userdoc/annotations"/>
    1312     <mkdir dir="${docbook.html.out}/userdoc/platforms"/>
    1313     <mkdir dir="${docbook.html.out}/userdoc/array_lims"/>
    1314     <mkdir dir="${docbook.html.out}/userdoc/biomaterials"/>
    1315     <mkdir dir="${docbook.html.out}/userdoc/analysis"/>
    1316     <mkdir dir="${docbook.html.out}/userdoc/filesystem"/>
    1317     <mkdir dir="${docbook.html.out}/userdoc/subtypes"/>
    1318     <mkdir dir="${docbook.html.out}/userdoc/wares"/>
    1319     <mkdir dir="${docbook.html.out}/userdoc/import"/>
    1320     <mkdir dir="${docbook.html.out}/userdoc/export"/>
    1321     <mkdir dir="${docbook.html.out}/userdoc/jobs"/>
    1322     <mkdir dir="${docbook.html.out}/userdoc/project_permission"/>
    1323     <mkdir dir="${docbook.html.out}/userdoc/protocols"/>
    1324     <mkdir dir="${docbook.html.out}/userdoc/reporters"/>
    1325     <mkdir dir="${docbook.html.out}/userdoc/trashcan"/>
    1326     <mkdir dir="${docbook.html.out}/userdoc/webclient"/>
    1327     <mkdir dir="${docbook.html.out}/userdoc/overview"/>
    1328     <mkdir dir="${docbook.html.out}/faqsdoc" />
    1329     <mkdir dir="${docbook.html.out}/faqsdoc/faqs" />
     1288    <mkdir dir="${docbook.html.out}/admin"/>
     1289    <mkdir dir="${docbook.html.out}/developer"/>
     1290    <mkdir dir="${docbook.html.out}/overview"/>
     1291    <mkdir dir="${docbook.html.out}/user"/>
     1292    <mkdir dir="${docbook.html.out}/faq" />
    13301293    <mkdir dir="${docbook.html.out}/appendix" />
    13311294       
  • trunk/doc/src/docbook/admin/accounts.xml

    r5737 r5738  
    2525-->
    2626
    27 <chapter id="user_administration">
    28   <?dbhtml dir="user_administration"?>
     27<chapter id="accounts">
    2928  <title>Account administration</title>
    3029
     
    3938  </important>
    4039
    41   <sect1 id="user_administration.users">
     40  <sect1 id="accounts.users">
    4241    <title>Users administration</title>
    4342    <para>
     
    5049    </para>
    5150
    52     <sect2 id="user_administration.users.edit">
     51    <sect2 id="accounts.users.edit">
    5352      <title>Edit user</title>
    5453      <para>
     
    5756        shows the user's memberships.
    5857      </para>
    59       <sect3 id="user_administration.users.edit.properties">       
     58      <sect3 id="accounts.users.edit.properties">       
    6059        <title>Properties</title>
    6160        <helptext external_id="user.edit" title="Edit user account">
     
    337336      </sect3>
    338337
    339       <sect3 id="user_administration.users.edit.additional">
     338      <sect3 id="accounts.users.edit.additional">
    340339        <title>Additional information</title>
    341340        <helptext external_id="user.edit.additional" title="Additional information">
     
    396395      </sect3>
    397396
    398       <sect3 id="user_administration.users.edit.membership">
     397      <sect3 id="accounts.users.edit.membership">
    399398        <title>Group and role membership</title>
    400399        <helptext external_id="user.edit.membership" title="Group and role membership">
     
    479478    </sect2>
    480479   
    481     <sect2 id="user_administration.users.default_membership">
     480    <sect2 id="accounts.users.default_membership">
    482481      <title>Default group and role membership</title>
    483482     
     
    530529  </sect1>
    531530
    532   <sect1 id="user_administration.groups">
     531  <sect1 id="accounts.groups">
    533532    <title>Groups administration</title>
    534533    <para>
     
    546545    </para>
    547546
    548     <sect2 id="user_administration.groups.edit">
     547    <sect2 id="accounts.groups.edit">
    549548      <title>Edit group</title>
    550549      <para>
     
    554553        <guilabel>Members</guilabel>.
    555554      </para>
    556       <sect3 id="user_administration.groups.edit.properties">
     555      <sect3 id="accounts.groups.edit.properties">
    557556        <title>Properties</title>
    558557        <helptext external_id="group.edit" title="Edit group">
     
    652651      </sect3>
    653652
    654       <sect3 id="user_administration.groups.edit.members">
     653      <sect3 id="accounts.groups.edit.members">
    655654        <title>Group members</title>
    656655        <helptext external_id="group.edit.membership" title="Edit group members">
     
    727726  </sect1>
    728727
    729   <sect1 id="user_administration.roles">
     728  <sect1 id="accounts.roles">
    730729    <title>Roles administration</title>
    731730    <para>
     
    737736
    738737
    739     <sect2 id="user_administration.roles.defaultroles">
     738    <sect2 id="accounts.roles.defaultroles">
    740739      <title>Pre-defined system roles</title>
    741740      <para>
     
    811810    </sect2>
    812811
    813     <sect2 id="user_administration.roles.edit">
     812    <sect2 id="accounts.roles.edit">
    814813      <title>Edit role</title>
    815814      <para>
     
    819818        permissions.
    820819      </para>
    821       <sect3 id="user_administration.roles.edit.properties">
     820      <sect3 id="accounts.roles.edit.properties">
    822821        <title>Properties</title>
    823822        <helptext external_id="role.edit" title="Edit role">
     
    908907      </sect3>
    909908
    910       <sect3 id="user_administration.roles.edit.permissions">
     909      <sect3 id="accounts.roles.edit.permissions">
    911910        <title>Permissions</title>
    912911        <helptext external_id="role.edit.permissions" title="Edit role permissions">
     
    991990      </sect3>
    992991
    993       <sect3 id="user_administration.roles.edit.members">
     992      <sect3 id="accounts.roles.edit.members">
    994993        <title>Members</title>
    995994        <helptext external_id="role.edit.members" title="Role members">
     
    10421041  </sect1>
    10431042
    1044   <sect1 id="user_administration.quota">
     1043  <sect1 id="accounts.quota">
    10451044    <title>Disk space/quota</title>
    10461045    <para>
     
    10611060    <para>
    10621061      Read
    1063       <xref linkend="user_administration.users.edit" />
    1064       and <xref linkend="user_administration.groups.edit" />
     1062      <xref linkend="accounts.users.edit" />
     1063      and <xref linkend="accounts.groups.edit" />
    10651064      for information about how to set a quota for a user and
    10661065      group.
     
    10741073    </para>
    10751074
    1076     <sect2 id="user_administration.quota.edit">
     1075    <sect2 id="accounts.quota.edit">
    10771076      <title>Edit quota</title>
    10781077      <para>
     
    10801079        limits are defined.
    10811080      </para>
    1082       <sect3 id="user_administration.quota.edit.properties">
     1081      <sect3 id="accounts.quota.edit.properties">
    10831082        <title>Properties</title>
    10841083        <helptext external_id="quota.edit" title="Edit properties">
     
    11171116      </sect3>
    11181117
    1119       <sect3 id="user_administration.quota.edit.values">
     1118      <sect3 id="accounts.quota.edit.values">
    11201119        <title>Values</title>
    11211120        <helptext external_id="quota.edit.values" title="Edit quota values">
     
    11821181    </sect2>
    11831182   
    1184     <sect2 id="user_administration.quota.diskusage">
     1183    <sect2 id="accounts.quota.diskusage">
    11851184      <title>Disk usage</title>
    11861185     
  • trunk/doc/src/docbook/admin/index.xml

    r5737 r5738  
    2424  along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2525-->
    26 <part id="admindoc">
    27   <?dbhtml dir="admindoc"?>
     26<part id="admin">
     27  <?dbhtml dir="admin"?>
    2828  <title>Admin documentation</title>
    29   <include file="installation_upgrade.xml"/>
     29  <include file="installation.xml"/>
    3030  <include file="plugins.xml"/>
    31   <include file="user_administration.xml"/>
     31  <include file="accounts.xml"/>
    3232</part>
  • trunk/doc/src/docbook/admin/installation.xml

    r5737 r5738  
    2727-->
    2828
    29 <chapter id="installation_upgrade">
    30   <?dbhtml dir="installation_upgrade"?>
     29<chapter id="installation">
    3130
    3231  <title>Installation and upgrade instructions</title>
     
    4241  </note>
    4342
    44   <sect1 id="installation_upgrade.upgrade">
     43  <sect1 id="installation.upgrade">
    4544    <title>Upgrade instructions</title>
    4645
    47     <important id="installation_upgrade.upgrade.important">
     46    <important id="installation.upgrade.important">
    4847      <title>Important information for upgrading from BASE 2.17 to BASE 3.0-alfa</title>
    4948     
     
    159158              If there are users logged in to your BASE server, it may
    160159              be nice of you to notify them a few minutes prior to shutting
    161               down the BASE server. See <xref linkend="installation_upgrade.broadcast" />.
     160              down the BASE server. See <xref linkend="installation.broadcast" />.
    162161            </para>
    163162          </tip>
     
    300299  </sect1>      <!-- Upgrade instructions -->
    301300
    302   <sect1 id="installation_upgrade.installation">
     301  <sect1 id="installation.main">
    303302    <title>Installation instructions</title>
    304303
     
    493492      </varlistentry>
    494493
    495       <varlistentry id="installation_upgrade.installation.database">
     494      <varlistentry id="installation.main.database">
    496495        <term>BASE (database engine)</term>
    497496        <listitem>
     
    611610      </varlistentry>
    612611
    613       <varlistentry id="installation_upgrade.installation.configuration">
     612      <varlistentry id="installation.main.configuration">
    614613        <term>BASE (configuration)</term>
    615614        <listitem>
     
    755754            creating a couple user accounts, for more information on
    756755            how to create user accounts please refer to
    757             <xref linkend="user_administration"/>.
     756            <xref linkend="accounts"/>.
    758757          </para>
    759758        </listitem>
     
    764763  </sect1>      <!-- Installation instructions -->
    765764
    766   <sect1 id="installation_upgrade.jobagents">
     765  <sect1 id="installation.jobagents">
    767766    <title>Installing job agents</title>
    768767
     
    837836    </para>
    838837
    839     <sect2 id="installation_upgrade.jobagents.serverside">
     838    <sect2 id="installation.jobagents.serverside">
    840839      <title>BASE application server side setup</title>
    841840      <para>
     
    855854            </listitem>
    856855          </varlistentry>
    857           <varlistentry id="installation_upgrade.jobagent.user_account">
     856          <varlistentry id="installation.jobagent.user_account">
    858857            <term>Enable the job agent user account</term>
    859858            <listitem>
     
    867866                <filename>jobagent.properties</filename> file, see
    868867                item
    869                 <xref linkend="installation_upgrade.jobagent.client.properties"/>
     868                <xref linkend="installation.jobagent.client.properties"/>
    870869                below.
    871870              </para>
     
    876875    </sect2>
    877876
    878     <sect2 id="installation_upgrade.jobagents.database">
     877    <sect2 id="installation.jobagents.database">
    879878      <title>Database server setup</title>
    880879      <para>
    881880        <variablelist>
    882           <varlistentry id="installation_upgrade.jobagent.database">
     881          <varlistentry id="installation.jobagent.database">
    883882            <term>Create a user account on the database</term>
    884883            <listitem>
     
    888887                installation, cf.
    889888                <xref
    890                 linkend="installation_upgrade.installation.database"/>.
     889                linkend="installation.main.database"/>.
    891890                You must create an account in the database that is
    892891                allowed to connect from the job agent server. MySQL
     
    899898                agent. You should also set password. This password is
    900899                used in item
    901                 <xref linkend="installation_upgrade.jobagent.client.config"/>
     900                <xref linkend="installation.jobagent.client.config"/>
    902901                below in job agent server setup. You can use the same
    903902                database user and password as in the regular database
     
    910909    </sect2>
    911910
    912     <sect2 id="installation_upgrade.jobagents.client">
     911    <sect2 id="installation.jobagents.client">
    913912      <title>Job agent client setup</title>
    914913      <para>
     
    926925            </listitem>
    927926          </varlistentry>
    928           <varlistentry id="installation_upgrade.jobagent.client.config">
     927          <varlistentry id="installation.jobagent.client.config">
    929928            <term>Edit the <filename>base.config</filename> file</term>
    930929            <listitem>
     
    934933                installation, cf.
    935934                <xref
    936                 linkend="installation_upgrade.installation.configuration"/>,
     935                linkend="installation.main.configuration"/>,
    937936                to use the same database as the web server
    938937                application. The most important settings are
     
    943942                      user you created in item
    944943                      <xref
    945                       linkend="installation_upgrade.jobagent.database"/>
     944                      linkend="installation.jobagent.database"/>
    946945                      above.
    947946                    </para>
     
    984983            </listitem>
    985984          </varlistentry>
    986           <varlistentry id="installation_upgrade.jobagent.client.properties">
     985          <varlistentry id="installation.jobagent.client.properties">
    987986            <term>Edit
    988987            the <filename>jobagent.properties</filename> file</term>
     
    998997                      you set for the job agent user account in item
    999998                      <xref
    1000                       linkend="installation_upgrade.jobagent.user_account"/>
     999                      linkend="installation.jobagent.user_account"/>
    10011000                      above.
    10021001                    </para>
     
    10571056
    10581057
    1059     <sect2 id="installation_upgrade.jobagents.configuration">
     1058    <sect2 id="installation.jobagents.configuration">
    10601059      <title>Configuring the job agent</title>
    10611060   
     
    12101209  </sect1>      <!-- job agent setup -->
    12111210
    1212   <sect1 id="installation_upgrade.serverconfigurations">
     1211  <sect1 id="installation.serverconfigurations">
    12131212    <title>Server configurations</title>
    12141213    <para>
     
    13941393    </variablelist>
    13951394   
    1396     <sect2 id="installation_upgrade.broadcast">
     1395    <sect2 id="installation.broadcast">
    13971396      <title>Sending a broadcast message to logged in users</title>
    13981397
  • trunk/doc/src/docbook/admin/plugins.xml

    r5737 r5738  
    2828
    2929<chapter id="plugins">
    30   <?dbhtml dir="plugins"?>
    3130  <title>Plug-ins and extensions</title>
    3231
     
    299298            the internal job queue is used this setting has no effect and the
    300299            plug-in may use as much memory as it likes.
    301             <nohelp>See <xref linkend="installation_upgrade.jobagents.configuration" /> for more information.</nohelp>
     300            <nohelp>See <xref linkend="installation.jobagents.configuration" /> for more information.</nohelp>
    302301          </para>
    303302        </listitem>
     
    602601              same as the permission list for roles.
    603602              <nohelp>
    604                 See <xref linkend="user_administration.roles.edit.permissions" />.
     603                See <xref linkend="accounts.roles.edit.permissions" />.
    605604              </nohelp>
    606605            </para>
  • trunk/doc/src/docbook/appendix/base.config.xml

    r5680 r5738  
    451451    <para>
    452452      This section contains settings that BASE uses when communicating
    453       with external job agents. See <xref linkend="installation_upgrade.jobagents"/>
     453      with external job agents. See <xref linkend="installation.jobagents"/>
    454454      for more information about job agents.
    455455    </para>
     
    805805          Defines if already existing helptexts in BASE should be overwritten when
    806806          updating the program,
    807           <xref linkend="installation_upgrade.upgrade" />
     807          <xref linkend="installation.upgrade" />
    808808          <itemizedlist>
    809809            <listitem>
  • trunk/doc/src/docbook/appendix/update_warnings.xml

    r5677 r5738  
    3030    This document is a list of things that may have to be considered
    3131    when updating a BASE installation to a newer version. The <xref
    32     linkend="installation_upgrade.upgrade" /> section only include the most
     32    linkend="installation.upgrade" /> section only include the most
    3333    recent information that is needed for updating the previous BASE version
    3434    to the current version.
  • trunk/doc/src/docbook/developer/api_overview.xml

    r5737 r5738  
    2626
    2727<chapter id="api_overview">
    28   <?dbhtml dir="api"?>
    2928  <title>API overview (how to use and code examples)</title>
    3029
     
    16361635        <title>See also</title>
    16371636        <listitem><xref linkend="plugins.installation" /></listitem>
    1638         <listitem><xref linkend="installation_upgrade.jobagents" /></listitem>
     1637        <listitem><xref linkend="installation.jobagents" /></listitem>
    16391638      </itemizedlist>
    16401639     
  • trunk/doc/src/docbook/developer/base_overview.xml

    r5633 r5738  
    2626
    2727<chapter id="base_develop_overview" chunked="0">
    28   <?dbhtml dir="develop_overview"?>
    2928  <title>Developer overview of BASE</title>
    3029
  • trunk/doc/src/docbook/developer/core_ref.xml

    r5689 r5738  
    2626
    2727<chapter id="core_ref">
    28   <?dbhtml dir="core_ref"?>
    2928  <title>Core developer reference</title>
    3029
  • trunk/doc/src/docbook/developer/documentation.xml

    r5071 r5738  
    2626
    2727<chapter id="documentation">
    28   <?dbhtml dir="write_doc"?>
    2928  <title>Write documentation</title>
    3029
  • trunk/doc/src/docbook/developer/extensions.xml

    r5737 r5738  
    2626
    2727<chapter id="extensions_developer">
    28   <?dbhtml dir="extensions"?>
    2928  <title>Extensions developer</title>
    3029
  • trunk/doc/src/docbook/developer/index.xml

    r5634 r5738  
    2525-->
    2626<part id="developerdoc">
    27   <?dbhtml dir="developerdoc"?>
     27  <?dbhtml dir="developer"?>
    2828  <title>Developer documentation</title>
    2929  <include file="migrate_2_3.xml" />
  • trunk/doc/src/docbook/developer/migrate_2_3.xml

    r5704 r5738  
    2525-->
    2626<chapter id="migrate_2_3" chunked="0">
    27   <?dbhtml dir="migrate_2_3"?>
    2827  <title>Migrating code from BASE 2 to BASE 3</title>
    2928
  • trunk/doc/src/docbook/developer/plugin_developer.xml

    r5737 r5738  
    2626
    2727<chapter id="plugin_developer">
    28   <?dbhtml dir="plugin_developer"?>
    2928  <title>Plug-in developer</title>
    3029  <sect1 id="plugin_developer.organize">
     
    16901689          Normally, the creation of a job and the execution of it are
    16911690          two different events. The execution may as well be done on a
    1692           different server. See <xref linkend="installation_upgrade.jobagents" />.
     1691          different server. See <xref linkend="installation.jobagents" />.
    16931692          This means that the execution takes place in a different instance
    16941693          of the plug-in class than what was used for creating the job.
  • trunk/doc/src/docbook/developer/webservices.xml

    r5655 r5738  
    2626
    2727<chapter id="webservices">
    28   <?dbhtml dir="webservices"?>
    2928  <title>Web services</title>
    3029  <para>
  • trunk/doc/src/docbook/faq/faqs.xml

    r5682 r5738  
    2727
    2828<part id="faqsdoc">
    29   <?dbhtml dir="faqsdoc"?>
     29  <?dbhtml dir="faq"?>
    3030  <title>FAQ</title>
    3131
    3232  <chapter id="faqs" chunked="0">
    33     <?dbhtml dir="faqs"?>
    3433    <title>Frequently Asked Questions with answers</title>
    3534
     
    6766              reporters, you will need modify the <filename>extended-properties.xml</filename>
    6867              file and run a BASE update. Please refer to section
    69               <xref linkend="installation_upgrade.installation" />
     68              <xref linkend="installation.main" />
    7069              for information about both processes. Once done with the upgrade, you'll
    7170              have to define a new reporter import plug-in. Instructions can be found
     
    337336              by marking their checkboxes. Then click on the <guibutton>Pool</guibutton>
    338337              button. For more information see
    339               <xref linkend="biomaterials.samples.create" />.
     338              <xref linkend="biomaterial.samples.create" />.
    340339              Pooling can also be applied to extracts.
    341340            </para>
     
    355354              permission to create subtypes. Contact your BASE administrator.
    356355              For more information about permissions, please refer to
    357               <xref linkend="user_administration" />.
     356              <xref linkend="accounts" />.
    358357            </para>
    359358          </answer>
     
    419418              Then, you will have to run the <filename>updatedb.sh</filename>
    420419              to make the new raw data type available to the system. See
    421               <xref linkend="installation_upgrade.upgrade" />.
     420              <xref linkend="installation.upgrade" />.
    422421            </para>
    423422            <para>
  • trunk/doc/src/docbook/index.xml

    r5676 r5738  
    2424  along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2525-->
    26 <book id="base2_documentation">
     26<book id="base_documentation">
    2727  <bookinfo>
    2828    <releaseinfo>Last modified: <lastmodified/></releaseinfo>
     
    3030  <title>BASE <baseversion/> Documentation</title>
    3131 
    32   <include file="overviewdoc/index.xml"/>
    33   <include file="userdoc/index.xml"/>
    34   <include file="admindoc/index.xml"/>
    35   <include file="developerdoc/index.xml"/>
     32  <include file="overview/index.xml"/>
     33  <include file="user/index.xml"/>
     34  <include file="admin/index.xml"/>
     35  <include file="developer/index.xml"/>
    3636  <include file="faq/faqs.xml" />
    3737  <include file="appendix/index.xml" />
  • trunk/doc/src/docbook/overview/base_overview.xml

    r4509 r5738  
    2626
    2727<chapter id="base_overview">
    28   <?dbhtml dir="overview"?>
    2928  <title>Overview of BASE</title>
    3029    <sect1 id="nolabelhereyet2">
  • trunk/doc/src/docbook/overview/features.xml

    r4889 r5738  
    2727
    2828<chapter id="features" chunked="0">
    29   <?dbhtml dir="features"?>
    3029  <title>BASE features</title>
    3130
  • trunk/doc/src/docbook/overview/index.xml

    r4889 r5738  
    2626-->
    2727<part id="overviewdoc">
    28   <?dbhtml dir="overviewdoc"?>
     28  <?dbhtml dir="overview"?>
    2929  <title>Overview</title>
    3030
  • trunk/doc/src/docbook/overview/resources.xml

    r5036 r5738  
    2626
    2727<chapter id="resources" chunked="0">
    28   <?dbhtml dir="resources"?>
    2928  <title>Resources</title>
    3029  <para>
  • trunk/doc/src/docbook/overview/why_base.xml

    r4509 r5738  
    2626
    2727<chapter id="why_base">
    28   <?dbhtml dir="why_base"?>
    2928  <title>Why use BASE</title>
    3029    <sect1 id="nolabelhereyet">
  • trunk/doc/src/docbook/user/annotations.xml

    r5706 r5738  
    2626
    2727<chapter id="annotations">
    28   <?dbhtml dir="annotations"?>
    2928  <title>Annotations</title>
    3029 
  • trunk/doc/src/docbook/user/array_lims.xml

    r4889 r5738  
    2727
    2828<chapter id="array_lims" chunked="0">
    29   <?dbhtml dir="array_lims"?>
    3029  <title>Array LIMS</title>
    3130
  • trunk/doc/src/docbook/user/biomaterials.xml

    r5724 r5738  
    2626-->
    2727<chapter id="biomaterials">
    28   <?dbhtml dir="biomaterials"?>
    2928  <title>Biomaterial</title>
    3029  <sect1 id="biomaterial.introduction">
  • trunk/doc/src/docbook/user/experiments_analysis.xml

    r4905 r5738  
    2626
    2727<chapter id="experiments_analysis">
    28   <?dbhtml dir="analysis"?>
    2928  <title>Experiments and analysis</title>
    3029  <include file="scans_images.xml"/>
  • trunk/doc/src/docbook/user/export_data.xml

    r5372 r5738  
    3838-->
    3939<chapter id="export_data" chunked="0">
    40   <?dbhtml dir="export"?>
    4140  <title>Export of data</title>
    4241  <para>
  • trunk/doc/src/docbook/user/file_system.xml

    r5705 r5738  
    2626
    2727<chapter id="file_system">
    28   <?dbhtml dir="filesystem"?>
    2928  <title>File management</title>
    3029  <sect1 id="file_system.system">
     
    216215     
    217216      <para>
    218         See <xref linkend="user_administration.quota" /> for more information about
     217        See <xref linkend="accounts.quota" /> for more information about
    219218        the quota system.
    220219      </para>
  • trunk/doc/src/docbook/user/import_data.xml

    r5372 r5738  
    3838-->
    3939<chapter id="import_data" chunked="0">
    40   <?dbhtml dir="import"?>
    4140  <title>Import of data</title>
    4241  <para>
  • trunk/doc/src/docbook/user/index.xml

    r5706 r5738  
    2424  along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2525-->
    26 <part id="userdoc">
    27   <?dbhtml dir="userdoc"?>
     26<part id="user">
     27  <?dbhtml dir="user"?>
    2828  <title>User documentation</title>
    2929  <include file="overview.xml"/>
  • trunk/doc/src/docbook/user/jobs.xml

    r5705 r5738  
    2626
    2727<chapter id="jobs" chunked="0">
    28   <?dbhtml dir="jobs"?>
    2928  <title>Jobs</title>
    3029 
     
    301300                This options is normally only given to powers users and
    302301                needs the <emphasis>Select job agent</emphasis> permission.
    303                 See <xref linkend="user_administration.roles.edit" />.
     302                See <xref linkend="accounts.roles.edit" />.
    304303              </para>
    305304            </listitem>
  • trunk/doc/src/docbook/user/overview.xml

    r5684 r5738  
    2626
    2727<chapter id="userdoc_overview" chunked="0">
    28   <?dbhtml dir="overview"?>
    2928  <title>Overview of user documentation</title>
    3029  <para> The 'User documentation' part is quite extensive and covers everything from how to Log in on
     
    129128            <para>
    130129              Information related to user-accounts can be found at
    131               <xref linkend="user_administration" />.
     130              <xref linkend="accounts" />.
    132131            </para>
    133132          </listitem>
  • trunk/doc/src/docbook/user/platforms.xml

    r5706 r5738  
    2525-->
    2626<chapter id="platforms" chunked="0">
    27   <?dbhtml dir="platforms"?>
    2827  <title>Experimental platforms and data file types</title>
    2928 
  • trunk/doc/src/docbook/user/project_permission.xml

    r5706 r5738  
    2626
    2727<chapter id="project_permission">
    28   <?dbhtml dir="project_permission"?>
    2928  <title>Projects and the permission system</title>
    3029    <sect1 id="project_permission.permissions">
  • trunk/doc/src/docbook/user/protocols.xml

    r5706 r5738  
    2525-->
    2626<chapter id="protocols" chunked="0">
    27   <?dbhtml dir="protocols"?>
    2827  <title>Protocols</title>
    2928
  • trunk/doc/src/docbook/user/reporters.xml

    r5706 r5738  
    2626-->
    2727<chapter id="reporters" chunked="0">
    28   <?dbhtml dir="reporters"?>
    2928  <title>Reporters</title>
    3029  <sect1 id="reporters.introduction">
     
    275274            to the next.     
    276275            <nohelp>
    277             See <xref linkend="installation_upgrade.installation" />
     276            See <xref linkend="installation.main" />
    278277            and <xref linkend="appendix.extendedproperties" />
    279278            for more information.
  • trunk/doc/src/docbook/user/subtypes.xml

    r5706 r5738  
    2626
    2727<chapter id="subtypes" chunked="0">
    28   <?dbhtml dir="subtypes"?>
    2928  <title>Item subtypes</title>
    3029
  • trunk/doc/src/docbook/user/wares.xml

    r5706 r5738  
    2525-->
    2626<chapter id="wares" chunked="0">
    27   <?dbhtml dir="wares"?>
    2827  <title>Hardware and software</title>
    2928
  • trunk/doc/src/docbook/user/webclient.xml

    r5684 r5738  
    2626
    2727<chapter id="webclient">
    28   <?dbhtml dir="webclient"?>
    2928  <title>Using the web client</title>
    3029    <sect1 id="webclient.introduction">
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