Changeset 5684


Ignore:
Timestamp:
Aug 2, 2011, 5:00:19 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

User documentation chapter 5 and 6 but not screenshots and still some incorrect information about validating labeled extracts in the "Item overview" section.

Location:
trunk/doc/src/docbook/userdoc
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/userdoc/overview.xml

    r4509 r5684  
    9898   
    9999   
    100     <sect2 id="userdoc_overview.start2work.getgoing">
    101       <title>Get going</title>
    102       <para>
    103         This description will guide you from the initiating tasks of creating the first account to
    104         running an analysis plug-in. Most of the steps below ends with a reference to somewhere in the
    105         documentation where more information can be found.
    106       </para>
    107      
    108       <sect3 id="userdoc_overview.start2work.getgoing.administrative">
    109         <title>Administrative tasks</title>
     100    <sect2 id="userdoc_overview.start2work.administrative">
     101      <title>Administrative tasks</title>
    110102        <para>
    111103          Most of the tasks in this section require more privileges than the normal user
     
    137129            <para>
    138130              Information related to user-accounts can be found at
    139               <xref linkend="user_administration" />
    140               .
     131              <xref linkend="user_administration" />.
    141132            </para>
    142133          </listitem>
     
    163154          </listitem>
    164155        </orderedlist>
    165       </sect3>
    166       <sect3 id="userdoc_overview.start2work.getgoing.user">
     156      </sect2>
     157      <sect2 id="userdoc_overview.start2work.user">
    167158        <title>User tasks</title>
    168159        <para>
     
    183174            <para>
    184175              The first thing for an user to do is creating a project to work in and set this as
    185               <prompt>active project</prompt>
    186               . This should be done before any other items are created.
     176              <emphasis>the active project</emphasis>.
     177              This should be done before any other items are created.
    187178              <xref linkend="project_permission.projects" />
    188               tell you more how working in project can help you and your co-workers.
     179              tell you more about how working in projects can help you and your co-workers.
    189180            </para>
    190181          </listitem>
     
    243234          analysis.
    244235        </para>
    245       </sect3>
    246236    </sect2>
    247237  </sect1>
  • trunk/doc/src/docbook/userdoc/webclient.xml

    r5442 r5684  
    4646        <para>
    4747          You may, for example, try the BASE demo server. Go to the
    48           URL <ulink url="http://base2.thep.lu.se:8080/demo/">http://base2.thep.lu.se:8080/demo/</ulink>
     48          URL <ulink url="http://base2.thep.lu.se/demo/">http://base2.thep.lu.se/demo/</ulink>
    4949          and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
    5050          for the password.
     
    130130            cooperating with other users. We recommend
    131131            that you always use a project when working with BASE.
    132             For more information read <xref linkend="project_permission"/>.
     132            For more information read <xref linkend="project_permission"/>. The list
     133            displays the most recently used projects first and then fills up
     134            with the rest sorted by name.
    133135            </para>
    134136          </listitem>
     
    197199       
    198200      <variablelist>
     201        <varlistentry>
     202          <term>
     203            <guiicon>
     204              <inlinemediaobject>
     205              <imageobject><imagedata fileref="figures/project.gif" format="GIF" align="left"/></imageobject>
     206              </inlinemediaobject>
     207            </guiicon>
     208            <interface>
     209            Projects
     210            </interface>
     211          </term>
     212          <listitem>
     213            <para>
     214            A list of all projects you are a member of. The most recently used projects are
     215            listed first, then the list is filled with the rest of your projects up to a
     216            maximum of 15. If you have more projects an option to display the remaining
     217            projects is activated. Selecting a project in the list will make that project
     218            the active project.
     219            </para>
     220            <tip>
     221              <para>
     222              The sort order in the menu of non-recent projects is the same as the sort order on the
     223              projects list page. If you, for example, want to sort the newest
     224              project first (after the most recently used ones), select to sort by the
     225              <guilabel>Registered</guilabel> column in descending order on the list page.
     226              The menu will automatically use the same order.
     227              </para>
     228            </tip>
     229          </listitem>
     230        </varlistentry>
    199231        <varlistentry>
    200232          <term>           
     
    247279            for configuration information.
    248280            </para>
    249           </listitem>
    250         </varlistentry>
    251        
    252         <varlistentry>
    253           <term>
    254             <guiicon>
    255               <inlinemediaobject>
    256               <imageobject><imagedata fileref="figures/project.gif" format="GIF" align="left"/></imageobject>
    257               </inlinemediaobject>
    258             </guiicon>
    259             <interface>
    260             Projects
    261             </interface>
    262           </term>
    263           <listitem>
    264             <para>
    265             A list of all projects you are a member of. Selecting a project in the
    266             list will make that project the active project. The list can display
    267             a maximum of 25 projects. If you are a member of more projects, the last
    268             menu entry will take you to the complete list of projects.
    269             </para>
    270             <tip>
    271               <para>
    272               The sort order in the menu is the same as the sort order on the
    273               projects list page. If you, for example, want to sort the newest
    274               project first, select to sort by the <guilabel>Registered</guilabel>
    275               column in descending order on the list page. The menu will automatically
    276               use the same order.
    277               </para>
    278             </tip>
    279281          </listitem>
    280282        </varlistentry>
     
    624626          menu to bring up the preferences dialog.
    625627          This dialog has three tabs, <guilabel>Appearance</guilabel>,
    626           <guilabel>Plugins</guilabel> and <guilabel>Most recent</guilabel>.
     628          <guilabel>Plugins</guilabel> and <guilabel>Recent items</guilabel>.
    627629        </para>
    628630       
     
    684686                  <listitem>
    685687                    <simpara>
    686                     <guilabel>Always</guilabel>: The full text is always displayed.
     688                    <guilabel>Always</guilabel>: The full text is always displayed. This may
     689                    cause tables, etc. to become hard to read since cells will automatically
     690                    grow to be able to display the full text.
    687691                    </simpara>
    688692                  </listitem>
     
    736740                data that is suitable for color coding, for
    737741                example the intensity ratio in two-color
    738                 experiments. The default setting is blue-black-yellow.
     742                experiments. The default setting is blue-white-yellow.
    739743                The list of presets contains other useful color combinations
    740744                (for example, the BASE version 1 red-yellow-green) and the most
     
    752756                We support all formatting options supported by the Java
    753757                language. For more information see:
    754                 <ulink url="http://java.sun.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
     758                <ulink url="http://download.oracle.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
    755759                The most useful format patterns are:
    756760                </para>
     
    782786                We support all formatting options supported by the Java
    783787                language. For more information see:
    784                 <ulink url="http://java.sun.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
     788                <ulink url="http://download.oracle.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
    785789                The most useful time-format patterns are:
    786790                </para>
     
    803807              <listitem>
    804808                <para>
    805                 The number of decimals to display for numeric values.
     809                The number of decimals to display for numerical floating point values.
    806810                The default is 2.
    807811                </para>
     
    833837                Mark the checkbox if you want to have a message sent
    834838                to you when a plug-in completes execution. This setting
    835                 can be overridden each time you start a plug-in.
     839                can be overridden each time you start a plug-in. You'll
     840                receive the message as a notification in BASE, but it may
     841                also be possible to get the message as an email.
    836842                </para>
    837843              </listitem>
     
    878884          <para>
    879885            This tab contains settings that affect the <guilabel>Recent
    880             items</guilabel> menu.
     886            items</guilabel> menu and selection lists in many edit dialogs.
    881887          </para>
    882888         
     
    10751081            <guilabel>Recently used items</guilabel> setting (default is 4),
    10761082            allowing you to quickly select one of those protocols.
    1077             <xref linkend="webclient.configuration.preferences.appearance"/>
     1083            <xref linkend="webclient.configuration.preferences.mostrecent" />
    10781084            contains more information about the setting.
    10791085            </para>
     
    11851191          the list view, or from the single-item view. This section
    11861192          only covers the last two cases. The trashcan is described in
    1187           another section (<xref linkend="webclient.trashcan"/>).
     1193          <xref linkend="webclient.trashcan"/>.
    11881194        </para>
    11891195
     
    14821488      </sect2>
    14831489     
    1484       <sect2 id="webclient.items.export">
    1485         <title>Export items</title>
    1486         <para>
    1487           This has a chapter of it's own. See <xref linkend="export_data"/>.
    1488         </para>
    1489       </sect2>
    1490 
    14911490    </sect1>
    14921491   
     
    15271526          <listitem>
    15281527            <para>
    1529               It support only a limited set of columns (type, name and description)
    1530               since these are the only properties that are common
    1531               among all items.
     1528              It support only a limited set of columns (id, item type, name and description)
     1529              since these are the only properties that are common among all items. It is also
     1530              possible to display sharing information.
    15321531            </para>
    15331532          </listitem>
     
    18831882              configurations. The list of presets is the same as the one
    18841883              described <link linkend="webclient.itemlist.presets">below</link>,
    1885               but if used from this dialog the presets does not affect filters,
    1886               sort order, etc.
     1884              but if used from this dialog the presets only affects the visible columns
     1885              and not filters or sort order.
    18871886            </para>
    18881887          </listitem>
     
    22872286    <para>
    22882287      With the <guilabel>Item overview</guilabel>
    2289       function you can get an overview of all hybridizations,
     2288      function you can get an overview of all bioassays,
    22902289      extracts, samples, annotations, raw data sets, etc. that are
    22912290      related to a given item. In the overview you can also validate
     
    23992398          The validation procedure is highly
    24002399          configurable and you can select what you want to
    2401           ignore, or something should be displayed as an error
     2400          ignore, and what should be displayed as an error
    24022401          or warning.
    24032402        </para>
     
    24492448         
    24502449          <varlistentry>
     2450            <term><guilabel>Subtypes</guilabel></term>
     2451            <listitem>
     2452              <para>
     2453              The options in this section are used to check that related items
     2454              have a subtype that matches the subtype of the main item. For example,
     2455              if we have an <emphasis>extract</emphasis>
     2456              which is a <emphasis>labeled extract</emphasis> subtype the subtype for
     2457              the related tag should be <emphasis>label</emphasis>, but if the extract
     2458              is a <emphasis>library</emphasis> the subtype of the tag should be
     2459              <emphasis>barcode</emphasis>.
     2460              </para>
     2461            </listitem>
     2462          </varlistentry>
     2463
     2464          <varlistentry>
    24512465            <term><guilabel>Annotations</guilabel></term>
    24522466            <listitem>
     
    25182532            </listitem>
    25192533          </varlistentry>
     2534         
     2535          <varlistentry>
     2536            <term><guilabel>Files</guilabel></term>
     2537            <listitem>
     2538              <para>
     2539              The options in this section are related to the validity of
     2540              data files that can be attached to some items, for example,
     2541              raw bioassays and array designs. The data files are usually
     2542              validated immediately when they are used and the result is saved
     2543              to the database. The options in this dialog can be used to find
     2544              (or ignore) problems with data files.
     2545              </para>
     2546            </listitem>
     2547          </varlistentry>
     2548
    25202549         
    25212550          <varlistentry>
     
    25442573                <listitem>
    25452574                  <simpara>
    2546                   <emphasis>Array deign mismatch</emphasis>:
     2575                  <emphasis>Array design mismatch</emphasis>:
    25472576                  Checks if the array design specified for
    25482577                  a raw bioassay is the same array design
    2549                   specified for the hybridization.
     2578                  specified for the physical bioassay.
    25502579                  </simpara>
    25512580                </listitem>
     
    25622591                <listitem>
    25632592                  <simpara>
    2564                   <emphasis>Incorrect number of labled extracts</emphasis>:
     2593                  <emphasis>(Incorrect number of labled extracts)</emphasis>:
    25652594                  Checks if the number of labeled extracts
    25662595                  match the number of channels for the experiment.
     
    25732602                  <emphasis>Non-unique name</emphasis>:
    25742603                  Checks if two items of the same type
    2575                   have the same name. A unique name if important
    2576                   when exporting data in Tab2Mage format.
     2604                  have the same name. It is usually a good idea to
     2605                  have unique names within an experiment if the data is
     2606                  going to be exported and in other circumstances.
    25772607                  </simpara>
    25782608                </listitem>
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