build.xml

<?xml version="1.0" encoding="utf-8"?>
<project name="biobank" basedir="." default="deploy"
	 xmlns:ivy="antlib:org.apache.ivy.ant"
	 xmlns:flyway="antlib:com.googlecode.flyway.ant">
  <!--

      Overall build file
      use command "ant -projecthelp" to display the targets.

  -->

  <property environment="env" />
  <property name="doxygen" location="/usr/bin/doxygen" />
  <property name="xsltproc" location="/usr/bin/xsltproc" />

  <!-- TODO: move as many properties as possible into build.properties -->
  <!-- TODO: add tasks to push database properties to various files -->
  <!-- TODO: create a cacore directory with all the cacore stuff in it
       that we can throw into the war file and use to create the database -->
  <property file="build.properties" />
  <property file="client.properties" />
  <property file="db.properties" />

  <!-- must use a property with a LOCATION attribute because it is converted
       to be an absolute value, which the product builder seems to require in
       order to load its build.properties in product/build.properties -->
  <property name="product.dir" location="product" />
  <property name="buildDirectory" value="${product.dir}/buildDirectory" />

  <path id="flyway.lib.path">
    <fileset dir="${lib.dir}/flyway" includes="*.jar"/>
  </path>

  <path id="flyway.classpath">
    <fileset dir="${lib.dir}/build" includes="mysql-connector-java.jar"/>
    <fileset dir="${lib.dir}/flyway" includes="*.jar"/>
  </path>

  <import file="build-db.xml"/>
  <import file="build-i18n.xml"/>
  <import file="build-eclipse.xml"/>
  <import file="build-tests.xml"/>
  <import file="build-tools.xml"/>

  <condition property="databse.exec.haveUserAndPassword">
    <and>
      <isset property="database.exec.username" />
      <isset property="database.exec.password" />
    </and>
  </condition>

  <condition property="perl" value="perl" else="/usr/bin/perl">
    <os family="windows" />
  </condition>
  <condition property="debugFileExtension" value="-debug" else="">
    <equals arg1="${debug}" arg2="true" casesensitive="false" trim="true" />
  </condition>

  <fileset id="biobank.common.server.build.classpath" dir="${eclipse.proj.dir.common}/lib/server">
    <include name="csmapi.jar" />
    <include name="flyway-core.jar" />
    <include name="jta.jar" />
    <include name="sdk-core.jar" />
    <include name="sdk-writable-core.jar" />
    <include name="spiffy-all.jar" />
    <include name="supercsv.jar" />
    <include name="commons-lang.jar" />
  </fileset>

  <fileset id="biobank.common.client.build.classpath" dir="${eclipse.proj.dir.common}/lib/client">
    <include name="acegi-security.jar" />
    <include name="antlr.jar" />
    <include name="asm.jar" />
    <include name="axis.jar" />
    <include name="caGrid-CQL-cql.jar" />
    <include name="castor.jar" />
    <include name="cglib.jar" />
    <include name="cog-jglobus.jar" />
    <include name="commons-codec.jar" />
    <include name="commons-collections.jar" />
    <include name="commons-discovery.jar" />
    <include name="commons-lang.jar" />
    <include name="commons-logging.jar" />
    <include name="dom4j.jar" />
    <include name="ehcache.jar"/>
    <include name="gettext-commons.jar" />
    <include name="hibernate-commons-annotations.jar"/>
    <include name="hibernate-core.jar" />
    <include name="hibernate-ehcache.jar"/>
    <include name="hibernate-envers.jar" />
    <include name="hibernate-jpa-2.0-api.jar" />
    <include name="hibernate-validator.jar" />
    <include name="javassist.jar" />
    <include name="jaxrpc.jar" />
    <include name="jdom.jar"/>
    <include name="jsse.jar" />
    <include name="jta.jar" />
    <include name="log4j.jar" />
    <include name="messages.jar" />
    <include name="mysql-connector-java.jar" />
    <include name="ognl.jar" />
    <include name="saaj.jar" />
    <include name="sdk-client-framework.jar" />
    <include name="sdk-grid-remoting.jar" />
    <include name="sdk-security.jar" />
    <include name="sdk-writable-client-framework.jar" />
    <include name="slf4j-api.jar" />
    <include name="slf4j-log4j12.jar" />
    <include name="spring.jar" />
    <include name="validation-api.jar" />
    <include name="wsdl4j.jar" />
    <include name="xercesImpl.jar" />
    <include name="xpp3.jar" />
    <include name="xstream.jar" />
  </fileset>

  <path id="biobank.common.build.classpath">
    <fileset refid="biobank.common.server.build.classpath" />
    <fileset refid="biobank.common.client.build.classpath" />
  </path>

  <!-- for tests -->
  <path id="biobank.common.run.classpath">
    <fileset refid="biobank.common.server.build.classpath" />
    <fileset refid="biobank.common.client.build.classpath" />
    <pathelement location="${eclipse.proj.dir.common}/output" />
  </path>

  <target name="flyway-set-properties" depends="resolve,get-db-executor,build-common-project">
    <taskdef uri="antlib:com.googlecode.flyway.ant"
             resource="com/googlecode/flyway/ant/antlib.xml"
             classpathref="flyway.lib.path"
	     onerror="ignore" />

    <property name="flyway.driver" value="${database.driver}"/>
    <property name="flyway.url" value="${database.url}"/>
    <property name="flyway.user" value="${database.exec.username}"/>
    <property name="flyway.password" value="${database.exec.password}"/>
    <property name="flyway.schemas" value="${database.name}"/>
    <!--property name="flyway.locations"
	value="edu.ualberta.med.biobank.migration,db/migrations"/-->
    <property name="flyway.locations" value="edu.ualberta.med.biobank.migration,db/migrations"/>

    <copy file="${secu-log.dir}/jboss/flyway-application-config.xml.template"
	  tofile="${lib.dir}/flyway/flyway-application-config.xml"/>
    <replace file="${lib.dir}/flyway/flyway-application-config.xml">
      <replacefilter token="@database.url@" value="${database.url}"/>
      <replacefilter token="@database.driver@" value="${database.driver}"/>
      <replacefilter token="@database.username@" value="${database.username}"/>
      <replacefilter token="@database.password@" value="${database.password}"/>
    </replace>

    <jar destfile="${lib.dir}/flyway/migrations.jar"
	 basedir="."
	 includes="db/migration/**">
      <fileset dir="${eclipse.proj.dir.common}/output" includes="**/migration/*.class"/>
    </jar>
  </target>

  <target name="flyway-clean" depends="flyway-set-properties">
    <flyway:clean/>
  </target>

  <target name="flyway-info" depends="flyway-set-properties">
    <flyway:info/>
  </target>

  <target name="flyway-init" depends="flyway-set-properties">
    <flyway:init/>
  </target>

  <target name="flyway-migrate" depends="flyway-set-properties">
    <flyway:migrate/>
  </target>

  <target name="flyway-repair" depends="flyway-set-properties">
    <flyway:repair/>
  </target>

  <target name="flyway-validate" depends="flyway-set-properties">
    <flyway:validate/>
  </target>

  <property name="ivy.install.version" value="2.2.0" />
  <condition property="ivy.home" value="${env.IVY_HOME}">
    <isset property="env.IVY_HOME" />
  </condition>
  <property name="ivy.home" value="${user.home}/.ant" />
  <property name="ivy.jar.dir" value="${ivy.home}/lib" />
  <property name="ivy.jar.file" value="${ivy.jar.dir}/ivy.jar" />

  <target name="download-ivy" unless="offline">

    <mkdir dir="${ivy.jar.dir}"/>
    <!-- download Ivy from web site so that it can be used even without any special installation -->
    <get src="http://repo2.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/ivy-${ivy.install.version}.jar"
         dest="${ivy.jar.file}" usetimestamp="true"/>
  </target>

  <target name="init-ivy" depends="download-ivy">
    <!-- try to load ivy here from ivy home, in case the user has not already dropped
         it into ant's lib dir (note that the latter copy will always take precedence).
         We will not fail as long as local lib dir exists (it may be empty) and
         ivy is in at least one of ant's lib dir or the local lib dir. -->
    <path id="ivy.lib.path">
      <fileset dir="${ivy.jar.dir}" includes="*.jar"/>

    </path>
    <taskdef resource="org/apache/ivy/ant/antlib.xml"
             uri="antlib:org.apache.ivy.ant" classpathref="ivy.lib.path"/>
  </target>

  <target name="check-dependencies-uptodate">
    <uptodate property="dependencies.uptodate">
      <srcfiles dir="." includes="ivy.xml"/>
      <mapper type="merge" to="${lib.dir}/.dependencies.resolved"/>
    </uptodate>
  </target>

  <target name="resolve" depends="init-ivy,check-dependencies-uptodate" unless="dependencies.uptodate"
	  description="--> retrieve dependencies with ivy">

    <ivy:retrieve pattern="lib/build/[artifact].[ext]" conf="biobank.build"  type="jar" />
    <ivy:retrieve pattern="lib/[conf]/[artifact].[ext]"
		  conf="hibernatetool,biobank.webapp"  type="jar" />

    <ivy:retrieve pattern="lib/[conf]/[artifact].[ext]" conf="flyway"  type="jar" />
    <ivy:retrieve pattern="lib/[conf]//[artifact]-[type].[ext]" conf="flyway" type="source" />

    <ivy:retrieve pattern="eclipse_ws/biobank.common/lib/client/[artifact].[ext]" conf="biobank.common.client" type="jar" />
    <ivy:retrieve pattern="eclipse_ws/biobank.common/lib/client/[artifact]-[type].[ext]" conf="biobank.common.client" type="source" />

    <ivy:retrieve pattern="eclipse_ws/biobank.common/lib/server/[artifact].[ext]" conf="biobank.common.server" type="jar" />
    <ivy:retrieve pattern="eclipse_ws/biobank.common/lib/server/[artifact]-[type].[ext]" conf="biobank.common.server" type="source" />

    <ivy:retrieve pattern="eclipse_ws/[conf]/lib/[artifact].[ext]"
		  conf="biobank.gui.common,biobank.mvp,biobank2,biobank2.tools,biobank2.tests"
		  type="jar" />

    <ivy:retrieve pattern="eclipse_ws/[conf]/lib/[artifact]-[type].[ext]"
		  conf="biobank.gui.common,biobank.mvp,biobank2,biobank2.tools,biobank2.tests"
		  type="source" />
    <touch file="${lib.dir}/.dependencies.resolved" />
  </target>

  <target name="report" depends="resolve" description="--> generates a report of dependencies">
    <ivy:report todir="${output.dir}"
		conf="biobank.common.client,biobank.common.server,biobank.gui.common,biobank.mvp,biobank2,biobank2.tools,biobank2.tests" />
  </target>

  <target name="clean-ivy" depends="init-ivy"
	  description="--> cleans ivy temporary files">
    <delete>
      <fileset dir="${lib.dir}" includes=".dependencies.resolved"/>
    </delete>
  </target>

  <target name="clean-cache" depends="init-ivy" description="--> cleans the ivy cache">
    <ivy:cleancache />
  </target>

  <target name="check-messages-jar-exists">
    <available file="${lib.dir}/messages.jar" property="messages-jar-exists" />
  </target>

  <target name="create-messages-jar" depends="check-messages-jar-exists"
	  unless="messages-jar-exists">
    <antcall target="messages-jar"/>
  </target>


  <target name="versions-update"
          depends="server-manifest,biobank-version-modify"
	  description="--> update version strings on server and client">
  </target>

  <target name="deploy-eclipse" depends="resolve,client-branding,create-messages-jar,biobank-version-modify"
	  description="--> retrieve dependencies for eclipse projects">
    <copy file="${lib.dir}/messages.jar" todir="${eclipse.proj.dir}/lib"/>
    <copy file="${lib.dir}/messages.jar" todir="${eclipse.proj.dir.common}/lib/client"/>

      <!-- File needed in the test project to call csm api methods -->
    <copy file="sdk_conf/biobank.csm.new.hibernate.cfg.xml" todir="${eclipse.proj.dir.tests}/src" />
  </target>

  <target name="get-db-executor" unless="databse.exec.haveUserAndPassword">
    <input message="Enter database executor's username (to execute database commands)"
           addProperty="database.exec.username"
           defaultValue="root" />
    <input message="Enter password"
           addProperty="database.exec.password"
           defaultValue="">
      <handler type="secure" />
    </input>
  </target>

  <target name="check-db-user"
          depends="check-db">
  </target>

  <target name="check-db"
          depends="get-db-executor">
  </target>

  <!-- JBoss -->
  <target name="check-jboss-uptodate">
    <!-- remove the upt.war because it requires db name/url/username/pw variables
         inside the war -->
    <delete includeemptydirs="true">
      <fileset dir="${env.JBOSS_HOME}/server/default/deploy">
        <include name="upt*.war"/>
      </fileset>
    </delete>
    <uptodate property="jboss.uptodate"
              targetfile="${env.JBOSS_HOME}/server/default/deploy/biobank.war">
      <srcfiles file="${war.file}" />
      <srcfiles file="db.properties" />
    </uptodate>
  </target>

  <target name="keystore-gen">
    <hostinfo prefix="local" />

    <echo message="Helping you to generate a TEMPORARY THROW-AWAY TEST key..." />
    <input message="Enter CN:"
           addproperty="dName.CN"
           defaultValue="localhost" />
    <input message="Enter subjectAltName:"
           addproperty="subjectAltName"
           defaultValue="IP:${local.ADDR4},DNS:localhost" />
    <input message="Enter an alias:"
           addproperty="keystore.alias"
           defaultValue="${dName.CN}" />

    <copy file="scripts/ssl/cert.cnf.template"
          tofile="scripts/ssl/cert.cnf" overwrite="true" />
    <replace file="scripts/ssl/cert.cnf">
      <replacefilter token="@@dName.CN@@" value="${dName.CN}" />
      <replacefilter token="@@subjectAltName@@" value="${subjectAltName}" />
    </replace>

    <exec executable="openssl" dir="scripts/ssl">
      <arg line="req -newkey rsa:2048 -x509 -outform DER -out cert.der -days 3650 -config cert.cnf" />
    </exec>
    <exec executable="openssl" dir="scripts/ssl">
      <arg line="pkcs8 -topk8 -nocrypt -in key.pem -inform PEM -out key.der -outform DER" />
    </exec>
    <exec executable="java" dir="scripts/ssl">
      <arg line="-Dkeystore=biobank.keystore ImportKey key.der cert.der ${keystore.alias}" />
    </exec>
    <exec executable="keytool" dir="scripts/ssl">
      <arg line="-keystore biobank.keystore -alias ${keystore.alias} -storepass importkey -keypasswd -keypass importkey -new biobank2" />
    </exec>
    <exec executable="keytool" dir="scripts/ssl">
      <arg line="-keystore biobank.keystore -storepasswd -storepass importkey -new biobank2" />
    </exec>
    <copy file="scripts/ssl/biobank.keystore"
          tofile="${secu-log.dir}/jboss/biobank.keystore"  overwrite="true" />
  </target>

  <target name="keystore-check">
    <available file="${secu-log.dir}/jboss/biobank.keystore" property="keystore.available" />
  </target>

  <target name="keystore-copy" depends="keystore-check">
    <fail unless="keystore.available"
          message="${secu-log.dir}/jboss/biobank.keystore not found. Use target 'keystore-gen' to generate a temporary key or create your own manually." />
    <copy file="${secu-log.dir}/jboss/biobank.keystore"
          tofile="${env.JBOSS_HOME}/server/default/conf/biobank.keystore"
          overwrite="true" />
  </target>

  <!-- version number on server side -->
  <target name="server-manifest">
    <manifest file="${eclipse.proj.dir.common}/META-INF/MANIFEST.MF"
              mode="update">
      <attribute name="Bundle-Version" value="${server.version.num}" />
    </manifest>
    <fixcrlf srcdir="${eclipse.proj.dir.common}/META-INF"
             eol="lf"
             eof="asis">
      <include name="**/*.MF" />
    </fixcrlf>
    <propertyfile file="${eclipse.proj.dir.common}/src/edu/ualberta/med/biobank/server/applicationservice/version.properties">
      <entry key="server.version" value="${server.version.num}" />
    </propertyfile>
  </target>

  <target name="update-db-config"
          description="copies db configuration information from db.properties to various config files">

    <copy todir="${secu-log.dir}/jboss" overwrite="true">
      <fileset dir="${secu-log.dir}/jboss">
	<exclude name="**/console/**" />
      </fileset>
      <globmapper from="*.template" to="*"/>
      <filterset>
        <filter token="database.url" value="${database.url}"/>
        <filter token="database.driver" value="${database.driver}"/>
        <filter token="database.username" value="${database.username}"/>
        <filter token="database.password" value="${database.password}"/>
      </filterset>
    </copy>
    <move file="${secu-log.dir}/jboss/application-config.xml"
          tofile="webapp/WEB-INF/classes/application-config.xml"
	  overwrite="true" />
    <move file="${secu-log.dir}/jboss/biobank.csm.new.hibernate.cfg.xml"
          tofile="webapp/WEB-INF/classes/biobank.csm.new.hibernate.cfg.xml"
	  overwrite="true" />
    <move file="${secu-log.dir}/jboss/log4j.xml"
          tofile="webapp/WEB-INF/classes/log4j.xml"
	  overwrite="true" />
  </target>

  <target name="check-db-properties">
    <available file="db.properties" property="db.properties.available" />
  </target>

  <target name="db-properties-copy" depends="check-db-properties">
    <fail unless="db.properties.available"
          message="File 'db.properties' not found in project's root directory. Copy 'db.properties.template' to 'db.properties' and modify accordingly." />
    <copy file="db.properties.template"
          tofile="db.properties"
          overwrite="false" />
  </target>

  <target name="jboss.home.env">
    <fail unless="env.JBOSS_HOME"
          message="JBOSS_HOME environment variable not defined" />
  </target>

  <target name="deploy-jboss"
          depends="jboss.home.env,update-db-config,package-webapp,check-jboss-uptodate,keystore-copy"
          description="deploys the caCORE SDK webapp to JBoss"
          unless="jboss.uptodate">
    <copy file="${secu-log.dir}/jboss/login-config.xml"
          tofile="${env.JBOSS_HOME}/server/default/conf/login-config.xml"
          overwrite="true" verbose="true" />
    <copy file="${secu-log.dir}/jboss/server${debugFileExtension}.xml"
          tofile="${env.JBOSS_HOME}/server/default/deploy/jbossweb-tomcat55.sar/server.xml"
          overwrite="true" verbose="true" />
    <!-- for compatibility: this file has been split -->
    <delete file="${env.JBOSS_HOME}/server/default/deploy/mysql-ds.xml" />
    <copy file="${lib.dir}/build/mysql-connector-java.jar"
          tofile="${env.JBOSS_HOME}/server/default/lib/mysql-connector-java.jar"
          overwrite="true" verbose="true" />
    <copy file="${secu-log.dir}/jboss/upt-ds.xml"
          tofile="${env.JBOSS_HOME}/server/default/deploy/upt-ds.xml"
          overwrite="true" verbose="true" />
    <copy file="${secu-log.dir}/jboss/biobank-ds.xml"
          tofile="${env.JBOSS_HOME}/server/default/deploy/biobank-ds.xml"
          overwrite="true" verbose="true" />
    <!-- ignore this war for now
    <copy file="${secu-log.dir}/jboss/upt.war"
          tofile="${env.JBOSS_HOME}/server/default/deploy/upt.war"
         overwrite="true" verbose="true" />
    -->
    <delete includeemptydirs="true">
      <fileset dir="${env.JBOSS_HOME}/server/default/deploy">
        <include name="upt*.war"/>
      </fileset>
    </delete>
    <copy file="${war.file}"
          tofile="${env.JBOSS_HOME}/server/default/deploy/biobank.war"
          overwrite="true" verbose="true"/>
  </target>

  <target name="build-eclipse-projects"
	  description="builds the Biobank client Eipse projects">
    <antcall target="eclipse-projects" />
  </target>

  <target name="deploy" description="deploys to JBoss and Eclipse project"
	  depends="deploy-eclipse,deploy-jboss">
  </target>

  <target name="build-common-project"
          depends="resolve,create-messages-jar,server-manifest">
    <copy file="${lib.dir}/messages.jar" todir="${eclipse.proj.dir.common}/lib/client" overwrite="true"/>
    <mkdir dir="${eclipse.proj.dir.common}/output" />
    <copy includeemptydirs="false" todir="${eclipse.proj.dir.common}/output" overwrite="false">
      <fileset dir="${eclipse.proj.dir.common}/src">
        <exclude name="**/*.launch" />
        <exclude name="**/*.java" />
      </fileset>
    </copy>
    <javac debug="true"
           debuglevel="source,lines,vars"
           srcdir="${eclipse.proj.dir.common}/src"
           destdir="${eclipse.proj.dir.common}/output"
           source="1.6"
           target="1.6"
           includeantruntime="false">
      <classpath refid="biobank.common.build.classpath" />
    </javac>
  </target>

  <target name="package-webapp" depends="build-common-project">
    <mkdir dir="${output.dir}" />
    <delete dir="webapp/db"/>
    <copy includeemptydirs="false" todir="webapp">
      <fileset dir=".">
        <include name="db/migration/*.sql" />
      </fileset>
    </copy>
    <war destfile="${war.file}"
         webxml="webapp/WEB-INF/web.xml">
      <manifest>
        <attribute name="Version" value="${server.version.num}" />
      </manifest>
      <lib dir="${req.jars.dir}">
        <include name="messages.jar" />
      </lib>
      <lib dir="${req.jars.dir}/biobank.webapp">
        <include name="*.jar" />
      </lib>
      <lib dir="${req.jars.dir}/flyway">
        <include name="flyway-core.jar" />
      </lib>
      <fileset dir="webapp">
        <exclude name="**/WEB-INF/**" />
      </fileset>
      <classes dir="${eclipse.proj.dir.common}/output">
        <exclude name="**/client/**" />
      </classes>
      <webinf dir="webapp/WEB-INF">
        <include name="**/*" />
	<exclude name="**/web.xml" />
      </webinf>
    </war>
  </target>

  <target name="clean-jars" depends="clean-ivy" description="deletes jars from eclipse projects">
    <delete>
      <fileset dir="${eclipse.proj.dir}/lib" includes="**/*.jar" />
      <fileset dir="${eclipse.proj.dir.mvp}/lib" includes="**/*.jar" />
      <fileset dir="${eclipse.proj.dir.gui.common}/lib" includes="**/*.jar" />
      <fileset dir="${eclipse.proj.dir.common}/lib" includes="**/*.jar" />
      <fileset dir="${eclipse.proj.dir.tests}/lib" includes="**/*.jar" />
      <fileset dir="${eclipse.proj.dir.tools}/lib" includes="**/*.jar" />
    </delete>
  </target>

  <target name="clean"
          depends="clean-tests,clean-tools,clean-jars,clean-product,clean-doxygen,clean-package-biobank-server"
          description="cleans project output, tests, and jars">
    <delete dir="${eclipse.proj.dir.common}/output" />
    <delete dir="${eclipse.proj.dir.tools}/output" />
    <delete dir="${lib.dir}/biobank.webapp" />
    <delete dir="${lib.dir}/hibernatetool" />
    <delete dir="${lib.dir}/build" />
    <delete dir="${lib.dir}/flyway" />
    <antcall target="clean-eclipse-projects" />
  </target>

  <property name="doxygen.output" location="docs/doxygen" />


  <target name="clean-product">
    <delete dir="${buildDirectory}" />
  </target>

  <condition property="client.branding.cbsr">
    <equals arg1="${client.branding}" arg2="cbsr" />
  </condition>

  <condition property="client.branding.stanford">
    <equals arg1="${client.branding}" arg2="stanford" />
  </condition>

  <target name="client-branding-cbsr" if="client.branding.cbsr">
    <copy file="branding/cbsr_splash.bmp"
          tofile="${eclipse.proj.dir}/splash.bmp" overwrite="true" />
  </target>

  <target name="client-branding-stanford" if="client.branding.stanford">
    <copy file="branding/stanford_splash.bmp"
          tofile="${eclipse.proj.dir}/splash.bmp" overwrite="true" />
  </target>

  <target name="client-branding" depends="client-branding-cbsr,client-branding-stanford">
    <fail message="Client branding is invalid: ${client.branding}">
      <condition>
	<and>
	  <not>
	    <isset property="client.branding.cbsr" />
	  </not>
	  <not>
	    <isset property="client.branding.stanford" />
	  </not>
	</and>
      </condition>
    </fail>
  </target>

  <target name="product"
	  depends="clean-product,versions-update,deploy,client-branding"
	  description="build the product">
    <!-- buildDirectory is the folder where the plugins and products are found and build -->
    <!-- plugins and features are copied into the buildDirectory -->
    <copy todir="${buildDirectory}/plugins/biobank2" verbose="true">
      <fileset dir="${eclipse.workspace.dir}/biobank2" />
    </copy>
    <!-- TODO : copy all project containing .nl1. into the plugins folder -->
    <copy todir="${buildDirectory}/plugins/biobank.nl1.fr_CA">
      <fileset dir="${eclipse.workspace.dir}/biobank.nl1.fr_CA" />
    </copy>
    <copy todir="${buildDirectory}/plugins/scannerConfig">
      <fileset dir="${eclipse.workspace.dir}/scannerConfig" />
    </copy>
    <copy todir="${buildDirectory}/plugins/biobank.common">
      <fileset dir="${eclipse.workspace.dir}/biobank.common" />
    </copy>
    <copy todir="${buildDirectory}/plugins/labelPrinter">
      <fileset dir="${eclipse.workspace.dir}/labelPrinter" />
    </copy>
    <copy todir="${buildDirectory}/plugins/biobank.gui.common">
      <fileset dir="${eclipse.workspace.dir}/biobank.gui.common" />
    </copy>
    <copy todir="${buildDirectory}/plugins/biobank.mvp">
      <fileset dir="${eclipse.workspace.dir}/biobank.mvp" />
    </copy>
    <copy todir="${buildDirectory}/features/biobank2.feature.core">
      <fileset dir="${eclipse.workspace.dir}/biobank2.feature.core" />
    </copy>
    <copy todir="${buildDirectory}/features/biobank2.feature.platform">
      <fileset dir="${eclipse.workspace.dir}/biobank2.feature.platform" />
    </copy>
    <!-- get current org.eclipse.equinox.launcher jar. If find more than one, will use the last one in the list (should be the last version)-->
    <fileset id="launcher.id.all"
             dir="${env.ECLIPSE_HOME}/plugins/"
             includes="org.eclipse.equinox.launcher_*.jar" />
    <last id="launcher.id" count="1">
      <fileset refid="launcher.id.all" />
    </last>
    <!-- get current org.eclipse.pde.build folder. If find more than one, will use the last one in the list (should be the last version) -->
    <fileset id="pde.build.id.all"
             dir="${env.ECLIPSE_HOME}/plugins/"
             includes="org.eclipse.pde.build_*/scripts/productBuild/productBuild.xml" />
    <last id="pde.build.id" count="1">
      <fileset refid="pde.build.id.all" />
    </last>
    <!-- launch product creation -->
    <java classpath="${toString:launcher.id}"
          classname="org.eclipse.equinox.launcher.Main"
          failonerror="true"
          fork="true">
      <arg line="-application org.eclipse.ant.core.antRunner" />
      <arg line="-buildfile ${toString:pde.build.id}" />
      <arg line="-Dbuilder=${product.dir}" />
      <!-- product.dir is used in product/customTarget.xml -->
      <arg line="-Dproduct.dir=${product.dir}" />
      <!-- instead of fixed paths in product/build.properties: -->
      <arg line="-Dproduct=${eclipse.proj.dir}/biobank2.product" />
      <arg line="-DbuildDirectory=${product.dir}/buildDirectory" />
      <arg line="-DbaseLocation=${env.ECLIPSE_HOME}" />
      <arg line="-Djava.client.version.num=${java.client.version.num}" />

      <!-- uncomment line below to build a single executable product -->
      <!-- arg line="-Dconfigs='win32, win32, x86'" / -->
      <!-- arg line="-Dconfigs='linux, gtk, x86_64'" / -->
    </java>
    <antcall target="updateSiteMetadata" />
  </target>


  <target name="updateSiteMetadata"
	  description="Build the update site folder">
    <property name="buildDirectory" value="${product.dir}/buildDirectory" />
    <property name="updateSiteFolder" value="${buildDirectory}/updateSite" />
    <copy todir="${updateSiteFolder}/features/">
      <fileset dir="${buildDirectory}/buildRepo/features/" />
    </copy>
    <copy todir="${updateSiteFolder}/plugins/">
      <fileset dir="${buildDirectory}/buildRepo/plugins/" />
    </copy>
    <fileset id="featureJar.id"
             dir="${updateSiteFolder}/features/"
             includes="biobank2.feature.core_*.jar" />
    <property name="featureJar" refid="featureJar.id" />
    <taskdef resource="net/sf/antcontrib/antcontrib.properties">
      <classpath>
        <pathelement location="${product.dir}/ant-contrib/ant-contrib-1.0b3.jar" />
      </classpath>
    </taskdef>
    <propertyregex property="featureVersion"
                   input="${featureJar}"
                   regexp="biobank2.feature.core_(.*)\.jar"
                   select="\1"
                   casesensitive="true" />
    <copy file="${product.dir}/site.xml"
          tofile="${updateSiteFolder}/site.xml" />
    <replace file="${updateSiteFolder}/site.xml"
             token="@VERSION@"
             value="${featureVersion}" />


    <!-- get current org.eclipse.equinox.launcher jar. If find more than one, will use the last one in the list (should be the last version)-->
    <fileset id="launcher.id.all"
             dir="${env.ECLIPSE_HOME}/plugins/"
             includes="org.eclipse.equinox.launcher_*.jar" />
    <last id="launcher.id" count="1">
      <fileset refid="launcher.id.all" />
    </last>
    <java classpath="${toString:launcher.id}"
          classname="org.eclipse.equinox.launcher.Main"
          failonerror="true"
          fork="true">
      <arg line="-application org.eclipse.equinox.p2.publisher.UpdateSitePublisher" />
      <arg line="-source ${updateSiteFolder}" />
      <arg line="-compress" />
      <arg line="-publishArtifacts" />
      <arg line="-consoleLog" />
      <arg line="-artifactRepository file:${updateSiteFolder}" />
      <arg line="-metadataRepository file:${updateSiteFolder}" />
    </java>
  </target>

  <target name="doxygen" description="generates documentation for the model classes">
    <exec executable="${doxygen}">
      <arg value="docs/doxygen/doxygen.cfg" />
    </exec>
    <echo message="point your browser to: file://${doxygen.output}/html/index.html" />
    <exec executable="${xsltproc}" dir="docs/doxygen/xml" output="docs/doxygen/xml/all.xml">
      <arg value="combine.xslt" />
      <arg value="index.xml" />
    </exec>
  </target>

  <target name="clean-doxygen">
    <delete dir="docs/doxygen/html" />
    <delete dir="docs/doxygen/xml" />
  </target>

  <target name="clean-package-biobank-server">
    <delete dir="${package.jboss.target.dir}" />
    <delete dir="${package.jboss.root.dir}/templates" />
    <delete dir="${package.jboss.root.dir}/tools" />
    <delete file="biobank-server-*.deb"/>
  </target>

  <target name="package-biobank-server"
	  depends="deploy-jboss"
	  description="Generates an Ubuntu package file for the Biobank server.">

    <!-- Use command line unzip to keep file permissions -->
    <exec executable="unzip">
      <arg line="-q -o ${env.JBOSS_HOME}/../jboss-4.0.5.GA.zip -d ${package.jboss.root.dir}" />
    </exec>

    <copy file="${secu-log.dir}/jboss/overwrite/run.conf"
	  tofile="${package.jboss.target.dir}/bin/run.conf"
	  overwrite="true" verbose="true"/>

    <copy file="${secu-log.dir}/jboss/overwrite/server/default/conf/jboss-service.xml"
	  tofile="${package.jboss.target.dir}/server/default/conf/jboss-service.xml"
	  overwrite="true" verbose="true"/>

    <copy file="${secu-log.dir}/jboss/server.xml"
	  tofile="${package.jboss.target.dir}/server/default/deploy/jbossweb-tomcat55.sar/server.xml"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/overwrite/server/default/deploy/jmx-console.war/WEB-INF/jboss-web.xml"
	  tofile="${package.jboss.target.dir}/server/default/deploy/jmx-console.war/WEB-INF/jboss-web.xml"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/overwrite/server/default/deploy/jmx-console.war/WEB-INF/web.xml"
	  tofile="${package.jboss.target.dir}/server/default/deploy/jmx-console.war/WEB-INF/web.xml"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/overwrite/server/default/deploy/management/console-mgr.sar/web-console.war/WEB-INF/jboss-web.xml"
	  tofile="${package.jboss.target.dir}/server/default/deploy/management/console-mgr.sar/web-console.war/WEB-INF/jboss-web.xml"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/overwrite/server/default/deploy/management/console-mgr.sar/web-console.war/WEB-INF/web.xml"
	  tofile="${package.jboss.target.dir}/server/default/deploy/management/console-mgr.sar/web-console.war/WEB-INF/web.xml"
	  overwrite="true" />

    <mkdir dir="${package.jboss.root.dir}/tools"/>

    <copy file="${scripts.proj.dir}/ssl/ImportKey.class"
	  tofile="${package.jboss.root.dir}/tools/ImportKey.class"
	  overwrite="true" />

    <mkdir dir="${package.jboss.root.dir}/templates"/>

    <copy file="${secu-log.dir}/jboss/application-config.xml.template"
	  tofile="${package.jboss.root.dir}/templates/application-config.xml.template"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/biobank-ds.xml.template"
	  tofile="${package.jboss.root.dir}/templates/biobank-ds.xml.template"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/login-config.xml.template"
	  tofile="${package.jboss.root.dir}/templates/login-config.xml.template"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/log4j.xml.template"
	  tofile="${package.jboss.root.dir}/templates/log4j.xml.template"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/biobank.csm.new.hibernate.cfg.xml.template"
	  tofile="${package.jboss.root.dir}/templates/biobank.csm.new.hibernate.cfg.xml.template"
	  overwrite="true" />
    <copy file="${secu-log.dir}/jboss/upt-ds.xml.template"
	  tofile="${package.jboss.root.dir}/templates/upt-ds.xml.template"
	  overwrite="true" />

    <copy file="db/empty_db.sql.template"
	  tofile="${package.jboss.root.dir}/templates/empty_db.sql.template"
	  overwrite="true" />

    <copy file="${scripts.proj.dir}/ssl/cert.cnf.template"
	  tofile="${package.jboss.root.dir}/templates/cert.cnf.template"
	  overwrite="true" />


    <copy file="${secu-log.dir}/jboss/console/jmx-console-users.properties.template"
	  tofile="${package.jboss.root.dir}/templates/jmx-console-users.properties.template"
	  overwrite="true" />

    <copy file="${secu-log.dir}/jboss/console/web-console-users.properties.template"
 	  tofile="${package.jboss.root.dir}/templates/web-console-users.properties.template"
	  overwrite="true" />

    <copy file="${war.file}"
	  tofile="${package.jboss.target.dir}/server/default/deploy/biobank.war"
	  overwrite="true" />

    <copy file="${war.file}"
	  tofile="${package.jboss.target.dir}/server/default/deploy/biobank.war"
	  overwrite="true" />

    <copy file="${lib.dir}/build/mysql-connector-java.jar"
          tofile="${package.jboss.target.dir}/server/default/lib/mysql-connector-java.jar"
          overwrite="true" verbose="true" />

    <exec executable="dpkg" dir="package-jboss">
      <arg line="--build debian" />
    </exec>

    <move file="package-jboss/debian.deb"
	  tofile="biobank-server-${server.version.num}.deb"
	  overwrite="true" />


  </target>

<!-- (setq nxml-slash-auto-complete-flag t) -->


</project>

<!--
    Local Variables:
    compile-command: "ant"
    End:
-->