source: trunk/build.xml @ 3911

<?xml version="1.0" encoding="UTF-8"?>
<!--
    $Id: build.xml 3908 2007-11-05 18:46:31Z martin $

    Copyright (C) 2005 Samuel Andersson, Johan Enell, Jari Hakkinen, Nicklas Nordborg, Gregory Vincic
    Copyright (C) 2006, 2007 Johan Enell, Jari Hakkinen, Nicklas Nordborg, Martin Svensson

    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
    webservices:  Build webservices for local use
    test:         Build test programs
    web:          Build web client application for local use

    Documentation:
    doc:          Build all documentation for local use
    docbook:      Build only html and pdf from docbook
    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="5" />
  <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>
  
  <taskdef
    name="java2WSDL"
    classname="org.apache.ws.java2wsdl.Java2WSDLTask"
    description="Task for creating wsdl files for the web services"
    >
    <classpath>
      <fileset dir="${lib}/webservices">
        <include name="**/*.jar"/>
      </fileset>
      <fileset dir="${lib}/dist">
        <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/conf" defaultexcludes="no" />
      <fileset dir="www/WEB-INF/services" defaultexcludes="no" />
      <fileset dir="www/WEB-INF" includes="web.xml" defaultexcludes="no" />
      <fileset dir="doc/api" defaultexcludes="no" />
      <fileset dir="doc/html" defaultexcludes="no" />
      <fileset file="doc/base.pdf" />
      <fileset file="doc/download/exampleplugins.tar.gz" />
    </delete>
  </target>
  
  <target
    name="dist"
    depends="clean,dist.init,core.jar,coreplugins.jar,web.jar,webservices.aar,
          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>
      <fileset dir="${webservices.build}" description="Webservice WSDL files">
          <include name="wsdl/**/*"/>
      </fileset>
    </copy>
    <copy todir="${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,webservices,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="webservices"
      depends="web,webservices.aar"
      description="Build webservices for local use"
  />
  
  <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="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" />
    <property name="plugins" location="${dist}/plugins" />
    <mkdir dir="${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" />
    <property name="plugins" location="plugins" />
    <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"
    >
    <mkdir dir="${config}/../conf" />
    <!--<move file="${config}/axis2.xml" todir="${config}/../conf" /> -->
  </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>
      <fileset dir="${lib}/webservices">
        <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"
    >
    <mkdir dir="${plugins}" />
    <jar
      basedir="${exampleplugins.build}"
      jarfile="${plugins}/ExamplePlugins.jar"
      manifest="${exampledir}/MANIFEST.MF"
      >
      <metainf file="${exampledir}/base-plugins.xml"></metainf>
       <metainf file="${exampledir}/base-configurations.xml"></metainf>
    </jar>
  </target>

  <target
    name="exampleplugins.tar"
    depends="exampleplugins.jar"
    description="Create a downloadable tar file with the example plugins"
    >
    <mkdir dir="${doc}/download" />
    <tar
      destfile="${doc}/download/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,webservices.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="webservices.classpath"/>
      <pathelement location="${core.build}" />
      <pathelement location="${coreplugins.build}" />
      <pathelement location="${jobagent.build}" />
      <pathelement location="${webservices.build}" />
    </path>
  </target>
  
  <target
    name="test.compile"
    depends="test.init,core.compile,coreplugins.compile,jobagent.compile,webservices.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*,Base1NullPlugin*"
      excludes="JarPlugin.jar,JarPluginAbout.*"
      manifest="${test.src}/data/JarPluginManifest.txt"
      >
      <metainf file="${test.src}/base-plugins.xml"></metainf>
       <metainf file="${test.src}/base-configurations.xml"></metainf>
    </jar>
    <delete>
      <fileset dir="${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>
  
  <!-- webservices targets -->
  <target
    name="webservices.init"
    depends="core.init"
    >
    <property name="webservices.src" location="${src}/webservices" 
      description="Location of source files" />
    <property name="webservices.build" location="${build}/webservices" 
      description="Location of compiled files" />
    <path id="webservices.classpath" description="Class path for compiling webservices">
      <path refid="core.classpath"/>
      <pathelement location="${core.build}"/>
      <pathelement location="${coreplugins.build}"/>
      <fileset dir="${lib}/webservices">
        <include name="**/*.jar"/>
      </fileset>
    </path>
  </target>

  <target
    name="webservices.compile"
    depends="webservices.init,core.compile"
    description="Compile the core web services"
    >
    <mkdir dir="${webservices.build}" />
    <javac
      destdir="${webservices.build}"
      classpathref="webservices.classpath"
      encoding="ISO-8859-1"
      debug="true"
      deprecation="true"
      >
      <src path="${webservices.src}/server" />
      <src path="${webservices.src}/client/java" />
      <compilerarg value="${javac.arg}" />
    </javac>
    
    <!-- Create WSDL files for services -->
    <webservices.wsdl serviceClassName="ArrayDesignService"/>
    <webservices.wsdl serviceClassName="BioAssaySetService"/>
    <webservices.wsdl serviceClassName="ExperimentService"/>
    <webservices.wsdl serviceClassName="ProjectService"/>
    <webservices.wsdl serviceClassName="RawBioAssayService"/>
    <webservices.wsdl serviceClassName="SessionService"/>
    
    <copy todir="${webservices.build}" 
      description="Resource files needed by the webservices; excludes documentation and source files"
      includeEmptyDirs="false"
      >
      <fileset dir="${webservices.src}/server">
        <include name="**/*" />
        <exclude name="**/*.java" />
        <exclude name="**/doc-files/" />
        <exclude name="**/package.html" />
      </fileset>
    </copy>   
  </target>
  
  <!-- Creates a WSDL file for a Webservice class -->
    <macrodef name="webservices.wsdl">
        <attribute name="serviceClassName"/>
        <sequential>
          <java2WSDL
        classpath="${webservices.build};${core.build}"
        className="net.sf.basedb.ws.server.@{serviceClassName}"
        outputLocation="${webservices.build}/wsdl"      
        serviceName="@{serviceClassName}"
        outputFileName="@{serviceClassName}.wsdl"
        >   
      </java2WSDL>    
        </sequential>
    </macrodef>
  
  <target
    name="webservices.aar"
    depends="webservices.compile"
    description="Create the core webservices aar file: core.aar"
    >
    <mkdir dir="${config}/../services" />
    <jar
      basedir="${webservices.build}"
      jarfile="${config}/../services/core.aar"
    />
  </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"
    depends="core.init"
    >
    <property name="javadoc.src" location="doc/src/javadoc" 
      description="Location of javadoc source files" />
    <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="${lib}/servlet">
        <include name="**/*.jar"/>
      </fileset>
    </path>
    <property name="docbook.html.out" location="${doc}/html" />
    <property name="docbook.pdf.out" location="${doc}" />
  </target>
  
  <target
    name="doc.javadoc"
    depends="doc.init,core.init,coreplugins.init,web.init,migrate.init,jobagent.init,webservices.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}:${jobagent.src}:${webservices.src}/server:${webservices.src}/client/java"
      destdir="${doc}/api"
      author="true"
      version="true"
      use="false"
      private="true"
      windowtitle="BASE ${base.version} API documentation"
      stylesheetfile="${javadoc.src}/javadoc.css"
      classpathref="javadoc.classpath"
      linksource="false"
      breakiterator="yes"
      encoding="iso-8859-1"
      overview="${javadoc.src}/overview.html"
      >
      <group title="Public API"
        packages="net.sf.basedb.core:net.sf.basedb.core.plugin:net.sf.basedb.core.query:net.sf.basedb.util*:net.sf.basedb.clients.web.taglib*:net.sf.basedb.plugins:net.sf.basedb.core.authentication"
      />
      <group title="Mixed Public and Internal API"
        packages="net.sf.basedb.core.data:net.sf.basedb.clients.web:net.sf.basedb.clients.web.util"
      />
      <group title="Extension API"
        packages="net.sf.basedb.core.dbengine:net.sf.basedb.clients.jobagent:net.sf.basedb.ws.server*"
      />
      <group title="Internal API"
        packages="net.sf.basedb.core.data.keyring:net.sf.basedb.clients.jobagent.*:net.sf.basedb.clients.migrate*:net.sf.basedb.clients.web.*"
      />
      
      <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.developer" description="Developer info" />
      <tag name="base.internal" description="This class/package is not part of the Public API" scope="overview,packages,types" />
      <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="${docbook.html.out}" />
    <!--Create subdirectories to store the chunked files in-->
    <mkdir dir="${docbook.html.out}/admindoc"/>
    <mkdir dir="${docbook.html.out}/admindoc/user_administration"/>
    <mkdir dir="${docbook.html.out}/admindoc/installation_upgrade"/>
    <mkdir dir="${docbook.html.out}/admindoc/plugin_installation"/>
    <mkdir dir="${docbook.html.out}/admindoc/coreplugin_configuration"/>
    <mkdir dir="${docbook.html.out}/developerdoc"/>
    <mkdir dir="${docbook.html.out}/developerdoc/api"/>
    <mkdir dir="${docbook.html.out}/developerdoc/develop_overview"/>
    <mkdir dir="${docbook.html.out}/developerdoc/core_ref"/>
    <mkdir dir="${docbook.html.out}/developerdoc/javadoc"/>
    <mkdir dir="${docbook.html.out}/developerdoc/plugin_developer"/>
    <mkdir dir="${docbook.html.out}/developerdoc/webservices"/>
    <mkdir dir="${docbook.html.out}/developerdoc/write_doc"/>
    <mkdir dir="${docbook.html.out}/overviewdoc/overview"/>
    <mkdir dir="${docbook.html.out}/overviewdoc"/>
    <mkdir dir="${docbook.html.out}/overviewdoc/why_base"/>
    <mkdir dir="${docbook.html.out}/overviewdoc/resources"/>
    <mkdir dir="${docbook.html.out}/userdoc"/>
    <mkdir dir="${docbook.html.out}/userdoc/about"/>
    <mkdir dir="${docbook.html.out}/userdoc/annotations"/>
    <mkdir dir="${docbook.html.out}/userdoc/platforms"/>
    <mkdir dir="${docbook.html.out}/userdoc/array_lims"/>
    <mkdir dir="${docbook.html.out}/userdoc/biomaterials"/>
    <mkdir dir="${docbook.html.out}/userdoc/analysis"/>
    <mkdir dir="${docbook.html.out}/userdoc/filesystem"/>
    <mkdir dir="${docbook.html.out}/userdoc/hardware"/>
    <mkdir dir="${docbook.html.out}/userdoc/import_export"/>
    <mkdir dir="${docbook.html.out}/userdoc/jobs"/>
    <mkdir dir="${docbook.html.out}/userdoc/project_permission"/>
    <mkdir dir="${docbook.html.out}/userdoc/protocols"/>
    <mkdir dir="${docbook.html.out}/userdoc/reporters"/>
    <mkdir dir="${docbook.html.out}/userdoc/software"/>
    <mkdir dir="${docbook.html.out}/userdoc/trashcan"/>
    <mkdir dir="${docbook.html.out}/userdoc/webclient"/>
    <mkdir dir="${docbook.html.out}/userdoc/overview"/>
    <mkdir dir="${docbook.html.out}/faqs" />
    <mkdir dir="${docbook.html.out}/appendix" />
        
    <mkdir dir="${build}/docbook/html" />
    <delete description="Delete existing documents">
      <fileset dir="${build}/docbook" defaultexcludes="no" />
      <fileset dir="${docbook.html.out}" defaultexcludes="no" />
    </delete>
    <delete file="data/helptexts.xml" />
    <ant antfile="${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="${docbook.src}/figures" />
      <property name="distribution.dir" location="${docbook.html.out}" />
      <property name="build.dir" location="${build}/docbook/html" />
      <property name="base.version" value="${base.version}"/>
    </ant>
     <copy todir="${docbook.html.out}">
         <fileset dir="${docbook.src}" includes="css/*.*" />
         <fileset dir="${docbook.src}" includes="script/*.*" />
     </copy>
    
    <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="${docbook.src}/figures" />
      <property name="distribution.dir" location="${docbook.pdf.out}" />
      <property name="build.dir" location="${build}/docbook/pdf" />
      <property name="pdf.name" value="base.pdf" />
      <property name="base.version" value="${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>