build.xml

<!-- Genoogle: Similar DNA Sequences Searching Engine and Tools. (http://genoogle.pih.bio.br) -->
<!-- Copyright (C) 2008,2009  Felipe Fernandes Albrecht (felipe.albrecht@gmail.com)           -->
<!--                                                                                          -->
<!-- For further information check the LICENSE file.                                          -->

<project name="genoogle" default="compile" basedir=".">
	<description> Build script for Genoogle project</description>


	<target name="init" description="Checks environment and setup variables">

		<!-- Check the current system classpath for JUnit -->
		<available classpath="${java.class.path}" classname="junit.framework.TestCase" property="junit.present" />

		<!-- Check for JUnit support in Ant (only in >= 1.3) -->
		<available classpath="${java.class.path}" classname="org.apache.tools.ant.taskdefs.optional.junit.JUnitTest" property="junit.support" />

		<property name="name" value="Genoogle" />
		<property name="version" value="0.80" />

		<property name="docs.dir" location="./doc/javadoc" />
		<property name="src.dir" location="./src" />
		<property name="src_tmp.dir" location="src_tmp/" />

		<property name="tests.src.dir" location="./tests" />

		<!-- Main build directory -->
		<property name="build.dir" location="./ant-build" />
		<property name="build.classes.dir" location="${build.dir}/classes" />

		<!-- Jar configuration -->
		<property name="manifest.dir" location="./manifest" />
		<property name="jar.genoogle" location="${build.dir}/genoogle.jar" />
		<property name="targz.genoogle" location="genoogle.tar.gz" />
		<property name="jar.genoogle-src" location="genoogle-src.jar" />
		<property name="jar.genoogle-javadoc" location="genoogle-javadoc.jar" />



		<!-- Javac properties -->
		<property name="javac.deprecation" value="false" />
		<property name="javac.source" value="6" />
		<property name="javac.target" value="6" />

		<!-- Javadoc properties -->
		<property name="build.docs" location="${build.dir}/docs" />
		<property name="packages" value="bio.pih.*" />

        <!-- Packing info -->
		<property name="packing.dir" location="packing/genoogle" />


		<!-- Tests properties -->
		<property name="reports.tests" value="${build.dir}/tests/report" />

		<echo message="JUnit present:                      ${junit.present}" />
		<echo message="JUnit supported by Ant:             ${junit.support}" />
		<echo message="Keep it up, rock 'n' roll, good music save your soul" />
	</target>

	<!-- Prepares the biojava source code -->
	<target name="prepare" depends="init">
		<mkdir dir="${build.dir}" />
		<mkdir dir="${build.classes.dir}" />
		<mkdir dir="${build.docs}" />
		<mkdir dir="${reports.tests}" />
	</target>

	<!-- Compile the Genoogle Sources -->
	<target name="compile" depends="prepare">
		<javac includeantruntime="false" encoding="ISO-8859-15" srcdir="${src.dir}" destdir="${build.classes.dir}" depend="${javac.depend}" deprecation="${javac.deprecation}" source="${javac.source}" target="${javac.target}"  debug="true" debuglevel="lines,vars,source">
			<classpath>
				<fileset dir="./lib">
					<include name="**/*.jar" />
				</fileset>
			</classpath>
		</javac>
	</target>

	<!-- Generate the Genoogle jar file -->
	<target name="jar" depends="compile">
		<jar jarfile="${jar.genoogle}" manifest="${manifest.dir}/genoogle.txt">
			<fileset dir="${build.classes.dir}" />
		</jar>
	</target>

	<!-- Compile the Genoogle Sources -->
	<target name="tests-compile" depends="jar">
		<javac includeantruntime="false" encoding="ISO-8859-15" srcdir="${tests.src.dir}" destdir="${tests.src.dir}" depend="${javac.depend}" deprecation="${javac.deprecation}" source="${javac.source}" target="${javac.target}"  debug="true" debuglevel="lines,vars,source">
			<classpath>
				<fileset dir="./lib">
					<include name="**/*.jar" />
				</fileset>
				<fileset dir="${build.dir}">
					<include name="**/*.jar" />
				</fileset>
			</classpath>
		</javac>
	</target>

	<!-- Generate the Genoogle source jar file -->
	<target name="src_jar" depends="init">
		<mkdir dir="${src_tmp.dir}"/>

		<copy todir="${src_tmp.dir}">
			<fileset dir="${src.dir}">
				<exclude name="**/.svn"/>
			</fileset>
		</copy>
		<jar jarfile="${jar.genoogle-src}">
			<fileset dir="${src_tmp.dir}"/>
		</jar>
		<delete dir="${src_tmp.dir}"/>
    </target>

	<!-- Pre processing to generate the jar file-->
	<target name="packing_dir" depends="jar">
		<mkdir dir="${packing.dir}"/>

		<copy file="${jar.genoogle}" tofile="${packing.dir}/genoogle.jar"/>

                <copy file="format_db.sh" tofile="${packing.dir}/format_db.sh"/>

		<copy file="run_console.sh" tofile="${packing.dir}/run_console.sh"/>
		<copy file="run_web.sh" tofile="${packing.dir}/run_web.sh"/>
		<copy file="run_standalone_web.sh" tofile="${packing.dir}/run_standalone_web.sh"/>

		<copy file="./conf/genoogle_default.xml" tofile="${packing.dir}/conf/genoogle.xml"/>
		<copy file="./conf/log4j.properties" tofile="${packing.dir}/conf/log4j.properties"/>

		<mkdir dir="${packing.dir}/files/fasta"/>
		<copy file="files/fasta/AE000657.fna" tofile="${packing.dir}/files/fasta/AE000657.fna"/>

		<copy todir="${packing.dir}/lib">
			<fileset dir="./lib"/>
		</copy>

		<copy todir="${packing.dir}/webapps">
			<fileset dir="./webapps">
				<exclude name="**/work/"/>
			</fileset>
		</copy>
	</target>

	<!-- create the genoogle.tar.gz file -->
	<target name="packing" depends="packing_dir">
		<tar destfile="genoogle.tar" basedir="./packing"/>
		<gzip destfile="${targz.genoogle}" src="genoogle.tar"/>

		<delete file="genoogle.tar"/>
		<delete dir="./packing"/>
	</target>


	<!-- Creates the API documentation -->
	<target name="javadoc" depends="compile" description="Creates the API documentation">
		<javadoc encoding="ISO-8859-1" packagenames="${packages}" sourcepath="${src.dir}" destdir="${build.docs}" author="true" version="true" use="true" source="1.6" windowtitle="${name}-${version} API" doctitle="${name}-${version}" maxmemory="192m">

			<classpath>
				<fileset dir="./lib">
					<include name="**/*.jar" />
				</fileset>
			</classpath>

			<link href="http://java.sun.com/javase/6/docs/api/" offline="false" />

			<excludepackage name="bio.pih.tests.*" />

			<group title="Indexer" packages="bio.pih.indexer" />
			<group title="Scheduler" packages="bio.pih.scheduler" />
			<group title="Search" packages="bio.pih.search" />
			<group title="Seq" packages="bio.pih.seq:bio.pih.seq.*" />
			<group title="util" packages="bio.pih.util" />

		</javadoc>
	</target>

	<!-- Create the jar file with the API documentation -->
	<target name="javadoc_jar" depends="javadoc">
		<jar jarfile="${jar.genoogle-javadoc}">
			<fileset dir="${build.docs}"/>
		</jar>
	</target>

	<!-- Runs tests if the Ant optional JUnit support is available -->
	<target name="run-tests" depends="compile, tests-compile">
		<property name="test.subtree" value="**" />
		<echo message="Running tests:           ${test.subtree}" />

		<echo message="${build.classes.dir}" />
		<echo message="${classpath}" />
		<echo message="${java.class.path}" />

		<junit fork="true" maxmemory="128m" printsummary="yes" haltonfailure="no">
			<formatter type="plain" usefile="true" />
			<classpath>
				<!-- main classes from build -->
				<pathelement path="${build.classes.dir}" />
				<!-- classes specified in this file -->
				<pathelement path="${classpath}" />
				<!-- classes specified in system classpath -->
				<pathelement path="${java.class.path}" />
				<pathelement path="${tests.src.dir}" />
				<fileset dir="./lib">
					<include name="**/*.jar" />
				</fileset>
			</classpath>

			<!-- The junit task doesn't support 'if' so we test for JUnit here -->
			<batchtest fork="yes" todir="${reports.tests}">
				<fileset dir="${tests.src.dir}">
					<include name="${test.subtree}/*Test*.class" />
					<include name="${test.subtree}/*TestSuite*.class" />
					<exclude name="**/Abstract*Test.class" />
				</fileset>
			</batchtest>
		</junit>
	</target>

	<!-- Create a zip with all genoogle libs -->
	<target name="libs_package">
		<zip destfile="genoogle-libs.zip"
       		basedir="./lib"
	        excludes="**/.svn"
		  />
	</target>


	<target name="all" depends="packing,libs_package,javadoc_jar,src_jar"/>


</project>