source: trunk/doc/historical/admin/extended-properties.html @ 7982

Last change on this file since 7982 was 7982, checked in by Nicklas Nordborg, 21 months ago

Merge BASE 3.18.2 to the trunk
  • Property svn:eol-style set to native
  • Property svn:keywords set to Id Date
File size: 6.9 KB
Line 
1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2
3<!--
4    $Id: extended-properties.html 7982 2021-06-14 08:01:21Z nicklas $
5
6    Copyright (C) 2006 Jari H�kkinen, Nicklas Nordborg
7    Copyright (C) 2007 Jari H�kkinen
8
9    This file is part of BASE - BioArray Software Environment.
10    Available at http://base.thep.lu.se/
11
12    BASE is free software; you can redistribute it and/or modify it
13    under the terms of the GNU General Public License as published by
14    the Free Software Foundation; either version 3 of the License, or
15    (at your option) any later version.
16
17    BASE is distributed in the hope that it will be useful, but
18    WITHOUT ANY WARRANTY; without even the implied warranty of
19    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20    General Public License for more details.
21
22    You should have received a copy of the GNU General Public License
23    along with BASE. If not, see <http://www.gnu.org/licenses/>.
24-->
25
26<html>
27  <head>
28    <title>BASE 2.0 - Administrator documentation: extended-properties.xml</title>
29    <link rel=stylesheet type="text/css" href="../styles.css">
30  </head>
31  <body>
32
33    <div class="navigation">
34      <a href="../index.html">BASE</a>
35      <img src="../next.gif">
36      <a href="index.html">Administrator documentation</a>
37      <img src="../next.gif">
38      extended-properties.xml
39    </div>
40
41    <h1>BASE 2.0 - Administrator documentation: extended-properties.xml</h1>
42
43    <div class="abstract">
44
45      <p>
46        This document describes how to setup extended-properties.xml
47      </p>
48
49      <b>Contents</b>
50      <ol>
51        <li><a href="#whatisit">What is extended properties?</a></li>
52        <li><a href="#samples">Sample extended properties setups?</a></li>
53        <li><a href="#howtochange">How to change extended properties.</a></li>
54      </ol>
55
56      <b>See also</b>
57      <ul>
58        <li> <a
59        href="../api/net/sf/basedb/core/data/ExtendableData.html">Javadoc
60        for ExtendableData</a> </li>
61        <li> <a
62        href="https://base.thep.lu.se/browser/trunk/src/core/net/sf/basedb/core/dtd/extended-properties.dtd">extended-properties.dtd</a> </li>
63      </ul>
64
65      <p class="authors">
66        <b>Last updated:</b> $Date: 2021-06-14 08:01:21 +0000 (Mon, 14 Jun 2021) $<br>
67        <b>Copyright &copy;</b> 2006 The respective authors. All rights reserved.
68      </p>
69
70    </div>
71
72    <a name="whatisit"></a>
73    <h2>1. What is extended-properties.xml?</h2>
74
75    <p>
76      A server administrator may modify the information stored about
77      reporters in BASE. The setup of additional data storage is made
78      in the <tt>extended-properties.xml</tt> file, and the storage
79      request will affect the ReporterData table. The format of
80      the <tt>extended-properties.xml</tt> file is described by the
81      <a
82         href="../api/net/sf/basedb/core/data/ExtendableData.html">ExtendableData
83        interface</a>.
84    </p>
85
86    <p>
87      It is important, but not vital, to setup the extended properties
88      before initializing the database since the
89      default <tt>extended-properties.xml</tt> file is biased towards
90      the BASE 1.2 setup for 2-spotted microarray data. It is possible
91      to change the extended properties after initialization but if the
92      amount of additional data to store is decreased, the extra
93      columns will not be removed. On the other hand if additional
94      data is added to the extended properties, the ReporterData table
95      is easily expanded by running the database update script. Thus,
96      starting with a too restrictive set of additional reporter data
97      can always be resolved later.
98    </p>
99
100    <a name="samples"></a>
101    <h2>2. Sample extended properties setups?</h2>
102
103    <p>
104      After installing BASE the <tt>extended-properties.xml</tt> is
105      located in <tt>/path/to/base/www/WEB-INF/classes/</tt>. There
106      are currently two sample <tt>extended-properties.xml</tt> files:
107      <ul>
108        <li>
109          <p>
110            The
111            <a
112            href="https://base.thep.lu.se/browser/trunk/config/dist/extended-properties.xml">default
113            extended properties</a> file. The properties described in
114            this sample file is required when migration from BASE 1.2
115            to BASE 2 will be performed. The default setup of extended
116            information is inherited from BASE 1.2.
117          </p>
118          <p>
119            This sample file is biased towards 2 spotted cDNA arrays.
120          </p>
121        </li>
122        <li>
123          <p>
124            A
125            <a
126            href="https://base.thep.lu.se/browser/trunk/misc/config/minimalistic_extended-properties.xml">minimalistic
127            setup</a>. This is useful when, at BASE installation time,
128            it is not known what reporter data will be stored in the
129            database. The addition of more properties later is
130            straightforward.
131          </p>
132        </li>
133        <li>
134          <p>
135            An Affymetrix sample file should be added to the list.
136          </p>
137        </li>
138      </ul>
139    </p>
140
141    <a name="howtochange"></a>
142    <h2>3. How to change extended properties</h2>
143
144    <p>
145      In order to add properties to store into the database you need
146      to follow the straightforward format of
147      <a
148      href="https://base.thep.lu.se/browser/trunk/src/extended-properties.xml">default
149      extended properties</a>. The problem is that some knowledge of
150      the underlying database schema is needed.
151    </p>
152
153    <p>
154      In order to remove extra properties entries from a live BASE 2
155      server you need to remove the corresponding entries from the
156      extended properties file. This will make the extra properties
157      inaccessible for BASE but not remove the excess data from the
158      database. If the excess data should be removed, the data must be
159      removed manually by modifying the reporter data table directly
160      (after changing the extended properties file).
161    </p>
162
163    <p>
164      Adding extra information (columns) to the reporters
165      (ReporterData table) is simply done by adding
166      a <tt>&lt;property></tt> tag into the <tt>&lt;class
167      name="ReporterData"></tt> tag:
168<pre>
169  &lt;property
170  name="clusterId"
171  title="Cluster ID"
172  description="A unique identifier for a UniGene entry"
173  column="clusterId"
174  type="string"
175  length="255"
176  >
177</pre>
178      where <tt>name</tt> is the name to be used by
179      Hibernate, <tt>title</tt> is what is used in the GUI when the
180      extended data is displayed, <tt>description</tt> is information
181      about the column, <tt>column</tt> is the underlying database
182      engine name of the column (this cannot be changed after
183      initialization of the database table, <tt>type</tt> is the data
184      type, and here <tt>length</tt> is needed since the <tt>type</tt>
185      is a string.
186    </p>
187
188    <p>
189      A more detailed information about the attributes is available in
190      the <a
191      href="../api/net/sf/basedb/core/data/ExtendableData.html">javadoc
192      for the ExtendableData class</a>.
193    </p>
194
195    <p>
196      If you change the extended-properties.xml on an already running
197      BASE 2 server, you should shutdown the server after changing the
198      extended properties file and run the <tt>updatedb.sh</tt>
199      followed by the <tt>updateindexes.sh</tt> script. This will push
200      your changes into into the database.
201    </p>
202
203    <p>
204      If you make the changes during first time install of BASE 2 all
205      changes take effect automatically. You only need to change the
206      extended properties file.
207    </p>
208
209  </body>
210</html>
Note: See TracBrowser for help on using the repository browser.