build.xml

<?xml version="1.0" encoding="utf-8"?>

<project name="StarBiochem" default="build" basedir=".">
	<taskdef name="apt" classname="org.apache.tools.ant.taskdefs.Apt" />
		<property name="src" value="${basedir}/src" />
	<property name="build" value="${basedir}/build" />
	<property name="preprocess.dir" value="${basedir}/generated_src" />

	<path id="apt.classpath">
		<pathelement path="${basedir}/bin" />
		<pathelement path="../java3d/bin" />
		<pathelement path="lib/jaxrpc.jar" />
		<pathelement path="lib/Jmol.jar" />
		<pathelement path="../STAR_SignalSystem/" />
		<pathelement path="../Plugin-Commons/bin" />
		<pathelement path="../CommonLibrariesBin/swing/miglayout15-swing.jar" />
		<pathelement path="../Plugin-Commons/lib/junit-4.1.jar" />
		<pathelement path="../CommonLibrariesBin/swing/swing-worker.jar" />
		<pathelement path="../CommonLibrariesBin/microsoft_office/poi/poi-3.2-FINAL-20081019.jar" />
		<pathelement path="../CommonLibraries/cos-05Nov2002/lib/cos.jar" />
		<pathelement path="../CommonLibrariesBin/lib/json.jar" />		
		<pathelement path="../CommonLibrariesBin/jetty/jetty-all-7.2.2.v20101205.jar" />		
		<pathelement path="../CommonLibrariesBin/jetty/servlet-api-2.5.jar" />
	</path>
	
	
	<target name="build" depends="apt,compile,jar">
	</target>

	<target name="clean" depends="">
		<echo>Force regenerate</echo>
		<delete>
			<fileset dir="build">
				<include name="**/*.class"/>
			</fileset>
			<fileset dir="generated_src">
				<include name="**/*.class"/>
			</fileset>
			<fileset dir="src">
				<include name="**/*.class"/>
			</fileset>			
		</delete>
	</target>
	
	<target name="apt" depends="clean">
		<echo>Precompiling</echo>
		
		<apt srcdir="${src}" debug="on" includes="**/*.java" classpathref="apt.classpath" factory="star.annotations.ProcessorFactory" preprocessdir="${preprocess.dir}" fork="on" target="1.5" source="1.5"/>
	</target>

	<target name="compile" depends="apt">
		<echo>Updating build date</echo>

		<echo>Compiling</echo>
		<javac srcdir="${src};${preprocess.dir}" classpathref="apt.classpath" destdir="${build}" debug="on" includes="**/*.java" optimize="on" target="1.5" source="1.5" includeantruntime="false" />
	</target>
	
	<target name="messagesbuilder" >
		<java classpathref='apt.classpath' classname="xls.MessagesBuilder" ></java>
		<echo>Working!!</echo>
	</target>

	<target name="jar" depends="compile">
		<echo>Creating JAR</echo>
		<jar destfile="biochem.jar">
			<fileset dir="build" id="build">
				<include name="**" />
				<exclude name=".classpath" />
				<exclude name=".project" />
				<exclude name=".settings" />
			</fileset>
			<fileset dir="src" id="pref">
				<include name="**/app/**.properties" />
				<include name="**/app/**.properties" />
			</fileset>
			<fileset dir="src" id="jmolscripts">
				<include name="**/JmolScripts/**" />
			</fileset>
			<fileset dir="bin" id="interfaces">
				<include name="**/interfaces/**" />
			</fileset>
			<fileset dir="../STAR_SignalSystem">
				<include name="**" />
				<exclude name=".classpath" />
				<exclude name=".project" />
				<exclude name=".settings" />
				<exclude name="SignalSystem.jar"/>
			</fileset>

		</jar>
	</target>

	<target name="buildsamples" depends="jar">
		<echo>Creating .jmol files from .pdb files</echo>
		<echo>and Loading .jmol files and .pdb files</echo>
		
		<echo> Each of the executables in the samples target should be run before a release of StarBiochem</echo>
		
		<!--
		<echo> Show help message on standard out </echo>
		<exec executable="java" dir="src">
			<arg value="-Xmx999m"/>
			<arg value="-classpath" />
			<arg value="../biochem.jar" />
			<arg value="app.StarBiochemMain"/>
			<arg value="-help"/>
		</exec>
		-->
		
		<!--
		<echo> Load 1A3N.pdb </echo>
		<exec executable="java" dir="src">
			<arg value="-Xmx999m"/>
			<arg value="-classpath" />
			<arg value="../biochem.jar:../lib/Jmol.jar" />
			<arg value="app.StarBiochemMain"/>
			<arg value="-load"/>
			<arg value="../src/SamplePDBfiles/Water.pdb"/>
		</exec>
		-->

		<!--
		<echo> Load 1A3N.jmol </echo>
		<exec executable="java" dir="src">
			<arg value="-Xmx999m"/>
			<arg value="-classpath" />
			<arg value="../biochem.jar:../lib/Jmol.jar" />
			<arg value="app.StarBiochemMain"/>
			<arg value="-load"/>
			<arg value="../src/SampleJMOLfiles/1A3N.jmol"/>
		</exec>
		-->

		<!--
		<echo> Load all the pdb files in SamplePDBfiles </echo>
		<exec executable="java" dir="src">
			<arg value="-Xmx999m"/>
			<arg value="-classpath" />
			<arg value="../biochem.jar:../lib/Jmol.jar" />
			<arg value="app.StarBiochemMain"/>
			<arg value="-load"/>
			<arg value="../src/SamplePDBfiles"/>
		</exec>
		-->

		<!--
		<echo> Load all the jmol files in SampleJMOLfiles </echo>
		<exec executable="java" dir="src">
			<arg value="-Xmx999m"/>
			<arg value="-classpath" />
			<arg value="../biochem.jar:../lib/Jmol.jar" />
			<arg value="app.StarBiochemMain"/>
			<arg value="-load"/>
			<arg value="../src/SampleJMOLfiles"/>
		</exec>
		-->

		<!--
		<echo> Load 1BA4.pdb and create 1BA4.jmol in SampleJMOLfiles </echo>
		<exec executable="java" dir="src">
			<arg value="-Xmx999m"/>
			<arg value="-classpath" />
			<arg value="../biochem.jar:../lib/Jmol.jar" />
			<arg value="app.StarBiochemMain"/>
			<arg value="-create"/>
			<arg value="../src/SamplePDBfiles/1BA4.pdb"/>
			<arg value="../src/SampleJMOLfiles"/>
		</exec>
		-->

		<echo> Load all the pdb files in SamplePDBfiles and create jmol files from them in SampleJMOLfiles </echo>
		<exec executable="java" dir="src">
			<arg value="-Xmx5999m"/>
			<arg value="-classpath" />
			<arg value="../biochem.jar:../lib/Jmol.jar" />
			<arg value="app.StarBiochemMain"/>
			<arg value="-create"/>
			<arg value="../src/SamplePDBfiles"/>
			<arg value="../src/SampleJMOLfiles"/>
		</exec>

	</target>	

	<target name="packedsamples" depends="buildsamples">
		<echo>Creating jar from .jmol files </echo>
		
		<exec executable="jar">
			<arg value="cfv0" />
			<arg value="samples.jar" />
			<arg value="-C"/>
			<arg value="src/SampleJMOLfiles"/>
			<arg value="."/>
		</exec>

		<exec executable="jar">
			<arg value="cf" />
			<arg value="PackedSamples.jar" />
			<arg value="samples.jar"/>
		</exec>

	</target>

	<target name="jarsamples" >
		<echo>Creating jar from .jmol files </echo>
		
		<exec executable="jar">
			<arg value="cfv0" />
			<arg value="samples.jar" />
			<arg value="-C"/>
			<arg value="src/SampleJMOLfiles"/>
			<arg value="."/>
		</exec>

		<exec executable="jar">
			<arg value="cf" />
			<arg value="PackedSamples.jar" />
			<arg value="samples.jar"/>
		</exec>

	</target>
	

	<target name="publish" depends="jar">
		<echo>Publishing and signing</echo>
		<echo>	To publish:
	Go to menu: Eclipse->Preferences
		In left menu click on: Ant->Runtime->Properties 
			Add Property
				Name: publish_user
				Value: your root Kerberos Principal
		</echo>

		<exec executable="kinit">
			<arg value="${publish_user}" />
		</exec>

		<exec executable="scp">
				<arg value="lib/Jmol.jar" />
				<arg value="${publish_user}@starapp.mit.edu:/home/star/star/media/uploads/star/jar/biochem3/Jmol.jar" />
			</exec>
		<exec executable="scp">
			<arg value="biochem.jar" />
			<arg value="${publish_user}@starapp.mit.edu:/home/star/star/media/uploads/star/jar/biochem3/biochem.jar" />
		</exec>
			<exec executable="scp">
				<arg value="PackedSamples.jar" />
				<arg value="${publish_user}@starapp.mit.edu:/home/star/star/media/uploads/star/jar/biochem3/PackedSamples.jar" />
			</exec>
		<exec executable="ssh">
			<arg value="starapp.mit.edu" />
			<arg value="-l" />
			<arg value="${publish_user}" />
			<arg value="/home/star/build/sign_biochem3.sh" />
		</exec>
	</target>

</project>