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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE appendix PUBLIC |
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"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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<!-- |
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$Id$ |
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|
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Copyright (C) 2007 Nicklas Nordborg, Martin Svensson |
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|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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|
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<appendix id="appendix.extendedproperties"> |
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<?dbhtml filename="extendedproperties.html" ?> |
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<title>extended-properties.xml reference</title> |
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|
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|
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<bridgehead>What is extended-properties.xml?</bridgehead> |
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|
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<para> |
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The <filename>extended-properties.xml</filename> file is a configuration |
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file for customizing some of the tables in the BASE database. |
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It is located in the <filename><basedir>/www/WEB-INF/classes</filename> |
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directory. Only a limited number of tables support this feature, the most important |
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one is the table for storing reporter information. |
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</para> |
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|
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<tip> |
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<para> |
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It is also possible to put additional extended property definitions in the |
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<filename><basedir>/www/WEB-INF/classes/extended-properties</filename> |
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subdirectory. BASE will merge all <filename>*.xml</filename> it finds with |
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the main <filename>extended-properties.xml</filename> file. The extra |
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configuration files should have the same format as the main |
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<filename>extended-properties.xml</filename> file. The extra files |
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may contain extra columns for classes that are already |
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defined in the main file, but existing columns can't be removed or |
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re-defined. |
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We recommend that you don't modify the default <filename>extended-properties.xml</filename> |
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file at all (unless you want to remove some of the columns). This will make it |
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easier when upgrading BASE since you don't have to worry about losing |
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your own changes. |
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|
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</para> |
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</tip> |
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|
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|
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<para> |
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The default <filename>extended-properties.xml</filename> that ships |
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with BASE is biased towards the BASE version 1.2 setup for 2-spotted microarray |
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data. If you want your BASE installation to be configured differently we |
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recommend that you do it before the first initialisation of the database. |
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It is possible to change the configuration of an existing BASE installation but it |
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may require manual updates to the database. Follow this procedure: |
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</para> |
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|
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<orderedlist> |
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<listitem> |
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<para> |
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Shut down the BASE web server. If you have installed job agents you should shut |
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down them as well. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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Modify the <filename>extended-properties.xml</filename> file or create a new file |
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in the <filename>extended-properties</filename> subdirectory. If you have installed |
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job agents, make sure they all have the same version as the web server. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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Run the <filename>updatedb.sh</filename> script. New |
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columns will automatically be created, but the script can't delete columns that |
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have been removed, or modify columns that have changed data type. You will have to |
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do these kind of changes by manually executing SQL against your database. Check your |
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database documentation for information about SQL syntax. |
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</para> |
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|
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<tip> |
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<title>Create a parallel installation</title> |
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<para> |
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You can always create a new temporary parallel installation to check |
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what the table generated by installation script looks like. Compare the |
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new table to the existing one and make sure they match. |
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</para> |
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</tip> |
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</listitem> |
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|
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<listitem> |
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<para> |
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Start up the BASE web server and job agents, if any, again. |
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</para> |
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</listitem> |
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|
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</orderedlist> |
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|
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<tip> |
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<title>Start with few columns</title> |
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<para> |
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It is better to start with too few columns, since it is easier to add |
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more columns than it is to remove columns that are not needed. |
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</para> |
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</tip> |
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|
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<bridgehead>Sample extended properties setups</bridgehead> |
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|
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<itemizedlist> |
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<listitem> |
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<para> |
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After installing BASE the default <filename>extended-properties.xml</filename> |
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is located in the <filename><basedir>/www/WEB-INF/classes</filename> directory. |
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This setup is biased towards the BASE version 1.2 setup for |
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2-spotted cDNA arrays. If you are migrating from BASE version 1.2 |
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you <emphasis>must</emphasis> to use the default setup. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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A <filename>minimalistic_extended-properties.xml</filename> setup which doesn't |
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define any extra columns at all. This file |
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can be found in the <filename><basedir>/misc/config</filename> directory, |
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and should be used if it is not known what reporter data will be stored in the |
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database. The addition of more columns later is straightforward. |
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</para> |
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</listitem> |
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</itemizedlist> |
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|
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<bridgehead>Format of the extended-properties.xml file</bridgehead> |
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<para> |
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The <filename>extended-properties.xml</filename> is an XML file. |
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The following example will serve as a description of the format: |
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</para> |
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|
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<programlisting language="xml"> |
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<?xml version="1.0" ?> |
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<!DOCTYPE extended-properties SYSTEM "extended-properties.dtd"> |
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<extended-properties> |
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<class name="ReporterData"> |
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<property |
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name="extra1" |
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column="extra1" |
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title="Extra property" |
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type="string" |
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length="255" |
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null="true" |
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update="true" |
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insert="true" |
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averagemethod="max" |
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restricted-edit="false" |
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hidden="false" |
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description="An extra property for all reporters" |
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> |
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<link |
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regexp=".*" |
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url="http://www.myexternaldb.com/find?{value}" |
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/> |
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</property> |
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</class> |
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</extended-properties> |
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</programlisting> |
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|
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<para> |
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Each table that can be customized is represented by a <sgmltag class="starttag">class</sgmltag> |
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tag. The value of the <sgmltag>name</sgmltag> attribute is the name of the Java class |
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that handles the information in that table. In the case of reporters |
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the class name is <constant>ReporterData</constant>. |
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</para> |
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|
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<para> |
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Each <sgmltag class="starttag">class</sgmltag> tag may contain one or more |
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<sgmltag class="starttag">property</sgmltag> tags, each one describing a single |
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column in the table. The possible attributes of the <sgmltag class="starttag">property</sgmltag> |
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tag are: |
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</para> |
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|
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<table frame="all" id="appendix.extendedproperties.property"> |
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<title>Attributes for the <sgmltag class="starttag">property</sgmltag> tag</title> |
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<tgroup cols="3" align="left"> |
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<colspec colname="attribute" align="left" /> |
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<colspec colname="required" /> |
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<colspec colname="comment" /> |
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<thead> |
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<row> |
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<entry>Attribute</entry> |
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<entry>Required</entry> |
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<entry>Comment</entry> |
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</row> |
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</thead> |
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<tbody> |
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<row> |
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<entry>name</entry> |
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<entry>yes</entry> |
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<entry> |
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A unique name (within the class) of the extra property. |
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The name must only contain letters, numbers and underscores but the first character |
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can't be a number. The name is used to identify the extra column in the Java code |
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and in the Query API. |
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</entry> |
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</row> |
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<row> |
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<entry>column</entry> |
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<entry>yes</entry> |
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<entry> |
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The name of the database column. This value must be unique within the |
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class. Valid names depends on the database, but it should be safe |
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to follow the same rules as for the <sgmltag>name</sgmltag> attribute. |
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In most cases, it makes sense to use the same value for both the |
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<sgmltag>name</sgmltag> and <sgmltag>column</sgmltag> attributes. |
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</entry> |
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</row> |
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<row> |
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<entry>title</entry> |
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<entry>no</entry> |
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<entry> |
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The title of the extra property as it is displayed in client applications. |
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If not specified the value of the <sgmltag>name</sgmltag> attribute is used. |
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</entry> |
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</row> |
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<row> |
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<entry>description</entry> |
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<entry>no</entry> |
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<entry> |
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A longer (but still short!) description of the extra property which can be |
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used in client applications to provide help. |
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</entry> |
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</row> |
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<row> |
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<entry>type</entry> |
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<entry>yes</entry> |
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<entry> |
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The data type of the column. Allowed values are: |
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<itemizedlist> |
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<listitem> |
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<simpara>int</simpara> |
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</listitem> |
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<listitem> |
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<simpara>long</simpara> |
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</listitem> |
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<listitem> |
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<simpara>float</simpara> |
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</listitem> |
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<listitem> |
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<simpara>double</simpara> |
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</listitem> |
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<listitem> |
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<simpara>boolean</simpara> |
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</listitem> |
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<listitem> |
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nicklas |
267 |
<simpara>string</simpara> |
3612 |
31 Jul 07 |
nicklas |
268 |
</listitem> |
3612 |
31 Jul 07 |
nicklas |
269 |
<listitem> |
3612 |
31 Jul 07 |
nicklas |
270 |
<simpara>date</simpara> |
3612 |
31 Jul 07 |
nicklas |
271 |
</listitem> |
5436 |
30 Sep 10 |
nicklas |
272 |
<listitem> |
5436 |
30 Sep 10 |
nicklas |
273 |
<simpara>timestamp</simpara> |
5436 |
30 Sep 10 |
nicklas |
274 |
</listitem> |
3612 |
31 Jul 07 |
nicklas |
275 |
</itemizedlist> |
3612 |
31 Jul 07 |
nicklas |
276 |
|
3612 |
31 Jul 07 |
nicklas |
277 |
<para> |
3612 |
31 Jul 07 |
nicklas |
278 |
Note that the given types are converted into the most appropriate database |
3612 |
31 Jul 07 |
nicklas |
279 |
column type by Hibernate. |
3612 |
31 Jul 07 |
nicklas |
280 |
</para> |
3612 |
31 Jul 07 |
nicklas |
281 |
</entry> |
3612 |
31 Jul 07 |
nicklas |
282 |
</row> |
3612 |
31 Jul 07 |
nicklas |
283 |
<row> |
3612 |
31 Jul 07 |
nicklas |
284 |
<entry>length</entry> |
3612 |
31 Jul 07 |
nicklas |
285 |
<entry>no</entry> |
3612 |
31 Jul 07 |
nicklas |
286 |
<entry> |
3612 |
31 Jul 07 |
nicklas |
287 |
If the column is a string type, this is the maximum length that can |
3612 |
31 Jul 07 |
nicklas |
288 |
be stored in the database. If no value is given, 255 is assumed. |
3612 |
31 Jul 07 |
nicklas |
289 |
</entry> |
3612 |
31 Jul 07 |
nicklas |
290 |
</row> |
3612 |
31 Jul 07 |
nicklas |
291 |
<row> |
3612 |
31 Jul 07 |
nicklas |
292 |
<entry>null</entry> |
3612 |
31 Jul 07 |
nicklas |
293 |
<entry>no</entry> |
3612 |
31 Jul 07 |
nicklas |
294 |
<entry> |
3612 |
31 Jul 07 |
nicklas |
295 |
If the column should allow <constant>null</constant> values or not. |
3612 |
31 Jul 07 |
nicklas |
296 |
Allowed values are <constant>true</constant> (default) and |
3612 |
31 Jul 07 |
nicklas |
297 |
<constant>false</constant>. |
3612 |
31 Jul 07 |
nicklas |
298 |
</entry> |
3612 |
31 Jul 07 |
nicklas |
299 |
</row> |
3612 |
31 Jul 07 |
nicklas |
300 |
<row> |
3612 |
31 Jul 07 |
nicklas |
301 |
<entry>insert</entry> |
3612 |
31 Jul 07 |
nicklas |
302 |
<entry>no</entry> |
3612 |
31 Jul 07 |
nicklas |
303 |
<entry> |
3660 |
13 Aug 07 |
martin |
304 |
If values for this property should be inserted into the database or not. |
3612 |
31 Jul 07 |
nicklas |
305 |
Allowed values are <constant>true</constant> (default) and |
3612 |
31 Jul 07 |
nicklas |
306 |
<constant>false</constant>. |
3612 |
31 Jul 07 |
nicklas |
307 |
</entry> |
3612 |
31 Jul 07 |
nicklas |
308 |
</row> |
3612 |
31 Jul 07 |
nicklas |
309 |
<row> |
3612 |
31 Jul 07 |
nicklas |
310 |
<entry>update</entry> |
3612 |
31 Jul 07 |
nicklas |
311 |
<entry>no</entry> |
3612 |
31 Jul 07 |
nicklas |
312 |
<entry> |
3660 |
13 Aug 07 |
martin |
313 |
If values for this property should be updated in the database or not. |
3612 |
31 Jul 07 |
nicklas |
314 |
Allowed values are <constant>true</constant> (default) and |
3612 |
31 Jul 07 |
nicklas |
315 |
<constant>false</constant>. |
3612 |
31 Jul 07 |
nicklas |
316 |
</entry> |
3612 |
31 Jul 07 |
nicklas |
317 |
</row> |
3612 |
31 Jul 07 |
nicklas |
318 |
<row> |
6428 |
03 Mar 14 |
nicklas |
319 |
<entry>restricted-edit</entry> |
6428 |
03 Mar 14 |
nicklas |
320 |
<entry>no</entry> |
6428 |
03 Mar 14 |
nicklas |
321 |
<entry> |
6428 |
03 Mar 14 |
nicklas |
322 |
Allowed values are <constant>false</constant> (default) and |
6428 |
03 Mar 14 |
nicklas |
323 |
<constant>true</constant>. If set, there is some restriction |
6428 |
03 Mar 14 |
nicklas |
324 |
on who may change the values. This is currently only implemented |
6428 |
03 Mar 14 |
nicklas |
325 |
for users. If the property is restricted only an administrator is allowed |
6428 |
03 Mar 14 |
nicklas |
326 |
to change the value, not the user itself. |
6428 |
03 Mar 14 |
nicklas |
327 |
</entry> |
6428 |
03 Mar 14 |
nicklas |
328 |
</row> |
6428 |
03 Mar 14 |
nicklas |
329 |
<row> |
7497 |
11 Jul 18 |
nicklas |
330 |
<entry>hidden</entry> |
7497 |
11 Jul 18 |
nicklas |
331 |
<entry>no</entry> |
7497 |
11 Jul 18 |
nicklas |
332 |
<entry> |
7497 |
11 Jul 18 |
nicklas |
333 |
Allowed values are <constant>false</constant> (default) and |
7497 |
11 Jul 18 |
nicklas |
334 |
<constant>true</constant>. If set, the property is normally |
7497 |
11 Jul 18 |
nicklas |
335 |
not visible in the user interface. It is still possible for |
7497 |
11 Jul 18 |
nicklas |
336 |
plug-ins and extensions to access and modify the property |
7497 |
11 Jul 18 |
nicklas |
337 |
(using regular access permission rules). |
7497 |
11 Jul 18 |
nicklas |
338 |
</entry> |
7497 |
11 Jul 18 |
nicklas |
339 |
</row> |
7497 |
11 Jul 18 |
nicklas |
340 |
<row> |
3612 |
31 Jul 07 |
nicklas |
341 |
<entry>averagemethod</entry> |
3612 |
31 Jul 07 |
nicklas |
342 |
<entry>no</entry> |
3612 |
31 Jul 07 |
nicklas |
343 |
<entry> |
3612 |
31 Jul 07 |
nicklas |
344 |
The method to use when calculating the average of a set of values. |
3612 |
31 Jul 07 |
nicklas |
345 |
This attribute replaces the <sgmltag>averagable</sgmltag> attribute. |
3612 |
31 Jul 07 |
nicklas |
346 |
The following values can be used: |
3612 |
31 Jul 07 |
nicklas |
347 |
|
3612 |
31 Jul 07 |
nicklas |
348 |
<itemizedlist> |
3612 |
31 Jul 07 |
nicklas |
349 |
<listitem> |
3612 |
31 Jul 07 |
nicklas |
350 |
<simpara> |
3612 |
31 Jul 07 |
nicklas |
351 |
<constant>none</constant>: average values are not supported |
3612 |
31 Jul 07 |
nicklas |
352 |
(default for non-numerical columns) |
3612 |
31 Jul 07 |
nicklas |
353 |
</simpara> |
3612 |
31 Jul 07 |
nicklas |
354 |
</listitem> |
3612 |
31 Jul 07 |
nicklas |
355 |
<listitem> |
3612 |
31 Jul 07 |
nicklas |
356 |
<simpara> |
3612 |
31 Jul 07 |
nicklas |
357 |
<constant>arithmetic_mean</constant>: calculate the arithmetic mean |
3612 |
31 Jul 07 |
nicklas |
358 |
(default for numerical columns; not supported for non-numerical columns) |
3612 |
31 Jul 07 |
nicklas |
359 |
</simpara> |
3612 |
31 Jul 07 |
nicklas |
360 |
</listitem> |
3612 |
31 Jul 07 |
nicklas |
361 |
<listitem> |
3612 |
31 Jul 07 |
nicklas |
362 |
<simpara> |
3612 |
31 Jul 07 |
nicklas |
363 |
<constant>geometric_mean</constant>: calculate the geometric mean |
3612 |
31 Jul 07 |
nicklas |
364 |
(not supported for non-numerical columns) |
3612 |
31 Jul 07 |
nicklas |
365 |
</simpara> |
3612 |
31 Jul 07 |
nicklas |
366 |
</listitem> |
3612 |
31 Jul 07 |
nicklas |
367 |
<listitem> |
3612 |
31 Jul 07 |
nicklas |
368 |
<simpara> |
5678 |
29 Jun 11 |
nicklas |
369 |
<constant>quadratic_mean</constant>: calculate the quadtratic mean |
5678 |
29 Jun 11 |
nicklas |
370 |
(not supported for non-numerical columns) |
5678 |
29 Jun 11 |
nicklas |
371 |
</simpara> |
5678 |
29 Jun 11 |
nicklas |
372 |
</listitem> |
5678 |
29 Jun 11 |
nicklas |
373 |
<listitem> |
5678 |
29 Jun 11 |
nicklas |
374 |
<simpara> |
3612 |
31 Jul 07 |
nicklas |
375 |
<constant>min</constant>: use the minimum value of the values in the set |
3612 |
31 Jul 07 |
nicklas |
376 |
</simpara> |
3612 |
31 Jul 07 |
nicklas |
377 |
</listitem> |
3612 |
31 Jul 07 |
nicklas |
378 |
<listitem> |
3612 |
31 Jul 07 |
nicklas |
379 |
<simpara> |
3612 |
31 Jul 07 |
nicklas |
380 |
<constant>max</constant>: use the maximum value of the values in the set |
3612 |
31 Jul 07 |
nicklas |
381 |
</simpara> |
3612 |
31 Jul 07 |
nicklas |
382 |
</listitem> |
3612 |
31 Jul 07 |
nicklas |
383 |
</itemizedlist> |
3612 |
31 Jul 07 |
nicklas |
384 |
|
3612 |
31 Jul 07 |
nicklas |
385 |
</entry> |
3612 |
31 Jul 07 |
nicklas |
386 |
</row> |
3612 |
31 Jul 07 |
nicklas |
387 |
</tbody> |
3612 |
31 Jul 07 |
nicklas |
388 |
</tgroup> |
3996 |
23 Nov 07 |
nicklas |
389 |
</table> |
3612 |
31 Jul 07 |
nicklas |
390 |
|
3612 |
31 Jul 07 |
nicklas |
391 |
<para> |
3612 |
31 Jul 07 |
nicklas |
392 |
Each <sgmltag class="starttag">property</sgmltag> tag may contain zero or more |
3612 |
31 Jul 07 |
nicklas |
393 |
<sgmltag class="starttag">link</sgmltag> tags that can be used by client |
3612 |
31 Jul 07 |
nicklas |
394 |
application to provide clickable links to other databases. Each |
3612 |
31 Jul 07 |
nicklas |
395 |
<sgmltag class="starttag">link</sgmltag> has a <sgmltag>regexp</sgmltag> |
3612 |
31 Jul 07 |
nicklas |
396 |
and an <sgmltag>url</sgmltag> attribute. If the regular expression matches |
3612 |
31 Jul 07 |
nicklas |
397 |
the value a link will be created, otherwise not. The order of the |
3612 |
31 Jul 07 |
nicklas |
398 |
<sgmltag class="starttag">link</sgmltag> tags are important, since only |
3612 |
31 Jul 07 |
nicklas |
399 |
the first one that matches is used. The <sgmltag>url</sgmltag> attribute may |
3612 |
31 Jul 07 |
nicklas |
400 |
contain the string <constant>{value}</constant> which will be replaced by the |
3612 |
31 Jul 07 |
nicklas |
401 |
actual value when the link is generated. |
3612 |
31 Jul 07 |
nicklas |
402 |
</para> |
3612 |
31 Jul 07 |
nicklas |
403 |
|
3612 |
31 Jul 07 |
nicklas |
404 |
<note> |
3612 |
31 Jul 07 |
nicklas |
405 |
<para> |
3612 |
31 Jul 07 |
nicklas |
406 |
If the link contains the character <constant>&</constant> it must be |
4487 |
08 Sep 08 |
jari |
407 |
escaped as <constant>&amp;</constant>. For example, to link to a UniGene |
3612 |
31 Jul 07 |
nicklas |
408 |
entry: |
3612 |
31 Jul 07 |
nicklas |
409 |
</para> |
3612 |
31 Jul 07 |
nicklas |
410 |
<programlisting> |
3612 |
31 Jul 07 |
nicklas |
411 |
<link |
3612 |
31 Jul 07 |
nicklas |
412 |
regexp="\w+\.\d+" |
3612 |
31 Jul 07 |
nicklas |
413 |
url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&amp;term={value}[ClusterID]" |
3612 |
31 Jul 07 |
nicklas |
414 |
/> |
3612 |
31 Jul 07 |
nicklas |
415 |
</programlisting> |
3612 |
31 Jul 07 |
nicklas |
416 |
</note> |
3612 |
31 Jul 07 |
nicklas |
417 |
|
3612 |
31 Jul 07 |
nicklas |
418 |
|
3334 |
14 May 07 |
nicklas |
419 |
</appendix> |
3334 |
14 May 07 |
nicklas |
420 |
|