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Revision 6abb0164

ID6abb016422e52a7a219de6d551114e4100735bf4
Parent 65b1cba1
Child 7fa1eea8

Added by Andreas Kohlbecker about 5 years ago

moving site folder to root and setting up the pom.xml, also updating the site content

View differences:

modules/cdm_dataportal/pom.xml.offline
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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
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	http://maven.apache.org/xsd/maven-4.0.0.xsd">
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	<!--
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		xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
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		http://maven.apache.org/maven-v4_0_0.xsd"
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	-->
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	<modelVersion>4.0.0</modelVersion>
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	<groupId>eu.etaxonomy</groupId>
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	<artifactId>portal</artifactId>
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	<version>3.5.1</version>
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	<packaging>jar</packaging>
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	<name>CDM Dataportal</name>
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	<properties>
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		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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	</properties>
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	<scm>
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		<connection>scm:svn:http://dev.e-taxonomy.eu/svn/trunk/drupal/</connection>
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		<developerConnection>scm:svn:https://dev.e-taxonomy.eu/svn/trunk/drupal/</developerConnection>
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		<url>http://dev.e-taxonomy.eu/trac/browser/trunk/drupal/</url>
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	</scm>
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  <prerequisites>
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    <maven>3.0.5</maven>
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  </prerequisites>
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	<mailingLists>
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		<mailingList>
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			<name>dev-edit</name>
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			<subscribe>
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				https://webmail.mnhn.fr/wws/subrequest/dev-edit
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			</subscribe>
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			<unsubscribe>
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				https://webmail.mnhn.fr/wws/sigrequest/dev-edit
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			</unsubscribe>
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			<post>dev-edit@mnhn.fr</post>
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			<archive>https://webmail.mnhn.fr/wws/arc/dev-edit/</archive>
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		</mailingList>
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		<mailingList>
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			<name>cdm-edit</name>
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			<post>cdm-edit@mnhn.fr</post>
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			<subscribe>
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				https://webmail.mnhn.fr/wws/subrequest/cdm-edit
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			</subscribe>
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			<unsubscribe>
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				https://webmail.mnhn.fr/wws/sigrequest/cdm-edit
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			</unsubscribe>
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			<archive>https://webmail.mnhn.fr/wws/arc/cdm-edit/</archive>
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		</mailingList>
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	</mailingLists>
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	<licenses>
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		<license>
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			<name>Mozilla Public License Version 1.1</name>
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			<url>http://www.mozilla.org/MPL/MPL-1.1.html</url>
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			<distribution>repo</distribution>
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		</license>
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	</licenses>
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	<developers>
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		<developer>
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			<!-- your SVN account id please! -->
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			<id>a.kohlbecker</id>
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			<name>
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				Andreas Kohlbecker
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			</name>
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			<email>a.kohlbecker [at] bgbm.org</email>
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			<organization>
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				Botanical Garden Botanical Museum Berlin
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			</organization>
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			<organizationUrl>http://www.bgbm.org/BioDivInf/</organizationUrl>
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			<timezone>+1</timezone>
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			<roles>
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				<role>Developer</role>
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			</roles>
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			<url></url>
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		</developer>
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		<developer>
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<!-- your SVN account id please! -->
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			<id>f.revilla</id>
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			<name>
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				Francisco Revilla
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			</name>
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			<email>f.revilla [at] bgbm.org</email>
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			<organization>
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				Botanical Garden Botanical Museum Berlin
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			</organization>
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			<organizationUrl>http://www.bgbm.org/BioDivInf/</organizationUrl>
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			<timezone>+1</timezone>
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			<roles>
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				<role>Developer</role>
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			</roles>
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			<url></url>
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		</developer>
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	</developers>
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	<!--contributors>
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		<contributor>
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			<name>Test-Contributor</name>
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		</contributor>
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	</contributors-->
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	<issueManagement>
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		<system>Trac</system>
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		<url>http://dev.e-taxonomy.eu/trac/</url>
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	</issueManagement>
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	<!-- **** REPOSITORIES **** -->
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	<repositories>
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		<repository>
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			<id>EditRepository</id>
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			<url>http://wp5.e-taxonomy.eu/cdmlib/mavenrepo/</url>
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		</repository>
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	</repositories>
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	<!-- **** PLUGINS **** -->
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	<build>
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		<plugins>
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			<plugin>
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				<groupId>org.codehaus.mojo</groupId>
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				<artifactId>buildnumber-maven-plugin</artifactId>
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				<version>1.3</version>
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				<executions>
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					<execution>
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						<!--<phase>deploy</phase>-->
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						<goals>
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							<goal>create</goal>
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						</goals>
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					</execution>
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				</executions>
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				<configuration>
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					<doCheck>false</doCheck>
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					<!--
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						Only create the build number if there are no local modifications
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					-->
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					<doUpdate>false</doUpdate>
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					<!--
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						automatically update the local svn copy
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					-->
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				</configuration>
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			</plugin>
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			<plugin>
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				<groupId>org.apache.maven.plugins</groupId>
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				<artifactId>maven-site-plugin</artifactId>
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				<version>3.4</version>
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				<configuration>
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					<locales>en</locales>
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                    <outputEncoding>UTF-8</outputEncoding>
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					<siteDirectory>${basedir}/site</siteDirectory>
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                    <!-- chmod: not not use chmod, rather adapt the umask of the user at the server to which the site is deployed -->
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                    <chmod>false</chmod>
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				</configuration>
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			</plugin>
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			<plugin>
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				<groupId>org.apache.maven.plugins</groupId>
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				<artifactId>maven-source-plugin</artifactId>
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                <version>2.4</version>
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				<executions>
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					<execution>
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						<id>attach-sources</id>
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						<phase>verify</phase>
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						<goals>
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							<goal>jar</goal>
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						</goals>
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					</execution>
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				</executions>
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			</plugin>
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			<plugin>
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				<groupId>org.apache.maven.plugins</groupId>
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				<artifactId>maven-javadoc-plugin</artifactId>
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                <version>2.10.2</version>
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				<configuration>
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					<aggregate>true</aggregate>
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					<stylesheet>maven</stylesheet>
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				</configuration>
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			</plugin>
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			<plugin>
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				<groupId>org.apache.maven.plugins</groupId>
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				<artifactId>maven-eclipse-plugin</artifactId>
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                <version>2.9</version>
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				<configuration>
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					<downloadSources>true</downloadSources>
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					<downloadJavadocs>true</downloadJavadocs>
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				</configuration>
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			</plugin>
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			<!-- DEPLOY -->
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			<plugin>
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				<artifactId>maven-antrun-plugin</artifactId>
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				<version>1.8</version>
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				<executions>
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					<execution>
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						<phase>install</phase>
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						<configuration>
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							<tasks>
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								<!--
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									${project.patchversion} is explicitly set in this pom
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								-->
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								<property name="project.fullversionstring"
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								    value="${project.fullversionstring}" />
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								<ant antfile="${project.basedir}/src/main/installer/linux/build-deb.xml"
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									dir="${project.basedir}" />
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							</tasks>
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						</configuration>
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						<goals>
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							<goal>run</goal>
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						</goals>
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					</execution>
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				</executions>
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			</plugin>
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		</plugins>
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		<!-- EXTENSIONS -->
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		<extensions>
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			<extension>
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				<groupId>org.apache.maven.wagon</groupId>
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				<artifactId>wagon-scm</artifactId>
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				<version>1.0-beta-6</version>
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			</extension>
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			<extension>
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				<groupId>org.apache.maven.wagon</groupId>
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				<artifactId>wagon-ssh</artifactId>
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				<version>1.0-beta-6</version>
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			</extension>
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			<extension>
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				<groupId>org.apache.maven.wagon</groupId>
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				<artifactId>wagon-ssh-external</artifactId>
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				<version>1.0-beta-6</version>
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			</extension>
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			<extension>
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				<groupId>org.apache.maven.scm</groupId>
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				<artifactId>maven-scm-manager-plexus</artifactId>
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				<version>1.0</version>
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			</extension>
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			<extension>
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				<groupId>org.apache.maven.scm</groupId>
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				<artifactId>maven-scm-provider-svnexe</artifactId>
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				<version>1.0</version>
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			</extension>
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			<!-- WebDAV plugin to upload snapshots -->
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			<extension>
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				<groupId>org.apache.maven.wagon</groupId>
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				<artifactId>wagon-webdav</artifactId>
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				<version>1.0-beta-2</version>
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			</extension>
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		</extensions>
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	</build>
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	<reporting>
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		<plugins>
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			<plugin>
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				<!-- you will want to start by publishing your classes' Javadocs -->
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				<groupId>org.apache.maven.plugins</groupId>
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				<artifactId>maven-javadoc-plugin</artifactId>
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                <version>2.10.3</version>
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				<configuration>
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					<links>
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						<link>http://java.sun.com/j2se/1.6.0/docs/api/</link>
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						<link>http://static.springframework.org/spring/docs/2.5.x/api/</link>
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						<link>http://www.hibernate.org/hib_docs/v3/api/</link>
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						<!-- more libraries? -->
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					</links>
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				</configuration>
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			</plugin>
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			<plugin>
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				<!--
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					this will generate an indexed and cross-referenced HTML version of
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					your source code
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				-->
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				<groupId>org.apache.maven.plugins</groupId>
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				<artifactId>maven-jxr-plugin</artifactId>
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                <version>2.5</version>
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			</plugin>
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			<plugin>
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				<!--
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					if you use @todo tags to remind you of things to be done (which is
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					a good coding practice), the taglist report will generate a list of
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					all the items marked @todo or TODO
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				-->
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				<groupId>org.codehaus.mojo</groupId>
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				<artifactId>taglist-maven-plugin</artifactId>
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                <version>2.4</version>
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			</plugin>
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			<plugin>
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				<!--
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					Test coverage can be a useful indication of the quality of your
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					unit tests. It basically tells you how much of your code is
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					actually run by your unit tests, which, in turn, can give you a
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					good idea of the tests' quality
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				-->
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				<groupId>org.codehaus.mojo</groupId>
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				<artifactId>cobertura-maven-plugin</artifactId>
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                <version>2.7</version>
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			</plugin>
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			<plugin>
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				<groupId>org.apache.maven.plugins</groupId>
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				<artifactId>maven-changes-plugin</artifactId>
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				<version>2.11</version>
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				<configuration>
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					<issueLinkTemplatePerSystem>
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						<default>%URL%/ticket/%ISSUE%</default>
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					</issueLinkTemplatePerSystem>
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				</configuration>
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				<reportSets>
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					<reportSet>
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						<reports>
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							<report>changes-report</report>
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						</reports>
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					</reportSet>
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				</reportSets>
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			</plugin>
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		</plugins>
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	</reporting>
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	<!--	 DISTRIBUTION MANAGEMENT -->
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	<distributionManagement>
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		<site>
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			<id>wp5.e-taxonomy.eu</id>
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			<url>
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				scpexe://wp5.e-taxonomy.eu/var/www/wp5.e-taxonomy.eu/portal/
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			</url>
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		</site>
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	</distributionManagement>
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</project>
modules/cdm_dataportal/site/apt/configuration.apt
1

  
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    {{{http://drupal.org}Drupal}} is an open source 
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    {{{http://en.wikipedia.org/wiki/Web_content_management_system}content managent system}}
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    which can be expanded, builded and custimized by developing modules and themes.
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    <<CDM Dataportal module>> is a drupal module developed for supporting the front end or presentation layer of the 
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    {{{http://wp5.e-taxonomy.eu/cdm-server/}EDIT CDM Server}}.
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    It allows taxonomist to look up for taxa, search taxa and other features. Besides 
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    the CDM Dataportal module there are several <<drupal themes>>
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    which personalized the layout (colours, images and others) of the CDM Dataportal module results.
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    On this basis, it can be possible, for example, to have two different taxonomy collections whith differents selected looks
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    thanks to the different drupal themes (each one per collection). However both collections will have the same features (such
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    taxa search) thanks to the CDM Dataportal module.
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    More documentation about the CDM (Common Data Library) where the CDM dataportal belongs could be found at the following locations:
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    * {{{http://wp5.e-taxonomy.eu/cdmlib/}CDM Library}}
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    * {{{http://wp5.e-taxonomy.eu/taxeditor/}Taxonomic Editor}}
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    * {{{http://wp5.e-taxonomy.eu/cdm-server/}CDM Server}}
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    * {{{http://wp5.e-taxonomy.eu/printpublisher/}Print Publisher}}
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    * {{{http://wp5.e-taxonomy.eu/cdm-setups/}CDM Setups}}
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Drupal module and theme activation
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    To activate the datataportal module go to 
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    <Administer-\>Site building-\>Modules>
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    and at the CDM section select the modules CDM API, CDM Dataportal and CDM Taxon Tree. The other two 
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    modules are optional.
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    To change your default theme just navigate to      
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    <Administer-\>Site building-\>Themes>
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    where you can select your default theme as well as configured it. 
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CDM Dataportal Settings
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    If you are using the CDM Dataportal module, you will need to configure it in order to make it run. Here you will find how to
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    explore and configure the module.
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    First step to configure the module is making sure your user has access to the settings options of CDM Dataportal module.
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    You can find the configurations options under <Administer-\>Site Configuration-\>CDM Dataportal>. Once you are in the
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    configuration site you will see four different sections:
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*General
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    Drupal's CDM Dataportal module dialogues with the <CDM Server> asking for taxa data 
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   	and classification of taxa. The first thing the <CDM Dataportal module> needs to know
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   	is where is the CDM Server located in order to access it. Such parameters are configurable
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    via the general tag of the settings.
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    The general settings has enough documentation that explains itself. However the same
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    documentation with some extra details is avaible
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    <a href="./?q=admin/help/cdm_dataportal_general" title="General">here</a>
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    as one html site. If you prefer to go directly to the general settings just click 
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    <Administer-\>Site Configuration-\>CDM Dataportal>
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    to start the configuration click here. 
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*Geo & Map
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    As with <CDM Server>, CDM Dataportal module also dialogues with a Map Server to 
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    generate all the maps displayed on your web site. Again the module needs to know where
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    the map server is located and this parameter as well as others related with the maps
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    appaerance like map legends, map size, map background ... are configurable via
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    {{{./?q=admin/settings/cdm_dataportal/geo}Geo & Map settings}}.
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    This configuration site also explain all the configurable options itself. Same documentation with some extra details is avaible
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    <a href="./?q=admin/help/cdm_dataportal_geo" title="Geo & Map">here</a> as one html site.
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91
	 	
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*Layout		
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    <a target="_blank" href="./?q=admin/settings/cdm_dataportal/layout" >Here</a> 
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    you will find the settings for configuring the layout issues such pictures size or
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    number of search results to show. Layout section itself contains three subsections; 
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    <a target="_blank" href="./?q=admin/settings/cdm_dataportal/layout/taxon">Taxon Layout Settings</a>,
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    <Administer-\>Site Configuration-\>CDM Dataportal-\>Layout-\>Search> and
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    <Administer-\>Site Configuration-\>CDM Dataportal-\>Layout-\>Media>. 
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    Each one of the listed links forward you to the settings configuration site where each site explains 
101
    itself the different options.
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103
	
104
    
105
	A html site with more level of details is available 
106
	<a target="_blank" href="./?q=admin/settings/cdm_dataportal_layout">here</a>.
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109
	
110
*Cache
111
    
112
    It is possible to increase the portal time response when serving taxa sites. The mechanism 
113
    is quite simple. It works caching all taxa sites available in your portal in a way that when
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    a user wants to visit new taxa, the module will not create the new taxon site from scratch.
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    Instead of that the taxon site will be loaded from the cache and therefore will be no
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    dialogue with the CDM Server. 		 
117
    
118
		 
119
    
120
    <a href="./?q=admin/help/cdm_dataportal_cache.html" title="Cache">Here</a>
121
    you can read the cache configuration help or much better go directly to the
122
    {{{./?q=admin/help/settings/cdm_dataportal/cachesite}cache settings site}}.
123
    
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modules/cdm_dataportal/site/apt/download.apt
1
CDM Dataportal Download
2

  
3
   Coming soon
modules/cdm_dataportal/site/apt/getting-started.apt
1
Developing with Drupal
2
    
3
    Drupal is a free software package that allows anyone to easily publish, 
4
    manage and organize a wide variety of content on a website. Hundreds of 
5
    thousands of people and organizations are using Drupal to power an 
6
    endless variety of sites.
7
    
8
    CDM Dataportal have been developed with Drupal version 5. If you want to
9
    learn or experience more about Drupal visit the 
10
    {{{http://drupal.org}Drupal's oficial site}}.
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    If you already know what Drupal is and you want to configure the CDM 
12
    Dataportal module to interacte with your CDM Server visit our 
13
    {{{http://wp5.e-taxonomy.eu/cdm-setups/?q=node/17}CDM Setup->Group Installation}}
14
    
15
Enviroment Setup
16

  
17
    The development enviroment here described is based on following elements 
18
    technologies Drupal + Apache + Php + MySQL + Eclipse.
19
    
20
    For windows  {{{http://dev.e-taxonomy.eu/trac/wiki/DeveloperEnvironmentSetup}Windows 1}} and
21
    {{{http://dev.e-taxonomy.eu/trac/wiki/InstallingDrupal}Windows 2}}. For Os X 
22
    {{{http://dev.e-taxonomy.eu/trac/wiki/DeveloperEnvironmentSetupOsX}Apple}}
23

  
24
External Resources
25

  
26
   Some useful resources for developers are the following
27
   
28
   *Drupal
29
   
30
      Useful documentation for Drupal can be founded on the Drupal official web sites, such as
31
   
32
     *{{{http://drupal.org}Drupal Home}}
33
     
34
     *{{{api.drupal.org}Drupal API}}, or
35
     
36
     *{{{http://drupal.org/documentation}Drupal Documentation}} (with installation guides included).
37
          
38
   *JavaScript
39
     
40
     *{{{http://docs.jquery.com/Main_Page}JQuery}}
41
   
42
   
43
   *Firefox
44
   
45
      Useful Firefox addons for developers:
46
   
47
     *{{{https://addons.mozilla.org/de/firefox/addon/1843/}Firebug}}
48
     
49
     *{{{https://addons.mozilla.org/de/firefox/addon/60/}Web Developer Toolbar}}
50
     
51
     *{{{https://addons.mozilla.org/en-US/firefox/addon/10869/}JSONView}}
modules/cdm_dataportal/site/apt/index.apt
1
EDIT CDM Data Portal
2

  
3
    The EDIT Data Portal publishes taxonomic data data hosted in a CommunityStore
4
    either to a closed community or to the public at large. It has been implemented
5
    as a module for the content management system Drupal. The term
6
    {{{http://en.wikipedia.org/wiki/Web_content_management_system}content managent system}}
7
    is somewhat misleading here: since the actual content is stored and managed
8
    by the CDM, ensuring scientific accuracy and reusability of data. Drupal offers
9
    a great deal of flexibility and can be extended almost indefinitely, making it
10
    possible to adapt the EDIT Data Portal to the individual needs of a community.
11
    Custom web pages, forums, and blogs are only a few of Drupal's capabilities
12
    available out of the box, and there is practically no limit to the number of
13
    modules that can be added to enhance a site with for example image galleries.
14
    The layout and look and feel of the application can be easily adapted to fit
15
    any taste.
16

  
17
    The EDIT Data Portal supports zoological and botanical names (support for viral
18
    and bacterial names should be available soon), as well as multiple concurrent
19
    taxonomies. Rules as specified by the nomenclatural codes ICNAFP (formerly ICBN) and ICZN are
20
    built into the CDM, ensuring that taxon names conform to these standards.
21

  
22
    User interface design was guided by the following design principles: provide
23
    easy access to all taxa and names; display all relevant information in one
24
    place where possible; and reduce complexity without compromising scientific
25
    accuracy. A challenge particular to taxonomy is keeping the user from losing
26
    his or her bearings while navigating through vast taxonomic trees; to this
27
    end, a sophisticated taxonomic tree browser has been developed to reduce
28
    confusion and make daily work with such trees more productive. A search
29
    function provides an additional way to access taxa.
30

  
31
    Each taxon is represented by an individual page, which displays the list
32
    of synonyms, related taxa, occurrences, descriptions, media, and more. The
33
    list of homotypic and heterotypic synonyms is ordered historically and grouped
34
    by types; its layout resembles that found in printed publications. Images of
35
    protologues and of type specimens are linked directly from taxon names and
36
    synonym lists. In addition, taxon pages will allow users to contribute
37
    annotations as text or images.
38

  
39
    Currently, EDIT Data Portals and CDM Community Stores are used to store and
40
    publish the work of the EDIT exemplar groups focusing on the taxonomic groups
41
    Cichorieae, Diptera and Palmae. Links to the demosites are found below.
42

  
43

  
44
Drupal
45

  
46
    The open source content management system Drupal becomes more and more widely
47
    used in the area of biodiversity informatics. This popularity is not only
48
    due to its capabilities to just manage content for
49
    websites. The genius of what the Drupal community has done, is to reduce all
50
    of the aspects of social software to the core and then build a platform that
51
    could be infinitely extended to allow the assembly of almost any styles of
52
    online social interaction. During the past years the community contributed
53
    over 3000 different modules extending the Drupal core and thus on one hand
54
    providing a highly flexible construction kit and on the other hand showing by
55
    many examples that nearly everything is possible, perhaps only limited by the
56
    human imagination.
57

  
58
    The EDIT Data Portal has been developed as a drupal module to take the
59
    advantage of the community support and already available resources. Since we
60
    offer CDM Data Portal as a package with drupal together it is not necessary
61
    to spend extra time learning about drupal.
62

  
63
~~Constructing the EDIT platform for cybertaxonomy
64

  
65
~~   Drupal is used to build up
66
~~   general web applications like forums, blogs, a central repository for users
67
~~   and taxonomists, the Experts Database and a software tracker and rating
68
~~   system. Last but not least also taxonomy related software like the
69
~~   Scratchpads and the CDM DataPortal is based on this system.
70
~~
71
~~   The CDM DataPortal is using Drupal as an application framework to publish
72
~~   taxonomic treatments to a closed community or to the public. The treatments,
73
~~   stored in database are, accessible via web services to which the
74
~~   CDM DataPortal connects to fetch the information to be displayed.
75
~~   Furthermore does the CDM DataPortal act as an easy to use web service
76
~~   allowing reusing fragments of its pages in other contexts already rendered
77
~~   as HTML.
78
~~
79
~~   The new TDWG standards architecture relies among others on semantic web
80
~~   technologies, which are tailored around a data format called RDF.
81
~~   Unfortunately there has always been a lack of common tools for easy
82
~~   processing and visualising data provided by the RDF based ontology.
83
~~
84
~~   Since the last big version switch to Drupal 6, some very interesting
85
~~   modules are being simmered, which will allow storing, aggregating and
86
~~   processing RDF data, making Drupal an highly interesting candidate for
87
~~   building applications which benefit from the new semantic capabilities
88
~~   of the TDWG standards architecture. Drupal is promising not only because
89
~~   of the interesting technical implementations but also because of its
90
~~   popularity and support from a vast community.
91
~~
92
~~   Some RDF related modules are already available although most of them
93
~~   still are in alpha status. One of these incorporates RDF taxonomies
94
~~   into Drupal, another one is actually an ensemble of modules providing
95
~~   comprehensive RDF functionality and interoperability.
96
~~
97
~~   With Exhibit and Potluck the SIMILE (Semantic Interoperability of
98
~~   Metadata and Information in unLike Environments) project of the MIT
99
~~   has developed interesting tools for visualizing, browsing and mixing
100
~~   data. Exhibit for example displays structured data in the form of rich
101
~~   visualizations that can be searched, filtered and sorted using faceted
102
~~   browsing. The Exhibit module will bring these abilities to Drupal.
103
~~
104
~~   Tools for efficiently using the TDWQG RDF ontology are in reach and
105
~~   await their evaluation. So the time has come to find out what is
106
~~   possible to vision the next generation biodiversity network tools.
modules/cdm_dataportal/site/apt/installation.apt
1
CDM Server Installation
2

  
3
   CDM Dataportal module publishes the data of the CDM Server,
4
   therefore an already working CDM Server is a prerequisite for retrieving the
5
   data to publish. To learn more about the CDM Server visit the {{{http://wp5.e-taxonomy.eu/cdm-server/}CDM Server's web}}.
6
   To install a CDM Server instance follow the instructions at our {{{http://wp5.e-taxonomy.eu/node/2}cdm-setups web}}.
7

  
8
Drupal Installation
9

  
10
   Since the CDM Dataportal is a drupal module you will need to install at first Drupal
11
   (currently we are working with <<Drupal 7>>). There are two different possibilities of
12
   installing the CDM Data Portal. The first one is installing Drupal 7 and afterwards to
13
   enable the CDM Data Portal Module. The second and recomended is to download Drupal with
14
   the CDM Data Portal Module installed and already enable to use.
15

  
16
   For the first option visit {{{http://drupal.org}Drupal's site}} for more information.
17

  
18
   You can download the CDM Data Portal module from our download site.
19
   For the second option follow the instruction at our
20
   {{{http://cybertaxonomy.eu/node/7}cdm-setups web}}.
21

  
22
CDM Data Portal Configuration
23

  
24
   Once you have been installed Drupal and CDM Data Portal Module is enabled you will find
25
   how to configure the CDM Data Portal Module inside Drupal itself.
26

  
27
   Open a browser and go to your drupal site. Once you are in your drupal web site go to
28
   <<Configuration>CDM Data Portal>> where you will find a general documentation for
29
   configuring the module properly as well as links to specific configurations sites
30
   and documentation. We recommend to read and understand the documentation before starting
31
   to configure the module.
32

  
33
FAQ and contact
34

  
35
   If you have any problems or questions do not hesitate to contact us and to read our
36
   famous answer and questions site.
37

  
38

  
39

  
modules/cdm_dataportal/site/apt/screenshots.apt
1
Examples
2

  
3
   It is possible to see the data portal in action, the following links contains some collections using it.
4
   
5
   *{{{http://wp6-cichorieae.e-taxonomy.eu/portal/}Cichorieae}} group of plants.
6
   
7
   *{{{http://www.palmweb.org}Palmae}} group of plants.
8
   
9
   *{{{http://160.45.63.151/dataportal/diptera/}Diptera}} group of flies and mosquitoes.
10
   
11
Screenshots
12

  
13
    The welcome site of the palmweb with the <<taxon tree>> (the classification box) and
14
    the <<search>> (the search box) at the link side of the page. On the 
15
    middle of the page is the welcome text.
16

  
17
[./images/palmae2.png] Figure caption
18

  
19
    
20
    The welcome site of the cichorieae with the <<taxon tree>> (the classification box),
21
    the <<search>> (the search box) and the <<user login>> at the link side of the page. On the 
22
    middle of the page is the welcome text.
23
    
24
[./images/cichorieae2.png] Figure caption
25

  
26

  
27
   A screenshot of the palmweb portal after performing a search for the string "Coc"
28
   
29
[./images/palmae5.png] Figure caption
30

  
31

  
32
   Screenshot of the <<Lactuca Alpina>> from cichorieae portal. We can see how a taxon 
33
   profil (general tab) page looks like with his <<profile picture>> and 
34
   <<distribution map>>. We can see the <<footnotes>> for the distribution references 
35
   (the small red numbers). Also the <<taxon tree>> is focused at the Lactuca Alpina
36
   taxon under Cichorieae->Lactucinae->Lactuca->L. alpina at the left side of the page.
37
   
38
[./images/cichorieae4.png] Figure caption
39

  
40
   Screenshot of the Crepis Mollis taxon from cichorieae portal. This is how the 
41
   synonymy tab looks like. The heterotypic synonyms are grouped and ordered by date.
42
   The footnotes are displayed at the end of the page and the red links 
43

  
44
[./images/cichorieae5.PNG] Figure caption
45

  
46
   The following screenshot is from one of the configuration pages of the data portal,
47
   it contains the instructions for a correct configuration. At the top right corner 
48
   are the different configurable options (general, geo & map, layout and cache).
49
   
50
[./images/settings1.PNG] Figure caption
modules/cdm_dataportal/site/changes/changes.xml
1
<document xmlns="http://maven.apache.org/changes/1.0.0"
2
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
3
	xsi:schemaLocation="http://maven.apache.org/changes/1.0.0 http://maven.apache.org/xsd/changes-1.0.0.xsd">
4
	<properties>
5
		<title>CDM Data Portal Releases</title>
6
		<author email="f.revilla@bgbm.org">Francisco Revilla</author>
7
	</properties>
8
	<body>
9

  
10
		<release version="3.0.0.beta" date="2010-09-07" description="Version 3.0 pre-release">
11
			<action dev="f.revilla" type="fix">
12
				Test
13
	      </action>
14
		</release>
15

  
16
	</body>
17
</document>
modules/cdm_dataportal/site/fml/admin-faq.fml
1
<?xml version="1.0" encoding="UTF-8"?>
2
<faqs xmlns="http://maven.apache.org/FML/1.0.1"
3
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
4
  xsi:schemaLocation="http://maven.apache.org/FML/1.0.1 http://maven.apache.org/xsd/fml-1.0.1.xsd"
5
  title="Adminstration of the EDIT CDM Dataportal - Frequently Asked Questions"
6
  toplink="false">
7

  
8
  <part id="general">
9
    <title>Layout &amp; visibility of elements</title>
10

  
11
    <faq id="autherinfo-get-rid-off">
12
      <question>
13
        How can I turn of authoring information like "<em>Fri, 04/15/2011 - 12:23 — Anonymous</em>" which appears on some pages?
14
      </question>
15
      <answer>
16
        <p>Display of the 'post information' can be configured in the administration area of the DataPortal.
17
        Login and go to Site building  &gt; Themes &gt; Configure (admin/build/themes/settings)
18
        and toggle the check boxes below the heading '<em>Display post information on</em>' according to your wishes.
19
        </p>
20
      </answer>
21
    </faq>
22

  
23
  </part>
24
  <part id="cdm">
25
    <title>Working on CDM data</title>
26

  
27
    <faq id="cdm_changes_not_visible">
28
      <question>
29
        Why do the changes I made on the CDM data not appear in the portal? Why do they not appear immediately but only after some time?
30
      </question>
31
      <answer>
32
        <p>Drupal provides a mechanism for caching data which is then displayed on the web pages to avoid querying the data base for every site request. The cache will be updated from time to time.
33
        This is the default setting for the 'Anonymous' user (not logged in). If you log in the caching will be disabled and the data should be up-to-date. 
34
        You can also clear the cache to update it for the 'Anonymous' user. In the administration menu go to Configuration &gt; Development &gt; Performance &gt; Clear all caches.
35
        </p>
36
      </answer>
37
    </faq>
38

  
39
  </part>
40

  
41
</faqs>
modules/cdm_dataportal/site/fml/troubleshooting.fml
1
<?xml version="1.0" encoding="UTF-8"?>
2
<faqs xmlns="http://maven.apache.org/FML/1.0.1"
3
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
4
  xsi:schemaLocation="http://maven.apache.org/FML/1.0.1 http://maven.apache.org/xsd/fml-1.0.1.xsd"
5
  title="Frequently Asked Questions"
6
  toplink="false">
7

  
8
  <part id="general">
9
    <title>General</title>
10

  
11
    <faq id="whats-foo">
12
      <question>
13
        What is Foo?
14
      </question>
15
      <answer>
16
        <p>some markup goes here</p>
17

  
18
        <source>some source code</source>
19

  
20
        <p>some markup goes here</p>
21
      </answer>
22
    </faq>
23

  
24
    <faq id="whats-bar">
25
      <question>
26
        What is Bar?
27
      </question>
28
      <answer>
29
        <p>some markup goes here</p>
30
      </answer>
31
    </faq>
32
  </part>
33

  
34
  <part id="install">
35

  
36
    <title>Installation</title>
37

  
38
    <faq id="how-install">
39
      <question>
40
        How do I install Foo?
41
      </question>
42
      <answer>
43
        <p>some markup goes here</p>
44
      </answer>
45
    </faq>
46

  
47
  </part>
48

  
49
</faqs>
modules/cdm_dataportal/site/site.xml
1
<?xml version="1.0"?>
2
<project xmlns="http://maven.apache.org/DECORATION/1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/DECORATION/1.0.0 http://maven.apache.org/xsd/decoration-1.0.0.xsd">
3
	<skin>
4
		<groupId>eu.etaxonomy.site</groupId>
5
		<artifactId>platform-site-skin</artifactId>
6
		<version>1.0</version>
7
	</skin>
8
	<body>
9
		<menu name="General Information">
10
			<item name="Overview" href="index.html"/>
11
			<item name="Screenshots" href="screenshots.html"/>
12
			<item name="Dataportal Installation" href="installation.html"/>
13
			<item name="Releases" href="changes-report.html"/>
14
			<item name="Download" href="download.html"/>
15

  
16
		</menu>
17

  
18
		<menu name="Getting Help">
19
			<item name="Admin FAQ" href="admin-faq.html"/>
20
		</menu>
21

  
22
		<menu name="Developer">
23
			<item name="Getting started" href="getting-started.html"/>
24
			<item name="Wiki" href="http://dev.e-taxonomy.eu/trac/wiki/CdmDataportalDev"/>
25
		</menu>
26

  
27
		<menu name="Project">
28
			<item name="Mailing Lists" href="mail-lists.html"/>
29
			<item name="Project Team" href="team-list.html"/>
30
			<item name="Continuous Integration" href="integration.html"/>
31
			<item name="Issue Tracking" href="http://dev.e-taxonomy.eu/trac/"/>
32
			<item name="Source Repository" href="source-repository.html"/>
33
			<item name="License" href="license.html"/>
34
		</menu>
35
	</body>
36
</project>
pom.xml
6 6
    <packaging>pom</packaging>
7 7
    <version>3.9.0</version>
8 8

  
9
    <mailingLists>
10
        <mailingList>
11
            <name>EDIT Platform Developers</name>
12
            <subscribe>
13
                https://lists.fu-berlin.de/listinfo/editplatformdevelopers#subscribe
14
            </subscribe>
15
            <unsubscribe>
16
                https://lists.fu-berlin.de/listinfo/editplatformdevelopers#options
17
            </unsubscribe>
18
        </mailingList>
19
        <mailingList>
20
            <name>EDIT User</name>
21
            <subscribe>
22
                https://lists.fu-berlin.de/listinfo/edituser#subscribe
23
            </subscribe>
24
            <unsubscribe>
25
                https://lists.fu-berlin.de/listinfo/edituser#options
26
            </unsubscribe>
27
        </mailingList>
28
    </mailingLists>
29
    <licenses>
30
        <license>
31
            <name>Mozilla Public License Version 1.1</name>
32
            <url>http://www.mozilla.org/MPL/MPL-1.1.html</url>
33
            <distribution>repo</distribution>
34
        </license>
35
    </licenses>
36
    <developers>
37
        <developer>
38
            <!-- your SVN account id please! -->
39
            <id>a.kohlbecker</id>
40
            <name>
41
                Andreas Kohlbecker
42
            </name>
43
            <email>a.kohlbecker [at] bgbm.org</email>
44
            <organization>
45
                Botanical Garden Botanical Museum Berlin
46
            </organization>
47
            <organizationUrl>http://www.bgbm.org/BioDivInf/</organizationUrl>
48
            <timezone>+1</timezone>
49
            <roles>
50
                <role>Developer</role>
51
            </roles>
52
            <url />
53
        </developer>
54
    </developers>
55

  
9 56
    <distributionManagement>
10 57
        <site>
11 58
            <id>wp5.e-taxonomy.eu</id>
......
31 78
                <version>2.8.2</version>
32 79
            </plugin>
33 80
            <plugin>
81
                <groupId>org.apache.maven.plugins</groupId>
82
                <artifactId>maven-site-plugin</artifactId>
83
                <version>3.4</version>
84
                <configuration>
85
                    <locales>en</locales>
86
                    <outputEncoding>UTF-8</outputEncoding>
87
                    <siteDirectory>${basedir}/site</siteDirectory>
88
                    <!-- chmod: not not use chmod, rather adapt the umask
89
                        of the user at the server to which the site is deployed
90
                    -->
91
                    <chmod>false</chmod>
92
                </configuration>
93
            </plugin>
94
            <plugin>
34 95
                <groupId>external.atlassian.jgitflow</groupId>
35 96
                <artifactId>jgitflow-maven-plugin</artifactId>
36 97
                <version>1.0-m6</version>
site/apt/configuration.apt
1

  
2
    {{{http://drupal.org}Drupal}} is an open source 
3
    {{{http://en.wikipedia.org/wiki/Web_content_management_system}content managent system}}
4
    which can be expanded, builded and custimized by developing modules and themes.
5
    <<CDM Dataportal module>> is a drupal module developed for supporting the front end or presentation layer of the 
6
    {{{http://wp5.e-taxonomy.eu/cdm-server/}EDIT CDM Server}}.
7
    It allows taxonomist to look up for taxa, search taxa and other features. Besides 
8
    the CDM Dataportal module there are several <<drupal themes>>
9
    which personalized the layout (colours, images and others) of the CDM Dataportal module results.
10

  
11

  
12

  
13
    On this basis, it can be possible, for example, to have two different taxonomy collections whith differents selected looks
14
    thanks to the different drupal themes (each one per collection). However both collections will have the same features (such
15
    taxa search) thanks to the CDM Dataportal module.
16

  
17

  
18

  
19
    More documentation about the CDM (Common Data Library) where the CDM dataportal belongs could be found at the following locations:
20

  
21
    * {{{http://wp5.e-taxonomy.eu/cdmlib/}CDM Library}}
22
    
23
    * {{{http://wp5.e-taxonomy.eu/taxeditor/}Taxonomic Editor}}
24
    
25
    * {{{http://wp5.e-taxonomy.eu/cdm-server/}CDM Server}}
26
    
27
    * {{{http://wp5.e-taxonomy.eu/printpublisher/}Print Publisher}}
28
    
29
    * {{{http://wp5.e-taxonomy.eu/cdm-setups/}CDM Setups}}
30
    
31

  
32

  
33

  
34

  
35
Drupal module and theme activation
36

  
37
    To activate the datataportal module go to 
38
    <Administer-\>Site building-\>Modules>
39
    and at the CDM section select the modules CDM API, CDM Dataportal and CDM Taxon Tree. The other two 
40
    modules are optional.
41
    
42

  
43
    To change your default theme just navigate to      
44
    <Administer-\>Site building-\>Themes>
45
    where you can select your default theme as well as configured it. 
46

  
47

  
48

  
49
CDM Dataportal Settings
50

  
51

  
52
    If you are using the CDM Dataportal module, you will need to configure it in order to make it run. Here you will find how to
53
    explore and configure the module.
54

  
55

  
56

  
57
    First step to configure the module is making sure your user has access to the settings options of CDM Dataportal module.
58
    You can find the configurations options under <Administer-\>Site Configuration-\>CDM Dataportal>. Once you are in the
59
    configuration site you will see four different sections:
60

  
61

  
62

  
63

  
64
*General
65
    
66
    Drupal's CDM Dataportal module dialogues with the <CDM Server> asking for taxa data 
67
   	and classification of taxa. The first thing the <CDM Dataportal module> needs to know
68
   	is where is the CDM Server located in order to access it. Such parameters are configurable
69
    via the general tag of the settings.
70
    
71
    The general settings has enough documentation that explains itself. However the same
72
    documentation with some extra details is avaible
73
    <a href="./?q=admin/help/cdm_dataportal_general" title="General">here</a>
74
    as one html site. If you prefer to go directly to the general settings just click 
75
    <Administer-\>Site Configuration-\>CDM Dataportal>
76
    to start the configuration click here. 
77
	
78

  
79
	
80
*Geo & Map
81
    
82
    As with <CDM Server>, CDM Dataportal module also dialogues with a Map Server to 
83
    generate all the maps displayed on your web site. Again the module needs to know where
84
    the map server is located and this parameter as well as others related with the maps
85
    appaerance like map legends, map size, map background ... are configurable via
86
    {{{./?q=admin/settings/cdm_dataportal/geo}Geo & Map settings}}.
87
    This configuration site also explain all the configurable options itself. Same documentation with some extra details is avaible
88
    <a href="./?q=admin/help/cdm_dataportal_geo" title="Geo & Map">here</a> as one html site.
89
   	 	
90

  
91
	 	
92
*Layout		
93
    
94
    <a target="_blank" href="./?q=admin/settings/cdm_dataportal/layout" >Here</a> 
95
    you will find the settings for configuring the layout issues such pictures size or
96
    number of search results to show. Layout section itself contains three subsections; 
97
    <a target="_blank" href="./?q=admin/settings/cdm_dataportal/layout/taxon">Taxon Layout Settings</a>,
98
    <Administer-\>Site Configuration-\>CDM Dataportal-\>Layout-\>Search> and
99
    <Administer-\>Site Configuration-\>CDM Dataportal-\>Layout-\>Media>. 
100
    Each one of the listed links forward you to the settings configuration site where each site explains 
101
    itself the different options.
102
	
103
	
104
    
105
	A html site with more level of details is available 
106
	<a target="_blank" href="./?q=admin/settings/cdm_dataportal_layout">here</a>.
107
    
108

  
109
	
110
*Cache
111
    
112
    It is possible to increase the portal time response when serving taxa sites. The mechanism 
113
    is quite simple. It works caching all taxa sites available in your portal in a way that when
114
    a user wants to visit new taxa, the module will not create the new taxon site from scratch.
115
    Instead of that the taxon site will be loaded from the cache and therefore will be no
116
    dialogue with the CDM Server. 		 
117
    
118
		 
119
    
120
    <a href="./?q=admin/help/cdm_dataportal_cache.html" title="Cache">Here</a>
121
    you can read the cache configuration help or much better go directly to the
122
    {{{./?q=admin/help/settings/cdm_dataportal/cachesite}cache settings site}}.
123
    
124

  
125

  
site/apt/getting-started.apt
1
Developing with Drupal
2
    
3
    Drupal is a free software package that allows anyone to easily publish, 
4
    manage and organize a wide variety of content on a website. Hundreds of 
5
    thousands of people and organizations are using Drupal to power an 
6
    endless variety of sites.
7
    
8
    CDM Dataportal have been developed with Drupal version 5. If you want to
9
    learn or experience more about Drupal visit the 
10
    {{{http://drupal.org}Drupal's oficial site}}.
11
    If you already know what Drupal is and you want to configure the CDM 
12
    Dataportal module to interacte with your CDM Server visit our 
13
    {{{http://wp5.e-taxonomy.eu/cdm-setups/?q=node/17}CDM Setup->Group Installation}}
14
    
15
Enviroment Setup
16

  
17
    The development enviroment here described is based on following elements 
18
    technologies Drupal + Apache + Php + MySQL + Eclipse.
19
    
20
    For windows  {{{http://dev.e-taxonomy.eu/trac/wiki/DeveloperEnvironmentSetup}Windows 1}} and
21
    {{{http://dev.e-taxonomy.eu/trac/wiki/InstallingDrupal}Windows 2}}. For Os X 
22
    {{{http://dev.e-taxonomy.eu/trac/wiki/DeveloperEnvironmentSetupOsX}Apple}}
23

  
24
External Resources
25

  
26
   Some useful resources for developers are the following
27
   
28
   *Drupal
29
   
30
      Useful documentation for Drupal can be founded on the Drupal official web sites, such as
31
   
32
     *{{{http://drupal.org}Drupal Home}}
33
     
34
     *{{{api.drupal.org}Drupal API}}, or
35
     
36
     *{{{http://drupal.org/documentation}Drupal Documentation}} (with installation guides included).
37
          
38
   *JavaScript
39
     
40
     *{{{http://docs.jquery.com/Main_Page}JQuery}}
41
   
42
   
43
   *Firefox
44
   
45
      Useful Firefox addons for developers:
46
   
47
     *{{{https://addons.mozilla.org/de/firefox/addon/1843/}Firebug}}
48
     
49
     *{{{https://addons.mozilla.org/de/firefox/addon/60/}Web Developer Toolbar}}
50
     
51
     *{{{https://addons.mozilla.org/en-US/firefox/addon/10869/}JSONView}}
site/apt/index.apt
1
EDIT CDM Data Portal
2

  
3
    The EDIT Data Portal publishes taxonomic data data hosted in a CommunityStore
4
    either to a closed community or to the public at large. It has been implemented
5
    as a module for the content management system Drupal. The term
6
    {{{http://en.wikipedia.org/wiki/Web_content_management_system}content managent system}}
7
    is somewhat misleading here: since the actual content is stored and managed
8
    by the CDM, ensuring scientific accuracy and reusability of data. Drupal offers
9
    a great deal of flexibility and can be extended almost indefinitely, making it
10
    possible to adapt the EDIT Data Portal to the individual needs of a community.
11
    Custom web pages, forums, and blogs are only a few of Drupal's capabilities
12
    available out of the box, and there is practically no limit to the number of
13
    modules that can be added to enhance a site with for example image galleries.
14
    The layout and look and feel of the application can be easily adapted to fit
15
    any taste.
16

  
17
    The EDIT Data Portal supports zoological and botanical names (support for viral
18
    and bacterial names should be available soon), as well as multiple concurrent
19
    taxonomies. Rules as specified by the nomenclatural codes ICNAFP (formerly ICBN) and ICZN are
20
    built into the CDM, ensuring that taxon names conform to these standards.
21

  
22
    User interface design was guided by the following design principles: provide
23
    easy access to all taxa and names; display all relevant information in one
24
    place where possible; and reduce complexity without compromising scientific
25
    accuracy. A challenge particular to taxonomy is keeping the user from losing
26
    his or her bearings while navigating through vast taxonomic trees; to this
27
    end, a sophisticated taxonomic tree browser has been developed to reduce
28
    confusion and make daily work with such trees more productive. A search
29
    function provides an additional way to access taxa.
30

  
31
    Each taxon is represented by an individual page, which displays the list
32
    of synonyms, related taxa, occurrences, descriptions, media, and more. The
33
    list of homotypic and heterotypic synonyms is ordered historically and grouped
34
    by types; its layout resembles that found in printed publications. Images of
35
    protologues and of type specimens are linked directly from taxon names and
36
    synonym lists. In addition, taxon pages will allow users to contribute
37
    annotations as text or images.
38

  
39
    Currently, EDIT Data Portals and CDM Community Stores are used to store and
40
    publish the work of the EDIT exemplar groups focusing on the taxonomic groups
41
    Cichorieae, Diptera and Palmae. Links to the demosites are found below.
42

  
43

  
44
Drupal
45

  
46
    The open source content management system Drupal becomes more and more widely
47
    used in the area of biodiversity informatics. This popularity is not only
48
    due to its capabilities to just manage content for
49
    websites. The genius of what the Drupal community has done, is to reduce all
50
    of the aspects of social software to the core and then build a platform that
51
    could be infinitely extended to allow the assembly of almost any styles of
52
    online social interaction. During the past years the community contributed
53
    over 3000 different modules extending the Drupal core and thus on one hand
54
    providing a highly flexible construction kit and on the other hand showing by
55
    many examples that nearly everything is possible, perhaps only limited by the
56
    human imagination.
57

  
58
    The EDIT Data Portal has been developed as a drupal module to take the
59
    advantage of the community support and already available resources. Since we
60
    offer CDM Data Portal as a package with drupal together it is not necessary
61
    to spend extra time learning about drupal.
62

  
63
~~Constructing the EDIT platform for cybertaxonomy
64

  
65
~~   Drupal is used to build up
66
~~   general web applications like forums, blogs, a central repository for users
67
~~   and taxonomists, the Experts Database and a software tracker and rating
68
~~   system. Last but not least also taxonomy related software like the
69
~~   Scratchpads and the CDM DataPortal is based on this system.
70
~~
71
~~   The CDM DataPortal is using Drupal as an application framework to publish
72
~~   taxonomic treatments to a closed community or to the public. The treatments,
73
~~   stored in database are, accessible via web services to which the
74
~~   CDM DataPortal connects to fetch the information to be displayed.
75
~~   Furthermore does the CDM DataPortal act as an easy to use web service
76
~~   allowing reusing fragments of its pages in other contexts already rendered
77
~~   as HTML.
78
~~
79
~~   The new TDWG standards architecture relies among others on semantic web
80
~~   technologies, which are tailored around a data format called RDF.
81
~~   Unfortunately there has always been a lack of common tools for easy
82
~~   processing and visualising data provided by the RDF based ontology.
83
~~
84
~~   Since the last big version switch to Drupal 6, some very interesting
85
~~   modules are being simmered, which will allow storing, aggregating and
86
~~   processing RDF data, making Drupal an highly interesting candidate for
87
~~   building applications which benefit from the new semantic capabilities
88
~~   of the TDWG standards architecture. Drupal is promising not only because
89
~~   of the interesting technical implementations but also because of its
90
~~   popularity and support from a vast community.
91
~~
92
~~   Some RDF related modules are already available although most of them
93
~~   still are in alpha status. One of these incorporates RDF taxonomies
94
~~   into Drupal, another one is actually an ensemble of modules providing
95
~~   comprehensive RDF functionality and interoperability.
96
~~
97
~~   With Exhibit and Potluck the SIMILE (Semantic Interoperability of
98
~~   Metadata and Information in unLike Environments) project of the MIT
99
~~   has developed interesting tools for visualizing, browsing and mixing
100
~~   data. Exhibit for example displays structured data in the form of rich
101
~~   visualizations that can be searched, filtered and sorted using faceted
102
~~   browsing. The Exhibit module will bring these abilities to Drupal.
103
~~
104
~~   Tools for efficiently using the TDWQG RDF ontology are in reach and
105
~~   await their evaluation. So the time has come to find out what is
106
~~   possible to vision the next generation biodiversity network tools.
site/apt/installation.apt
1
CDM Server Installation
2

  
3
   CDM Dataportal module publishes the data of the CDM Server,
4
   therefore an already working CDM Server is a prerequisite for retrieving the
5
   data to publish. To learn more about the CDM Server visit the {{{http://wp5.e-taxonomy.eu/cdm-server/}CDM Server's web}}.
6
   To install a CDM Server instance follow the instructions at our {{{http://wp5.e-taxonomy.eu/node/2}cdm-setups web}}.
7

  
8
Drupal Installation
9

  
10
   Since the CDM Dataportal is a drupal module you will need to install at first Drupal
11
   (currently we are working with <<Drupal 7>>). There are two different possibilities of
12
   installing the CDM Data Portal. The first one is installing Drupal 7 and afterwards to
13
   enable the CDM Data Portal Module. The second and recomended is to download Drupal with
14
   the CDM Data Portal Module installed and already enable to use.
15

  
16
   For the first option visit {{{http://drupal.org}Drupal's site}} for more information.
17

  
18
   You can download the CDM Data Portal module from our download site.
19
   For the second option follow the instruction at our
20
   {{{http://cybertaxonomy.eu/node/7}cdm-setups web}}.
21

  
22
CDM Data Portal Configuration
23

  
24
   Once you have been installed Drupal and CDM Data Portal Module is enabled you will find
25
   how to configure the CDM Data Portal Module inside Drupal itself.
26

  
27
   Open a browser and go to your drupal site. Once you are in your drupal web site go to
28
   <<Configuration>CDM Data Portal>> where you will find a general documentation for
29
   configuring the module properly as well as links to specific configurations sites
30
   and documentation. We recommend to read and understand the documentation before starting
31
   to configure the module.
32

  
33
FAQ and contact
34

  
35
   If you have any problems or questions do not hesitate to contact us and to read our
36
   famous answer and questions site.
37

  
38

  
39

  
site/apt/screenshots.apt
1
Examples
2

  
3
   It is possible to see the data portal in action, the following links contains some collections using it.
4
   
5
   *{{{http://wp6-cichorieae.e-taxonomy.eu/portal/}Cichorieae}} group of plants.
6
   
7
   *{{{http://www.palmweb.org}Palmae}} group of plants.
8
   
9
   *{{{http://160.45.63.151/dataportal/diptera/}Diptera}} group of flies and mosquitoes.
10
   
11
Screenshots
12

  
13
    The welcome site of the palmweb with the <<taxon tree>> (the classification box) and
14
    the <<search>> (the search box) at the link side of the page. On the 
15
    middle of the page is the welcome text.
16

  
17
[./images/palmae2.png] Figure caption
18

  
19
    
20
    The welcome site of the cichorieae with the <<taxon tree>> (the classification box),
21
    the <<search>> (the search box) and the <<user login>> at the link side of the page. On the 
22
    middle of the page is the welcome text.
23
    
24
[./images/cichorieae2.png] Figure caption
25

  
26

  
27
   A screenshot of the palmweb portal after performing a search for the string "Coc"
28
   
29
[./images/palmae5.png] Figure caption
30

  
31

  
32
   Screenshot of the <<Lactuca Alpina>> from cichorieae portal. We can see how a taxon 
33
   profil (general tab) page looks like with his <<profile picture>> and 
34
   <<distribution map>>. We can see the <<footnotes>> for the distribution references 
35
   (the small red numbers). Also the <<taxon tree>> is focused at the Lactuca Alpina
36
   taxon under Cichorieae->Lactucinae->Lactuca->L. alpina at the left side of the page.
37
   
38
[./images/cichorieae4.png] Figure caption
39

  
40
   Screenshot of the Crepis Mollis taxon from cichorieae portal. This is how the 
41
   synonymy tab looks like. The heterotypic synonyms are grouped and ordered by date.
42
   The footnotes are displayed at the end of the page and the red links 
43

  
44
[./images/cichorieae5.PNG] Figure caption
45

  
46
   The following screenshot is from one of the configuration pages of the data portal,
47
   it contains the instructions for a correct configuration. At the top right corner 
48
   are the different configurable options (general, geo & map, layout and cache).
49
   
50
[./images/settings1.PNG] Figure caption
site/fml/admin-faq.fml
1
<?xml version="1.0" encoding="UTF-8"?>
2
<faqs xmlns="http://maven.apache.org/FML/1.0.1"
3
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
4
  xsi:schemaLocation="http://maven.apache.org/FML/1.0.1 http://maven.apache.org/xsd/fml-1.0.1.xsd"
5
  title="Adminstration of the EDIT CDM Dataportal - Frequently Asked Questions"
6
  toplink="false">
7

  
8
  <part id="general">
9
    <title>Layout &amp; visibility of elements</title>
10

  
11
    <faq id="autherinfo-get-rid-off">
12
      <question>
13
        How can I turn of authoring information like "<em>Fri, 04/15/2011 - 12:23 — Anonymous</em>" which appears on some pages?
14
      </question>
15
      <answer>
16
        <p>Display of the 'post information' can be configured in the administration area of the DataPortal.
17
        Login and go to Site building  &gt; Themes &gt; Configure (admin/build/themes/settings)
18
        and toggle the check boxes below the heading '<em>Display post information on</em>' according to your wishes.
19
        </p>
20
      </answer>
21
    </faq>
22

  
23
  </part>
24
  <part id="cdm">
25
    <title>Working on CDM data</title>
26

  
27
    <faq id="cdm_changes_not_visible">
28
      <question>
29
        Why do the changes I made on the CDM data not appear in the portal? Why do they not appear immediately but only after some time?
30
      </question>
31
      <answer>
32
        <p>Drupal provides a mechanism for caching data which is then displayed on the web pages to avoid querying the data base for every site request. The cache will be updated from time to time.
33
        This is the default setting for the 'Anonymous' user (not logged in). If you log in the caching will be disabled and the data should be up-to-date. 
34
        You can also clear the cache to update it for the 'Anonymous' user. In the administration menu go to Configuration &gt; Development &gt; Performance &gt; Clear all caches.
35
        </p>
36
      </answer>
37
    </faq>
38

  
39
  </part>
40

  
41
</faqs>
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