Changeset 3388


Ignore:
Timestamp:
May 28, 2007, 9:13:56 AM (14 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #542. Major reorganisation. Added screen shots.

Location:
trunk/doc/src/docbook
Files:
2 added
1 edited

Legend:

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

    r3382 r3388  
    33    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
    44    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
    5     <!--
    6      $Id$
    7      
    8      Copyright (C) Authors contributing to this file.
    9      
    10      This file is part of BASE - BioArray Software Environment.
    11      Available at http://base.thep.lu.se/
    12      
    13      BASE is free software; you can redistribute it and/or
    14      modify it under the terms of the GNU General Public License
    15      as published by the Free Software Foundation; either version 2
    16      of the License, or (at your option) any later version.
    17      
    18      BASE is distributed in the hope that it will be useful,
    19      but WITHOUT ANY WARRANTY; without even the implied warranty of
    20      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    21      GNU General Public License for more details.
    22      
    23      You should have received a copy of the GNU General Public License
    24      along with this program; if not, write to the Free Software
    25      Foundation, Inc., 59 Temple Place - Suite 330,
    26      Boston, MA  02111-1307, USA.
    27     -->             
     5<!--
     6  $Id$
     7 
     8  Copyright (C) Authors contributing to this file.
     9 
     10  This file is part of BASE - BioArray Software Environment.
     11  Available at http://base.thep.lu.se/
     12 
     13  BASE is free software; you can redistribute it and/or
     14  modify it under the terms of the GNU General Public License
     15  as published by the Free Software Foundation; either version 2
     16  of the License, or (at your option) any later version.
     17 
     18  BASE is distributed in the hope that it will be useful,
     19  but WITHOUT ANY WARRANTY; without even the implied warranty of
     20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     21  GNU General Public License for more details.
     22 
     23  You should have received a copy of the GNU General Public License
     24  along with this program; if not, write to the Free Software
     25  Foundation, Inc., 59 Temple Place - Suite 330,
     26  Boston, MA  02111-1307, USA.
     27-->
    2828<chapter id="hardware">
    29 <?dbhtml dir="hardware"?>
    30  <title>Hardware</title>
    31  <sect1 id="hardware.introduction">
    32   <title>Introduction</title>
    33   <para>Information about laboratory equipment can be tracked in BASE2 using two structures, the use
    34    of which is detailed in the following sections. </para>
    35  </sect1>
    36  <sect1 id="hardware.manage">
    37   <title>Managing Hardware</title>
     29  <?dbhtml dir="hardware"?>
     30  <title>Hardware</title>
     31  <para>
     32    Information about laboratory equipment can be tracked in
     33    BASE using two structures, the use of which is detailed in
     34    the following sections.
     35  </para>
     36  <sect1 id="hardware.hardwaretypes">
     37    <title>Hardware types</title>
    3838
    39   <sect2 id="hardware.manage.typecreate">
    40    <title>Creating Hardware Types</title>
    41    <para><guilabel>Hardware Type</guilabel> allows classification of hardwares based on their usage
    42     and purpose in the laboratory workflow.</para>
    43    <para> By default, BASE2 creates the 3 main Hardware Types and those correspond to the main
    44     hardware families identified by <ulink url="http://www.mged.org/Workgroups/MIAME/miame.html"
    45      >MIAME requirements</ulink>. These 3 Hardware Types are <guilabel>Print Robot</guilabel>,
    46      <guilabel>Scanner</guilabel> and <guilabel>Hybridization station</guilabel>
    47    </para>
    48    <para>In case those built-in Hardware Type are not enough, it is possible to create new ones. To
    49     do so:</para>
    50    <para>Go To <menuchoice>
    51      <guimenu>Administrate</guimenu>
    52      <guimenuitem>Types</guimenuitem>
    53      <guisubmenu>Hardware Type</guisubmenu>
    54     </menuchoice>
    55    </para>
    56    <para> Click on <guibutton>New&hellip;</guibutton>. </para>
    57    <para>A 'Create' pop-up window opens</para>
    58    <para>Fill in <guilabel>Name</guilabel> and <guilabel>Description</guilabel></para>
    59    <figure id="write_docbook_doc.figures.hardwaretype">
    60     <title>The Hardware Type Create Window</title>
    61     <screenshot>
    62      <mediaobject>
    63       <imageobject>
    64        <imagedata contentwidth="7cm" width="7cm" fileref="figures/hardwaretype.png" format="PNG"/>
    65       </imageobject>
    66      </mediaobject>
    67     </screenshot>
    68    </figure>
    69    <tip><para>
    70     It is advised to define the Hardware Type <guilabel>Name</guilabel> attribute so that it is
    71     compatible with the MIAME requirements and recommendations issues by microarray data
    72     repositories.
    73    </para></tip>
    74    <para>Click on the
    75     <inlinemediaobject>
    76      <imageobject>
    77       <imagedata fileref="figures/save.gif" format="GIF"/>
    78      </imageobject>
    79     </inlinemediaobject>
    80     Save button to store the information in BASE2 or on the
    81     <inlinemediaobject>
    82      <imageobject>
    83       <imagedata fileref="figures/cancel.gif" format="GIF"/>
    84      </imageobject>
    85     </inlinemediaobject>       
    86     button to abort.
    87    </para>
    88   </sect2>
    89   <sect2 id="hardware.manage.create">
    90    <title>Creating Hardwares</title>
    91    <para>In BASE2, Hardwares can be created by 2 routes:</para>
    92    <orderedlist>
    93     <listitem>
    94      <para>Creating Hardwares from the Hardware Type List View page</para>
    95      <para>Clicking on the <inlinemediaobject>
    96       <imageobject>
    97        <imagedata fileref="figures/add.gif" format="GIF"/>
    98       </imageobject>
    99      </inlinemediaobject> add hardware button.
    100      </para>
    101      <figure id="write_docbook_doc.figures.hardware-frompt">
    102       <title>Create New hardware from the Hardware Type List View</title>
    103       <screenshot>
    104        <mediaobject>
    105         <imageobject>
    106          <imagedata contentwidth="10cm" width="10cm" fileref="figures/hardware-frompt.png" format="PNG"/>
    107         </imageobject>
    108        </mediaobject>
    109       </screenshot>
    110      </figure>
    111     </listitem>
    112     <listitem>
    113      <para>Creating Hardware from the Hardware List View page</para>
    114      <para>Go to
    115       <menuchoice>
    116        <guimenu>View</guimenu>
    117        <guimenuitem>Hardware</guimenuitem>
    118       </menuchoice></para>
    119       <para>Click on <guibutton>New&hellip;</guibutton> button
    120       </para>
    121     </listitem>
    122    </orderedlist>
     39    <helptext external_id="hardwaretype.view.properties"
     40      title="Hardware types">
    12341
    124      <para>In both cases, a Hardware Create pop-up window opens. The window contains 2 mandatory fields:</para>
    125       <itemizedlist>
    126        <listitem>
    127         <para>
    128         <guilabel>Name</guilabel> and <guilabel>Hardware type</guilabel>.</para>
    129      <para>The later is a select-list population from Hardware Types owned by or shared to the user.</para>
    130         </listitem>
    131         <listitem>
    132          <para><guilabel>Version</guilabel> and <guilabel>Description</guilabel>, the other 2 fields, are optional and self explanatory.</para>
    133     </listitem>
    134       </itemizedlist>
    135    <para>Click on the
    136     <inlinemediaobject>
    137      <imageobject>
    138       <imagedata fileref="figures/save.gif" format="GIF"/>
    139      </imageobject>
    140     </inlinemediaobject>
    141     Save button to store the information in BASE2 or on the
    142     <inlinemediaobject>
    143      <imageobject>
    144       <imagedata fileref="figures/cancel.gif" format="GIF"/>
    145      </imageobject>
    146     </inlinemediaobject>       
    147    button to abort.
    148    </para>
     42      <para>
     43        <guilabel>Hardware Type</guilabel>
     44        allows classification of hardwares based on their usage
     45        and purpose in the laboratory workflow. By default, BASE2
     46        creates the 3 main hardware types and
     47        those correspond to the main hardware families
     48        identified by
     49        <ulink
     50          url="http://www.mged.org/Workgroups/MIAME/miame.html">
     51          MIAME requirements</ulink>.
     52        These 3 hardware types are
     53        <guilabel>Print Robot</guilabel>,
     54        <guilabel>Scanner</guilabel>,
     55        and
     56        <guilabel>Hybridization station</guilabel>.
     57      </para>
     58      <para>
     59        In case those built-in types are not enough, it
     60        is possible to create new ones.
     61      </para>
     62    </helptext>
    14963
    150   </sect2>
    151   <sect2 id="hardware.manage.detail_view">
    152    <title>Viewing/Editing Hardwares</title>
    153    <itemizedlist>
    154     <listitem>
    155      <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
    156       <keycap>SHIFT</keycap> keys while clicking on the name of an Hardware Item, which is a live
    157       link. </para>
    158     </listitem>
    159     <listitem>
    160      <para> Alternately, navigating to the Hardware Item View, one can hit the
    161        <guibutton>Edit&hellip;</guibutton> to performed the task.</para>
    162      <para>In both cases, an Edit pop-up windows opens. It is essentially identical to a Create
    163       window and allows updating information about a particular Hardware item stored in BASE2</para>
    164      <figure id="write_docbook_doc.figures.hardware-itemview">
    165       <title>Hardware Item View</title>
    166       <screenshot>
    167       <mediaobject>
    168        <imageobject>
    169         <imagedata contentwidth="10cm" width="10cm" fileref="figures/hardware-itemview.png" format="PNG"/>
    170        </imageobject>
    171       </mediaobject>
    172      </screenshot>
    173      </figure>
    174     </listitem>
    175    </itemizedlist>
    176   </sect2>
    177   <sect2 id="hardware.manage.delete">
    178    <title>Deleting/Restoring Hardwares</title>
    179    <para>As for other items in BASE2, Hardwares can be removed and restored. To do so, do the
    180     following</para>
    181    <itemizedlist>
    182     <listitem>
    183      <para>Select one or more Hardwares and click <guibutton>Delete</guibutton> button in the menu
    184       bar. </para>
    185      <para>All the selected Hardwares have been marked as deleted and are no longer available from
    186       the interface. </para>
    187      <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
    188        <guilabel>Removed</guilabel> option, one can see those of the Hardwares earmarked for
    189       deletion. They will be shown with a symbol
    190       <inlinemediaobject>
    191        <imageobject>
    192         <imagedata fileref="figures/deleted.gif" format="GIF"/>
    193        </imageobject>
    194       </inlinemediaobject> in front of them. </para>
    195     </listitem>
    196     <listitem>
    197      <para>Alternately, navigating to the Hardware Item View, one can hit the
    198       <guibutton>Delete</guibutton> to performed the task. </para>
    199     </listitem>
    200     <listitem>
    201      <para>Deletion errors at this stage can be easily recovered. Select the item to recover from
    202       the List View (be sure to check the <guilabel>Removed</guilabel> option in the
    203        <guilabel>view/preset&hellip;</guilabel> filter) and hit the
    204       <guibutton>Restore</guibutton> button to performed the task. </para>
    205     </listitem>
    206    </itemizedlist>
    207    <important>
    208     <para>To really delete an item from the database you must use the trashcan. Items
    209      deleted from the Trashcan can not be recovered. To learn more about the trashcan function, please refer to <xref linkend="trashcan"/> </para>
    210    </important>
    211   </sect2>
    212  </sect1>
     64    <para>
     65      You can manage the hardware types by going to
     66      <menuchoice>
     67        <guimenu>Administrate</guimenu>
     68        <guimenuitem>Types</guimenuitem>
     69        <guisubmenu>Hardware types</guisubmenu>
     70      </menuchoice>.
     71    </para>
     72   
     73    <figure
     74      id="hardware.figures.hardwaretype">
     75      <title>Hardware type properties</title>
     76      <screenshot>
     77        <mediaobject>
     78          <imageobject>
     79            <imagedata
     80              fileref="figures/edit_hardwaretype.png" format="PNG" />
     81          </imageobject>
     82        </mediaobject>
     83      </screenshot>
     84    </figure>
     85
     86    <helptext external_id="hardwaretype.edit"
     87      title="Edit hardware type">
     88   
     89      <variablelist>
     90      <varlistentry>
     91        <term><guilabel>Name</guilabel></term>
     92        <listitem>
     93          <para>
     94            The name of the hardware type.
     95            <tip>
     96              <para>
     97                It is advised to define the name
     98                so that it is compatible with the MIAME
     99                requirements and recommendations issues by
     100                microarray data repositories.
     101              </para>
     102            </tip>
     103          </para>
     104        </listitem>
     105      </varlistentry>
     106      <varlistentry>
     107        <term><guilabel>Description</guilabel></term>
     108        <listitem>
     109          <para>
     110            A description of the hardware type.
     111          </para>
     112        </listitem>
     113      </varlistentry>
     114      </variablelist>
     115    </helptext>
     116  </sect1>
     117 
     118  <sect1 id="hardware.hardware">
     119    <title>Hardware</title>
     120   
     121    <para>
     122      In BASE, hardware can be created by 2 routes. Either
     123      from the single-item view of a hardware type or from the
     124      list view of hardware.
     125    </para>
     126   
     127    <figure
     128      id="hardware.figures.edit_hardware">
     129      <title>Hardware properties</title>
     130      <screenshot>
     131        <mediaobject>
     132          <imageobject>
     133            <imagedata
     134              fileref="figures/edit_hardware.png" format="PNG" />
     135          </imageobject>
     136        </mediaobject>
     137      </screenshot>
     138    </figure>
     139   
     140    <helptext external_id="hardware.edit"
     141      title="Edit hardware">
     142      <variablelist>
     143      <varlistentry>
     144        <term><guilabel>Name</guilabel></term>
     145        <listitem>
     146          <para>
     147          The name of the hardware.
     148          </para>
     149        </listitem>
     150      </varlistentry>
     151      <varlistentry>
     152        <term><guilabel>Version</guilabel></term>
     153        <listitem>
     154          <para>
     155          The version number or model of the hardware.
     156          </para>
     157        </listitem>
     158      </varlistentry>
     159      <varlistentry>
     160        <term><guilabel>Type</guilabel></term>
     161        <listitem>
     162          <para>
     163          The hardware type of the hardware. The list
     164          may evolve depending on additions by the server
     165          administrator.
     166          </para>
     167        </listitem>
     168      </varlistentry>
     169      <varlistentry>
     170        <term><guilabel>Description</guilabel></term>
     171        <listitem>
     172          <para>
     173          A description of the hardware.
     174          </para>
     175        </listitem>
     176      </varlistentry>
     177      </variablelist>
     178    </helptext>
     179   
     180  </sect1>
    213181</chapter>
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