build.xml

<?xml version="1.0"?>
<project name="ClusterONE" default="usage" basedir=".">
    <!-- Package name and version number -->
    <loadproperties>
        <file file="etc/cl1.properties"/>
    </loadproperties>

    <!-- Compiler constants -->
    <property name="debug" value="on"/>
    <property name="optimize" value="on"/>
    <property name="deprecation" value="on"/>

    <!-- Directories -->
    <property name="build" location="build" />
    <property name="src" location="src" />
    <property name="test" location="test" />
    <property name="doc" location="doc" />
    <property name="etc" location="etc" />
    <property name="lib" location="lib" />
    <property name="reports" location="reports" />
    <property name="tools" location="tools" />

    <!-- DON'T CHANGE ANYTHING BELOW THIS LINE
    UNLESS YOU KNOW WHAT YOU'RE DOING -->
    <property name="src.java" location="${src}/java" />
    <property name="src.java.tests" location="${test}/java" />
    <property name="src.web" location="${src}/web" />
    
    <property name="build.java" location="${build}/java" />
    <property name="build.java.tests" location="${build}/tests" />
    <property name="build.webinf" location="${build}/WEB-INF" />

    <property name="build.doc" location="${build}/doc" />
    <property name="build.doc.cmdline" location="${build.doc}/cmdline" />
    <property name="build.doc.cytoscape" location="${build}/java/${package.name.slashed}/ui/cytoscape/help" />
    <property name="build.doc.cytoscape3" location="${build}/java/${package.name.slashed}/ui/cytoscape3/help" />
    <property name="build.doc.procope" location="${build.doc}/procope" />

    <property name="tool.bnd.path" location="${lib}/bnd-2.0.0.jar" />
    
    <property name="ant.build.javac.source" value="1.5" />
    <property name="ant.build.javac.target" value="1.5" />

    <!-- Access to environment -->
    <property environment="os" />

    <!-- External dependencies -->
    <condition property="lib.cytoscape.path" value="${cytoscape.path}/cytoscape.jar">
        <available file="${cytoscape.path}/cytoscape.jar" />
    </condition>
    <condition property="lib.cytoscape3.path" value="${cytoscape3.api.jar}">
        <available file="${cytoscape3.api.jar}" />
    </condition>
    <condition property="lib.procope.path" value="${procope.path}/lib/procope_core-${procope.version}.jar">
        <available file="${procope.path}/lib/procope_core-${procope.version}.jar" />
    </condition>
    <condition property="lib.jsr311.path" value="${jersey.path}/lib/jsr311-api-${jersey.jsr311.version}.jar">
        <available file="${jersey.path}/lib/jsr311-api-${jersey.jsr311.version}.jar" />
    </condition>
    <condition property="lib.jersey-core.path" value="${jersey.path}/lib/jersey-core-${jersey.version}.jar">
        <available file="${jersey.path}/lib/jersey-core-${jersey.version}.jar" />
    </condition>
    <condition property="lib.jersey-json.path" value="${jersey.path}/lib/jersey-json-${jersey.version}.jar">
        <available file="${jersey.path}/lib/jersey-json-${jersey.version}.jar" />
    </condition>
    <condition property="lib.jersey-multipart.path" value="${jersey.path}/contribs/jersey-multipart-${jersey.version}.jar">
        <available file="${jersey.path}/contribs/jersey-multipart-${jersey.version}.jar" />
    </condition>
    <condition property="lib.osgi-core.path" value="${osgi.core.jar}">
        <available file="${osgi.core.jar}" />
    </condition>
    <condition property="tool.rst2html" value="rst2html">
        <available file="rst2html" filepath="${os.PATH}" />
    </condition>
    <condition property="tool.rst2html" value="rst2html.py">
        <available file="rst2html.py" filepath="${os.PATH}" />
    </condition>

    <!-- Set up the default classpath -->
    <path id="classpath.base">
        <pathelement location="lib/tclib.jar" />
        <pathelement location="lib/commons-cli-1.2.jar" />
        <pathelement location="lib/tablelayout.jar" />
        <pathelement location="${lib.cytoscape.path}" />
        <pathelement location="${lib.cytoscape3.path}" />
        <pathelement location="${lib.procope.path}" />
        <pathelement location="${lib.jsr311.path}" />
        <pathelement location="${lib.jersey-core.path}" />
        <pathelement location="${lib.jersey-json.path}" />
        <pathelement location="${lib.jersey-multipart.path}" />
        <pathelement location="${lib.osgi-core.path}" />
    </path>

    <tstamp>
        <format property="TODAY" pattern="MMMM dd, yyyy" locale="en" />
    </tstamp>

    <!-- Initializes the build tree, creates the necessary directories -->
    <target name="-init" depends="-cytoscape_warning,-cytoscape3_warning,-procope_warning,-rst2html_warning,-web_warning"
            description="Initializes the build process">
        <mkdir dir="${build}" />
        <mkdir dir="${build.java}" />
        <mkdir dir="${build.java.tests}" />
        <mkdir dir="${build.webinf}" />
        <mkdir dir="${reports}" />
    </target>
    <target name="-cytoscape_warning" unless="lib.cytoscape.path">
        <echo message="Cytoscape 2.x plugin will not be built: cytoscape.jar not found."
              level="warning" />
    </target>
    <target name="-cytoscape3_warning" unless="lib.cytoscape3.path">
        <echo message="Cytoscape 3.x plugin will not be built: cytoscape.jar not found."
              level="warning" />
    </target>
    <target name="-procope_warning" unless="lib.procope.path">
        <echo message="Procope plugin will not be built: procope_core-${procope.version}.jar not found" level="warning" />
    </target>
    <target name="-rst2html_warning" unless="tool.rst2html">
        <echo message="Documentation will not be built: rst2html or rst2html.py not found." level="warning" />
    </target>
    <target name="-web_warning" unless="lib.jsr311.path">
        <echo message="Web interface will not be built: jsr311-api-${jersey.jsr311.version}.jar not found" level="warning" />
    </target>

    <!-- Deletes the existing build -->
    <target name="clean" description="Cleans up the build directories">
        <!-- Delete build directories -->
        <delete dir="${build.java}" />
        <delete dir="${build.webinf}" />
        <delete dir="${reports}" />
    </target>

    <!-- Compiles the Java source code -->
    <target name="compile_java"
        depends="-init,compile_java_base,compile_java_cytoscape_plugin,compile_java_cytoscape3_plugin,compile_java_procope_plugin,compile_java_rest_api"
        description="--> compile Java code">
    </target>

    <!-- Compiles the base classes -->
    <target name="compile_java_base" depends="-init">
        <javac srcdir="${src.java}" destdir="${build.java}"
               debug="${debug}" deprecation="${deprecation}"
               optimize="${optimize}" includeAntRuntime="false">
            <exclude name="**/cytoscape/*" />
            <exclude name="**/cytoscape3/*" />
            <exclude name="**/procope/*" />
            <exclude name="**/api/**/*" />
            <exclude name="**/CommitmentStatisticsCalculator.java" />
            <classpath>
                <path refid="classpath.base" />
            </classpath>
        </javac>
    </target>

    <!-- Compiles the Cytoscape 2.x plugin -->
    <target name="compile_java_cytoscape_plugin" if="lib.cytoscape.path"
            depends="compile_java_base">
        <javac srcdir="${src.java}" destdir="${build.java}"
               debug="${debug}" deprecation="${deprecation}"
               optimize="${optimize}" includeAntRuntime="false">
            <include name="${package.name.slashed}/ui/cytoscape/*.java" />
            <classpath>
                <path refid="classpath.base" />
            </classpath>
        </javac>
        <copy file="${etc}/cytoscape/plugin.props.in"
            tofile="${build.java}/${package.name.slashed}/ui/cytoscape/plugin.props" />
        <replace file="${build.java}/${package.name.slashed}/ui/cytoscape/plugin.props">
            <replacefilter token="@today@" value="${TODAY}" />
            <replacefilter token="@package.name@" value="${package.name}" />
            <replacefilter token="@package.version@" value="${package.version}" />
        </replace>
    </target>

    <!-- Compiles the Cytoscape 3.x plugin -->
    <target name="compile_java_cytoscape3_plugin" if="lib.cytoscape3.path"
            depends="compile_java_base">
        <javac srcdir="${src.java}" destdir="${build.java}"
               debug="${debug}" deprecation="${deprecation}"
               optimize="${optimize}" includeAntRuntime="false">
            <include name="${package.name.slashed}/ui/cytoscape3/*.java" />
            <classpath>
                <path refid="classpath.base" />
            </classpath>
        </javac>
    </target>

    <!-- Compiles the Procope plugin -->
    <target name="compile_java_procope_plugin" if="lib.procope.path"
            depends="compile_java_base">
        <javac srcdir="${src.java}" destdir="${build.java}"
               debug="${debug}" deprecation="${deprecation}"
               optimize="${optimize}" includeAntRuntime="false">
            <include name="${package.name.slashed}/ui/procope/*.java" />
            <classpath>
                <path refid="classpath.base" />
            </classpath>
        </javac>
    </target>
    
    <!-- Compiles the web interface -->
    <target name="compile_java_rest_api" if="lib.jsr311.path"
            depends="compile_java_base">
        <javac srcdir="${src.java}" destdir="${build.java}"
               debug="${debug}" deprecation="${deprecation}"
               optimize="${optimize}" includeAntRuntime="false">
            <include name="${package.name.slashed}/api/rest/*.java" />
            <exclude name="${package.name.slashed}/api/rest/StandaloneWebServer.java" />
            <classpath>
                <path refid="classpath.base" />
            </classpath>
        </javac>
        <copy file="${etc}/web/web.xml.in" tofile="${build.webinf}/web.xml" />
        <replace file="${build.webinf}/web.xml">
            <replacefilter token="@ant.project.name@" value="${ant.project.name}" />
            <replacefilter token="@package.name@" value="${package.name}" />
            <replacefilter token="@package.version@" value="${package.version}" />
        </replace>
    </target>
    
    <!-- Compiles the Java tests -->
    <target name="compile_tests" depends="-init"
        description="--> compile Java tests">
        <javac srcdir="${src.java.tests}" destdir="${build.java.tests}">
            <classpath>
                <path refid="classpath.base" />
                <pathelement location="${build.java}" />
                <pathelement location="${lib}/junit-4.7.jar" />
            </classpath>
        </javac>
    </target>

    <!-- Compiles the whole thing -->
    <target name="compile" depends="compile_java" description="Compiles all the source files">
    </target>

    <!-- Copies resource files to the build tree -->
    <target name="-copy_resources" depends="compile_java" description="Copies resource files to the build tree">
        <copy todir="${build.java}/${package.name.slashed}/resources">
            <fileset dir="${src.java}/${package.name.slashed}/resources" />
            <fileset file="${doc}/images/logo.png" />
        </copy>
    </target>
 
    <!-- Creates the JAR file -->
    <target name="jar" depends="compile,doc,-copy_resources" description="Creates the JAR file">
        <taskdef resource="aQute/bnd/ant/taskdef.properties" classpath="${tool.bnd.path}" />
        <copy file="${etc}/cl1.bnd.in"
            tofile="${build}/cluster_one-${package.version}.bnd" />
        <replace file="${build}/cluster_one-${package.version}.bnd">
            <replacefilter token="@ant.project.name@" value="${ant.project.name}" />
            <replacefilter token="@package.name@" value="${package.name}" />
            <replacefilter token="@package.version@" value="${package.version}" />
        </replace>
        <bnd
            classpath="${build.java}:${lib}/tclib.jar:${lib}/commons-cli-1.2.jar:${lib}/tablelayout.jar"
            sourcepath="${src.java}" eclipse="false"
            files="${build}/cluster_one-${package.version}.bnd"
            output="cluster_one-${package.version}.jar" />

        <!-- Old version that builds the JAR using Ant's built-in JAR task.
             This is not suitable for OSGi bundles -->
        <!--
        <jar destfile="cluster_one-${package.version}.jar" basedir="${build.java}"
             excludes="**/api/**/*.class">
            <zipfileset src="lib/tclib.jar" includes="**/*.class" />
            <zipfileset src="lib/commons-cli-1.2.jar" includes="**/*.class" />
            <zipfileset src="lib/tablelayout.jar" includes="**/*.class" />
            <manifest>
                <attribute name="Manifest-Version" value="1.0" />
                <attribute name="Extension-Name" value="${package.name}" />
                <attribute name="Implementation-Version" value="${package.version}" />
                <attribute name="Main-Class" value="${package.name}.ui.cmdline.CommandLineApplication" />
                <attribute name="Cytoscape-Plugin" value="${package.name}.ui.cytoscape.CytoscapePlugin" />
                <attribute name="Cytoscape-App-Version" value="${package.version}" />
                <attribute name="Cytoscape-App-Name" value="${ant.project.name}" />
                <attribute name="Cytoscape-App-Works-With" value="3.0" />

                <attribute name="Bundle-ManifestVersion" value="2" />
                <attribute name="Bundle-Name" value="ClusterONE plugin for Cytoscape 3" />
                <attribute name="Bundle-SymbolicName" value="${package.name}.ui.cytoscape3" />
                <attribute name="Bundle-Version" value="${package.version}" />
                <attribute name="Bundle-Activator" value="${package.name}.ui.cytoscape3.CytoscapeAppActivator" />
                <attribute name="Import-Package"
                    value="javax.help,javax.swing,javax.swing.event,org.cytoscape.application;version=&quot;[3.0,4)&quot;,org.cytoscape.application.swing;version=&quot;[3.0,4)&quot;,org.cytoscape.service.util;version=&quot;[3.0,4)&quot;,org.cytoscape.model;version=&quot;[3.0,4)&quot;,org.cytoscape.task;version=&quot;[3.0,4)&quot;,org.cytoscape.view.model;version=&quot;[3.0,4)&quot;,org.cytoscape.work;version=&quot;[3.0,4)&quot;" />
            </manifest>
        </jar>
        -->
    </target>
    
    <!-- Creates the WAR file -->
    <target name="war" depends="jar" description="Creates the WAR file">
        <war destfile="cluster_one-${package.version}.war"
             webxml="${build.webinf}/web.xml">
            <fileset dir="${src.web}" />
            <zipfileset file="${etc}/logo/png/cl1_logo_64x64.png" prefix="img" />
            <lib dir="lib/">
                <include name="tclib.jar" />
            </lib>
            <lib dir=".">
                <include name="cluster_one-${package.version}.jar" />
            </lib>
            <classes dir="${build.java}">
                <include name="**/api/**/*.class" />
                <exclude name="web.xml" />
            </classes>
            <metainf dir="${etc}/web">
                <include name="**/context.xml" />
            </metainf>
        </war>
    </target>

    <!-- Creates a distributable ZIP file -->
    <target name="zip" depends="jar,doc" description="Creates a distributable ZIP file">
        <mkdir dir="${build.doc}/license" /> 
        <copy todir="${build.doc}/license">
            <fileset dir="doc/license" />
        </copy>
        <zip destfile="cluster_one-${package.version}.zip">
            <zipfileset dir="${build.doc}" prefix="doc" />
            <fileset dir="doc" includes="LICENSE.txt" />
            <fileset dir="." includes="cluster_one-${package.version}.jar, COPYING" />
        </zip>
    </target>

    <!-- Creates a ZIP file containing the source code -->
    <target name="source_zip" description="Creates a ZIP file containing the source code">
        <zip destfile="cluster_one-${package.version}_src.zip">
            <fileset dir=".">
                <include name="build.xml" />
            </fileset>
            <zipfileset dir="${doc}" prefix="doc" />
            <zipfileset dir="${etc}" prefix="etc" />
            <zipfileset dir="${lib}" prefix="lib">
                <exclude name="junit*.jar" />
            </zipfileset>
            <zipfileset dir="${src}" prefix="src" />
            <zipfileset dir="${test}" prefix="test" />
            <zipfileset dir="${tools}" prefix="tools" />
        </zip>
    </target>

    <!-- Tests the whole thing -->
    <target name="test" depends="compile, compile_tests" description="Runs JUnit tests in the distribution">
        <junit printsummary="yes" fork="yes" failureproperty="tests.failed">
            <classpath>
                <path refid="classpath.base" />
                <pathelement location="${build.java.tests}" />
                <pathelement location="${build.java}" />
                <pathelement location="${lib}/junit-4.7.jar" />
            </classpath>

            <formatter type="plain" />

            <batchtest todir="${reports}">
                <fileset dir="${build.java.tests}">
                    <include name="**/*Test.class" />
                    <exclude name="**/AllTests.class" />
                </fileset>
            </batchtest>
        </junit>
        <fail message="Test failure detected, check test results" if="tests.failed" />
    </target>

    <!-- Command line interface documentation -->
    <target name="doc_cmdline" description="Builds the command line interface documentation" if="tool.rst2html">
        <mkdir dir="${build.doc.cmdline}" />
        <mkdir dir="${build.doc.cmdline}/images" />
        <exec executable="${tool.rst2html}">
            <arg value="${doc}/cmdline/index.rst" />
            <arg value="${build.doc.cmdline}/index.html" />
        </exec>
        <copy todir="${build.doc.cmdline}/images">
            <fileset dir="${doc}/images">
                <include name="*.*" />
            </fileset>
        </copy>
    </target>

    <!-- Cytoscape documentation -->
    <target name="-doc_cytoscape_check">
        <condition property="doc_cytoscape_run">
            <and>
                <isset property="tool.rst2html" />
                <isset property="lib.cytoscape.path" />
            </and>
        </condition>
    </target>
    <target name="doc_cytoscape" description="Builds the Cytoscape 2.x plugin documentation"
        depends="-doc_cytoscape_check" if="doc_cytoscape_run">
        <mkdir dir="${build.doc.cytoscape}" />
        <mkdir dir="${build.doc.cytoscape}/images" />
        <exec executable="${tool.rst2html}">
            <arg value="${doc}/cytoscape/index.rst" />
            <arg value="${build.doc.cytoscape}/index.html" />
        </exec>
        <exec executable="python">
            <arg value="${tools}/generate_javahelp.py" />
            <arg value="${build.doc.cytoscape}/index.html" />
        </exec>
        <copy todir="${build.doc.cytoscape}/images">
            <fileset dir="${doc}/images">
                <include name="*.*" />
            </fileset>
            <fileset dir="${doc}/cytoscape/images">
                <include name="*.*" />
            </fileset>
        </copy>
        <copy file="${doc}/cytoscape/cl1.hs"
            tofile="${build.doc.cytoscape}/cl1.hs" />
    </target>

    <!-- Cytoscape3 documentation -->
    <target name="-doc_cytoscape3_check">
        <condition property="doc_cytoscape3_run">
            <and>
                <isset property="tool.rst2html" />
                <isset property="lib.cytoscape3.path" />
            </and>
        </condition>
    </target>
    <target name="doc_cytoscape3" description="Builds the Cytoscape 3.x plugin documentation"
        depends="-doc_cytoscape3_check" if="doc_cytoscape3_run">
        <mkdir dir="${build.doc.cytoscape3}" />
        <mkdir dir="${build.doc.cytoscape3}/images" />
        <exec executable="${tool.rst2html}">
            <arg value="${doc}/cytoscape/index.rst" />
            <arg value="${build.doc.cytoscape3}/index.html" />
        </exec>
        <exec executable="python">
            <arg value="${tools}/generate_javahelp.py" />
            <arg value="${build.doc.cytoscape3}/index.html" />
        </exec>
        <copy todir="${build.doc.cytoscape3}/images">
            <fileset dir="${doc}/images">
                <include name="*.*" />
            </fileset>
            <fileset dir="${doc}/cytoscape3/images">
                <include name="*.*" />
            </fileset>
        </copy>
        <copy file="${doc}/cytoscape3/cl1.hs"
            tofile="${build.doc.cytoscape3}/cl1.hs" />
    </target>

    <!-- ProCope documentation -->
    <target name="-doc_procope_check">
        <condition property="doc_procope_run">
            <and>
                <isset property="tool.rst2html" />
                <isset property="procope.path" />
            </and>
        </condition>
    </target>
    <target name="doc_procope" description="Builds the ProCope plugin documentation"
        depends="-doc_procope_check" if="doc_procope_run">
        <mkdir dir="${build.doc.procope}" />
        <mkdir dir="${build.doc.procope}/images" />
        <copy file="${doc}/cmdline/description.rst" todir="${build.doc.procope}" />
        <copy file="${doc}/procope/index.rst" todir="${build.doc.procope}" />
        <exec executable="${tool.rst2html}" dir="${build.doc.procope}">
            <arg value="index.rst" />
            <arg value="index.html" />
        </exec>
        <delete>
            <fileset dir="${build.doc.procope}" includes="*.rst" />
        </delete>
        <copy todir="${build.doc.cmdline}/images">
            <fileset dir="${doc}/images">
                <include name="*.*" />
            </fileset>
        </copy>
    </target>

    <target name="doc" depends="doc_cmdline, doc_cytoscape, doc_cytoscape3, doc_procope" description="Builds the documentation" />

    <!-- Main targets -->
    <target name="build" depends="compile, doc, jar" description="Builds the whole project" />
    <target name="rebuild" depends="clean, build" description="Rebuilds the project from scratch" />

    <!-- Usage information target -->
    <target name="usage" description="Display usage information">
        <echo message="  Execute 'ant -projecthelp' for build file help." />
        <echo message="  Execute 'ant -help' for Ant help." />
    </target>
    <target name="help" depends="usage" />
</project>