build.xml

<project name="Mauve" default="compile">
	<description>
	This buildfile tells the ant build tool how to build and package the Mauve Java 
	visualization environment.
	</description>
	
	<!-- set the release version, unless making a snapshot -->
	<target name="release_properties" unless="env.MAUVE_SNAPSHOT">
		<property name="release.version" value="2.4.1"/>
	</target>

	<!-- deployment locations for production ASAP integration -->
	<property name="deploy.asapdir" value="/srv/asap/htdocs/mauve" />
	<property name="asap.codebase" value="http://asap.ahabs.wisc.edu/asap/mauve/" />
	<!-- deployment locations for devel ASAP integration -->
	<!--
	<property name="deploy.asapdir" value="/srv/asap-devel/htdocs/mauve" />
	<property name="asap.codebase" value="http://asap.ahabs.wisc.edu/asap-devel/mauve/" />
	-->
	<!-- deployment locations for standalone releases -->
	<property name="deploy.address" value="darlini8@darlinglab.org" />
	<property name="deploy.bareaddress" value="darlinglab.org" />
	<property name="deploy.username" value="darlini8" />
	<property name="deploy.win32.keyfile" value="C:\Documents and Settings\koadman\plonk.ppk" />
	<property name="deploy.serverdir" value="/home3/darlini8/www/mauve/downloads" />
	<property name="key.alias" value="mauve" />
	<property name="key.keystore" value="C:\Documents and Settings\koadman\My Documents\mauve-keystore" />
	
	<!-- set global properties for this build -->
	<property name="src" location="src"/>
	<property name="build" location="bin"/>
	<property name="dist"  location="dist"/>
	<property name="ext" location="ext"/>
 	<property name="support" location="build_support"/>

	<!-- Make datestamp for update checks -->
	<tstamp>
		<format property="datestamp" pattern="yyyyMMdd" />
	</tstamp>
	
	<!-- increment the build number-->
	<buildnumber/>
	
	<!-- get any environment variables -->	
	<property environment="env" />

	<!-- osxant.jar creates Mac OS X disk images -->
	<taskdef name="dmg" classname="com.amberarcher.ant.osx.DmgTask">
		<classpath>
			<pathelement path="${support}/osxant.jar"/>
		</classpath>
	</taskdef>
	<!-- maverick-ant.jar supports secure FTP for deployment -->
    <taskdef name="ssh" classname="com.sshtools.ant.Ssh" classpath="${support}/maverick-ant.jar"/>
	<taskdef resource="net/sf/antcontrib/antcontrib.properties">
		<classpath>
			<pathelement path="${support}/ant-contrib-1.0b3.jar"/>
		</classpath>
	</taskdef>
	
	<target name="init">
		<!-- Create the time stamp -->
		<tstamp/>
	</target>
	
	<!-- set the timestamp if building a snapshot -->
	<target name="snapshot_properties" if="env.MAUVE_SNAPSHOT">
		<property name="release.version" value="${datestamp}"/>
	</target>

	<!-- set the version number -->
	<target name="create_properties" depends="snapshot_properties,release_properties">
		<propertyfile 
			file="${src}/version.properties"
			comment="Stores version and build information">
			<entry key="release.version" value="${release.version}"/>
			<entry key="build.number" value="${build.number}"/>
			<entry key="build.timestamp" value="${datestamp}"/>
		</propertyfile>
	</target>
	  
	<target name="compile" depends="init,create_properties" description="compile the java source">
		<!-- Create the build directory structure used by compile -->
		<mkdir dir="${build}" />
				
		<!-- Build all java source files -->
		<javac
			classpath="
				${ext}/core-1.9.2-SNAPSHOT.jar;
				${ext}/bytecode-1.9.2-SNAPSHOT.jar;
				${ext}/gui-1.9.2-SNAPSHOT.jar;
				${ext}/commons-cli-1.2.jar;
				${support}/junit.jar;
				${ext}/zeus-jscl.jar;
				${ext}/goose.jar;
				${ext}/ant-1.7.1.jar;
				${ext}/dbus-2.6.jar;
				${ext}/jebl-0.4.jar;
				${ext}/unix-0.5.jar"
			srcdir="${src}"
			destdir="${build}"
			target="1.6"
			source="1.6"
		>
			<compilerarg value="-Xbootclasspath/p:${env.JAVA_6_RT_PATH}"/>
		</javac>
		<mkdir dir="${build}/images"/>
		<copy todir="${build}/images">
			<fileset dir="${src}/images"/>
		</copy>
		<copy file="${src}/version.properties" todir="${build}"/>
	</target>

	<target name="rmic" depends="compile">
		<rmic base="${build}" classname="org.gel.mauve.remote.RemoteControlImpl" />
	</target>
	
	<target name="jar" depends="rmic">
		<!-- Make list of external dependencies -->
		<fileset dir="${ext}" id="ext.jars">
			<include name="**/*.jar"/>
		</fileset>
		<pathconvert pathsep=" " property="ext.path" refid="ext.jars">
			<mapper>
				<chainedmapper>
					<mapper type="flatten" />
					<mapper type="glob" from="*.jar" to="ext/*.jar"/>
				</chainedmapper>
			</mapper>
		</pathconvert>
		
	    <!-- Put everything in ${build} into the Mauve.jar file -->
		<delete file="Mauve.jar"/>
	    <jar jarfile="Mauve.jar">
			<fileset dir="${build}" includes="**/*" />

	    	<!-- Create a manifest file to tell java the name of the main class -->
			<manifest>
				<attribute name="Main-Class" value="org.gel.mauve.gui.Mauve"/>
				<attribute name="Built-By" value="${user.name}"/>
				<attribute name="Class-Path" value="${ext.path}" />
				<section name="common">
					<attribute name="Specification-Title" value="Mauve"/>
					<attribute name="Specification-Version" value="${version}"/>
					<attribute name="Specification-Vendor" value="Aaron E. Darling"/>
					<attribute name="Implementation-Title" value="Mauve"/>
					<attribute name="Implementation-Version" value="${version} ${TODAY}"/> 
					<attribute name="Implementation-Vendor" value="Aaron E. Darling"/>
				</section>
			</manifest>
		 </jar>
	</target>
	
	<target name="appletjar" depends="rmic">
		<delete file="mauveApplet.jar" />
		<jar jarfile="mauveApplet.jar">
			<fileset dir="${build}">
				<include name="org/gel/mauve/remote/*" />
			</fileset>
		</jar>
	</target>

	

	

	<target name="checkkeyprops" unless="key.password">
		<fail message="key.password must be set on command line, using -Dkey.password=&lt;password&gt;" />
	</target>
	
	<target name="signjars" depends="checkkeyprops,jar,appletjar">
		<signjar jar="Mauve.jar" alias="${key.alias}" storepass="${key.password}" keystore="${key.keystore}" />
		<signjar jar="mauveApplet.jar" alias="${key.alias}" storepass="${key.password}" keystore="${key.keystore}" />
	</target>
	
	<target name="signextjars" depends="checkkeyprops">
		<signjar alias="${key.alias}" storepass="${key.password}" keystore="${key.keystore}">
			<fileset dir="./ext">
				<include name="*.jar" />
			</fileset>
		</signjar>
	</target>
	
	<target name="testdist" depends="signjars">
		<copy todir="C:\htdocs" file="Mauve.jar" />
		<copy todir="C:\htdocs" file="mauveApplet.jar" />
		<copy todir="C:\htdocs" file="./testdata/smallAlignment.jar" />
		<copy todir="C:\htdocs" file="./jws/index.html" />
		<copy todir="C:\htdocs" file="./jws/mauve.jnlp" />
	</target>
		
	<target name="dist" depends="jar,getChangeLog" description="generate the distribution" >
		<!-- Create the distribution directory -->
		<mkdir dir="${dist}" />
		
		<!-- Set the tarball OS name based on the build host OS -->
		<condition property="OSNAME" value="linux">
			<os name="Linux"/>
		</condition>
		<condition property="OSNAME" value="OSX">
			<os name="Mac OS X"/>
		</condition>

		<!-- Make the tarball -->
		<tar destfile="${dist}/mauve_${OSNAME}_${release.version}.tar.gz" compression="gzip">
			<!-- Copy various support files into the dist directory-->
			<tarfileset dir="." prefix="/mauve_${release.version}">
				<include name="Mauve.jar" />
				<include name="COPYING" />
				<include name="README" />
				<include name="ChangeLog.html" />
			</tarfileset>
			<tarfileset dir="linux-x64" prefix="/mauve_${release.version}/" mode="755">
				<include name="Mauve" />
			</tarfileset>
			<tarfileset dir="linux-x64" prefix="/mauve_${release.version}/linux-x64" mode="755">
				<include name="mauveAligner" />
				<include name="progressiveMauve" />
			</tarfileset>
			<tarfileset dir="${ext}" prefix="/mauve_${release.version}/ext" includes="*.jar" />
		</tar>
	</target>

	<taskdef name="bundleapp"
		classname="com.oracle.appbundler.AppBundlerTask"   
		classpath="build_support/appbundler-1.0.jar" />

<!-- Create a DMG - This only works on MacOSX (requires hdiutil) -->
<target name="dmg" depends="macdist" description="Create a DMG package for MacOSX (only works on MacOSX)">
    
    <!-- Set this property value to your application name -->
    <property name="app.name" value="Mauve-${release.version}"/>
    
    <!-- Set this property value to a directory where you can
     mount temporarily your images, for example /tmp -->
    <property name="mountdir"  value="/tmp"/>
    
    <!-- Delete previously created DMG -->
    <delete file="${dist}/${app.name}.dmg" quiet="yes" failonerror="false"/>
    
    <!-- Create a temporary Disk Image -->
    <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true">
        <arg value="create"/>
        <arg value="-srcfolder"/>
        <arg value="staging"/>
        <arg value="-volname"/>
        <arg value="${app.name}"/>
        <arg value="-ov"/>
        <arg value="${dist}/${app.name}-tmp.dmg"/>
        <arg value="-format"/>
        <arg value="UDRW"/>
    </exec>
    
    <!-- Attach the temporary image -->
    <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true">
        <arg value="attach"/>
        <arg value="${dist}/${app.name}-tmp.dmg"/>
        <arg value="-mountroot"/>
        <arg value="${mountdir}/"/>
    </exec>
    
    <!-- Copy the background, the volume icon and DS_Store files -->
    <mkdir dir="${mountdir}/${app.name}/.background"/>
    <copy file="osx/background.png" tofile="${mountdir}/${app.name}/.background/background.png" overwrite="true"/>
    <copy file="osx/mauve.icns" tofile="${mountdir}/${app.name}/.VolumeIcon.icns" overwrite="true"/>
    <copy file="osx/DS_Store" tofile="${mountdir}/${app.name}/.DS_Store" overwrite="true"/>


    <!-- Indicate that we want a custom icon -->
    <exec executable="SetFile" os="Mac OS X">
        <arg value="-a"/>
        <arg value="C"/>
        <arg value="${mountdir}/${app.name}"/>
    </exec>
    
    <!-- Add a symbolic link to the Applications directory -->
    <symlink link="${mountdir}/${app.name}" resource="/Applications"/>



    <!-- Detach the temporary image -->
    <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true">
        <arg value="detach"/>
        <arg value="${mountdir}/${app.name}"/>
    </exec>
    
    <!-- Compress it to a new image -->
    <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true">
        <arg value="convert"/>
        <arg value="${dist}/${app.name}-tmp.dmg"/>
        <arg value="-format"/>
        <arg value="UDZO"/>
        <arg value="-o"/>
        <arg value="${dist}/${app.name}.dmg"/>
    </exec>
    
    <!-- Delete the temporary image -->
    <delete file="${dist}/${app.name}-tmp.dmg" quiet="yes" failonerror="false"/>
</target>


	<!-- Create an OS X application and disk image -->
	<target name="macdist" depends="jar,getChangeLog" description="Generate a Mac OS X disk image" >
		<!-- Create the distribution directory -->
		<mkdir dir="${dist}" />
		<delete dir="${dist}/Mauve.app"/>

        <!-- get the java home -->
        <exec executable="/usr/libexec/java_home" os="Mac OS X" failonerror="true" outputproperty="osx.java.home"/>
		<bundleapp outputdirectory="${dist}"
			name="Mauve"
			displayname="Mauve ${release.version}"
			identifier="components.Mauve"
			icon="osx/mauve.icns"
			shortversion="${release.version}"
			copyright="(c) 2003-2015  http://darlinglab.org/mauve"
			mainclassname="org.gel.mauve.gui.Mauve">
			<classpath file="Mauve.jar" />
			<classpath file="ext/*.jar" />
			<librarypath file="osx/progressiveMauve" />
			<librarypath file="osx/mauveAligner" />
            <runtime dir="${osx.java.home}" />
            <option value="-Dapple.laf.useScreenMenuBar=false"/>
            <option value="-Xmx500m"/>
		</bundleapp>
		
		<!-- Create a staging directory for the Disk Image filesystem -->
		<mkdir dir="staging"/>
        <exec executable="ditto" failonerror="true">
                <arg value="-v"/>
                <arg value="${dist}/Mauve.app"/>
                <arg value="staging/Mauve.app"/>
        </exec>
		<copy todir="staging">
			<fileset dir="${basedir}">
				<include name="ChangeLog.html"/>
			</fileset>
		</copy>
		
		<!-- copy text files to the staging directory, adding .txt
		     to their filename -->
		<copy todir="staging">
			<fileset dir="${basedir}">
				<include name="COPYING"/>
			</fileset>
			<mapper type="glob" from="*" to="*.txt"/>
		</copy>
		<chmod file="staging/Mauve.app/Contents/MacOS/JavaAppLauncher" perm="755"/>
		<chmod file="staging/Mauve.app/Contents/MacOS/mauveAligner" perm="755"/>
		<chmod file="staging/Mauve.app/Contents/MacOS/progressiveMauve" perm="755"/>

<!-- sign the app -->
<exec executable="/usr/bin/codesign" os="Mac OS X" failonerror="true">
    <arg value="-s"/>
    <arg value="Developer ID Application: Aaron Darling"/>
    <arg value="--deep"/>
    <arg value="staging/Mauve.app"/>
</exec>
<!---->

<!--        <dmg destfile="${dist}/Mauve-${release.version}.dmg" name="Mauve ${release.version}" srcdir="staging" compressed="true"/> -->
	</target>

	<target name="srcdist" depends="init" description="package a source distribution">
		<tar destfile="${dist}/mauve_source_${datestamp}.tar.gz" compression="gzip">
			<!-- Copy support files into the dist directory-->
			<tarfileset dir="." prefix="/mauve-src">
				<include name="COPYING" />
				<include name="Mauve" />
				<include name="README" />
				<include name="TODO" />
				<include name="ChangeLog.html" />
				<include name="build.xml" />
				<include name="mauve.nsi" />
				<include name="mauve.dox" />
				<include name="mauve.ico" />
				<include name=".project" />
				<include name=".classpath" />
				<include name="mauve.icns" />
				<include name="Mauve Online Documentation.url" />
				<include name="Mauve.lnk" />
			</tarfileset>
			<tarfileset dir="${src}" includes="**/*" prefix="/mauve-src/src" />
		</tar>
	</target>

	<target name="getChangeLog" >
		<get src="http://darlinglab.org/mauve/user-guide/versions.html" dest="ChangeLog.html" usetimestamp="true"/>
		<copy file="ChangeLog.html" tofile="ChangeLog"/>
	</target>

	<target name="nsicompile" depends="jar,getChangeLog" description="make windows installer" >

		<!-- create output directory -->
		<mkdir dir="${dist}" />

		<!-- Make timestamp and timestampdash for installer making -->
		<property environment="env" />
		<echo message="Program files: ${env.ProgramFiles}"/>
		<exec executable="C:\Program Files (x86)\NSIS\makensis.exe" dir=".">
			<arg line="/V2 /NOCD win32\mauve.nsi" />
			<env key="release_version" value="${release.version}" />
			<env key="datestamp" value="${datestamp}" />
		</exec>
	</target>
		
	
	<target name="run" depends="jar" description="run Mauve">
		<java jar="Mauve.jar" fork="true" />
	</target>
	
	<target name="asapResources">
		<pathconvert property="asap.resources" pathsep=" ">
			<path>
				<fileset dir="./ext">
					<include name="*.jar" />
				</fileset>
			</path>
			<mapper>			
		        <chainedmapper>
		    		<mapper type="flatten" />
		    		<mapper type="glob" from="*" to="&lt;jar href=&quot;*&quot; /&gt;&#13;&#10;"/>
		        </chainedmapper>
			</mapper>
		</pathconvert>
	</target>
	
	<target name="deployASAP" depends="signjars, asapResources">
		
		<echo message="Deploying mauve ASAP stuff to directory ${asap.dir}" />
		<echo message="Using codebase of ${asap.codebase}" />
		
		<!-- update and copy mauve.jnlp to dist-->
		<copy file="./jws/mauve.jnlp.template" tofile="${dist}/mauve.jnlp" overwrite="yes">
			<filterset>
				<filter token="CODEBASE" value="${asap.codebase}"/>
				<filter token="RESOURCES" value="${asap.resources}"/>
				<filter token="ARGUMENTS" value=""/>
			</filterset>
		</copy>

		<!-- copy unmodified files to the server -->
		<ssh host="${deploy.bareaddress}"
			username="${deploy.username}"
			version="2"
			keyfile="${deploy.win32.keyfile}">
			<sftp action="put" remotedir="${deploy.asapdir}" verbose="true" newer="true">
				<fileset dir=".">
					<include name="Mauve.jar" />
					<include name="mauveApplet.jar" />
				</fileset>
				<fileset dir="./ext">
					<include name="*.jar"/>
				</fileset>
				<fileset dir="./src/images">
					<include name="mauve_icon.gif" />
					<include name="mauve_logo.png" />
				</fileset>
				<fileset dir="${dist}">
					<include name="mauve.jnlp"/>
				</fileset>
			</sftp>
			<!-- set the permissions so others in the group can modify them -->
			<exec cmd="chgrp annotation ${deploy.asapdir}/*"/>
			<exec cmd="chmod 664 ${deploy.asapdir}/*"/>
			<!-- jar files should have the execute bit set -->
			<exec cmd="chmod 775 ${deploy.asapdir}/*.jar"/>
		</ssh>
	</target>
	
	<!-- assumes that an ssh key has been registered with the web server -->
	<target name="deployWin32" depends="nsicompile">
		<echo file="${dist}\latest" message="${datestamp}"/>
		<echo file="${dist}\latest.windows" message="${datestamp}"/>
		<ssh host="${deploy.bareaddress}"
			username="${deploy.username}"
			version="2"
			keyfile="${deploy.win32.keyfile}">

			<sftp action="put" remotedir="${deploy.serverdir}" verbose="true">
				<fileset dir="${dist}">
					<include name="mauve_installer_${release.version}.exe"/>
					<include name="${dist}\latest"/>
					<include name="${dist}\latest.windows"/>
				</fileset>
			</sftp>
			<exec cmd="cp ${deploy.serverdir}/mauve_installer_${release.version}.exe ${deploy.serverdir}/mauve_installer_${datestamp}.exe"/>
		</ssh>
	</target>

	<!-- assumes that passwordless ssh authentication has been configured to the web server -->
	<target name="deployMacOSX" depends="dmg">
		<exec executable="scp">
			<arg value="${dist}/Mauve-${release.version}.dmg" />
			<arg value="${deploy.address}:${deploy.serverdir}" />
		</exec>
		<echo file="${dist}/latest.mac" message="${datestamp}"/>
		<exec executable="scp">
			<arg value="${dist}/latest.mac" />
			<arg value="${deploy.address}:${deploy.serverdir}" />
		</exec>
	</target>

	<!-- assumes that passwordless ssh authentication has been configured to the web server -->
	<target name="deployLinux" depends="dist">
		<exec executable="scp">
			<arg value="${dist}/mauve_linux_${release.version}.tar.gz" />
			<arg value="${deploy.address}:${deploy.serverdir}" />
		</exec>
		<echo file="${dist}/latest.linux" message="${datestamp}"/>
		<exec executable="scp">
			<arg value="${dist}/latest.linux" />
			<arg value="${deploy.address}:${deploy.serverdir}" />
		</exec>
	</target>
</project>