xqtl_jar.xml

<?xml version="1.0" encoding="UTF-8"?>
<project name="xqtl_jar" default="create_zip" basedir=".">
	<description>
        Build a runnable JAR with a standalone xQTL application.
		Work in progress, but must be kept stable to ensure the dependencies don't break.
		Needs a properly connected Selenium test: right now we test on the folder that
		is JARred instead of the JAR itself, because TestNG does not support this.
    </description>
	
	<!-- Import development script for reuse -->
	<import file="xqtl_dev.xml" />

	<!-- Import TestNG as an Ant task -->
	<taskdef resource="testngtasks" classpath="../molgenis/lib/testng-5.14.10.jar" />

	<!-- Path of Molgenis libs -->
	<property name="mlibs" value="../molgenis/lib/"/>
	
	<!-- Path of application libs -->
	<property name="alibs" value="WebContent/WEB-INF/lib/"/>
	
	<!-- Path of all unjarred and build content, to be JARred at the end -->
	<property name="jarme" value="${app_build_dir}/jarme"/>
	
	<!-- Path of dist folder where the resulting JAR will be put -->
	<property name="dist" value="dist"/>
	
	<!-- Delete content of jarme dir -->
	<target name="clean_jarme" description="Delete stuff">
		<!-- create dir if it doesn't exist -->
		<mkdir dir="${jarme}"/>
		<!-- remove content -->
		<delete includeemptydirs="true">
			<fileset dir="${jarme}" includes="**/*" />
		</delete>
	</target>
	
	<target name="unjar" description="Unjar all Molgenis and application jars">
		<!-- Molgenis jars -->
		<unjar src="${mlibs}hibernate/hibernate-jpa-2.0-api-1.0.0.Final.jar" dest="${jarme}" overwrite="false"/> <!-- JPA common -->
		<unjar src="${mlibs}hibernate/hibernate3.jar" dest="${jarme}" overwrite="false"/> <!-- JPA common -->
		<unjar src="${mlibs}hibernate/hibernate-search-3.4.1.Final.jar" dest="${jarme}" overwrite="false"/> <!-- JPA search-->
		<unjar src="${mlibs}hibernate-validator-4.1.0.Final/validation-api-1.0.0.GA.jar" dest="${jarme}" overwrite="false"/> <!-- JPA validation-->
		<unjar src="${mlibs}lucene-core-3.0.2.jar" dest="${jarme}" overwrite="false"/> <!-- JPA search -->
		<unjar src="${mlibs}gridgain/spring-2.5.6.jar" dest="${jarme}" overwrite="false"/> <!-- Spring framework -->
		<unjar src="${mlibs}ganymed-ssh2-build250.jar" dest="${jarme}" overwrite="false"/> <!-- SSH utils -->
		<unjar src="${mlibs}ant-1.8.1.jar" dest="${jarme}" overwrite="false"/> <!-- ProjectHelper Molgenis.java -->
		<unjar src="${mlibs}ant-apache-log4j.jar" dest="${jarme}" overwrite="false"/> <!-- Log4jListener Molgenis.java -->
	  	<unjar src="${mlibs}commons-dbcp-1.2.1.jar" dest="${jarme}" overwrite="false"/> <!-- BasicDataSource -->
	  	<unjar src="${mlibs}commons-fileupload-1.1.jar" dest="${jarme}" overwrite="false"/> <!-- HttpServletRequestTuple files -->
		<unjar src="${mlibs}commons-io-2.4.jar" dest="${jarme}" overwrite="false"/> <!-- File I/O helpers -->
	  	<unjar src="${mlibs}cxf-bundle-minimal-2.5.2.jar" dest="${jarme}" overwrite="false"/> <!-- CXFNonSpringJaxrsServlet -->
	  	<unjar src="${mlibs}freemarker.jar" dest="${jarme}" overwrite="false"/> <!-- Template processing -->
	  	<unjar src="${mlibs}jxl.jar" dest="${jarme}" overwrite="false"/> <!-- Excel import/export -->
	  	<unjar src="${mlibs}log4j-1.2.15.jar" dest="${jarme}" overwrite="false"/> <!-- org.apache.log4j.Logger -->
	  	<unjar src="${mlibs}mail.jar" dest="${jarme}" overwrite="false"/> <!-- Email utils -->
	  	<unjar src="${mlibs}tar.jar" dest="${jarme}" overwrite="false"/> <!-- TarGz utils -->
		<unjar src="${mlibs}testng-5.14.10.jar" dest="${jarme}" overwrite="false"/> <!-- TestNG -->
	  	<unjar src="${mlibs}jsr311-api-1.1.1.jar" dest="${jarme}" overwrite="false"/>  <!-- Rest API JSON -->
		<unjar src="${mlibs}selenium-server-standalone-2.19.0.jar" dest="${jarme}" overwrite="false" /> <!-- Selenium webtests -->
		<unjar src="${mlibs}hsqldb.jar" dest="${jarme}" overwrite="false"/> <!-- RUNTIME ??: HyperSQL database-->
		<unjar src="${mlibs}commons-pool-1.5.2.jar" dest="${jarme}" overwrite="false"/> <!-- RUNTIME FrontController only??: GenericObjectPool -->
		<unjar src="${mlibs}wsdl4j-1.6.2.jar" dest="${jarme}" overwrite="false"/><!-- RUNTIME AbstractServlet only??: WSDL Locator -->
		<unjar src="${mlibs}quartz-1.6.0.jar" dest="${jarme}" overwrite="false"/><!-- Scheduling -->
		<unjar src="${mlibs}gson-2.2.1.jar" dest="${jarme}" overwrite="false"/><!-- GSON for XrefService-->
		<unjar src="${mlibs}tjws-1.98.jar" dest="${jarme}" overwrite="false"/><!-- Webserver -->
		<!-- Application jars -->
		<unjar src="${alibs}jaxrpc.jar" dest="${jarme}" overwrite="false" /> <!-- xQTL: KEGG tools -->
		<unjar src="${alibs}axis.jar" dest="${jarme}" overwrite="false" /> <!-- xQTL: KEGG tools -->
		<unjar src="${alibs}keggapi.jar" dest="${jarme}" overwrite="false" /> <!-- xQTL: KEGG tools -->
		<unjar src="${alibs}mindterm.jar" dest="${jarme}" overwrite="false" /> <!-- xQTL: Mindterm SSH -->
		<unjar src="${alibs}commons-math-2.2.jar" dest="${jarme}" overwrite="false" /> <!-- xQTL: Report builder statistics -->
		<unjar src="${alibs}simplecaptcha-1.2.1.jar" dest="${jarme}" overwrite="false" /> <!-- Auth captcha service -->
		<unjar src="${alibs}jopenid-1.07.jar" dest="${jarme}" overwrite="false" /> <!-- Auth OpenID login -->
		<unjar src="${alibs}spssw-1.66.jar" dest="${jarme}" overwrite="false" /> <!-- SPSS writer -->
		<unjar src="${alibs}pircbot.jar" dest="${jarme}" overwrite="false" /> <!-- IRC client -->
		<unjar src="${alibs}lambdaj-2.3.3-with-dependencies.jar" dest="${jarme}" overwrite="false" />  <!-- Used in: matrix/component/sqlbackend/EAVBackend.java -->
	</target>
	
	<!-- Compile Molgenis on the unjarred content in jarme -->
	<target name="compile_molgenis_jarme" description="Compile MOLGENIS on unjarred classes">
		<!-- Run javac on molgenis, using the unjarred content as classpath -->
		<javac srcdir="../molgenis/src" destdir="${jarme}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath path="{jarme}" />
			<exclude name="**/org/molgenis/framework/db/lifewise**" />
		</javac>
		<!-- Copy the res folder to the build dir so it can be found by MolgenisResourceCopyGen -->
		<copy todir="${jarme}/org/molgenis/framework/ui/res" verbose="true">
			<fileset dir="../molgenis/src/org/molgenis/framework/ui/res" includes="**/*.*" />
		</copy>
		<!-- Copy all Freemarker templates anywhere in MOLGENIS too -->
		<copy todir="${jarme}" verbose="true">
			<fileset dir="../molgenis/src" includes="**/*.ftl" />
		</copy>
	</target>
	
	<!-- Generate app on the unjarred content in jarme -->
	<target name="generate_app_jarme" description="Generate the application">
		<java classname="org.molgenis.Molgenis" fork="yes" failonerror="true">
			<arg value="apps/xgap/org/molgenis/xgap/xqtlworkbench/xqtl.properties" />
			<classpath path="${jarme}" />
		</java>
	</target>
	
	<target name="compile_datatypes_jarme" description="Compile generated datatypes">
		<javac srcdir="generated/java/org" excludes="**/*Decorator.java" destdir="${jarme}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath path="${jarme}" />
		</javac>
	</target>
	
	<target name="compile_app_jarme" description="Compile application">
		<pathconvert targetos="unix" property="app_src" refid="app.class.path" />
		<javac srcdir="${app_src}" destdir="${jarme}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath path="${jarme}" />
		</javac>
	</target>
	
	<target name="compile_other_jarme" description="Compile other generated">
		<javac srcdir="generated/java/app" destdir="${jarme}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath path="${jarme}" />
		</javac>
		<javac srcdir="generated/java/test" destdir="${jarme}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath path="${jarme}" />
		</javac>
	</target>
	
	<target name="copy_resources_jarme">
		<pathconvert pathsep="/**/*," refid="app.class.path" property="app_fileset_pattern">
			<regexpmapper from=".*/(.*/.*)" to="\1" />
		</pathconvert>

		<fileset dir="." id="app_fileset" includes="${app_fileset_pattern}/**/*">
			<exclude name="**/*.java" />
		</fileset>

		<copy todir="${jarme}" verbose="true">
			<fileset refid="app_fileset" />
			<mapper type="regexp" from="^[-_a-zA-Z0-9]*/[-_a-zA-Z0-9]*/(.*)" to="\1" />
		</copy>

		<copy todir="${jarme}" verbose="true">				
			<fileset dir="generated/sql" includes="**/*.sql" />
		</copy>
	</target>
	
	<target name="build_jarme">
		<antcall target="clean_jarme" />
		<antcall target="unjar" />
		<antcall target="compile_molgenis_jarme" />
		<antcall target="generate_app_jarme" />
		<antcall target="compile_datatypes_jarme" />
		<antcall target="compile_app_jarme" />
		<antcall target="compile_other_jarme" />
		<antcall target="copy_resources_jarme" />
	</target>
	
	<target name="jar_jarme">
		<mkdir dir="${dist}" />
		
		<!-- copy resources to JAR specific locations -->
		<copy todir="${dist}">
			<fileset dir="handwritten/standalone">
				<include name="**/*.*" />
			</fileset>
		</copy>
		
		<copy todir="${dist}/WebContent">
			<fileset dir="WebContent">
				<exclude name="META-INF/**" />
				<exclude name="WEB-INF/**" />
				<exclude name="animaldb/**" />
				<exclude name="designgg/**" />
				<include name="**/*.*" />
			</fileset>
		</copy>
		
		<copy todir="${jarme}">
			<fileset dir="publicdata/xqtl">
				<include name="**/*.*" />
			</fileset>
		</copy>
			
		<!-- JAR the jarme folder into dist/Application.jar -->
		<jar jarfile="${dist}/Application.jar" basedir="${jarme}" update="false">
			<manifest>
				<attribute name="Built-By" value="GCC" />
				<attribute name="Main-Class" value="boot.RunStandalone" />
			</manifest>
		</jar>
	</target>
	
	<target name="zip_jarme" description="Package the distribution into a ZIP">
		<mkdir dir="${dist}" />
		
		<!-- copy resources to ZIP specific locations -->
		<copy todir="${jarme}/WebContent">
			<fileset dir="WebContent">
				<exclude name="META-INF/**" />
				<exclude name="WEB-INF/**" />
				<exclude name="animaldb/**" />
				<exclude name="designgg/**" />
				<include name="**/*.*" />
			</fileset>
		</copy>
		
		<copy todir="${jarme}/publicdata/xqtl">
			<fileset dir="publicdata/xqtl">
				<include name="**/*.*" />
			</fileset>
		</copy>
		
		<!-- Windows/Unix startup scripts-->
		<echo file="${jarme}/run.sh">java -Xmx512m boot/RunStandalone</echo>
		<echo file="${jarme}/run.bat">java -Xmx512m boot/RunStandalone</echo>
		
		<zip destfile="${dist}/xqtl_workbench.zip" basedir="${jarme}" update="false" />
	</target>
	
	<target name="create_zip">
		<antcall target="build_jarme" />
		<antcall target="zip_jarme" />
	</target>
	
	<target name="create_jar">
		<antcall target="build_jarme" />
		<antcall target="jar_jarme" />
	</target>
	
	<!--
	Run webtest on the directory that was JARred because it's not possible
	to run TestNG from inside a jar. (needs ref to class or XML files)
	TODO: find a way to make it possible? it's a bit silly now..
	-->
	<target name="webtest_jar" description="Start the Selenium test">
		<testng haltOnFailure="true">
			<classfileset dir="${app_build_dir}" includes="**/XqtlSeleniumTest.class"/>
			<classpath path="${jarme}" />
		</testng>
	</target>
	
	<!-- Unzip and run webtest -->
	<target name="webtest_zip" description="Start the Selenium test on unzipped app">
		
		<unzip src="${dist}/xqtl_workbench.zip" dest="${dist}/xqtl_unzipped" />
		
		<testng haltOnFailure="true">
			<classfileset dir="${dist}/xqtl_unzipped" includes="**/XqtlSeleniumTest.class"/>
			<classpath path="${dist}/xqtl_unzipped" />
		</testng>
	</target>
	
	<!-- Wrapper to make the JAR and run the webtest -->
	<target name="create_jar_webtest">
		<antcall target="create_jar" />
		<antcall target="webtest_jar" />
	</target>
	
	<!-- Wrapper to make the ZIP and run the webtest -->
		<target name="create_zip_webtest">
			<antcall target="create_zip" />
			<antcall target="webtest_zip" />
		</target>
	
	<!-- Run the application from JAR file. Not efficient because
	when running from here we need to make a copy first. (JAR needs
	to find stuff from the basedir where it was launched) -->
	<target name="run_jar" description="Start the application">
		<!-- in order to work properly, JAR must be started from basedir -->
		<echo message="moving application files from ${dist} to ${basedir}" />
		<copy todir="${basedir}" overwrite="true">
			<fileset dir="${dist}">
				<include name="**/*.*" />
			</fileset>
		</copy>
		<!--delete includeemptydirs="true">
			<fileset dir="${dist}" includes="**/*" />
		</delete-->
		<java maxmemory="512m" jar="Application.jar" fork="yes" failonerror="true" />
	</target>

</project>