build_lifelinesresearchportal_test.xml

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

<project>
	<!-- this name is used to name the war file -->
	<property name="app_name" value="lifelines_researchportal" />

	<!-- this holds all the settings for the generator -->
	<property name="app_properties" value="apps/lifelinesresearchportal/org/molgenis/lifelinesresearchportal/lifelinesresearchportal.test.properties"/>

	<!-- this determines what handwritten modules should be loaded 
	
	<pathelement location="apps/catalogue" />
	<pathelement location="modules/decorators/data" />
	<pathelement location="apps/xgap" />
			<pathelement location="modules/pheno" />
		<pathelement location="modules/search" />
		<pathelement location="publicdata" />
		<pathelement location="modules/import" />
		<pathelement location="modules/settings" />
		<pathelement location="modules/decorators/pheno" />
	-->
	<path id="app.class.path">
		<pathelement location="apps/lifelinesresearchportal" />
		<pathelement location="apps/lifelinesresearchportalimporter" />
			
		<pathelement location="modules/datamodel" />
		<pathelement location="modules/auth" />
		<pathelement location="modules/file" />
		
		<pathelement location="modules/webserver" />
		

		<pathelement location="modules/matrix" />
		<pathelement location="modules/decorators/core" />
		<pathelement location="modules/decorators/auth" />

		
		
	</path>
	
	<target name="runOn" description="Start the application">
	    <java maxmemory="128m" classname="boot.RunStandalone" fork="yes" failonerror="true">
	        <arg value="${port}"/>
	        <classpath>
	            <path refid="molgenis.classpath" />
	            <path location="${build.dir}" />
	        </classpath>
	    </java>
	</target>

	<!-- import all tasks from build_common: clean, generate, compile, test, war, standalone-jar -->
	<import file="build_common.xml" />
</project>
	
<!--project name="build_lifelinesresearchportal" default="run" basedir=".">
	
	<description>
		
        ANT file for xQTL development. Complete compilation and run script.
		Work in progress, may need fixes and will be updated with more doc to
		explain things. Includes developer functions and basic tests.
		
		The application can be installed and started using:
		
		svn co http://www.molgenis.org/svn/molgenis/trunk/ molgenis
		svn co http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps
		ant -f molgenis_apps/xqtl_dev.xml make_run

    </description>
	
	<-
	The properties file supplied to the generator
	-
	<property name="app_properties" value="apps/lifelinesresearchportal/org/molgenis/lifelinesresearchportal/lifelinesresearchportal.properties"/>

	<-
	Application class path. Describes the location of the app and the modules it consists of.
	-
	<path id="app.class.path">
		<pathelement location="apps/lifelinesresearchportal" />
		<pathelement location="apps/xgap" />
		<pathelement location="apps/lifelines" />
		<pathelement location="generated/java" />
		<pathelement location="modules/datamodel" />
		<pathelement location="modules/auth" />
		<pathelement location="modules/file" />
		<pathelement location="modules/import" />
		<pathelement location="modules/webserver" />
		<pathelement location="modules/settings" />
		<pathelement location="modules/pheno" />
		<pathelement location="modules/search" />
		<pathelement location="modules/matrix" />
		<pathelement location="modules/decorators/core" />
		<pathelement location="modules/decorators/auth" />
		<pathelement location="modules/decorators/pheno" />
		<pathelement location="modules/decorators/data" />
		<pathelement location="publicdata" />
	</path>
	
	<- Path refs to build dirs -
	<property name="mol_build_dir" value="../molgenis/bin" />
	<property name="app_build_dir" value="build/classes" />

	<- Path ref to the molgenis libraries -
	<path id="molgenis-libs">
		<fileset dir="../molgenis/lib">
			<include name="**/*.jar" />
		</fileset>
	</path>

	<- Path ref to the application libraries -
	<path id="app-libs">
		<fileset dir="WebContent/WEB-INF/lib">
			<include name="**/*.jar" />
		</fileset>
	</path>
	
	<- path to MOLGENIS toolkit -
	<path id="molgenis.classpath">
		<pathelement location="${build.dir}" />
		<fileset dir="../molgenis/lib">
			<include name="**/*.jar" />
		</fileset>
		<fileset dir="WebContent/WEB-INF/lib">
			<include name="**/*.jar" />
		</fileset>
	</path>
	
	<target name="update-eclipse">
		<taskdef name="xmltask" classpathref="molgenis.classpath" classname="com.oopsconsultancy.xmltask.ant.XmlTask"/>

		<pathconvert property="app_xml" refid="app.class.path" pathsep="&quot;/&gt;&lt;classpathentry kind=&quot;src&quot; path=&quot;">
			<map from="${basedir}/" to="" />
		</pathconvert>
		
		<- add generated src as well -
		<property name="app_xml2" value="&lt;classpathentry kind=&quot;src&quot; path=&quot;${app_xml}&quot;/&gt;"/>
		<property name="app_xml3" value="${app_xml2}&lt;classpathentry kind=&quot;src&quot; path=&quot;${output_sql}&quot;/&gt;&lt;classpathentry kind=&quot;src&quot; path=&quot;${output_src}&quot;/&gt;"/>
		<echo message="eclipse .classpath xml: ${app_xml3}"/>
	
		<xmltask source=".classpath" dest=".classpath" outputter="simple">
			<remove path="classpath/classpathentry[@kind='src' and not(@exported)]"/>
			<insert path="classpath" position="under" xml="${app_xml3}"/>
		</xmltask>
	</target>

	<-
	CLEAN - Step 1: Delete the content of the app build, app generated and Molgenis build folders.
	-
	<target name="clean" description="Delete generated and build content">
		<- create build dirs if they doesn't exist -
		<mkdir dir="${mol_build_dir}"/>
		<mkdir dir="${app_build_dir}"/>
		
		<- remove content of build, ${mol_build_dir} and generated -
		<delete includeemptydirs="true">
			<fileset dir="${app_build_dir}" includes="**/*" />
		</delete>
		<delete includeemptydirs="true">
			<fileset dir="${mol_build_dir}" includes="**/*" />
		</delete>
		<delete includeemptydirs="true">
			<fileset dir="generated" includes="**/*" />
		</delete>
	</target>

	<-
	MAKE - Step 2: Compile MOLGENIS. This is assumed to be in your 'workspace'. (e.g. you run
	this script in '/somedir/molgenis_apps', then molgenis must be in '/somedir/molgenis')
	-
	<target name="compile_molgenis" description="Compile MOLGENIS">
		<- create build dir if it doesn't exist -
		<mkdir dir="${mol_build_dir}"/>
		
		<- Run javac on the src dir to be compiled into build, using the molgenis-libs fileset as classpath -
		<javac srcdir="../molgenis/src" destdir="${mol_build_dir}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath>
				<path refid="molgenis-libs" />
			</classpath>
		</javac>
		<- Copy the res folder to the build dir so it can be found by MolgenisResourceCopyGen -
		<copy todir="${mol_build_dir}/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="${mol_build_dir}" verbose="true">
			<fileset dir="../molgenis/src" includes="**/*.ftl" />
		</copy>
	</target>

	<-
	MAKE - Step 3: Generate the application. This assumes you have compiled molgenis.
	The molgenis/build and libraries are used as classpath.
	-
	<target name="generate_app" description="Generate the application">
		<java classname="org.molgenis.Molgenis" fork="yes" failonerror="true">
			<arg value="${app_properties}" />
			<classpath>
				<path refid="molgenis-libs" />
				<path location="${mol_build_dir}" />
			</classpath>
		</java>
	</target>

	<-
	MAKE - Step 4: Compile generated datatypes. However we must exclude the
	security decorators, which depend on the org.molgenis.auth.service module.
	 -
	<target name="compile_datatypes" description="Compile generated datatypes">
		<- create build dir if it doesn't exist -
		<mkdir dir="${app_build_dir}"/>
		
		<- Run javac into app_build, using molgenis-libs and molgenis_build -
		<javac srcdir="generated/java/org" excludes="**/*Decorator.java" destdir="${app_build_dir}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath>
				<path refid="molgenis-libs" />
				<path location="${mol_build_dir}" />
			</classpath>
		</javac>
	</target>

	<-
	MAKE - Step 5: Compile the actual application using the components specified in app.class.path.
	-
	<target name="compile_app" description="Compile application">
		<pathconvert targetos="unix" property="app_src" refid="app.class.path" />
		<javac srcdir="${app_src}" destdir="${app_build_dir}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath>
				<path refid="molgenis-libs" />
				<path refid="app-libs" />
				<path location="${mol_build_dir}" />
			</classpath>
		</javac>
	</target>

	<-
	MAKE - Step 6: Compile other generated parts that depends on having the application compiled first.
	-
	<target name="compile_other" description="Compile other generated">
		<javac srcdir="generated/java/app" destdir="${app_build_dir}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath>
				<path refid="molgenis-libs" />
				<path location="${mol_build_dir}" />
				<path location="WebContent/WEB-INF/lib/simplecaptcha-1.2.1.jar" />
			</classpath>
		</javac>
		<javac srcdir="generated/java/test" destdir="${app_build_dir}" includeantruntime="false" debug="true" debuglevel="lines,vars,source">
			<classpath>
				<path refid="molgenis-libs" />
				<path location="${mol_build_dir}" />
			</classpath>
		</javac>
	</target>


	<-
	MAKE - Step 7: Copy resources other than Java files from the locations of app.class.path into the build folder.
	-
	<target name="copy_resources">

		<- Grab the elements of app.class.path and convert to make a fileset pattern
		usable by fileset. We concatenate the elements with '/**/*,' to grab all files.
		The regexp cuts off everything until the original specified path location. Eg:
		"/Users/joerivandervelde/Workspaces/workspace-23-03-2010/molgenis_apps/apps/xgap"
		becomes "apps/xgap/**/*".
		-
		<pathconvert pathsep="/**/*," refid="app.class.path" property="app_fileset_pattern">
			<regexpmapper from=".*/(.*/.*)" to="\1" />
		</pathconvert>

		<- Grab all files from the fileset pattern, excluding Java files -
		<fileset dir="." id="app_fileset" includes="${app_fileset_pattern}/**/*">
			<exclude name="**/*.java" />
		</fileset>

		<- Copy to build dir. Use a regexp to remove the leading locations
		such as 'apps/xgap' or 'modules/pheno' -
		<copy todir="${app_build_dir}" verbose="true">
			<fileset refid="app_fileset" />
			<mapper type="regexp" from="^[-_a-zA-Z0-9]*/[-_a-zA-Z0-9]*/(.*)" to="\1" />
		</copy>
		
		<- Copy SQL files from generated/sql to build root -
		<copy todir="${app_build_dir}" verbose="true">				
			<fileset dir="generated/sql" includes="**/*.sql" />
		</copy>
	</target>
	
	<-
	RUN - Step 8: Start the application.
	-
	<target name="run" description="Start the application">
		<java maxmemory="512m" classname="boot.RunStandalone" fork="yes" failonerror="true">
			<classpath>
				<path refid="molgenis-libs" />
				<path refid="app-libs" />
				<path location="${mol_build_dir}" />
				<path location="${app_build_dir}" />
			</classpath>
		</java>
	</target>
	
	<-
	Deploy help: run on a specific port, and on that port only
	Usage: ant -f xqtl_dev.xml runOn -Dport=9000
	-
	<target name="runOn" description="Start the application">
		<java maxmemory="512m" classname="boot.RunStandalone" fork="yes" failonerror="true">
			<arg value="${port}"/>
			<classpath>
				<path refid="molgenis-libs" />
				<path refid="app-libs" />
				<path location="${mol_build_dir}" />
				<path location="${app_build_dir}" />
			</classpath>
		</java>
	</target>
	
	<-
	MAKE WRAPPER - All instructions to make the application in one bundle
	-
	<target name="make"  description="Make the application">
		<antcall target="compile_molgenis" />
		<antcall target="generate_app" />
		<antcall target="compile_datatypes" />
		<antcall target="compile_app" />
		<antcall target="compile_other" />
		<antcall target="copy_resources" />
	</target>
	
	<-
	CLEAN, MAKE - Clean and make the application.
	Used when setting up the app from scratch, but not starting the webserver
	or running any tests. Good for developing and running Selenium web
	tests separately later on.
	-
	<target name="clean_make" description="Clean and make the application">
		<antcall target="clean" />
		<antcall target="make" />
	</target>
	
	<-
	MAKE, RUN - The complete make & run procedure.
	Used when installing the app from a fresh SVN checkout.
	-
	<target name="make_run" description="Make and start the application">
		<antcall target="make" />
		<antcall target="run" />
	</target>
	
	<-
	CLEAN, MAKE, TEST - Clean and make the application, then run tests.
	Used for project validation on Hudson.
	-
	<target name="clean_make_test" description="Clean and make the application">
		<antcall target="clean" />
		<antcall target="make" />
		<antcall target="test" />
	</target>
	
	<-
	Dev help: Recompile/copy the app. Basically MAKE without the generation step.
	-
	<target name="recompile" description="Recompile/copy the application">
		<antcall target="compile_molgenis" />
		<antcall target="compile_datatypes" />
		<antcall target="compile_app" />
		<antcall target="compile_other" />
		<antcall target="copy_resources" />
	</target>
	
	<- Import TestNG as an Ant task -
	<taskdef resource="testngtasks" classpath="../molgenis/lib/testng-5.14.10.jar" />
	
	<-
	Dev help: Run xQTL tests on a compiled application.
	-
	<target name="test" description="Run all tests">
		<testng haltOnFailure="true">
			<classfileset dir="${app_build_dir}" includes="**/*_XqtlTestNG.class" />
			<classpath>
				<path refid="molgenis-libs" />
				<path refid="app-libs" />
				<path location="${mol_build_dir}" />
				<path location="${app_build_dir}" />
			</classpath>
		</testng>
	</target>
	
	<-
	Dev help: Remove HSQL database
	-
	<target name="deletedb" description="Delete generated and build content">
		<mkdir dir="hsqldb" />
		<delete includeemptydirs="true">
			<fileset dir="hsqldb" includes="**/*" />
		</delete>
	</target>
	
	<-
	Create a Java class with information about this build.
	SVN info part: http://stackoverflow.com/questions/166322/obtain-current-svn-revision-in-webapp
	Other listing from: http://www.ghidinelli.com/2008/04/01/built-in-ant-properties
	-
	<target name="generate_revision_info_class">
		<- Try to call SVN to get the revision number -
		<exec executable="svnversion" failifexecutionfails="no" outputproperty="revision">
			<arg value="."/> 
			<arg value="-n"/>
		</exec>
		
		<- If that failed, try a bash script. If ${revision} was already set, this has no effect -
		<exec executable="bash" failifexecutionfails="no" outputproperty="revision">
			<arg value="-c"/>
			<arg value="head .svn/entries | awk 'NR==4' | sed -e 's/\(.$\)/\1 (from bash, please install SVN)/g'"/>
		</exec>
		
		<- If that failed, set it to this message -
		<property name="revision" value="ERROR: Could not get revision number. Please install SVN and/or use Linux"/>
		
		<tstamp>
			<format property="time" pattern="MM/dd/yyyy hh:mm:ss aa" offset="0" unit="hour"/>
		</tstamp>

		<echo file="generated/java/app/servlet/BuildInfo.java">
		package app.servlet;
		import java.util.HashMap;
		/**
		* BuildInfo contains static build information for this project.
		* The class is generated by Ant the moment you compile your app.
		* This information can be helpful for provenance, testing or debugging.
		*/
		public class BuildInfo
		{
		public static HashMap&lt;String, String&gt; buildInfo = null;
		
		public BuildInfo(){
			buildInfo = new HashMap&lt;String, String&gt;();
			buildInfo.put("buildBy", "${user.name}");
			buildInfo.put("buildRevision", "${revision}");
			buildInfo.put("buildDate", "${time}");
			
			buildInfo.put("osName", "${os.name}");
			buildInfo.put("osArch", "${os.arch}");
			buildInfo.put("osVersion", "${os.version}");
			
			buildInfo.put("javaVersion", "${java.version}");
			buildInfo.put("javaVendor", "${java.vendor}");
			buildInfo.put("javaSpec", "${java.specification.version}");
			
			buildInfo.put("antVersion", "${ant.version}");
			buildInfo.put("antProjectName", "${ant.project.name}");
			buildInfo.put("antJavaVersion", "${ant.java.version}");
		}
		
		
		public static final String buildBy = "${user.name}";
		public static final String buildRevision = "${revision}";
		public static final String buildDate = "${time}";

		public static final String osName = "${os.name}";
		public static final String osArch = "${os.arch}";
		public static final String osVersion = "${os.version}";

		public static final String javaVersion = "${java.version}";
		public static final String javaVendor = "${java.vendor}";
		public static final String javaSpec = "${java.specification.version}";

		public static final String antVersion = "${ant.version}";
		public static final String antProjectName = "${ant.project.name}";
		public static final String antJavaVersion = "${ant.java.version}";
			
		<- can't output paths: unescaped backslash for MS Windows breaks the code
		printing file and line seps is also dangerous
		also put some pointless vars here
		public static final String fileSep = "${file.separator}";
		public static final String pathSep = "${path.separator}";
		public static final String lineSep = "${line.separator}";
		public static final String javaClassPath = "${java.class.path}";
		public static final String javaExtDirs = "${java.ext.dirs}";
		public static final String userHome = "${user.home}";
		public static final String userDir = "${user.dir}";
		public static final String javaVendorUrl = "${java.vendor.url}";
		public static final String javaHome = "${java.home}";
		public static final String basedir = "${basedir}";
		public static final String antFile =  "${ant.file}";
		public static final String antHome = "${ant.home}";
		public static final String javaSpecVendor = "${java.specification.vendor}";
		public static final String javaSpecName = "${java.specification.name}";
		public static final String javaClassVersion = "${java.class.version}";
		public static final String javaVmSpecVersion = "${java.vm.specification.version}";
		public static final String javaVmSpecVendor = "${java.vm.specification.vendor}";
		public static final String javaVmSpecName = "${java.vm.specification.name}";
		public static final String javaVmVersion = "${java.vm.version}";
		public static final String javaVmVendor = "${java.vm.vendor}";
		public static final String javaVmName = "${java.vm.name}";
		-
		}
		</echo>
	</target>
	
</project -->