Changeset 5738


Ignore:
Timestamp:
Sep 15, 2011, 8:53:11 AM (12 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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