build.xml

<?xml version="1.0"?>

<!-- This is version 16.2-SNAPSHOT -->

<project name="ManhattanViz" default="run" basedir=".">
    <description>
        Build file for solutions gwava

        Notes:
        This is a build file for use with the Jakarta Ant build tool version 1.6.5 or higher.

        Prerequisites:
        jdk-1.6.0					from http://java.sun.com/javase/downloads/
        ant-1.6.5					from http://ant.apache.org/

        Build Instructions:
        To build, run

        ant "target"

        on the directory where this file is located with the target you want.

        Most useful targets:
        usage
        compile-gwava
        test
        inst-plugins
        test-inst-plugins
        webstart
        compile-test
        junit
        transmartwar

        Author:
        Ami Khandeshi
    </description>

    <!-- locads tomcat.home and axis.home from this external properties file -->
    <property file="build.properties"/>
    <property name="project.title"             value="GWAVA" />
    <property name="project.rep"               value="ManhattanViz"/>
    <property name="project.name"              value="ManhattanViz" />
    <property name="project.display.version"   value="2.1g" />
    <property name="project.version"           value="2.1g" />
    <property name="webstart.name"             value="gwava"/>

    <property name="webstart.root"             value="http://localhost:8080/gwava http://localhost:8880/gwava http://amrl2lp3fwfd58:10080/ http://75.124.74.46 http://AMRL2LP3FWFD58:10080/gwava http://clinux22.pfizer.com http://amre1al336.pcld.pfizer.com:8080/pfizerWebstart http://amrndhl693.pfizer.com http://amrndhl1040.pfizer.com:10080/pfizerWebstart http://amrndhl1038.pfizer.com:8000/gwava http://amrndhl1040.pfizer.com:8000/gwava /"/>


    <!-- project modules   -->
    <property name="gwava.module"              value="gwava"/>

    <!-- module  directories -->
    <property name="gwava.dir"                 location="${basedir}"/>

    <!-- cy.jnlp file	  -->
    <property name="jnlpfile"                  location="${gwava.dir}/scripts/gwava.jnlp"/>
    <property name="jnlp1file"                 location="${gwava.dir}/scripts/resource.jnlp"/>
    <property name="webinfdir"                 location="${gwava.dir}/scripts/WEB-INF"/>

    <!-- module  src directories -->
    <property name="gwava.src.dir"             location="${gwava.dir}/src"/>
    <!--<property name="gwava.test.dir"            location="${gwava.dir}/test"/>-->
    <property name="gwava.lib.dir"             location="${gwava.dir}/lib"/>
    <property name="gwava.image.dir"           location="${gwava.dir}/images"/>
    <property name="gwava.help.dir"            location="${gwava.dir}/help"/>
    <property name="gwava.web-app.dir"         location="${gwava.dir}/web-app" />
    <!-- module  classes  directories -->
    <property name="gwava.docs.dir"            location="${gwava.dir}/docs" />
    <property name="gwava.docs.api.dir"        location="${gwava.docs.dir}/api" />
    <property name="gwava.dist.dir"            location="${gwava.dir}/dist"/>
    <property name="gwava.build.dir"           location="${gwava.dir}/builds"/>
    <property name="gwava.build.classes.dir"   location="${gwava.build.dir}/classes"/>
    <property name="gwava.build.image.dir"     location="${gwava.build.classes.dir}/images"/>
    <property name="gwava.build.help.dir"      location="${gwava.build.classes.dir}/help"/>
    <property name="gwava.build.dist.dir"      location="${gwava.build.dir}/dist"/>
    <property name="gwava.build.dist.lib.dir"  location="${gwava.build.dist.dir}/lib"/>
    <property name="gwava.keystore.dir"        location="${gwava.build.dir}/keystore" />


    <!-- test reports -->
    <property name="gwava.test.report"         location="${gwava.build.dir}/reports"/>

    <!-- compilation options -->
    <property name="compile.debug"             value="on"/>
    <property name="compile.optimize"          value="off"/>
    <property name="compile.deprecation"       value="on"/>
    <property name="compile.verbose"           value="off"/>

    <property name="keystore"                  location="${gwava.keystore.dir}"/>
    <property name="keystore.alias"            value="transmartKeyStore"/>
    <property name="keystore.password"         value="transmartKey"/>


    <!--===================================================================-->
    <!--====== Compilation classpath - add all JARs in lib directory ======-->
    <!--===================================================================-->
    <path id="gwava.classpath">
        <fileset dir="${gwava.lib.dir}">
            <include name="*.jar" />
        </fileset>
    </path>


    <taskdef resource="net/sf/antcontrib/antlib.xml">
        <classpath>
            <pathelement location="${gwava.lib.dir}/ant-contrib/ant-contrib-1.0b3.jar"/>
        </classpath>
    </taskdef>


    <!--unsing Macro	-->
    <macrodef name="unsignjar">

        <attribute name="jar"/>

        <sequential>
            <!-- Remove any existing signatures from a JAR file. -->
            <tempfile prefix="usignjar-" destdir="${java.io.tmpdir}" property="temp.file"/>
            <echo message="Removing signatures from JAR: @{jar}"/>
            <mkdir dir="${temp.file}"/>

            <unjar src="@{jar}" dest="${temp.file}">
                <patternset>
                    <include name="**"/>
                    <exclude name="META-INF/*.SF"/>
                    <exclude name="META-INF/*.DSA"/>
                    <exclude name="META-INF/*.RSA"/>
                </patternset>
            </unjar>

            <delete file="@{jar}" failonerror="true"/>

            <!-- Touch it in case the file didn't have a manifest.
            Otherwise the JAR task below will fail if the manifest
            file doesn't exist. -->
            <mkdir dir="${temp.file}/META-INF"/>
            <touch file="${temp.file}/META-INF/MANIFEST.MF"/>

            <jar destfile="@{jar}"
                 basedir="${temp.file}"
                 includes="**"
                 manifest="${temp.file}/META-INF/MANIFEST.MF"/>

            <delete dir="${temp.file}" failonerror="true"/>
        </sequential>
    </macrodef>

    <!--addManifestToLibMacro	-->
    <macrodef name="addManifestToLibMacro">
        <attribute name="jar"/>

        <sequential>
            <!-- Remove any existing signatures from a JAR file. -->
            <tempfile prefix="usignjar-" destdir="${java.io.tmpdir}" property="temp.file"/>
            <echo message="Adding manifest to lib JAR: @{jar} placed in ${java.io.tmpdir} as ${temp.file}"/>
            <mkdir dir="${temp.file}"/>

            <unjar src="@{jar}" dest="${temp.file}">
            </unjar>

       		<delete file="@{jar}" failonerror="true"/>

            <!-- Touch it in case the file didn't have a manifest.
            Otherwise the JAR task below will fail if the manifest
            file doesn't exist. -->
            <mkdir dir="${temp.file}/META-INF"/>
            <touch file="${temp.file}/META-INF/MANIFEST.MF"/>

            <jar destfile="@{jar}"
                 basedir="${temp.file}"
                 includes="**">
                <!--manifest="${temp.file}/META-INF/MANIFEST.MF">-->
                <manifest>
                    <attribute name="Permissions" value="all-permissions"/>
                    <attribute name="Application-Name" value="${project.title}"/>
                    <attribute name="Codebase"  value="${webstart.root}" />
                </manifest>
            </jar>

            <delete dir="${temp.file}" failonerror="true"/>
        </sequential>
    </macrodef>



    <!--============================================================================-->
    <!--============================  Help on usage ================================-->
    <!--============================================================================-->
    <target name="usage" description="list down all available targets">
        <echo message=""/>
        <echo message="${project.name} Build file"/>
        <echo message="-------------------------------------------------------------"/>
        <echo message=" available targets are:"/>
        <echo message=" 	usage/help/?		-> displays this message"/>
        <echo message=" 	compile-gwava		-> compiles all java files in src and create a ${project.name}-${gwava.module}-${project.display.version}.jar in dist directory"/>
        <echo message="		build-plugins		-> create a build/plugins folder and copies ${project.name}-${gwava.module}-${project.display.version}.jar and other dependant jars into this folder"/>
        <echo message="		test			-> executes particular test cases"/>
        <echo message="		clean			-> cleans up the build directories"/>
        <echo message="		all			-> it runs cleanup first then it runs inst-plugins and webstart"/>
        <echo message="     transmartwar -> creates signed jar files and packages for javastart-delivery war" />
        <echo message="-------------------------------------------------------------"/>
        <echo message=""/>
    </target>

    <target name="help" depends="usage"/>
    <target name="?" depends="usage"/>

    <target name="init" depends="clean">
        <!-- Create the time stamp -->
        <tstamp/>
        <!-- Create the build directory structure used by compile -->
        <mkdir dir="${gwava.build.dir}"/>
        <mkdir dir="${gwava.build.classes.dir}"/>
        <mkdir dir="${gwava.build.dist.dir}"/>
        <mkdir dir="${gwava.build.dist.lib.dir}"/>
        <mkdir dir="${gwava.dist.dir}"/>


        <echo message="--------- ${project.title} ${project.display.version} ---------"/>
        <echo message="java.home   = ${java.home}"/>
        <!--<echo message="java.home   = c:/Program Files/Java/jdk1.6.0_24"/>-->
        <echo message="base.dir   = ${basedir}"/>
        <echo message="proj.dir    = ${basedir}"/>
    </target>

    <!--=====================================================================-->
    <!--======================== compile solutions gwava ====================-->
    <!--=====================================================================-->
    <target name="compile-gwava" depends="init" description="compile the gwava source">
        <!-- Compile the java code from ${gwava.src.dir} into ${gwava.build.classes.dir} -->
        <javac srcdir="${gwava.src.dir}"
               destdir="${gwava.build.classes.dir}"
               debug="${compile.debug}"
               optimize="${compile.optimize}"
               verbose="${compile.verbose}"
               includeantruntime="false"
               deprecation="${compile.deprecation}">
            <classpath>
                <path refid="gwava.classpath"/>
            </classpath>

        </javac>
        <copy todir="${gwava.build.image.dir}">
            <fileset dir="${gwava.image.dir}" includes="*.*" />
        </copy>
        <copy todir="${gwava.build.help.dir}">
            <fileset dir="${gwava.help.dir}" includes="*.*" />
        </copy>
        <!-- Put everything in ${gwava.build.classes.dir} into the ${gwava.dist.dir} /solutions-gwava-1.0.jar  file -->
        <jar jarfile="${gwava.build.dist.dir}/${project.name}${project.version}.jar" basedir="${gwava.build.classes.dir}">
            <manifest>
                <attribute name="Specification-Title" value="Solutions gwava Library"/>
                <attribute name="Specification-Version" value="${project.version}"/>
                <attribute name="Specification-Vendor" value="Pfizer MRBT"/>
                <attribute name="Application-Name" value="${project.title}"/>
                <attribute name="Trusted-Only" value="true"/>
                <attribute name="Trusted-Library" value="false"/>
                <attribute name="Codebase"  value="${webstart.root}"/>
                <attribute name="Permissions" value="all-permissions"/>
                <!--<attribute name="Main-Class" value="com.pfizer.mrbt.genomics.Driver"/>
                <attribute name="Class-Path" value="gwava.classpath"/>-->
            </manifest>
        </jar>

        <copy todir="${gwava.build.dist.lib.dir}">
            <fileset dir="${gwava.lib.dir}" includes="*.jar" />
        </copy>
    </target>

    <!--==================================================================-->
    <!--=============== Run GWAVA ========================================-->
    <!--==================================================================-->
    <target name="run"  depends="compile-gwava" description="run GWAVA application" >
        <java jar="${gwava.build.dist.dir}/${project.name}${project.version}.jar"  fork="true" spawn="false" maxmemory="512m" >
            <arg value="-services=transmart"/>
        </java>
    </target>

    <target name="keytool">
        <delete file="${keystore}" failonerror="false" />
        <genkey alias="${keystore.alias}" storepass="${keystore.password}" keystore="${keystore}" validity="123456">
            <dname>
                <param name="CN" value="Pfizer RBT"/>
                <param name="OU" value="MRBT"/>
                <param name="O"  value="Translational Bioinformatics"/>
                <param name="L"  value="Cambridge"/>
                <param name="ST"  value="MA"/>
                <param name="C"  value="US"/>
            </dname>
        </genkey>
    </target>

    <target name="signJar" depends="addManifestToLib, keytool" >
        <signjar keystore="${keystore}" alias="${keystore.alias}" storepass="${keystore.password}" lazy="true" verbose="false">    <!-- from tianhong -->
            <path>
                <fileset dir="${gwava.build.dist.dir}" includes="${project.name}${project.version}.jar" />
                <fileset dir="${gwava.build.dist.lib.dir}" includes="*.jar" />
            </path>
        </signjar>
    </target>


    <!--==================================================================-->
    <!--===================== create war file ============================-->
    <!--==================================================================-->
    <target name="copyAdditionalWarContent" depends="init">
        <copy todir="${gwava.build.dir}/dist/help">
            <fileset dir="${gwava.help.dir}" />
        </copy>
         <copy file="${gwava.web-app.dir}/index.html" todir="${gwava.build.dir}/dist"/>
    </target>

    <target name="justwar" depends="signJar,copyAdditionalWarContent">
        <jar jarfile="${gwava.dist.dir}/${webstart.name}.war" basedir="${gwava.build.dir}" />
    </target>

    <target name="transmartwar" depends="signJar,copyAdditionalWarContent">
        <jar jarfile="${gwava.dist.dir}/${webstart.name}.war" basedir="${gwava.build.dir}/dist" />
    </target>

    <!--==================================================================-->
    <!--===================== cleans build directory =====================-->
    <!--==================================================================-->
    <target name="clean" description="clean up" >
        <delete dir="${gwava.build.dir}"/>
    </target>

    <target name="unsignjar" description="call macro to unsign jar">
        <for param="file">
            <path>
                <fileset dir="${gwava.build.dist.lib.dir}" includes="**/*.jar"/> <!-- pvh changed to builds not build -->
            </path>
            <sequential>
                <unsignjar jar="@{file}"/>
            </sequential>
        </for>
        <unsignjar jar="${gwava.build.dist.dir}/${project.name}${project.version}.jar"/> <!-- pvh changed to builds not build -->
    </target>

    <target name="addManifestToLib" depends="compile-gwava" description="call macro to unjar and add manifest to all library jars">
        <echo message="addManifestToLib operating on dir ${gwava.build.dist.lib.dir}" />
        <for param="file">
            <path>
                <fileset dir="${gwava.build.dist.lib.dir}" includes="**/*.jar"/>
            </path>
            <sequential>
                <addManifestToLibMacro jar="@{file}"/>
            </sequential>
        </for>
    </target>


</project>