build_compute.xml

<project name="compute">
	<!-- This name is used to name the war file -->
	<property name="app_name" value="compute" />
	
	<!-- This holds all the settings for the generator -->
	<property name="app_properties" value="apps/${app_name}/org/molgenis/${app_name}/${app_name}.properties" />
	
	<!-- This determines what handwritten modules should be loaded -->
	<path id="app.class.path">
		<pathelement location="apps/${app_name}" />
		<pathelement location="modules/_deprecated" />
		<pathelement location="modules/compute4" />
		<pathelement location="test/modules/compute4" />
		<pathelement location="modules/settings" />
		<pathelement location="modules/file" />
		<pathelement location="modules/datamodel" />
		<pathelement location="modules/decorators/core" />
		<pathelement location="modules/webserver" />
	</path>
	
	<!-- Import all tasks from build_common: clean, generate, compile, test, war, standalone-jar -->
	<import file="build_common.xml" />
	
	<!-- Set relative path to molgenis-pipeline repo. -->
	<!-- We need it to bundle some demo and production pipelines with a compute distro. -->
	<property name="pipelines_repo_dir" value="${basedir}/../molgenis-pipelines/" />
	
	<target name="test">
		<!-- combine classpaths -->
		<path id="combined.class.path">
			<path refid="molgenis.classpath" />
			<path refid="app.class.path" />
			<path location="${output_src}" />
		</path>
		
		<!-- run the tests -->
		<testng outputDir="${testng.report.dir}" haltOnFailure="true">
			<xmlfileset dir="${build.molgenis_apps.dir}" includes="org/molgenis/compute/commandline/testng-compute.xml" />
			<classpath location="${cb.instrument.dir}" />
			<classpath refid="combined.class.path"/>
			<classfileset dir="${build.molgenis.dir}" includes="**/*Test*.class" />
			<sysproperty key="net.sourceforge.cobertura.datafile" value="${cb.file}" />
			<jvmarg value="-noverify" />
			<jvmarg value="-ea" />
			<jvmarg value="-Xmx2048m" />
		</testng>
	</target>
		
	<!-- Get version and timestamp info from the commandline. -->
	<target name="currentversion">
		<!-- Get commit hashes from the commandline GIT client. -->
		<exec executable="git" outputproperty="git.version">
			<arg value="--version"/>
		</exec>
		<echo>Using ${git.version}</echo>
		<exec executable="git" dir="${basedir}" outputproperty="git.apps.hash-short">
			<arg value="rev-parse"/>
			<arg value="--short"/>
			<arg value="HEAD"/>
		</exec>
		<exec executable="git" dir="${basedir}" outputproperty="git.apps.hash-long">
			<arg value="rev-parse"/>
			<arg value="HEAD"/>
		</exec>
		<exec executable="git" dir="${molgenis.dir}" outputproperty="git.molgenis.hash-short">
			<arg value="rev-parse"/>
			<arg value="--short"/>
			<arg value="HEAD"/>
		</exec>
		<exec executable="git" dir="${molgenis.dir}" outputproperty="git.molgenis.hash-long">
			<arg value="rev-parse"/>
			<arg value="HEAD"/>
		</exec>
		<exec executable="git" dir="${pipelines_repo_dir}" outputproperty="git.pipelines.hash-short">
			<arg value="rev-parse"/>
			<arg value="--short"/>
			<arg value="HEAD"/>
		</exec>
		<exec executable="git" dir="${pipelines_repo_dir}" outputproperty="git.pipelines.hash-long">
			<arg value="rev-parse"/>
			<arg value="HEAD"/>
		</exec>
		<!-- Get timestamp for current build -->
		<exec executable="date" dir="${pipelines_repo_dir}" outputproperty="timestamp">
			<arg value="+%Y-%m-%dT%H:%M:%S%z"/>
		</exec>
		<echo>Creating MOLGENIS/compute distro based on Git commits: ${git.apps.hash-short} (molgenis_apps-legacy) depending on ${git.molgenis.hash-short} (molgenis-legacy) and bundled with ${git.pipelines.hash-short} (molgenis-pipelines).</echo>
	</target>
	
	<!-- Make a distribution:
		* Generate and compile this molgenis app
		* Bundle it with all associated dependencies and resources like manuals, example files, etc.
		* Create a *.zip archive -->
	<target name="makedistro" depends="currentversion">
		
		<!-- Create folder structure for distro -->
		<property name="root_distro_dir" value="${basedir}/dist/"/>
		<property name="app_distro_dir" value="${root_distro_dir}/molgenis_${app_name}/"/>
		
		<mkdir dir="${app_distro_dir}"/>
		
		<!-- Delete the old distro -->
		<delete includeEmptyDirs="true" failonerror="false">
				<fileset dir="${app_distro_dir}" />
		</delete>
		
		<!-- Create label for this release which includes the short git hashes for all repos: 
			MA = molgenis_apps-legacy 
			M  = molgenis-legacy
			MP = molgenis-pipelines -->
		<property name="app-r_label" value="molgenis_${app_name}-MA_${git.apps.hash-short}-M_${git.molgenis.hash-short}-MP_${git.pipelines.hash-short}"/>
		
		<!-- Create folder substructure for distro -->
		<property name="app-r_distro_dir" value="${app_distro_dir}/${app-r_label}/"/>
		<property name="lib_dir" value="${app-r_distro_dir}/lib/"/>
		
		<!-- Create RELEASE document with version numbers. -->
		<echo file="${app-r_distro_dir}/RELEASE.txt">
==========================================================================
 MOLGENIS/compute distro release details
==========================================================================
Git commit hash tags for the code in this release: 
 * molgenis_apps-legacy: ${git.apps.hash-long}
 * molgenis-legacy:      ${git.molgenis.hash-long}
 * molgenis-pipelines:   ${git.pipelines.hash-long}

Release compiled on:     ${timestamp}
==========================================================================
		</echo>
		
		<!-- Copy documentation to the distro dir -->
		<mkdir dir="${app-r_distro_dir}/docs/"/>
		<copy todir="${app-r_distro_dir}/docs/">
			<fileset dir="${basedir}/doc/${app_name}/">
				<include name="*"/>
			</fileset>
		</copy>
		
		<!-- Copy demo pipelines from molgenis_apps-legacy repo. -->
		<copy todir="${app-r_distro_dir}/pipelines/demo/">
			<fileset dir="${basedir}/modules/${app_name}/demo/" />
		</copy>
		
		<!-- Copy example script to analyze a test data set from a demo workflow from the molgenis_apps-legacy repo. -->
		<copy todir="${app-r_distro_dir}">
			<fileset dir="${basedir}/apps/${app_name}/org/molgenis/${app_name}/">
				<include name="test_molgenis_compute.sh"/>
			</fileset>
		</copy>
		
		<!-- Copy all generic templates from the molgenis_apps-legacy repo. -->
		<copy todir="${app-r_distro_dir}/templates/">
			<fileset dir="${basedir}/modules/${app_name}/templates/"/>
		</copy>
		
		<!-- Copy all generic templates, protocols and workflows from the molgenis-pipelines repo. -->
		<copy todir="${app-r_distro_dir}/pipelines/production/">
			<fileset dir="${pipelines_repo_dir}/compute4/"/>
		</copy>
		
		<!-- Copy all dependencies to the distro lib dir -->
		<!-- This is a manually maintained list of libs for now, but we should collect this from include statements -->
		<copy todir="${lib_dir}">
			<fileset dir="${molgenis.dir}/lib/">
				<include name="commons-io-2.4.jar"/>
				<include name="freemarker.jar"/>
				<include name="log4j-1.2.15.jar"/>
			</fileset>
		</copy>
		
		<!-- Create molgenis.jar -->
		<jar jarfile="${lib_dir}/molgenis-${git.molgenis.hash-short}.jar" basedir="${build.molgenis.dir}" update="false"/>
		
		<!-- Create molgenis_app.jar in folder dist/${app} -->
		<jar jarfile="${lib_dir}/molgenis-${app_name}-${git.apps.hash-short}.jar" basedir="${build.molgenis_apps.dir}" update="false"/>
		
		<!-- Make shell script to start molgenis app from the commandline -->
		<echo file="${app-r_distro_dir}/molgenis_${app_name}.sh">#!/bin/bash
#
# This script runs the MOLGENIS/compute commandline with only the jars needed added to the CLASSPATH.
#
# To get relative path to this script use $(dirname -- "$0").
#

# If -mcdir is not specified as argument then use the current (absolute) path:
MCDIR=$( cd -P "$( dirname "$0" )" &amp;&amp; pwd )

# If user has specified -mcdir, then use that one.
customMcdir=$(echo $* | grep -E "\-mcdir")
if [[ ! $customMcdir ]]; then mcDirArg="-mcdir=${MCDIR}"; else mcDirArg=""; fi;

java -cp \
${MCDIR}/lib/molgenis-${git.molgenis.hash-short}.jar:\
${MCDIR}/lib/molgenis-compute-${git.apps.hash-short}.jar:\
${MCDIR}/lib/commons-io-2.4.jar:\
${MCDIR}/lib/freemarker.jar:\
${MCDIR}/lib/log4j-1.2.15.jar \
org.molgenis.compute.commandline.ComputeCommandLine \
$* \
$mcDirArg

		</echo>
		<chmod file="${app-r_distro_dir}/molgenis_${app_name}.sh" perm="755"/>
		
		<!-- Make package with 'lib','workflows','protocols' and shell script -->
		<zip destfile="${root_distro_dir}/${app-r_label}.zip" basedir="${app_distro_dir}" update="false" />
		
		<!-- Cleanup -->
		<delete includeEmptyDirs="true" failonerror="false">
				<fileset dir="${app_distro_dir}" />
		</delete>
		
	</target>
	
	<target name="clean-generate-compile-test-makedistro" depends="clean,generate,compile,test,makedistro"/>
	
	<target name="clean-generate-compile-makedistro" depends="clean,generate,compile,makedistro"/>
	
</project>