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build.xml
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build.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE project [
<!ENTITY release_targets SYSTEM "./releaseTargets.xml">
]>
<project basedir="." default="targets" name="genepattern">
<import file="test/build.xml"/>
<description>JAR deployment for genepattern</description>
<property name="java.target" value="1.7" />
<property name="java.source" value="1.7" />
<property name="java.debug" value="off" />
<property name="java.optimize" value="on" />
<property name="java.visualizer.target" value="1.7" />
<property name="java.visualizer.source" value="1.7" />
<property location="lib" name="lib_compile" />
<property location="website/WEB-INF/lib" name="lib" />
<property location="src" name="src" />
<property location="build" name="build" />
<property name="junit.report.dir" location="${build}/junit/reports" />
<property location="." name="dist" />
<property name="classpath" value="${lib}/crimson.jar:${lib}/dom.jar:${lib}/ejb.jar:${lib}/genepattern.properties:${lib}/jaxb-rt-1.0-ea.jar:${lib}/jaxp-api.jar:${lib}/log4j-1.2.8.jar:${lib}/omnigene.jar:${lib}/oromatcher.jar:${lib}/runtask.jar:${lib}/sax.jar:${lib}/trove.jar:${lib}/xalan.jar:${lib}/xercesImpl.jar:${lib}/xsltc.jar:${lib}/image.jar:${lib}/colt.jar" />
<property name="common-manifest" value="gp-common.mf" />
<property name="uisupport-manifest" value="ui_support.mf" />
<property name="common-jarname" value="gp-common.jar" />
<property name="full-jarname" value="gp-full.jar" />
<property name="uisupport-jarname" value="ui_support.jar" />
<property name="runtask-jarname" value="runMain.jar" />
<property name="gp-library-jarname" value="GenePattern.jar" />
<!-- signed applet stuff for running visualizers from web page -->
<property name="runVisualizer-jarname" value="runVisualizer.jar" />
<path id="genepattern.root">
<pathelement location="${basedir}" />
</path>
<!-- bring in the release targets from their seperate file -->
&release_targets;
<property name="clover.dest" location="${basedir}/build/clover" />
<property name="clover.home" location="${user.home}/.gp_build/clover/clover-ant-3.2.0" />
<available file="${clover.home}/lib/clover.jar" property="clover.enabled" />
<target name="init-clover" if="clover.enabled">
<taskdef resource="cloverlib.xml" classpath="${clover.home}/lib/clover.jar"/>
<clover-env/>
</target>
<!-- Get all the files in the /lib directory and add them to the -->
<!-- Classpath -->
<target name="targets">
<echo>You probably want to use the following targets:</echo>
<echo>website: builds website (including R and Java clients)</echo>
<echo>tag: tags entire repository prior to an official build</echo>
</target>
<property name="tomcat.home" location="./installer-2014-sp1/gpdist/Tomcat" />
<target name="init" depends="init-clover">
<tstamp />
<property name="genepattern.root" value="${basedir}" />
<property name="genepattern.website" value="${genepattern.root}/website" />
<property name="genepattern.clients" value="${genepattern.root}/clients" />
<property name="genepattern.common" value="${genepattern.root}" />
<property name="genepattern.build" value="${genepattern.root}/build" />
<property name="defaultInstallDir" value="/xchip/gpint/gpdev03/gp-3.2" />
<property name="genepattern.installer" value="${genepattern.root}/installer-2014-sp1" />
<property name="genepattern.package" value="org/genepattern" />
<available file="post-compile.xml" property="post-compile.present" />
<!-- available file="${keyStore}" property="keyStore.present" / -->
<path id="library.classpath">
<fileset dir="${lib_compile}">
<include name="*.jar" />
<include name="*.zip" />
</fileset>
<fileset dir="${lib}">
<include name="*.jar" />
<include name="*.zip" />
</fileset>
<fileset dir="${genepattern.root}">
<include name="*.jar" />
<include name="*.zip" />
</fileset>
</path>
<path id="junit.classpath">
<fileset dir="lib">
<include name="*.jar" />
</fileset>
<fileset dir="test/lib">
<include name="*.jar" />
</fileset>
<pathelement location="${build}/junit/classes" />
<pathelement location="${build}" />
<fileset dir="website/WEB-INF/lib">
<!-- exclude older version of ant, so that we can use from the lib directory -->
<exclude name="ant-1.6.5.jar" />
<exclude name="ant-antlr-1.6.5.jar" />
<exclude name="ant-junit-1.6.5.jar" />
<exclude name="ant-launcher-1.6.5.jar" />
<exclude name="ant-swing-1.6.5.jar" />
<exclude name="groovy-all-1.0.jar" />
<!-- include the rest -->
<include name="*.jar" />
</fileset>
<!-- include src on classpath for tests which call getResourceAsStream -->
<pathelement location="test/src" />
<fileset dir="${clover.home}/lib" erroronmissingdir="false">
<include name="clover.jar" if="clover.enabled" />
</fileset>
</path>
<path id="jspc.classpath">
<pathelement location="${java.home}/../lib/tools.jar" />
<fileset dir="${tomcat.home}/bin">
<include name="*.jar" />
</fileset>
<fileset dir="${tomcat.home}/server/lib">
<include name="*.jar" />
</fileset>
<fileset dir="${tomcat.home}/common/lib">
<include name="*.jar" />
</fileset>
<fileset dir="build" includes="${full-jarname}" />
<fileset dir="lib" includes="*.jar" />
</path>
<mkdir dir="${build}" />
<mkdir dir="${build}/jars" />
<!-- for debugging only -->
<!-- echo message="My junit.classpath is ${toString:junit.classpath}" / -->
</target>
<target name="clover.clean" description="Deletes the clover database." depends="init" if="clover.enabled">
<clover-clean />
</target>
<target name="clean" depends="init">
<delete dir="applet-build" />
<delete quiet="true" failonerror="false">
<fileset dir="src/" includes="**/*.class" />
<fileset dir="website/" includes="**/*.class" />
<fileset dir="installer-2014-sp1/GP_server_Build_Output/" includes="**/*" />
<fileset dir="installer-2014-sp1/server_Build_Output/" includes="**/*" />
<fileset dir="installer-2014-sp1/" includes=".buildinstaller*.tmp/**" />
</delete>
<delete quiet="true" failonerror="false" includeemptydirs="true">
<fileset dir="build/" includes="**/*" excludes="placeholder.txt, log4j.properties, log4j2.xml" />
</delete>
<!-- <ant antfile="build.xml" dir="clients/MATLAB" target="clean" /> -->
<!--<ant antfile="build.xml" dir="clients/R" target="clean" >-->
<!--<property name="R.client.downloads" location="${R.client.downloads}" />-->
<!--</ant>-->
<delete quiet="true" failonerror="false" dir="${junit.report.dir}" />
<delete quiet="true" failonerror="false" dir="wartemp" />
<delete quiet="true" failonerror="false" dir="ziptemp" />
<delete quiet="true" failonerror="false" file="gp_war.zip" />
</target>
<target name="clean-jspc">
<delete quiet="true" failonerror="false">
<fileset dir="${webapp.path}/WEB-INF/classes/org/apache/jsp" includes="**/*.class" />
<fileset dir="${webapp.path}/WEB-INF/src/org/apache/jsp" includes="**/*.java" />
</delete>
</target>
<target name="clean-all" depends="init, clover.clean, clean-jspc, clean" />
<target name="findbugs" depends="init, compile, common" description="Findbugs static code analysis">
<property name="findbugs.home" value="build_tools/findbugs-3.0.1" />
<taskdef name="findbugs" classname="edu.umd.cs.findbugs.anttask.FindBugsTask">
<classpath>
<pathelement location="${findbugs.home}/lib/findbugs-ant.jar"/>
</classpath>
</taskdef>
<findbugs home="${findbugs.home}" output="xml" outputFile="findbugs.xml" excludeFilter="findbugsExcludeFilter.xml">
<auxClasspath path="${library.classpath}" />
<sourcePath path="${basedir}/src" />
<class location="${build}/${full-jarname}" />
</findbugs>
</target>
<target name="compile-junit" depends="init,compile">
<mkdir dir="${build}/junit/classes" />
<javac debug="true"
includeantruntime="false"
classpathref="junit.classpath"
destdir="${build}/junit/classes"
srcdir="test/src"
/>
</target>
<target name="junit" depends="compile-junit">
<mkdir dir="${junit.report.dir}" />
<mkdir dir="${junit.report.dir}/xml" />
<mkdir dir="${junit.report.dir}/html" />
<property name="junit.forkmode" value="once" /> <!-- set forkmode=once to create only a single JVM, set forkmode=perTest to fork a new JVM for each test -->
<!-- junit includeantruntime="yes" printsummary="withOutAndErr" haltonfailure="no" showoutput="yes" filtertrace="off"> -->
<junit includeantruntime="yes" printsummary="no" haltonfailure="no" showoutput="no" filtertrace="on" fork="true" forkmode="${junit.forkmode}">
<formatter type="xml"/>
<classpath refid="junit.classpath" />
<batchtest todir="${junit.report.dir}/xml" filtertrace="on">
<fileset dir="test/src">
<exclude name="org/genepattern/junitutil/*.java" />
<exclude name="**/RecordEulaStub.java" />
<!-- skip the FTP integration tests -->
<exclude name="org/genepattern/server/job/input/TestFileDownloader.java" />
<include name="**/*.java" />
</fileset>
</batchtest>
</junit>
<junitreport todir="${junit.report.dir}">
<fileset dir="${junit.report.dir}/xml">
<include name="*.xml" />
</fileset>
<report format="frames" todir="${junit.report.dir}/html" />
</junitreport>
</target>
<target name="compile" depends="init, initBuildProperties" description="Compiles all the source.">
<javac debug="true"
includeantruntime="false"
source="${java.source}" target="${java.target}"
classpathref="library.classpath"
destdir="${genepattern.build}"
srcdir="${src}"
excludes="org/genepattern/server/analysis/*,org/genepattern/server/handler/*,org/genepattern/jaxb/**"
/>
<copy todir="${genepattern.build}">
<fileset dir="${src}" includes="**/*.xml" />
</copy>
</target>
<target depends="init" name="get_dependencies">
<copy todir="${build}">
<fileset dir="${lib}" includes="**/*.jar" />
</copy>
</target>
<target name="gp-library-doc" depends="init" unless="skipdoc" description="Builds the javadoc for the Java programming API">
<!-- requires https://svnrepos/gp2/modules be checked out to ../modules -->
<property name="gp.modules.src.dir" value="../modules/common/src/" />
<javadoc destdir="clients/Java/doc" Author="no" Public="true" Verbose="false" sourcepath="website/WEB-INF/gp-modules.jar" classpathref="library.classpath">
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/cls/*.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/featureset/*.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/gct/*.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/mage/*.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/odf/*.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/res/*.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/snp/*.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/stanford/*.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/io/ParseException.java, org/genepattern/io/IOUtil.java,
org/genepattern/io/DefaultDatasetCreator.java, org/genepattern/io/DatasetWriter.java, org/genepattern/io/DatasetParser.java,
org/genepattern/io/DatasetHandler.java, org/genepattern/io/DatasetCreator.java, org/genepattern/module/AnalysisUtil.java,
org/genepattern/module/VisualizerUtil.java" />
<fileset dir="${gp.modules.src.dir}" includes="org/genepattern/matrix/*.java" />
<fileset dir="src">
<include name="org/genepattern/client/GPClient.java" />
<include name="org/genepattern/client/Util.java" />
<include name="org/genepattern/webservice/JobResult.java" />
<include name="org/genepattern/webservice/Parameter.java" />
</fileset>
</javadoc>
</target>
<target name="javadoc-all" depends="compile" unless="skipdoc"
description="Builds the javadoc for all classes in the GP project">
<javadoc destdir="build/javadoc/all" packagenames="org.genepattern.*"
sourcepath="src"
defaultexcludes="yes"
author="true"
version="true"
use="true"
windowtitle="GenePattern API"
classpathref="library.classpath"
>
<doctitle><![CDATA[<h1>GenePattern API</h1>]]></doctitle>
<bottom><![CDATA[<i>Copyright (c) 2003-2022 Regents of the University of California and Broad Institute</i>]]></bottom>
</javadoc>
</target>
<target name="javadoc-jobrunner" depends="compile" unless="skipdoc"
description="Builds the javadoc for the JobRunner API">
<javadoc
additionalparam="-Xdoclint:none"
destdir="build/javadoc/jobrunner"
defaultexcludes="yes"
author="true"
version="true"
use="true"
windowtitle="JobRunner API"
classpathref="library.classpath"
>
<!-- jobrunner api -->
<packageset dir="src" defaultexcludes="yes">
<include name="org/genepattern/drm/**" />
<include name="org/genepattern/server/config/**" />
<exclude name="com/dummy/test/doc-files/**"/>
</packageset>
<!-- awsbatch integration -->
<packageset dir="gp-jobrunner-awsbatch/src/main/java" defaultexcludes="yes">
<include name="org/genepattern/server/executor/awsbatch/**"/>
<exclude name="com/dummy/test/doc-files/**"/>
</packageset>
<doctitle><![CDATA[<h1>GenePattern JobRunner API</h1>]]></doctitle>
<bottom><![CDATA[<i>Copyright (c) 2003-2022 Regents of the University of California and Broad Institute</i>]]></bottom>
</javadoc>
</target>
<target name="gp-library" depends="init" description="builds GenePattern.zip, the zip file containing the Java programming API">
<jar basedir="${genepattern.build}" defaultexcludes="true" includes="log4j2.xml, log4j.properties, org/**/*.class, edu/**/*.class, **/*.xml" jarfile="${genepattern.build}/${gp-library-jarname}">
<manifest>
<attribute name="Class-Path" value="./lib/axis.jar ./lib/commons-codec-1.6.jar ./lib/commons-discovery-0.2.jar ./lib/commons-httpclient-3.1.jar ./lib/commons-logging.jar ./lib/gp-modules.jar ./lib/jaxb-rt-1.0-ea.jar ./lib/jaxrpc.jar ./lib/log4j-1.2-api-2.12.4.jar ./lib/log4j-api-2.12.4.jar ./lib/log4j-core-2.12.4.jar ./lib/javax.mail.jar ./lib/saaj.jar ./lib/trove.jar ./lib/wsdl4j-1.5.1.jar ./lib/Jama-1.0.1.jar ./lib/MAGEstk-2003-10-24-v1.1-compatible.jar " />
</manifest>
</jar>
<zip destfile="build/GenePattern.zip">
<zipfileset dir="${genepattern.build}">
<include name="${gp-library-jarname}" />
</zipfileset>
<zipfileset dir="website/WEB-INF/lib" prefix="lib" includes="axis.jar commons-codec-1.6.jar commons-discovery-0.2.jar commons-httpclient-3.1.jar commons-logging.jar gp-modules.jar jaxb-rt-1.0-ea.jar jaxrpc.jar log4j-1.2.17.jar javax.mail.jar saaj.jar trove.jar wsdl4j-1.5.1.jar Jama-1.0.1.jar MAGEstk-2003-10-24-v1.1-compatible.jar guava-15.0.jar" />
<zipfileset dir="clients/Java/doc" prefix="doc" />
</zip>
</target>
<target name="common" depends="init,compile,compile-jspc"
description="Create the gp-full.jar file in the build directory"
>
<!-- Makes gp-common.jar -->
<jar basedir="${genepattern.build}" defaultexcludes="true" excludes="org/genepattern/util/RunGenePatternTaskMain.class org/genepattern/util/GenePatternNetworkClassLoader.class,org/genepattern/server/**,org/genepattern/resources/**,**/*.java,**/*.form,**/*.nbattrs" includes="org/**/*.class" jarfile="${genepattern.build}/${common-jarname}" />
<!-- get code fragments for pipeline code generation -->
<copy todir="${build}">
<fileset dir="${src}" includes="**/*.code" />
</copy>
<jar basedir="${genepattern.build}" defaultexcludes="true" excludes="**/*.form,**/*.nbattrs" includes="org/**/*.class, edu/mit/genome/gp/ui/analysis/*.class, **/*.xml" jarfile="${genepattern.build}/${full-jarname}" />
<jar basedir="${genepattern.build}" defaultexcludes="true" excludes="**/*.form,**/*.nbattrs" includes="edu/mit/genome/gp/ui/analysis/*.class" jarfile="${genepattern.build}/analysis.jar">
<manifest>
<attribute name="Class-Path" value="${full-jarname} hsqldb.jar xalan.jar saaj.jar jaxrpc.jar jaxb-rt-1.0-ea.jar" />
</manifest>
</jar>
</target>
<target depends="init" name="runtask">
<javac debug="true"
includeantruntime="false"
classpathref="library.classpath"
destdir="${genepattern.build}"
srcdir="${src}"
source="${java.source}"
target="${java.target}"
includes="org/genepattern/util/RunGenePatternTaskMain.java"
/>
<!-- Makes runMain.jar -->
<jar basedir="${genepattern.build}" defaultexcludes="true" excludes="**/*.form,**/*.nbattrs" includes="org/genepattern/util/RunGenePatternTaskMain.class edu/mit/genome/gp/util/GenePatternNetworkClassLoader.class" jarfile="${genepattern.build}/${runtask-jarname}">
<manifest>
<attribute name="Main-Class" value="org.genepattern.RunGenePatternTaskMain" />
</manifest>
</jar>
</target>
<target depends="init,compile" name="uisupport">
<jar basedir="${genepattern.build}" defaultexcludes="true" excludes="**/*.java,**/*.form,**/*.nbattrs" includes="org/genepattern/modules/ui/,org/genepattern/module/" jarfile="${genepattern.build}/${uisupport-jarname}" />
</target>
<target depends="common,compile,get_dependencies,init,runtask,uisupport" name="package">
</target>
<target depends="init" name="jwhich">
<java classname="org.genepattern.debug.JWhich" classpathref="library.classpath" dir="${build}" fork="true">
<arg value="javax.ejb.EJBObject" />
</java>
</target>
<target depends="init" name="prepare-compile" unless="prepare.disable">
<mkdir dir="${genepattern.build}" />
</target>
<target depends="init" name="runsuite">
<java classname="org.genepattern.server.process.SuiteRepository">
<classpath>
<fileset dir="lib">
<include name="**/*.jar" />
</fileset>
<fileset dir="${build}" />
</classpath>
</java>
</target>
<target name="clients" depends="R-client,matlabclient">
</target>
<property name="R.client.downloads" location="clients/R/downloads" />
<target name="R-client" depends="init, gp-library">
<ant antfile="build.xml" dir="${genepattern.root}/clients/R">
<property name="R.client.downloads" location="${R.client.downloads}" />
</ant>
</target>
<target name="matlabclient" depends="gp-library, analysis">
<ant antfile="build.xml" dir="${genepattern.root}/clients/MATLAB" />
</target>
<target name="analysis" depends="init,common,runtask,uisupport">
<jar jarfile="${build}/gpwebservice.jar">
<fileset dir="${build}">
<include name="org/apache/xml/**" />
<include name="org/genepattern/**" />
</fileset>
</jar>
</target>
<target name="show-version" depends="initBuildProperties">
<echo>
genepattern.version: ${genepattern.version}
version.label: ${version.label}
version.revision.id: ${version.revision.id}
version.build.date: ${version.build.date}
</echo>
</target>
<target name="installers" depends="website">
<ant dir="${genepattern.installer}" inheritall="false" inheritrefs="false" target="installers" />
</target>
<target name="build-visualizer-applet" depends="jar-visualizer-applet" />
<target name="compile-visualizer-applet" depends="init">
<mkdir dir="applet-build" />
<javac debug="true"
includeantruntime="false"
destdir="applet-build"
srcdir="src"
classpathref="library.classpath"
includes="org/genepattern/visualizer/*.java"
target="${java.visualizer.target}"
source="${java.visualizer.source}" />
</target>
<target name="jar-visualizer-applet" depends="compile-visualizer-applet">
<mkdir dir="${genepattern.build}/META-INF" />
<manifest file="${genepattern.build}/META-INF/MANIFEST.MF">
<attribute name="Permissions" value="all-permissions" />
<attribute name="Trusted-Library" value="true" />
<attribute name="Application-Name" value="GenePattern Visualizer launcher" />
</manifest>
<jar basedir="applet-build"
manifest="${genepattern.build}/META-INF/MANIFEST.MF"
defaultexcludes="true"
includes="org/genepattern/visualizer/*.class"
jarfile="${genepattern.build}/${runVisualizer-jarname}">
</jar>
</target>
<macrodef name="signjar" uri="http://genepattern.org/gp">
<attribute name="jarfile" />
<element name="sysproperties" />
<sequential>
<echo>signing @{jarfile} with keystore=${signjar.keystore}</echo>
<signjar jar="@{jarfile}"
preservelastmodified="true"
keystore="${signjar.keystore}"
maxmemory="1024M"
alias="${signjar.alias}"
storepass="${signjar.storepass}"
tsaurl="${signjar.tsaurl}"
/>
</sequential>
</macrodef>
<target name="init-signjar">
<!-- load signjar.properties -->
<property file="${user.home}/.gp_build/signjar.properties" />
<property file="signjar.properties" />
<!-- for properties not set in 'signjar.properties', set defaults directly -->
<property name="signjar.keystore" location="${build}/keystore" />
<property name="signjar.alias" value="Genepattern" />
<!-- if not otherwise defined, prompt for password -->
<input message="Password for Jar Signing Key: " addproperty="signjar.storepass" defaultValue="gEnEpAtTeRn">
<handler classname="org.apache.tools.ant.input.SecureInputHandler" />
</input>
<available file="${signjar.keystore}" property="keyStore.present" />
<!--
Set the time-stamp authority url for signing the jar file.
signjar ... -t {signjar.tsaurl} ...
Time-stamping allows signed jar files to be used after the signing certificate expires.
Additional time-stamp authorities are listed here (https://www.entrust.com/what-is-time-stamping/):
RFC 3161 (SHA-1) – http://timestamp.entrust.net/TSS/RFC3161sha1TS
-->
<property name="signjar.tsaurl" value="https://timestamp.geotrust.com/tsa" />
</target>
<target name="makeKeystore" depends="init-signjar" unless="keyStore.present">
<genkey alias="GenePattern" keypass="${signjar.storepass}" storepass="${signjar.storepass}" keystore="${signjar.keystore}" keyalg="RSA">
<dname>
<param name="CN" value="GenePattern" />
<param name="OU" value="Cancer Genomics" />
<param name="O" value="Broad Institute" />
<param name="L" value="Cambridge" />
<param name="S" value="MA" />
<param name="C" value="US" />
<param name="EMAILADDRESS" value="genepattern-team@broadinstitute.org" />
</dname>
</genkey>
</target>
<target name="sign-visualizer-applet" depends="jar-visualizer-applet,init-signjar,makeKeystore"
description="Sign the visualizer applet jar files"
xmlns:gp="http://genepattern.org/gp"
>
<gp:signjar jarfile="${genepattern.build}/${runVisualizer-jarname}">
<sysproperties>
<sysproperty key="https.protocols" value="TLSv1.2" />
</sysproperties>
</gp:signjar>
<gp:signjar jarfile="external-src/commons-httpclient-3.0.1/dist/commons-httpclient.jar" />
<gp:signjar jarfile="website/WEB-INF/lib/commons-codec-1.6.jar" />
</target>
<!-- =================================================================== -->
<!-- Custom post-compilation step -->
<!-- =================================================================== -->
<target depends="init" if="post-compile.present" name="post-compile">
<ant antfile="post-compile.xml" dir="${genepattern.root}" />
</target>
<!-- classpathref="library.classpath" -->
<target depends="init,prepare-compile,common,analysis,build-visualizer-applet" name="website">
<mkdir dir="${genepattern.build}/website/classes" />
<mkdir dir="${genepattern.build}/website/lib" />
<ant antfile="build.xml" dir="${genepattern.root}/clients/MATLAB" />
<mkdir dir="${genepattern.website}/WEB-INF/classes" />
<javac debug="true"
includeantruntime="false"
destdir="${genepattern.build}/website/classes"
srcdir="${genepattern.website}/WEB-INF/classes"
classpathref="library.classpath"
/>
<!-- copy the web sites jar files to build/web-site/lib -->
<!-- ***** NOTE THAT THIS IS THE DEFINITIVE LIST ****** -->
<copy todir="${genepattern.build}/website/lib">
<fileset dir="${lib}">
<include name="axis.jar" />
<include name="axis-ant.jar" />
<include name="commons-discovery-0.2.jar" />
<include name="commons-logging.jar" />
<include name="commons-fileupload-1.1.1.jar" />
<include name="commons-io-2.0.1.jar" />
<include name="hsqldb.jar" />
<include name="jaxb-rt-1.0-ea.jar" />
<include name="jaxp.jar" />
<include name="jaxrpc.jar" />
<include name="jdom.jar" />
<include name="jspsmart.jar" />
<include name="log4j-1.2.8.jar" />
<include name="javax.mail.jar" />
<include name="PDFBox*.jar" />
<include name="saaj.jar" />
<include name="wsdl4j-1.5.1.jar" />
<include name="xalan.jar" />
</fileset>
<fileset dir="${genepattern.build}" includes="${full-jarname}" />
</copy>
<!-- Now call any custom post-compilation people want to do -->
<antcall target="post-compile" inheritall="true" inheritrefs="true" />
</target>
<target depends="init,common,analysis,build-visualizer-applet" name="quick-website">
<mkdir dir="${genepattern.build}/website/classes" />
<javac debug="true"
includeantruntime="false"
destdir="${genepattern.build}/website/classes"
srcdir="${genepattern.website}/WEB-INF/classes"
classpathref="library.classpath"
/>
<!-- Now call any custom post-compilation people want to do -->
<antcall target="post-compile" />
</target>
<target name="initBuildProperties"
description="Updates the build.properties file." >
<property file="build.versionNumbers" />
<property name="build.properties.file" value="website/WEB-INF/build.properties" />
<propertyfile file="${build.properties.file}" comment="Created by ANT; defines the build version, date etc.">
<entry key="genepattern.version" type="string" value="${genepattern.version}" />
<entry key="version.label" type="string" value="${version.label}" />
<entry key="version.revision.id" type="string" value="${version}" />
<entry key="version.build.date" type="date" pattern="yyyy-MM-dd HH:mm" value="${TSTAMP}" />
<entry key="builders.name" operation="=" type="string" value="${user.name}" />
<!-- add entries required for GenePattern Client installation -->
<entry key="build" operation="=" pattern="yyyyMMdd" type="date" value="now" />
<entry key="date" pattern="EEE, MMM d yyyy" type="date" value="now" />
<entry key="version.major" operation="=" type="int" value="${version.major}" />
<entry key="version.minor" operation="=" type="string" value="${version.minor}" />
<entry key="version.revision" operation="=" type="int" value="0" default="-1" />
<entry key="count" operation="+" type="int" default="0" />
<entry key="release" operation="=" type="string" value="" />
<entry key="program.name" operation="=" type="string" value="GenePattern Client" />
<entry key="build.tag" operation="=" type="string" value="${version}" />
</propertyfile>
<property file="${build.properties.file}" />
</target>
<target name="nightlyBuild" depends="initBuildProperties, website, gp-library, installers, createWar, copyWar" />
<property name="webapp.path" value="website" />
<target name="jspc" depends="init" description="generate .java files from .jsp files">
<property name="output.dir" value="${webapp.path}/WEB-INF/src" />
<mkdir dir="${webapp.path}/WEB-INF/src" />
<delete>
<fileset dir="${output.dir}" includes="**" />
</delete>
<taskdef classname="org.apache.jasper.JspC" name="jasper2" classpathref="jspc.classpath" />
<jasper2 validateXml="false" uriroot="${webapp.path}" addWebXmlMappings="true" webXmlFragment="${webapp.path}/WEB-INF/generated_web.xml" outputDir="${output.dir}" />
</target>
<target name="compile-jspc" depends="jspc, compile" description="generate .class files from .jsp files">
<mkdir dir="${webapp.path}/WEB-INF/classes" />
<javac debug="${java.debug}"
includeantruntime="false"
source="${java.source}" target="${java.target}"
optimize="${java.optimize}"
destdir="${webapp.path}/WEB-INF/classes"
srcdir="${webapp.path}/WEB-INF/src"
>
<classpath>
<path refid="library.classpath" />
<path refid="jspc.classpath" />
<pathelement location="${genepattern.build}" />
</classpath>
</javac>
</target>
</project>