source: trunk/doc/src/docbook/userdoc/software.xml @ 3372

Last change on this file since 3372 was 3372, checked in by philippe, 14 years ago
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: software.xml 3372 2007-05-24 08:45:06Z philippe $
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-->
28
29<chapter id="software">
30  <?dbhtml dir="software"?>
31  <title>Software</title>
32<sect1 id="software.manage">
33  <title>Managing Software</title>
34
35  <sect2 id="software.manage.typecreate">
36   <title>Software Types</title>
37   <para><guilabel>There is only Software Type</guilabel> in BASE2 and it is not possible to create new types. This is a difference compared to the way Hardware can be managed.</para>
38   <para> By default, BASE2 creates the 1 Software Type: Feature Extraction</para>
39  </sect2>
40  <sect2 id="software.manage.create">
41   <title>Creating Softwares</title>
42   <para>In BASE2, Softwares can be created by 2 routes:</para>
43   <orderedlist>
44    <listitem>
45     <para>Creating Softwares from the Software Type List View page</para>
46     <para>Clicking on the <inlinemediaobject>
47      <imageobject>
48       <imagedata fileref="figures/add.gif" format="GIF"/>
49      </imageobject>
50     </inlinemediaobject> add software button.
51     </para>
52     <figure id="write_docbook_doc.figures.software-frompt">
53      <title>Create New software from the Software Type List View</title>
54      <screenshot>
55       <mediaobject>
56        <imageobject>
57         <imagedata contentwidth="10cm" width="10cm" fileref="figures/software-frompt.png" format="PNG"/>
58        </imageobject>
59       </mediaobject>
60      </screenshot>
61     </figure>
62    </listitem>
63    <listitem>
64     <para>Creating Software from the Software List View page</para>
65     <para>Go to
66      <menuchoice>
67       <guimenu>View</guimenu>
68       <guimenuitem>Software</guimenuitem>
69      </menuchoice></para>
70      <para>Click on <guibutton>New&hellip;</guibutton> button
71      </para>
72    </listitem>
73   </orderedlist>
74
75     <para>In both cases, a Software Create pop-up window opens. The window contains 2 mandatory fields:</para>
76      <itemizedlist>
77       <listitem>
78        <para>
79        <guilabel>Name</guilabel> and <guilabel>Software type</guilabel>.</para>
80     <para>The later is a select-list population from Software Types owned by or shared to the user.</para>
81        </listitem>
82        <listitem>
83         <para><guilabel>Version</guilabel> and <guilabel>Description</guilabel>, the other 2 fields, are optional and self explanatory.</para>
84    </listitem>
85      </itemizedlist>
86   <para>Click on the
87    <inlinemediaobject>
88     <imageobject>
89      <imagedata fileref="figures/save.gif" format="GIF"/>
90     </imageobject>
91    </inlinemediaobject>
92    Save button to store the information in BASE2 or on the
93    <inlinemediaobject>
94     <imageobject>
95      <imagedata fileref="figures/cancel.gif" format="GIF"/>
96     </imageobject>
97    </inlinemediaobject>       
98   button to abort.
99   </para>
100
101  </sect2>
102  <sect2 id="software.manage.detail_view">
103   <title>Viewing/Editing Softwares</title>
104   <itemizedlist>
105    <listitem>
106     <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
107      <keycap>SHIFT</keycap> keys while clicking on the name of an Software Item, which is a live
108      link. </para>
109    </listitem>
110    <listitem>
111     <para> Alternately, navigating to the Software Item View, one can hit the
112       <guibutton>Edit&hellip;</guibutton> to performed the task.</para>
113     <para>In both cases, an Edit pop-up windows opens. It is essentially identical to a Create
114      window and allows updating information about a particular Software item stored in BASE2</para>
115     <figure id="write_docbook_doc.figures.software-itemview">
116      <title>Software Item View</title>
117      <screenshot>
118      <mediaobject>
119       <imageobject>
120        <imagedata contentwidth="10cm" width="10cm" fileref="figures/software-itemview.png" format="PNG"/>
121       </imageobject>
122      </mediaobject>
123     </screenshot>
124     </figure>
125    </listitem>
126   </itemizedlist>
127  </sect2>
128  <sect2 id="software.manage.delete">
129   <title>Deleting/Restoring Softwares</title>
130   <para>As for other items in BASE2, Softwares can be removed and restored. To do so, do the
131    following</para>
132   <itemizedlist>
133    <listitem>
134     <para>Select one or more Softwares and click <guibutton>Delete</guibutton> button in the menu
135      bar. </para>
136     <para>All the selected Softwares have been marked as deleted and are no longer available from
137      the interface. </para>
138     <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
139       <guilabel>Removed</guilabel> option, one can see those of the protocols earmarked for
140      deletion. They will be shown with a symbol
141      <inlinemediaobject>
142       <imageobject>
143        <imagedata fileref="figures/deleted.gif" format="GIF"/>
144       </imageobject>
145      </inlinemediaobject> in front of them. </para>
146    </listitem>
147    <listitem>
148     <para>Alternately, navigating to the Software Item View, one can hit the
149      <guibutton>Delete</guibutton> to performed the task. </para>
150    </listitem>
151    <listitem>
152     <para>Deletion errors at this stage can be easily recovered. Select the item to recover from
153      the List View (be sure to check the <guilabel>Removed</guilabel> option in the
154       <guilabel>view/preset&hellip;</guilabel> filter) and hit the
155      <guibutton>Restore</guibutton> button to performed the task. </para>
156    </listitem>
157   </itemizedlist>
158   <important>
159    <para>To really delete an item from the database you must use the trashcan. Items
160     deleted from the Trashcan can not be recovered. To learn more about the trashcan function, please refer to <xref linkend="trashcan"/> </para>
161   </important>
162  </sect2>
163 </sect1>
164</chapter>
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