source: branches/3.19-stable/build.xml @ 8080

<?xml version="1.0" encoding="UTF-8"?>
<!--
    $Id: build.xml 8080 2022-10-20 12:23:25Z nicklas $

    Copyright (C) 2005 Samuel Andersson, Johan Enell, Jari Häkkinen, Nicklas Nordborg, Gregory Vincic
    Copyright (C) 2006, 2007 Johan Enell, Jari Häkkinen, 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 3 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 BASE. If not, see <http://www.gnu.org/licenses/>.
-->

<project
  name="BASE"
  default="dev"
  basedir="."
  >
  <description>
    Build file for BASE. 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
    test:         Build test programs
    web:          Build web client application for local use

    Documentation:
    doc:          Build documentation for local use
    doc.javadoc:  Build javadoc for local use
    doc.docbook:  Build docbook documentation for local use
    helptext:     Generate help text import file from the docbook documentation

    Packaging:
    package:          Create *.tar.gz files with binary, source and exampele distributions
    package.bin       Create binary distribution only
    package.src       Create source distribution only
  </description>
  
  <!--create this file if you need to override values from properties below -->
  <property file="build.properties" />

  <!-- set BASE version
    Use numerical versions for bugfix (maintenance) releases starting
    with "1". Use "0" for the first release of a new trunk version.  Set
    "base.versionsuffix" to "-dev" for unreleased versions. Examples: 2.1.1-dev, 2.1.1,
    2.1.2-dev, 2.2.2, 2.2.0-dev, 2.2.0, 2.2.1-dev, 2.2.1 
  -->
  <property name="base.majorversion" value="3" />
  <property name="base.minorversion" value="19" />
  <property name="base.maintenanceversion" value="4" />
  <property name="base.versionsuffix" value="" />
  <property name="base.version" 
    value="${base.majorversion}.${base.minorversion}.${base.maintenanceversion}" />
  
  <!-- set other global properties for this build -->
  <property name="javac.arg" value="-Xlint:all,-varargs" 
    description="Extra arguments sent to Java compiler" />
  <property name="jsp.xlint" value="all,-serial" 
    description="Xlint parameter when compiling JSP files (-serial is needed since jasper doesn't generate a serialVersionUID)" />
  <!-- NOTE! Releae version is also in the config/dist/web.xml for the JSP servlet declaration -->
  <!-- If the value is changed here, it should also be changed in web.xml -->
  <property name="javac.release" value="11"
    description="Default value for the 'release' attribute when compiling java code" />
  <property name="javac.encoding" value="UTF-8"
    description="Default value for the 'encoding' attribute when compiling java code" />
  <property name="javadoc.arg" value="-Xdoclint:all,-missing"
    description="Extra arguments sent to Javadoc generation" />
  <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="package" location="package" description="Directory where packaged distribution files are 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" />
  
  <!-- classpaths to library files -->
  <path id="lib.dist.classpath">
    <fileset dir="${lib}/dist">
      <include name="**/*.jar"/>
    </fileset>
  </path>
  
  <path id="lib.svnkit.classpath">
    <fileset dir="${lib}/svnkit">
      <include name="**/*.jar"/>
    </fileset>
  </path>
  
  <path id="lib.hibernatedoclet.classpath">
    <fileset dir="${lib}/hibernatedoclet">
      <include name="**/*.jar"/>
    </fileset>
  </path>
  
  <path id="lib.servlet.classpath">
    <fileset dir="${lib}/servlet">
      <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>
      <path refid="lib.hibernatedoclet.classpath" />
    </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="${package}" defaultexcludes="no" />
      <fileset dir="bin/jar" defaultexcludes="no" />
      <fileset dir="www/WEB-INF/lib" defaultexcludes="no" />
      <fileset dir="www/WEB-INF/classes" defaultexcludes="no" />
      <fileset dir="www/WEB-INF/conf" defaultexcludes="no" />
      <fileset dir="www/WEB-INF/services" defaultexcludes="no" />
      <fileset dir="www/WEB-INF" includes="web.xml" defaultexcludes="no" />
      <fileset dir="doc/api" defaultexcludes="no" />
      <fileset dir="doc/html" defaultexcludes="no" />
      <fileset file="data/helptexts.xml" />
    </delete>
  </target>
  <target 
    name="old-jars"
    depends="dev.init"
    description="Remove BASE core JAR files created from older versions"
    >
    <delete>
      <fileset dir="${jar}" includes="base-*.jar" excludes="base-*-${base.version}.jar"></fileset>
    </delete>
    <delete>
      <fileset dir="${bin}/jar" includes="base-*.jar" excludes="base-*-${base.version}.jar"></fileset>
    </delete>
  </target>

  <target
    name="dist"
    depends="clean,dist.init,core.jar,coreplugins.jar,web.jar,xjspcompiler,
      installprg.jar,jobagent.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="${dist}/bin" description="Scripts, etc.">
      <fileset dir="bin">
      </fileset>
    </copy>
    <copy todir="${dist}/misc" description="Other files">
      <fileset dir="misc">
        <include name="sql/**/*" />
        <include name="config/**/*" />
      </fileset>
    </copy>
    <copy todir="${dist}" description="License and credits">
      <fileset file="base.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,old-jars,core,coreplugins,web,installprg,jobagent,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="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,xjspcompiler,copy.config,copy.jar"
    description="Build web client application for local use"
    >
  </target>
  
  <target
    name="installprg"
    depends="core,web,installprg.jar"
    description="Build installation programs for local use"
  />
  
  <target
    name="jobagent"
    depends="core,web,jobagent.jar"
    description="Build job agent for local use"
  />
  
  <target
    name="doc"
    depends="doc.javadoc,doc.docbook"
    description="Generate documentation (javadoc and docbook) for local use and distribution"
  />
  
  <!-- 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"
    >
    <java
      classname="org.tmatesoft.svn.cli.SVN"
      classpathref="lib.svnkit.classpath"
      outputproperty="svn.info.out"
      >
      <arg value="info" />
      <arg value="." />
    </java>
    <loadresource property="base.build"
      description="Scan output from 'svn info' and keep only the line with 'Last Changed Rev:'"
      >
      <concat>${svn.info.out}</concat>
      <filterchain>
        <linecontains><contains value="Last Changed Rev" /></linecontains>
        <replaceregex pattern=".*?(\d+)" replace="\1" />
        <striplinebreaks/>
      </filterchain>
    </loadresource>
    <echo message="Build #${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" />
    <path id="core.classpath">
      <path refid="lib.dist.classpath" />
    </path>
  </target>
  
  <target
    name="core.compile"
    depends="core.init"
    description="Compile the core"
    >
    <mkdir dir="${core.build}"/>
    <javac
      srcdir="${core.src}"
      destdir="${core.build}"
      classpathref="core.classpath"
      encoding="${javac.encoding}"
      debug="true"
      deprecation="true"
      release="${javac.release}"
      includeantruntime="false"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
    <delete file="${core.build}/base.version" failonerror="false" />
    <copy todir="${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}"
      />
      <replacefilter 
        token="@SUFFIX@"
        value="${base.versionsuffix}"
      />
    </replace>
    <replaceregexp 
      file="${core.build}/core-extensions.xml"
      match="&lt;version&gt;.*&lt;/version&gt;"
      replace="&lt;version&gt;${base.version}${base.versionsuffix}&lt;/version&gt;"
      encoding="UTF-8"
    />
  </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 failonerror="false">
      <fileset dir="${core.build}" includes="**/*.hbm.xml" />
      <fileset dir="${build}/hbm" includes="**/*" />
    </delete>
    <copy todir="${core.build}" 
      description="Hardcoded *.hbm.xml files">
      <fileset dir="${core.src}" includes="**/*.hbm.xml" />
    </copy>
    <copy todir="${build}/hbm"
      description="Copy our data class files so xdoclet doesn't parse other code">
      <fileset dir="${core.src}" includes="net/sf/basedb/core/data/**/*" />
    </copy>
    
    <hibernatedoclet
      destdir="${core.build}"
      excludedtags="@version,@author,@todo"
      mergedir="${core.build}"
      verbose="true"
      >
      <fileset dir="${build}/hbm">
        <include name="net/sf/basedb/core/data/**/*.java"/>
      </fileset>
      <hibernate version="2.0" />
    </hibernatedoclet>
    
    <replace
      dir="${core.build}"
      >
      <include name="**/*.hbm.xml"/>
      <replacefilter 
        token="&lt;hibernate-mapping"
        value="&lt;hibernate-mapping xmlns=&#34;http://www.hibernate.org/xsd/hibernate-mapping&#34;"
      />
      <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="outer-join=&#34;auto&#34;"
        value=""
      />
      <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>
    
    <!--
      Move the mappings files for all Extendable classes 
      because we are going to add more tags to them at runtime
    -->
    <!--
    <move 
      todir="${core.build}/net/sf/basedb/core/templates" 
      >
      <fileset dir="${core.build}/net/sf/basedb/core/data">
        <include name="ReporterData.hbm.xml"/>
        <include name="UserData.hbm.xml"/>
      </fileset>
      <mapper type="glob" from="*.hbm.xml" to="hibernate-properties-*.xml" />
    </move>
    -->
  </target>
  
  <target
    name="core.jar"
    depends="core.init,core.compile,core.hibernate"
    description="Create the core jar file: base-core-a.b.c.jar"
    >
    <jar
      basedir="${core.build}"
      jarfile="${jar}/base-core-${base.version}.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="${coreplugins.build}"
      classpathref="coreplugins.classpath"
      encoding="${javac.encoding}"
      debug="true"
      deprecation="true"
      release="${javac.release}"
      includeantruntime="false"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
    <copy todir="${coreplugins.build}" 
      description="Resource files needed by the core plug-ins; excludes documentation and source files">
      <fileset dir="${coreplugins.src}">
        <include name="**/*" />
        <exclude name="**/*.java" />
        <exclude name="**/doc-files/" />
        <exclude name="**/package.html" />
      </fileset>
    </copy>
    <replaceregexp 
      file="${coreplugins.build}/core-plugins.xml"
      match="&lt;version&gt;.*&lt;/version&gt;"
      replace="&lt;version&gt;${base.version}${base.versionsuffix}&lt;/version&gt;"
      encoding="UTF-8"
    />
  </target>
  
  <target
    name="coreplugins.jar"
    depends="coreplugins.compile"
    description="Create the plugin jar file: base-coreplugins-a.b.c.jar"
    >
    <jar
      basedir="${coreplugins.build}"
      jarfile="${jar}/base-coreplugins-${base.version}.jar"
    />
  </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="${test.build}"
      classpathref="test.classpath"
      encoding="${javac.encoding}"
      debug="true"
      deprecation="true"
      release="${javac.release}"
      includeantruntime="false"
      >
      <compilerarg value="${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"
    >
    <copy todir="${test.build}" description="Test data files needed inside JARs">
      <fileset dir="${test.src}">
        <include name="net/sf/basedb/test/**" />
        <exclude name="**/*.java" />
      </fileset>
    </copy>

    <jar 
      jarfile="${test.build}/JarPlugin.jar" 
      basedir="${test.build}" 
      includes="JarPlugin*,NullPlugin*,Base1*"
      excludes="JarPlugin.jar"
      manifest="${test.src}/data/JarPluginManifest.txt"
      >
    </jar>
    
    <jar jarfile="${test.build}/ExtensionOne.jar"
      basedir="${test.build}" 
      includes="net/sf/basedb/test/extension/jar1/** net/sf/basedb/test/extension/data/**"
      >
      <metainf file="${test.src}/net/sf/basedb/test/extension/jar1/extensions.xml" />
    </jar>

    <jar jarfile="${test.build}/ExtensionTwo.jar"
      basedir="${test.build}" 
      includes="net/sf/basedb/test/extension/jar2/** net/sf/basedb/test/extension/data/**"
      >
      <metainf file="${test.src}/net/sf/basedb/test/extension/jar2/extensions.xml" />
    </jar>

    <jar jarfile="${test.build}/ExtensionThree.jar"
      basedir="${test.build}" 
      includes="net/sf/basedb/test/extension/jar3/** net/sf/basedb/test/extension/data/**"
      >
      <metainf file="${test.src}/net/sf/basedb/test/extension/jar3/extensions.xml" />
      <manifest>
        <attribute name="Class-Path" value="ExtensionOne.jar ExtensionTwo.jar" />
      </manifest>
    </jar>
    
    <delete>
      <fileset dir="${test.build}" includes="JarPlugin*.class" />
      <fileset dir="${test.build}" includes="net/sf/basedb/test/extension/data/**" />
      <fileset dir="${test.build}" includes="net/sf/basedb/test/extension/jar1/**" />
      <fileset dir="${test.build}" includes="net/sf/basedb/test/extension/jar2/**" />
      <fileset dir="${test.build}" includes="net/sf/basedb/test/extension/jar3/**" />
    </delete>
  </target>

  <!-- web targets -->
  <target
    name="web.init"
    depends="core.init,coreplugins.init"
    >
    <property name="web.src" location="${src}/clients/web" 
      description="Location of source files" />
    <property name="xjspcompiler.src" location="${src}/misc/compiler" />    
    <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}" />
      <path refid="lib.servlet.classpath" />
    </path>
  </target>
  
  <target
    name="web.compile"
    depends="web.init,core.compile,coreplugins.compile"
    description="Compile the web client application"
    >
    <mkdir dir="${web.build}" />
    <javac
      srcdir="${web.src}"
      destdir="${web.build}"
      classpathref="web.classpath"
      encoding="${javac.encoding}"
      debug="true"
      deprecation="true"
      release="${javac.release}"
      includeantruntime="false"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
    <copy todir="${web.build}" 
      description="Resource files needed by the web client; excludes documentation and source files">
      <fileset dir="${web.src}">
        <include name="**/*" />
        <exclude name="**/*.java" />
        <exclude name="**/doc-files/" />
        <exclude name="**/package.html" />
      </fileset>
    </copy>
    <replaceregexp 
      file="${web.build}/web-extensions.xml"
      match="&lt;version&gt;.*&lt;/version&gt;"
      replace="&lt;version&gt;${base.version}${base.versionsuffix}&lt;/version&gt;"
      encoding="UTF-8"
    />
  </target>
  
  <target
    name="web.jar"
    depends="web.compile"
    description="Create the web client jar file: base-webclient-a.b.c.jar"
    >
    <jar
      basedir="${web.build}"
      jarfile="${jar}/base-webclient-${base.version}.jar"
    />
  </target>
  
  <!-- Targets for JSP precompilation. Useful for checking that eveything works before a release is made. -->
  <!-- Use as: 'ant web jsp' to also make sure that dependencies have been compiled -->
  <target 
    name="jsp"
    depends=""
    >
    <!-- check that tomcat.home exists and that required the required 'catalina-tasks.xml' is present -->
    <fail unless="tomcat.home" 
      message="{tomcat.home} has not been set. Create 'build.properties' in current directory and add 'tomcat.home' with path to your Tomcat installation directory. " />
    
    <available file="${tomcat.home}/bin/catalina-tasks.xml" property="catalina-tasks" />
    
    <fail unless="catalina-tasks" 
      message="File '${tomcat.home}/bin/catalina-tasks.xml' does not exists. You may have to install this from the Tomcat ZIP distribution." />
    
    <!-- we are good to go -->
    <mkdir dir="${build}/jsp" />
    <ant antfile="jsp-precompile.xml" inheritall="false" target="all" >
      <property name="tomcat.home" value="${tomcat.home}" />
      <property name="jsp.src" value="www" />
      <property name="jsp.build" value="${build}/jsp" />
      <property name="javac.bootclasspath" value="${javac.bootclasspath}" />
      <property name="javac.encoding" value="${javac.encoding}" />
      <property name="javac.release" value="${javac.release}" />
      <property name="jsp.xlint" value="${jsp.xlint}" />
    </ant>
  </target>
  
  <!-- Clean up after 'jsp' target -->
  <target 
    name="jsp.clean"
    >
    <delete dir="${build}/jsp" />
  </target>
  
  <!-- XJsp compiler targets -->
  <target
    name="xjspcompiler"
    depends="web.compile,core.compile"
    description="Compile the XJsp compiler and put JAR in ./bin/jar"
    >
    <mkdir dir="${build}/misc/compiler" />
    <javac
      srcdir="${xjspcompiler.src}"
      destdir="${build}/misc/compiler"
      classpathref="web.classpath"
      encoding="${javac.encoding}"
      debug="true"
      deprecation="true"
      release="${javac.release}"
      includeantruntime="false"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
    <jar
      basedir="${build}/misc/compiler"
      jarfile="${bin}/jar/base-xjsp-compiler-${base.version}.jar"
    />
  </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="${javac.encoding}"
      debug="true"
      deprecation="true"
      release="${javac.release}"
      includeantruntime="false"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="installprg.jar"
    depends="installprg.compile"
    description="Create the installation jar file: base-install-a.b.c.jar"
    >
    <jar
      basedir="${installprg.build}"
      jarfile="${bin}/jar/base-install-${base.version}.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="${javac.encoding}"
      debug="true"
      deprecation="true"
      release="${javac.release}"
      includeantruntime="false"
      >
      <compilerarg value="${javac.arg}" />
    </javac>
  </target>
  
  <target
    name="jobagent.jar"
    depends="jobagent.compile"
    description="Create the job agent jar file: base-jobagent-a.b.c.jar"
    >
    <jar
      basedir="${jobagent.build}"
      jarfile="${bin}/jar/base-jobagent-${base.version}.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" />
      <path refid="lib.servlet.classpath" />
    </path>
    <property name="docbook.html.out" location="${doc}/html" />
  </target>
  
  <target
    name="doc.javadoc"
    depends="doc.init,core.init,coreplugins.init,web.init,jobagent.init"
    description="Generate JavaDoc of entire API"
    >
    <!-- Create the time stamp -->
    <tstamp>
      <format property="TODAY" pattern="yyyy-MM-dd"/>
    </tstamp>
    <delete dir="${doc}/api" />
    <sleep milliseconds="1000"/>
    <mkdir dir="${doc}/api" />

    <javadoc
      packagenames="net.sf.basedb.*"
      sourcepath="${core.src}:${coreplugins.src}:${web.src}:${xjspcompiler.src}:${jobagent.src}"
      destdir="${doc}/api"
      author="true"
      version="true"
      use="false"
      private="true"
      windowtitle="BASE ${base.version}${base.versionsuffix} API documentation"
      classpathref="javadoc.classpath"
      linksource="false"
      breakiterator="yes"
      encoding="${javac.encoding}"
      overview="${javadoc.src}/overview.html"
      maxmemory="256M"
      additionalparam="${javadoc.arg}"
      >
      <group title="Public API">
        <package name="net.sf.basedb.info" />
        <package name="net.sf.basedb.core" />
        <package name="net.sf.basedb.core.plugin" />
        <package name="net.sf.basedb.core.query" />
        <package name="net.sf.basedb.core.signal" />
        <package name="net.sf.basedb.core.authentication" />
        <package name="net.sf.basedb.core.snapshot" />
        <package name="net.sf.basedb.plugins*" />
        <package name="net.sf.basedb.util*" />
        <package name="net.sf.basedb.clients.web.taglib*" />
        <package name="net.sf.basedb.clients.web.extensions*" />
      </group>
      <group title="Mixed Public and Internal API">
        <package name="net.sf.basedb.core.data" />
        <package name="net.sf.basedb.clients.web" />
        <package name="net.sf.basedb.clients.web.util" />
      </group>
      <group title="Extension API">
        <package name="net.sf.basedb.core.dbengine" />
        <package name="net.sf.basedb.core.log*" />
        <package name="net.sf.basedb.util.overview.*" />
        <package name="net.sf.basedb.util.extensions.manager.*" />
        <package name="net.sf.basedb.clients.jobagent" />
      </group>
      <group title="Internal API">
        <package name="net.sf.basedb.core.data.keyring" />
        <package name="net.sf.basedb.clients.jobagent.*" />
        <package name="net.sf.basedb.clients.web.*" />
        <package name="net.sf.basedb.core.hibernate" />
      </group>
      
      <header><![CDATA[${base.version}${base.versionsuffix}: ${TODAY}]]></header>
      <link href="https://docs.oracle.com/en/java/javase/11/docs/api/"/>
      <link href="https://docs.jboss.org/hibernate/orm/5.4/javadocs/" />
      <link href="http://www.jdom.org/docs/apidocs/" />
      <link href="https://tomcat.apache.org/tomcat-9.0-doc/servletapi/" />
      <link href="https://tomcat.apache.org/tomcat-9.0-doc/jspapi/" />
      <link href="https://tomcat.apache.org/tomcat-9.0-doc/api/" />
      <link href="http://www.singularsys.com/jep/doc/javadoc/" />
      <link href="https://www.jfree.org/jfreechart/api/gjdoc/" />
      <link href="https://logging.apache.org/log4j/1.2/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.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.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.component" description="Hibernate: component" 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" />
    </javadoc>
  </target>
  
  <target
    name="doc.docbook"
    depends="doc.init,doc.docbook.html"
    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}/admin"/>
    <mkdir dir="${docbook.html.out}/developer"/>
    <mkdir dir="${docbook.html.out}/developer/plugins"/>
    <mkdir dir="${docbook.html.out}/developer/extensions"/>
    <mkdir dir="${docbook.html.out}/developer/api"/>
    <mkdir dir="${docbook.html.out}/developer/documentation"/>
    <mkdir dir="${docbook.html.out}/user"/>
    <mkdir dir="${docbook.html.out}/user/webclient"/>
    <mkdir dir="${docbook.html.out}/user/projects"/>
    <mkdir dir="${docbook.html.out}/user/files"/>
    <mkdir dir="${docbook.html.out}/user/annotations"/>
    <mkdir dir="${docbook.html.out}/user/biomaterials"/>
    <mkdir dir="${docbook.html.out}/user/experiments"/>
    <mkdir dir="${docbook.html.out}/faq" />
    <mkdir dir="${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="${lib}/docbook" />
      <property name="svnkit.dir" location="${lib}/svnkit" />
      <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="${base.version}${base.versionsuffix}"/>
      <property name="dateformat" value="yyyy-MM-dd" />
    </ant>
    <copy todir="${docbook.html.out}">
      <fileset dir="${docbook.src}" includes="css/*.*" />
      <fileset dir="${docbook.src}" includes="script/*.*" />
      <fileset dir="${docbook.src}" includes="examples/*.*" />
     </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>
  </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="historical/**/*" />
      <fileset dir="doc" includes="test/**/*" />
      <!--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"
    >
    <mkdir dir="${package}" />
    <tar
      destfile="${package}/base-${base.version}${base.versionsuffix}.tar.gz"
      longfile="gnu"
      compression="gzip"
      >
      <tarfileset
        dir="${dist}"
        mode="755"
        prefix="base-${base.version}${base.versionsuffix}"
        preserveLeadingSlashes="true"
        >
        <include name="**/*.sh" />
      </tarfileset>
      <tarfileset
        dir="${dist}"
        prefix="base-${base.version}${base.versionsuffix}"
        preserveLeadingSlashes="true"
        >
        <exclude name="**/*.sh" />
      </tarfileset>
    </tar>
    <checksum file="${package}/base-${base.version}${base.versionsuffix}.tar.gz" />
  </target>
  
  <target
    name="package.src"
    depends="svn.revision"
    description="Create source distribution package"
    >
    <property name="tempdir" location="base-${base.version}${base.versionsuffix}-src" />
    <delete dir="${tempdir}" failonerror="false"/>
    <java
      classname="org.tmatesoft.svn.cli.SVN"
      classpathref="lib.svnkit.classpath"
      >
      <arg value="export" />
      <arg value="-q" />  <!--quiet: or we get a list of all files that are copied -->
      <arg value="." />
      <arg path="${tempdir}" />
    </java>
    
    <replaceregexp 
      description="replacs the 'java' call in svn.revision with a static property"
      file="${tempdir}/build.xml"
      match="&lt;java.*org.tmatesoft.svn.cli.SVN.*?&lt;/loadresource&gt;"
      replace="&lt;property name=&#34;base.build&#34; value=&#34;${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"
    />
    <mkdir dir="${package}" />
      <tar
      destfile="${package}/base-${base.version}${base.versionsuffix}-src.tar.gz"
      longfile="gnu"
      compression="gzip"
      >
      <tarfileset
        dir="${tempdir}"
        mode="755"
        prefix="base-${base.version}${base.versionsuffix}-src"
        preserveLeadingSlashes="true"
        >
        <include name="**/*.sh" />
      </tarfileset>
      <tarfileset
        dir="${tempdir}"
        prefix="base-${base.version}${base.versionsuffix}-src"
        preserveLeadingSlashes="true"
        >
        <exclude name="**/*.sh" />
      </tarfileset>
    </tar>
    <checksum file="${package}/base-${base.version}${base.versionsuffix}-src.tar.gz"/>
    <delete dir="${tempdir}" />
  </target>

</project>