source: trunk/build.xml @ 3377

<?xml version="1.0" encoding="UTF-8"?>
<!--
    $Id: build.xml 3377 2007-05-24 19:52:48Z nicklas $

    Copyright (C) 2005-2006
    Samuel Andersson, Jari H&auml;kkinen, Nicklas Nordborg, Gregory Vincic

    This file is part of BASE - BioArray Software Environment.
    Available at http://base.thep.lu.se/

    BASE is free software; you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    BASE is distributed in the hope that it will be useful, but
    WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
    General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
    02111-1307, USA.
-->

<project
  name="BASE2"
  default="dev"
  basedir="."
  >
  <description>
    Build file for BASE 2. The main targets are ('dev' is default):

    Clean up:
    clean:        Remove all generated files

    Compiling code
    core:         Build core for local use
    coreplugins:  Build core plugins for local use
    dev:          Build everything for local use
    dist:         Build everything (except test) for distribution (put in 'dist'
                  subdirectory)
    installprg:   Build installation programs for local use
    jobagent:     Build jobagent for local use
    migrate:      Build migration tool for local use
    test:         Build test programs
    web:          Build web client application for local use

    Documentation:
    doc:          Build documentation for local use
    docbook:      Build html and pdf from docbook (to be included in 'ant doc')
    helptext:     Generate help text import file from the docbook documentation

    Packaging:
    package:      Create *.tar.gz files with binary and source distributions
  </description>

  <!-- set BASE version
    Use numerical versions for bugix (maintenance) releases starting
    with "1". Use "0" for the first release of a new trunk version.  Add
    "pre" to unreleased versions.  Examples: 2.1.1pre, 2.1.1,
    2.1.2pre, 2.2.2, 2.2.0pre, 2.2.0, 2.2.1pre, 2.2.1 
  -->
  <property name="base.majorversion" value="2" />
  <property name="base.minorversion" value="3" />
  <property name="base.maintenanceversion" value="0pre" />
  <property name="base.version" 
    value="${base.majorversion}.${base.minorversion}.${base.maintenanceversion}" />
  
  <!-- set other global properties for this build -->
  <property name="javac.arg" value="-Xlint:unchecked" 
    description="Extra arguments sent to Java compiler" />
  <property name="src" location="src" description="Location of source files" />
  <property name="build" location="build" description="Location of compiled files" />
  <property name="dist" location="dist" description="Directory where distribution should be created" />
  <property name="lib" location="lib" description="Location of 3rd-party JAR files" />
  <property name="config.dist" location="config/dist" 
    description="Location of default configuration files" />
  <property name="config.local" location="config/local" 
    description="Location of local configuration files" />
  
  <!-- main class path for compilation -->
  <path id="core.classpath" 
    description="Main classpath to all 3rd-party JAR files required for compilation">
    <fileset dir="${lib}/dist">
      <include name="**/*.jar"/>
    </fileset>
  </path>

  <!-- pattern for configuration files use by copy.config -->
  <patternset id="config.files">
    <include name="*.*" />
    <exclude name="web.xml" />
    <exclude name="readme.txt" />
  </patternset>
  
  <!-- task definitions -->
  <taskdef
    name="hibernatedoclet"
    classname="xdoclet.modules.hibernate.HibernateDocletTask"
    description="Task for generating Hibernate mapping files from XDoclet tags"
    >
    <classpath>
      <fileset dir="${lib}/hibernatedoclet">
        <include name="**/*.jar"/>
      </fileset>
    </classpath>
  </taskdef>

  <taskdef
    name="svn"
    classname="org.tigris.subversion.svnant.SvnTask"
    description="Task for interacting with subversion"
    >
    <classpath>
      <fileset dir="${lib}/svn">
        <include name="**/*.jar"/>
      </fileset>
    </classpath>
  </taskdef>
  
  <!-- main targets -->
  <target
    name="clean"
    description="Remove all generated files and backup files" >
    <delete failonerror="false" includeemptydirs="true">
      <fileset dir="${build}" defaultexcludes="no" />
      <fileset dir="${dist}" defaultexcludes="no" />
      <fileset dir="bin/jar" defaultexcludes="no" />
      <fileset dir="www/WEB-INF/lib" defaultexcludes="no" />
      <fileset dir="www/WEB-INF/classes" defaultexcludes="no" />
      <fileset dir="www/WEB-INF" includes="web.xml" defaultexcludes="no" />
      <fileset dir="doc/api" defaultexcludes="no" />
      <fileset dir="doc/docbook" defaultexcludes="no" />
      <fileset file="doc/development/plugins/exampleplugins.tar.gz" />
    </delete>
  </target>
  
  <target
    name="dist"
    depends="clean,dist.init,core.jar,coreplugins.jar,web.jar,installprg.jar,
      jobagent.jar,migrate.jar,copy.config,copy.jar,doc,doc.dist"
    description="Create everything needed for distribution"
    >
    <copy file="${config.dist}/web.xml" todir="${config}/.." description="Default web.xml" />
    <copy todir="${dist}/www" description="JSP files, etc.">
      <fileset dir="www" />
    </copy>
    <copy todir="${dist}/data" description="Additional data files">
      <fileset dir="data" />
    </copy>
    <copy todir="${dist}/bin" description="Scripts, etc.">
      <fileset dir="bin" />
    </copy>
    <copy todir="${dist}/misc" description="Other files">
      <fileset dir="misc">
        <include name="sql/**/*" />
        <include name="config/**/*" />
      </fileset>
    </copy>
    <copy todir="${dist}" description="License and creadits">
      <fileset file="base2.license.txt" />
      <fileset file="credits.txt" />
    </copy>
    <chmod dir="." includes="**/*.sh" perm="a+x" description="Make all scripts executable" />
  </target>

  <target
    name="package"
    depends="package.bin,package.src"
    description="Generate tar.gz files for the binary and source distribution"
    >
  </target>
  
  <target
    name="dev"
    depends="dev.init,core,coreplugins,web,installprg,jobagent,migrate,test"
    description="Create a runnable local installation"
  />
  
  <target
    name="core"
    depends="dev.init,core.jar"
    description="Build the core for local use"
  />

  <target
    name="coreplugins"
    depends="core,coreplugins.jar"
    description="Build the core plugins for local use"
  />
  
  <target
    name="exampleplugins"
    depends="core,exampleplugins.jar"
    description="Build the example plugins for local use"
  />
  
  <target
    name="test"
    depends="test.jar,core.hibernate"
    description="Compile the test programs for local use"
    >
    <mkdir dir="${test.build}/data" />
    <copy todir="${test.build}/data" description="Test-data files">
      <fileset dir="${test.src}/data">
        <include name="**/*" />
      </fileset>
    </copy>
    <copy todir="${test.build}" description="Script files, etc.">
      <fileset dir="${test.src}">
        <include name="**/*" />
        <exclude name="**/*.java" />
      </fileset>
    </copy>
    <chmod dir="${test.build}" includes="*.sh" perm="a+x"/>
  </target>
  
  <target
    name="web"
    depends="core,coreplugins,web.jar,copy.config,copy.jar"
    description="Build web client application for local use"
    >
  </target>
  
  <target
    name="installprg"
    depends="web,installprg.jar"
    description="Build installation programs for local use"
  />
  
  <target
    name="jobagent"
    depends="web,jobagent.jar"
    description="Build job agent for local use"
  />
  
  <target
    name="migrate"
    depends="web,migrate.jar"
    description="Build migration tool for local use"
  />
  
  <target
    name="doc"
    depends="doc.javadoc,exampleplugins.tar,doc.docbook"
    description="Generate documentation for local use"
  />
  
  <target
    name="docbook"
    depends="dev.init,doc.docbook"
    description="Generate docbook documentation. This target is temporary. 
      It will be included in the 'doc' target in the future."
  />
  
  <!-- init targets -->
  <target
    name="init"
    depends="svn.revision"
    description="Initialise things"
    >
  </target>
  
  <target
    name="dist.init"
    depends="init"
    unless="isDev"
    >
    <property name="isDist" value="1" />
    <property name="jar" location="${dist}/www/WEB-INF/lib" />
    <property name="config" location="${dist}/www/WEB-INF/classes" />
    <property name="bin" location="${dist}/bin" />
    <property name="doc" location="${dist}/doc" />
    <mkdir dir="${jar}" />
    <mkdir dir="${config}" />
    <mkdir dir="${bin}" />
    <mkdir dir="${bin}/jar" />
    <mkdir dir="${dist}/data" />
    <mkdir dir="${dist}/doc" />
    <mkdir dir="${dist}/misc" />
  </target>
  
  <target
    name="dev.init"
    depends="init"
    unless="isDist"
    >
    <property name="isDev" value="1" />
    <property name="jar" location="www/WEB-INF/lib" />
    <property name="config" location="www/WEB-INF/classes" />
    <property name="bin" location="bin" />
    <property name="doc" location="doc" />
    <mkdir dir="${bin}/jar" />
    <mkdir dir="${jar}" />
    <mkdir dir="${config}" />
  </target>
  
  <target 
    name="svn.revision"
    description="Get the current revision number in the subversion and put the
      value into the base.build property; replaced by constant expression in source distributions"
    >
    <svn>
      <status path="." lastChangedRevisionProperty="base.build" />
    </svn>
    <echo message="Build #${base.build}" />
  </target>
  
  <!-- configuration targets -->
  <target
    name="copy.config"
    depends="copy.config.local,copy.config.dist"
    description="Copies configuration files to the appropriate folder"
    >
  </target>
    
  <target
    name="copy.config.dist"
    >
    <copy todir="${config}" description="Default configuration files">
      <fileset dir="${config.dist}">
        <patternset refid="config.files" />
        <present present="srconly" targetdir="${config}" />
      </fileset>
    </copy>
    <copy todir="${config}/.."  description="Default web.xml">
      <fileset dir="${config.dist}">
        <include name="web.xml" />
        <present present="srconly" targetdir="${config}/.." />
      </fileset>
    </copy>
  </target>
  
  <target
    name="copy.config.local"
    if="isDev"
    unless="isDist"
    >
    <copy todir="${config}" description="Local configuration files">
      <fileset dir="${config.local}">
        <patternset refid="config.files" />
      </fileset>
    </copy>
    <copy todir="${config}/.."  description="Local web.xml">
      <fileset dir="${config.local}">
        <include name="web.xml" />
      </fileset>
    </copy>
  </target>
  
  <target
    name="copy.jar"
    description="Copy required jar files to the appropriate folder"
    >
    <copy todir="${jar}" description="3rd-party JAR files">
      <fileset dir="${lib}/dist">
        <include name="**/*" />
      </fileset>
    </copy>
  </target>
  
  <!-- core targets -->
  <target
    name="core.init"
    depends="dev.init"
    >
    <property name="core.src" location="${src}/core" 
      description="Location of core source files" />
    <property name="core.build" location="${build}/core" 
      description="Location of compiled core files" />
  </target>
  
  <target
    name="core.compile"
    depends="core.init"
    description="Compile the core"
    >
    <mkdir dir="${core.build}"/>
    <javac
      srcdir="${core.src}"
      destdir="${core.build}"
      classpathref="core.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
    <copy todir="${core.build}" 
      description="Resource files needed by the core; excludes documentation and source files">
      <fileset dir="${core.src}">
        <include name="**/*" />
        <exclude name="**/*.java" />
        <exclude name="**/doc-files/" />
        <exclude name="**/package.html" />
      </fileset>
    </copy>
    <replace file="${core.build}/base.version">
      <replacefilter 
        token="@MAJOR@"
        value="${base.majorversion}"
      />
      <replacefilter 
        token="@MINOR@"
        value="${base.minorversion}"
      />
      <replacefilter 
        token="@MAINTENANCE@"
        value="${base.maintenanceversion}"
      />
      <replacefilter 
        token="@BUILD@"
        value="${base.build}"
      />
    </replace>
  </target>

  <target
    name="check.hibernate"
    depends="core.init"
    >
    <uptodate
      property="nohibernate"
      >
      <srcfiles dir="${core.src}/net/sf/basedb/core/data" includes="**/*.java">
        <contains text="@hibernate.class" />
      </srcfiles>
      <mapper type="glob" from="*.java" to="${core.build}/net/sf/basedb/core/data/*.hbm.xml" />
    </uptodate>
    <condition property="hibernate.message" 
      value="up to date; skipping" 
      >
      <istrue value="${nohibernate}" />
    </condition>
    <condition property="hibernate.message" 
      value="not up to date; generating new" 
      >
      <isfalse value="${nohibernate}" />
    </condition>
    <echo>Hibernate mapping files are ${hibernate.message}</echo>
  </target>
  
  <target
    name="core.hibernate"
    depends="core.init,core.compile,check.hibernate"
    description="Generates Hibernate mapping files from the source code"
    unless="nohibernate"
    >
    <delete>
      <fileset dir="${core.build}" includes="**/*.hbm.xml" />
    </delete>
    <copy todir="${core.build}" 
      description="Hardcoded *.hbm.xml files">
      <fileset dir="${core.src}" includes="**/*.hbm.xml" />
    </copy>
    <hibernatedoclet
      destdir="${core.build}"
      excludedtags="@version,@author,@todo"
      mergedir="${core.build}"
      verbose="${xdoclet.verbose}">
      <fileset dir="${core.src}">
        <include name="**/*.java"/>
      </fileset>
      <hibernate version="2.0"/>
    </hibernatedoclet>
    
    <replace
      dir="${core.build}"
      >
      <include name="**/*.hbm.xml"/>
      <replacefilter 
        token="2.0//EN"
        value="3.0//EN"
      />
      <replacefilter 
        token="2.0.dtd"
        value="3.0.dtd"
      />
      <replacefilter
        token="outer-join=&#34;false&#34;"
        value="fetch=&#34;select&#34;"
      />
      <replacefilter
        token="outer-join=&#34;true&#34;"
        value="fetch=&#34;join&#34;"
      />
      <replacefilter
        token="index-many-to-many"
        value="map-key-many-to-many"
      />
      <replacefilter
        token="&lt;index&gt;"
        value="&lt;list-index&gt;"
      />
      <replacefilter
        token="&lt;/index&gt;"
        value="&lt;/list-index&gt;"
      />
      <replacefilter
        token="composite-index"
        value="composite-map-key"
      />
    </replace>
  </target>
  
  <target
    name="core.jar"
    depends="core.init,core.compile,core.hibernate"
    description="Create the core jar file: BASE2Core.jar"
    >
    <jar
      basedir="${core.build}"
      jarfile="${jar}/BASE2Core.jar"
    />
  </target>

  <!-- core plugin targets -->
  <target
    name="coreplugins.init"
    depends="core.init"
    >
    <property name="coreplugins.src" location="${src}/plugins/core" 
      description="Location of source files" />
    <property name="coreplugins.build" location="${build}/plugins/core" 
      description="Location of compiled files" />
    <path id="coreplugins.classpath" description="Class path for compiling plugins">
      <path refid="core.classpath"/>
      <pathelement location="${core.build}"/>
    </path>
  </target>
  
  <target
    name="coreplugins.compile"
    depends="core.compile,coreplugins.init"
    description="Compile the core plugins"
    >
    <mkdir dir="${coreplugins.build}" />
    <javac
      srcdir="${coreplugins.src}"
      destdir="${coreplugins.build}"
      classpathref="coreplugins.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="coreplugins.jar"
    depends="coreplugins.compile"
    description="Create the plugin jar file: BASE2CorePlugins.jar"
    >
    <jar
      basedir="${coreplugins.build}"
      jarfile="${jar}/BASE2CorePlugins.jar"
    />
  </target>
  
  <!-- example plugin targets -->
  <target
    name="exampleplugins.init"
    depends="core.init"
    >
    <property name="exampledir" location="${src}/examples/plugins" />
    <property name="exampleplugins.src" location="${exampledir}/src" 
      description="Location of source files" />
    <property name="exampleplugins.build" location="${build}/plugins/example" 
      description="Location of compiled files" />
    <path id="exampleplugins.classpath" description="Class path for compiling plugins">
      <path refid="core.classpath"/>
      <pathelement location="${core.build}"/>
    </path>
  </target>
  
  <target
    name="exampleplugins.compile"
    depends="core.compile,exampleplugins.init"
    description="Compile the example plugins"
    >
    <mkdir dir="${exampleplugins.build}" />
    <javac
      srcdir="${exampleplugins.src}"
      destdir="${exampleplugins.build}"
      classpathref="exampleplugins.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="exampleplugins.jar"
    depends="exampleplugins.compile"
    description="Create the example plugins jar file: ExamplePlugins.jar"
    >
    <jar
      basedir="${exampleplugins.build}"
      jarfile="${jar}/ExamplePlugins.jar"
      manifest="${exampledir}/MANIFEST.MF"
    />
  </target>

  <target
    name="exampleplugins.tar"
    depends="exampleplugins.jar"
    description="Create a downloadable tar file with the example plugins"
    >
    <mkdir dir="${doc}/development/plugins" />
    <tar
      destfile="${doc}/development/plugins/exampleplugins.tar.gz"
      compression="gzip"
      >
      <tarfileset
        dir="${exampledir}"
        preserveLeadingSlashes="true"
      />
      <tarfileset
        dir="${exampleplugins.build}"
        prefix="bin"
        preserveLeadingSlashes="true"
      />
    </tar>
  </target>
  
  <!-- test targets -->
  <target
    name="test.init"
    depends="core.init,coreplugins.init,jobagent.init"
    >
    <property name="test.src" location="${src}/test" 
      description="Location of source files" />
    <property name="test.build" location="${build}/test" 
      description="Location of compiled files" />
    <path id="test.classpath" description="Class path for compiling">
      <path refid="core.classpath"/>
      <pathelement location="${core.build}" />
      <pathelement location="${coreplugins.build}" />
      <pathelement location="${jobagent.build}" />
    </path>
  </target>
  
  <target
    name="test.compile"
    depends="test.init,core.compile,coreplugins.compile,jobagent.compile"
    description="Compile the test programs"
    >
    <mkdir dir="${test.build}" />
    <javac
      srcdir="${test.src}"
      destdir="${test.build}"
      classpathref="test.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="test.jar"
    depends="test.compile"
    description="Create a JAR file used by the test programs; Delete corresponding .class files"
    >
    <jar 
      jarfile="${test.build}/JarPluginAbout.jar" 
      basedir="${test.build}" 
      includes="JarPluginAbout.class" 
    />
    <jar 
      jarfile="${test.build}/JarPlugin.jar" 
      basedir="${test.build}" 
      includes="JarPlugin*,NullPlugin*"
      excludes="JarPlugin.jar,JarPluginAbout.*"
      manifest="${test.src}/data/JarPluginManifest.txt"
    />
    <delete>
      <fileset dir="${test.build}" includes="JarPlugin*.class" />
    </delete>
  </target>

  <!-- web targets -->
  <target
    name="web.init"
    depends="core.init,coreplugins.init"
    >
    <property name="web.src" location="${src}/clients/web" 
      description="Location of source files" />
    <property name="web.build" location="${build}/clients/web" 
      description="Location of compiled files" />
    <property name="web.inf" location="www/WEB-INF" 
      description="Location of the WEB-INF folder" />
    <path id="web.classpath" description="Class path for compiling web client">
      <path refid="core.classpath"/>
      <pathelement location="${core.build}"/>
      <pathelement location="${coreplugins.build}" />
      <fileset dir="${lib}/servlet">
        <include name="**/*.jar"/>
      </fileset>
    </path>
  </target>
  
  <target
    name="web.compile"
    depends="web.init,core.compile"
    description="Compile the web client application"
    >
    <mkdir dir="${web.build}" />
    <javac
      srcdir="${web.src}"
      destdir="${web.build}"
      classpathref="web.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="web.jar"
    depends="web.compile"
    description="Create the web client jar file: BASE2Webclient.jar"
    >
    <jar
      basedir="${web.build}"
      jarfile="${jar}/BASE2Webclient.jar"
    />
  </target>
  
  <target 
    name="web.jsp"
    depends="web"
    description="Compile all JSP pages to a temporary directory; used for checking only"
    >
    <property name="jsp.build" location="${build}/jsp" />
    <property environment="env" />
    <mkdir dir="${jsp.build}/src" />
    <mkdir dir="${jsp.build}/classes" />
    
    <path id="jsp.precompile.classpath">
      <pathelement location="${java.home}/../lib/tools.jar" />
      <fileset dir="${env.CATALINA_HOME}/server/lib">
        <include name="*.jar" />
      </fileset>
      <fileset dir="${env.CATALINA_HOME}/common/lib">
        <include name="*.jar" />
      </fileset>
      <fileset dir="${env.CATALINA_HOME}/bin">
        <include name="*.jar" />
      </fileset>
    </path>
    
    <path id="jsp.compile.classpath">
      <path refid="web.classpath" />
      <pathelement location="${java.home}/../lib/tools.jar" />
      <fileset dir="${env.CATALINA_HOME}/common/lib">
        <include name="*.jar" />
      </fileset>
      <fileset dir="${env.CATALINA_HOME}/shared/lib">
        <include name="*.jar" />
      </fileset>
      <fileset dir="${web.inf}/lib">
        <include name="*.jar" />
      </fileset>
    </path>

    <taskdef
      classname="org.apache.jasper.JspC" 
      name="jasper2"
      classpathref="jsp.precompile.classpath"
    />
    <jasper2
      validateXml="false"
      uriroot="www"
      webXmlFragment="${jsp.build}/generated_web.xml"
      outputdir="${jsp.build}/src"
    />
    <javac
      destdir="${jsp.build}/classes"
      srcdir="${jsp.build}/src"
      debug="true"
      classpathref="jsp.compile.classpath"
      memoryinitialsize="256m"
      memorymaximumsize="512m"
      fork="true"
      >
    </javac>
  </target>
  
  <!-- installprg targets -->
  <target
    name="installprg.init"
    depends="core.init,coreplugins.init,web.init"
    >
    <property name="installprg.src" location="${src}/install" 
      description="Location of source files" />
    <property name="installprg.build" location="${build}/install" 
      description="Location of compiled files" />
    <path id="installprg.classpath" description="Class path for compiling installation programs">
      <path refid="core.classpath"/>
      <pathelement location="${core.build}"/>
      <pathelement location="${coreplugins.build}"/>
      <pathelement location="${web.build}"/>
    </path>
  </target>
  <target
    name="installprg.compile"
    depends="installprg.init,core.compile"
    description="Compile the installation programs"
    >
    <mkdir dir="${installprg.build}" />
    <javac
      srcdir="${installprg.src}"
      destdir="${installprg.build}"
      classpathref="installprg.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="installprg.jar"
    depends="installprg.compile"
    description="Create the installation jar file: BASE2Install.jar"
    >
    <jar
      basedir="${installprg.build}"
      jarfile="${bin}/jar/BASE2Install.jar"
    />
  </target>

  <!-- jobagent targets -->
  <target
    name="jobagent.init"
    depends="core.init,coreplugins.init,web.init"
    >
    <property name="jobagent.src" location="${src}/clients/jobagent" 
      description="Location of source files" />
    <property name="jobagent.build" location="${build}/clients/jobagent" 
      description="Location of compiled files" />
    <path id="jobagent.classpath" description="Class path for compiling jobagent">
      <path refid="core.classpath"/>
      <pathelement location="${core.build}"/>
    </path>
  </target>
  <target
    name="jobagent.compile"
    depends="jobagent.init,core.compile"
    description="Compile the job agent application"
    >
    <mkdir dir="${jobagent.build}" />
    <javac
      srcdir="${jobagent.src}"
      destdir="${jobagent.build}"
      classpathref="jobagent.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="jobagent.jar"
    depends="jobagent.compile"
    description="Create the job agent jar file: JobAgent.jar"
    >
    <jar
      basedir="${jobagent.build}"
      jarfile="${bin}/jar/JobAgent.jar"
    />
  </target>

  <!-- migrate targets -->
  <target
    name="migrate.init"
    depends="core.init,coreplugins.init,web.init"
    >
    <property name="migrate.src" location="${src}/clients/migrate" 
      description="Location of source files" />
    <property name="migrate.build" location="${build}/clients/migrate" 
      description="Location of compiled files" />
    <path id="migrate.classpath" description="Class path for compiling migration tool">
      <path refid="core.classpath"/>
      <pathelement location="${core.build}"/>
    </path>
  </target>
  <target
    name="migrate.compile"
    depends="migrate.init,core.compile"
    description="Compile the migration tool"
    >
    <mkdir dir="${migrate.build}" />
    <javac
      srcdir="${migrate.src}"
      destdir="${migrate.build}"
      classpathref="migrate.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="migrate.jar"
    depends="migrate.compile"
    description="Create the migration tool jar file: Migrate.jar"
    >
    <jar
      basedir="${migrate.build}"
      jarfile="${bin}/jar/Migrate.jar"
    />
  </target>
  
  <!-- documentation targets -->
  <target
    name="doc.init"
    >
    <property name="docbook.src" location="doc/src/docbook" 
      description="Location of docbook source XML files" />
    <path id="javadoc.classpath" description="Class path for generating javadoc">
      <path refid="core.classpath" />
      <fileset dir="${lib}/servlet">
        <include name="**/*.jar"/>
      </fileset>
    </path>
  </target>
  
  <target
    name="doc.javadoc"
    depends="doc.init,core.init,coreplugins.init,web.init,migrate.init,jobagent.init"
    description="Generate JavaDoc of entire API"
    >
    <!-- Create the time stamp -->
    <tstamp>
      <format property="TODAY" pattern="yyyy-MM-dd"/>
    </tstamp>
    <delete dir="${doc}/api" />
    <mkdir dir="${doc}/api"/>

    <javadoc
      packagenames="net.sf.basedb.*"
      sourcepath="${core.src}:${coreplugins.src}:${web.src}:${migrate.src}:${jobagent.src}"
      destdir="${doc}/api"
      author="true"
      version="true"
      use="false"
      private="true"
      windowtitle="BASE ${base.version} API documentation"
      stylesheetfile="doc/javadoc.css"
      classpathref="javadoc.classpath"
      linksource="false"
      breakiterator="yes"
      encoding="iso-8859-1"
      >
      <header><![CDATA[${base.version}: ${TODAY}]]></header>
      <link href="http://java.sun.com/j2se/1.5/docs/api"/>
      <link href="http://www.hibernate.org/hib_docs/v3/api"/>
      <link href="http://www.jdom.org/docs/apidocs/" />
      <link href="http://java.sun.com/products/servlet/2.2/javadoc/" />
      <link href="http://www.singularsys.com/jep/doc/javadoc/" />
      <link href="http://www.jfree.org/jfreechart/api/gjdoc/" />
      <link href="http://logging.apache.org/log4j/docs/api/" />
      <link href="http://java.sun.com/products/java-media/jai/forDevelopers/jai-apidocs/" />
      <tag name="base.internal" description="Developer info" />
      <tag name="base.modified" description="Last modified" />
      <tag name="hibernate.class" description="Hibernate: class" scope="types" />
      <tag name="hibernate.subclass" description="Hibernate: subclass" scope="types" />
      <tag name="hibernate.discriminator" description="Hibernate: discriminator" scope="types" />
      <tag name="hibernate.id" description="Hibernate: id" scope="methods" />
      <tag name="hibernate.generator-param" description="Hibernate: generator-param" scope="methods" />
      <tag name="hibernate.version" description="Hibernate: version" scope="methods" />
      <tag name="hibernate.property" description="Hibernate: property" scope="methods" />
      <tag name="hibernate.column" description="Hibernate: column" scope="methods" />
      <tag name="hibernate.map" description="Hibernate: map" scope="methods" />
      <tag name="hibernate.set" description="Hibernate: set" scope="methods" />
      <tag name="hibernate.list" description="Hibernate: list" scope="methods" />
      <tag name="hibernate.array" description="Hibernate: array" scope="methods" />
      <tag name="hibernate.one-to-one" description="Hibernate: one-to-one" scope="methods" />
      <tag name="hibernate.many-to-one" description="Hibernate: many-to-one" scope="methods" />
      <tag name="hibernate.many-to-many" description="Hibernate: many-to-many" scope="methods" />
      <tag name="hibernate.index-many-to-many" description="Hibernate: index-many-to-many" scope="methods" />
      <tag name="hibernate.collection-key" description="Hibernate: collection-key" scope="methods" />
      <tag name="hibernate.collection-index" description="Hibernate: collection-index" scope="methods" />
      <tag name="hibernate.collection-composite-index" description="Hibernate: collection-composite-index" scope="methods" />
      <tag name="hibernate.collection-element" description="Hibernate: collection-element" scope="methods" />
      <tag name="hibernate.collection-composite-element" description="Hibernate: collection-composite-element" scope="methods" />
      <tag name="hibernate.collection-one-to-many" description="Hibernate: collection-one-to-many" scope="methods" />
      <tag name="hibernate.collection-many-to-many" description="Hibernate: collection-many-to-many" scope="methods" />
      <tag name="hibernate.bag" description="Hibernate: bag" scope="methods" />
      <tag name="hibernate.many-to-any" description="Hibernate: many-to-any" scope="methods" />
      <tag name="hibernate.many-to-any-column" description="Hibernate: many-to-any-column" scope="methods" />
      <tag name="hibernate.component" description="Hibernate: component" scope="methods" />
    </javadoc>
  </target>
  
  <target
    name="doc.docbook"
    depends="doc.init,doc.docbook.html,doc.docbook.pdf"
    description="Generate docbook user and admin documentation."
    >
  </target>
    
  <target 
    name="doc.docbook.html"
    depends="dev.init,doc.init,xsltprocessor"
    >
    <mkdir dir="${doc}/docbook/html" />
    <!--Create subdirectories to store the chunked files in-->
    <mkdir dir="${doc}/docbook/html/admindoc"/>
    <mkdir dir="${doc}/docbook/html/admindoc/user_administration"/>
    <mkdir dir="${doc}/docbook/html/admindoc/installation_upgrade"/>
    <mkdir dir="${doc}/docbook/html/admindoc/plugin_installation"/>
    <mkdir dir="${doc}/docbook/html/admindoc/coreplugin_configuration"/>
    <mkdir dir="${doc}/docbook/html/developerdoc"/>
    <mkdir dir="${doc}/docbook/html/developerdoc/api"/>
    <mkdir dir="${doc}/docbook/html/developerdoc/develop_overview"/>
    <mkdir dir="${doc}/docbook/html/developerdoc/core_ref"/>
    <mkdir dir="${doc}/docbook/html/developerdoc/javadoc"/>
    <mkdir dir="${doc}/docbook/html/developerdoc/plugin_developer"/>
    <mkdir dir="${doc}/docbook/html/developerdoc/write_doc"/>
    <mkdir dir="${doc}/docbook/html/overviewdoc/overview"/>
    <mkdir dir="${doc}/docbook/html/overviewdoc"/>
    <mkdir dir="${doc}/docbook/html/overviewdoc/why_base"/>
    <mkdir dir="${doc}/docbook/html/overviewdoc/resources"/>
    <mkdir dir="${doc}/docbook/html/userdoc"/>
    <mkdir dir="${doc}/docbook/html/userdoc/about"/>
    <mkdir dir="${doc}/docbook/html/userdoc/annotations"/>
    <mkdir dir="${doc}/docbook/html/userdoc/array_lims"/>
    <mkdir dir="${doc}/docbook/html/userdoc/biomaterials"/>
    <mkdir dir="${doc}/docbook/html/userdoc/analysis"/>
    <mkdir dir="${doc}/docbook/html/userdoc/filesystem"/>
    <mkdir dir="${doc}/docbook/html/userdoc/hardware"/>
    <mkdir dir="${doc}/docbook/html/userdoc/import_export"/>
    <mkdir dir="${doc}/docbook/html/userdoc/jobs"/>
    <mkdir dir="${doc}/docbook/html/userdoc/project_permission"/>
    <mkdir dir="${doc}/docbook/html/userdoc/protocols"/>
    <mkdir dir="${doc}/docbook/html/userdoc/reporter"/>
    <mkdir dir="${doc}/docbook/html/userdoc/software"/>
    <mkdir dir="${doc}/docbook/html/userdoc/trashcan"/>
    <mkdir dir="${doc}/docbook/html/userdoc/webclient"/>
        
    <mkdir dir="${build}/docbook/html" />
    <delete description="Delete existing documents">
      <fileset dir="${build}/docbook" defaultexcludes="no" />
      <fileset dir="${doc}/docbook/html" defaultexcludes="no" />
    </delete>
    <delete file="data/helptexts.xml" />
  <ant antfile="${lib}/docbook/ant-build-docbook.xml" inheritall="false" target="html.chunked">
      <property name="ant.docbook.styler.dir" location="${lib}/docbook" />
      <property name="docbook.xml.dir" location="${docbook.src}" />
      <property name="docbook.resources.dir" location="${docbook.src}/figures" />
      <property name="distribution.dir" location="${doc}/docbook/html" />
      <property name="build.dir" location="${build}/docbook/html" />
      <property name="base.version" value="${base.version}"/>
    </ant>
    
    <property name="catalog.location" location="${lib}/docbook/preprocess/catalog.xml" />
    <path id="ant-extensions">
        <fileset dir="${lib}/docbook/ant-extensions" includes="**/*.jar" />
        <pathelement path="${lib}/docbook/ant-extensions" />
      </path>
    
    <xmlcatalog id="dtdcatalog">
          <catalogpath>
              <fileset file="${catalog.location}"/>
          </catalogpath>
      </xmlcatalog>

      <xslt
          in      = "${build}/docbook/html/docbook-ready-file.tmp"
          style   = "${lib}/docbook/preprocess/webclient_helptext.xsl"
          out     = "data/helptexts.xml"
          processor = "${xslt.processor}"
          >
          <xmlcatalog refid="dtdcatalog"/>
          <classpath refid="ant-extensions" />

          <param name="xsltproc.catalog" expression="${catalog.location}" />
          <param name="xsltproc.option.--nonet"  expression="" />
      </xslt>

    <replaceregexp 
      file="data/helptexts.xml"
      match="&lt;(?!/?name|/?description|/?helpitem|/?helptexts)(/?([a-z]+)[^>]*)&gt;"
      replace="&amp;lt;\$1&amp;gt;"
      flags="sg"
    />
  </target>
  
  <target 
    name="doc.docbook.pdf"
    depends="dev.init,doc.init"
    >
    <!-- Generate a pdf file from the documentation source -->
    <mkdir dir="${build}/docbook/pdf" />
    <echo>Generate pdf file</echo>
    <ant antfile="${lib}/docbook/ant-build-docbook.xml" inheritall="false" target="pdf.fop">
      <property name="ant.docbook.styler.dir" location="${lib}/docbook" />
      <property name="docbook.xml.dir" location="${docbook.src}" />
      <property name="docbook.resources.dir" location="${docbook.src}/figures" />
      <property name="distribution.dir" location="${doc}/docbook" />
      <property name="build.dir" location="${build}/docbook/pdf" />
      <property name="base.version" value="${base.version}"/>
    </ant>
  </target>
  
  <target 
    name="doc.dist"
    description="Copy documentation to the binary distribution"
    >
    <mkdir dir="dist/doc" />
    <copy todir="dist/doc">
      <fileset dir="doc" includes="admin/**/*" />
      <fileset dir="doc" includes="development/**/*" />
      <fileset dir="doc" includes="licenses/**/*" />
      <fileset dir="doc" includes="specifications/**/*" />
      <fileset dir="doc" includes="user/**/*" />
      <fileset dir="doc" includes="*.*" />
    </copy>
  </target>

  <target name="xsltprocessor">
      <property environment="env"/>

      <condition  property="executable.file.extension"
                  value=".exe">
              <os family="windows"/>
      </condition>
      <condition  property="executable.file.extension"
                  value="">
              <os family="unix"/>
      </condition>
      
      <condition  property="tmp:xsltproc.available"
                  value="xsltproc${executable.file.extension}">
          <or>
              <and>
                  <os family="windows"/>
                  <available file="xsltproc${executable.file.extension}" filepath="${env.Path}" />
              </and>
              <and>
                  <os family="unix"/>
                  <available file="xsltproc${executable.file.extension}" filepath="${env.PATH}" />
              </and>
          </or>
      </condition>
      
      <condition property="xslt.processor" value="com.dawidweiss.ant.taskdefs.XsltProcLiaison">
          <and>
              <isset property="tmp:xsltproc.available" />
              <not>
                  <isset property="disable.xsltproc" />
              </not>
          </and>
      </condition>
      
      <condition property="xslt.processor" value="com.dawidweiss.ant.taskdefs.SaxonLiaison">
          <not>
              <isset property="disable.saxon" />
          </not>
      </condition>

      <condition property="xslt.processor" value="trax">
          <not>
          <and>
                  <isset property="tmp:xsltproc.available" />
                  <not>
                      <isset property="disable.xsltproc" />
                  </not>
          </and>
          </not>
      </condition>

    </target>
  
  <!--package targets -->
  <target
    name="package.bin"
    depends="dist"
    description="Create binary distribution package"
    >
    <tar
      destfile="base-${base.version}.tar.gz"
      longfile="gnu"
      compression="gzip"
      >
      <tarfileset
        dir="${dist}"
        mode="755"
        prefix="base-${base.version}"
        preserveLeadingSlashes="true"
        >
        <include name="**/*.sh" />
      </tarfileset>
      <tarfileset
        dir="${dist}"
        prefix="base-${base.version}"
        preserveLeadingSlashes="true"
        >
        <exclude name="**/*.sh" />
      </tarfileset>
    </tar>
    <checksum file="base-${base.version}.tar.gz" />
  </target>
  
  <target
    name="package.src"
    depends="svn.revision"
    description="Create source distribution package"
    >
    <property name="tempdir" location="base-${base.version}-src" />
    <delete dir="${tempdir}" failonerror="false"/>
    <svn>
      <export srcPath="." destPath="${tempdir}" />
    </svn>
    <replaceregexp 
      file="${tempdir}/build.xml"
      match="&lt;svn&gt;.*&lt;status.*?&lt;/svn&gt;"
      replace="&lt;property name=&#34;base.build&#34; value=&#34;${base.build}&#34; /&gt;"
      flags="s"
    />
    <replace file="${tempdir}/build.xml"
      description="Remove references to package.src">
      <replacefilter 
        token="package.bin,package.src"
        value="package.bin"
      />
    </replace>
    <replaceregexp 
      file="${tempdir}/build.xml"
      match="&lt;target\s*?name=&#34;package.src&#34;.*?&lt;/target&gt;"
      replace=""
      flags="s"
      description="Remove package.src target"
    />
      <tar
      destfile="base-${base.version}-src.tar.gz"
      longfile="gnu"
      compression="gzip"
      >
      <tarfileset
        dir="${tempdir}"
        mode="755"
        prefix="base-${base.version}-src"
        preserveLeadingSlashes="true"
        >
        <include name="**/*.sh" />
      </tarfileset>
      <tarfileset
        dir="${tempdir}"
        prefix="base-${base.version}-src"
        preserveLeadingSlashes="true"
        >
        <exclude name="**/*.sh" />
      </tarfileset>
    </tar>
    <checksum file="base-${base.version}-src.tar.gz"/>
    <delete dir="${tempdir}" />
  </target>
  
</project>