build.xml

<?xml version="1.0"?>

<project name="PGKB PathVisio Plugin Builder" basedir=".">
  <description>
    Builds the pgkb-pathvisio-plugin OSGi bundle and the PGKB PathVisio distribution.
    Fully self-contained - can be run standalone (`cd pgkb-pathvisio-plugin &amp;&amp; ant dist`)
    or via the root build.xml's thin delegating targets (&lt;ant dir="pgkb-pathvisio-plugin" .../&gt;).
  </description>

  <property environment="env" />

  <property name="build.debug" value="true" />
  <property name="build.debuglevel" value="source,lines,vars" />
  <property name="build.optimize" value="off" />
  <property name="build.deprecation" value="off" />

  <tstamp>
    <format property="build.timestamp.gmt" pattern="EEE, d MMM yyyy HH:mm:ss zzz" timezone="GMT" />
    <format property="build.yearMonthDay" pattern="yyyy-MM-dd" />
    <format property="build.year" pattern="yyyy" />
  </tstamp>
  <exec executable="cmd" outputproperty="build.release" resultproperty="build.release.exit" osfamily="windows">
    <arg value="/c" />
    <arg value="git describe --tags" />
  </exec>
  <exec executable="git" outputproperty="build.release" resultproperty="build.release.exit" osfamily="unix">
    <arg line="describe --tags" />
  </exec>
  <fail message="'git describe --tags' failed (exit ${build.release.exit}) - build.release is unusable. Ensure this is a git checkout with at least one tag reachable.">
    <condition>
      <not>
        <equals arg1="${build.release.exit}" arg2="0" />
      </not>
    </condition>
  </fail>

  <property name="dir.pvPlugin" value="${basedir}" />
  <property name="dir.pvPlugin.lib" value="${dir.pvPlugin}/lib" />
  <property name="dir.pvPlugin.src" value="${dir.pvPlugin}/src/main/java" />
  <property name="dir.pvPlugin.res" value="${dir.pvPlugin}/src/main/resources" />
  <property name="dir.pvPlugin.test.src" value="${dir.pvPlugin}/src/test/java" />
  <property name="dir.pvPlugin.test.res" value="${dir.pvPlugin}/src/test/resources" />
  <property name="dir.build.pv" value="${basedir}/build" />
  <property name="dir.dist" value="${dir.build.pv}/dist" />
  <property name="pgkb.pvPlugin.jar" value="pgkb-pv-plugin.jar" />

  <property name="pv.classes" value="${dir.build.pv}/classes" />

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

  <target name="config" description="Sets up the PathVisio build classes dir and timestamp">
    <mkdir dir="${pv.classes}/org/pharmgkb/pathvisio/plugin" />
    <echo message="${build.timestamp.gmt}" encoding="UTF-8"
        file="${pv.classes}/org/pharmgkb/pathvisio/plugin/timestamp.txt" />
    <echo message="${build.release}" encoding="UTF-8"
        file="${pv.classes}/org/pharmgkb/pathvisio/plugin/version.txt" />
  </target>

  <target name="compile" depends="config" description="Compiles pgkb-pathvisio-plugin">
    <mkdir dir="${pv.classes}" />

    <echo message="Compiling pgkb-pathvisio-plugin" />
    <javac srcdir="${dir.pvPlugin.src}" destdir="${pv.classes}"
        release="8"
        classpathref="pvPlugin.classpath"
        includeantruntime="false"
        debug="${build.debug}"
        debuglevel="${build.debuglevel}"
        optimize="${build.optimize}"
        deprecation="${build.deprecation}"
        encoding="UTF-8"
        fork="true" />
    <!-- copy resources to the same location as .class files -->
    <copy todir="${pv.classes}">
      <fileset dir="${dir.pvPlugin.res}" />
    </copy>
  </target>

  <target name="compile-test" depends="compile" description="Compiles pgkb-pathvisio-plugin tests">
    <property name="pv.testClasses" value="${dir.build.pv}/test-classes" />
    <mkdir dir="${pv.testClasses}" />

    <javac srcdir="${dir.pvPlugin.test.src}" destdir="${pv.testClasses}"
        release="8"
        includeantruntime="false"
        debug="${build.debug}"
        debuglevel="${build.debuglevel}"
        optimize="${build.optimize}"
        deprecation="${build.deprecation}"
        encoding="UTF-8"
        fork="true">
      <compilerarg line="-parameters" />
      <classpath>
        <path refid="pvPlugin.classpath" />
        <pathelement location="${pv.classes}" />
        <pathelement location="${pv.testClasses}" />
      </classpath>
    </javac>
    <copy todir="${pv.testClasses}">
      <fileset dir="${dir.pvPlugin.test.res}" />
    </copy>
  </target>

  <target name="test" depends="compile-test" description="Runs pgkb-pathvisio-plugin tests">
    <property name="pvTestReportDir" value="${dir.build.pv}/test-reports" />
    <mkdir dir="${pvTestReportDir}" />
    <junitlauncher haltonfailure="true" printsummary="on">
      <classpath>
        <pathelement location="${pv.classes}" />
        <pathelement location="${pv.testClasses}" />
        <path refid="pvPlugin.classpath" />
      </classpath>
      <testclasses outputdir="${pvTestReportDir}">
        <fork includeJUnitPlatformLibraries="true" includeAntRuntimeLibraries="true" />
        <fileset dir="${pv.testClasses}">
          <include name="org/pharmgkb/pathvisio/**/*Test*.class" />
        </fileset>
        <listener type="legacy-xml" sendSysErr="false" sendSysOut="false" />
      </testclasses>
    </junitlauncher>
  </target>

  <target name="jar" depends="compile" description="Creates ${pgkb.pvPlugin.jar}">
    <mkdir dir="${dir.dist}" />
    <echo message="Building PGKB PathVisio jar file" />
    <taskdef resource="aQute/bnd/ant/taskdef.properties"
        classpath="${dir.pvPlugin.lib}/build/bnd.jar" />
    <bnd output="${dir.build.pv}/${pgkb.pvPlugin.jar}"
        classpath="${pv.classes}"
        eclipse="false"
        failok="false"
        exceptions="true"
        files="${dir.pvPlugin}/ant.bnd" />
  </target>

  <target name="dist" depends="jar" description="Builds the PGKB PathVisio distribution">
    <echo>Building PathVisio plugin</echo>

    <copy file="${pv.classes}/org/pharmgkb/pathvisio/plugin/timestamp.txt"
        tofile="${dir.dist}/pgkb-pathvisio.timestamp.txt" />

    <!-- Recreate staging so the distribution always uses the committed JARs. -->
    <delete dir="${dir.build.pv}/jar" />
    <unzip src="${dir.pvPlugin.lib}/build/pathvisio.jar" dest="${dir.build.pv}/jar" />
    <!-- add plugin and OSGI-aware jar files -->
    <copy todir="${dir.build.pv}/jar">
      <fileset file="${dir.build.pv}/${pgkb.pvPlugin.jar}" />
      <fileset dir="${dir.pvPlugin.lib}">
        <!-- guava -->
        <include name="guava.jar" />
        <include name="failureaccess.jar" />
        <!-- GSON -->
        <include name="gson.jar" />
        <!-- Commons Libraries -->
        <include name="commons-beanutils.jar" />
        <include name="commons-codec.jar" />
        <include name="commons-collections.jar" />
        <include name="commons-email.jar" />
        <include name="commons-io.jar" />
        <include name="commons-lang3.jar" />
        <include name="commons-text.jar" />
        <include name="joda-time.jar" />
        <!-- HttpComponents -->
        <include name="httpclient.jar" />
        <include name="httpcore.jar" />
        <!-- SLF4J, Logback and Log4J -->
        <include name="slf4j-api.jar" />
        <include name="jcl-over-slf4j.jar" />
        <include name="jul-to-slf4j.jar" />
        <include name="log4j-over-slf4j.jar" />
        <include name="logback-classic.jar" />
        <include name="logback-core.jar" />
        <include name="log4j-api.jar" />
        <include name="log4j-to-slf4j.jar" />
        <!-- Misc -->
        <include name="javax.mail.jar" />
        <include name="jakarta.xml.bind-api.jar" />
        <include name="jspecify.jar" />
        <include name="stax2-api.jar" />
      </fileset>
      <fileset dir="${dir.pvPlugin.lib}">
        <!-- formerly pgkb-core-pv/lib -->
        <include name="collections-generic.jar" />
        <include name="jdom.jar" />
        <include name="jena-arq.jar" />
        <include name="jena-core.jar" />
        <include name="jena-iri.jar" />
        <include name="org.bridgedb.bio.jar" />
        <include name="org.bridgedb.jar" />
        <include name="org.pathvisio.core.jar" />
        <include name="paxtools-core.jar" />
        <!-- OSGi support -->
        <include name="asm.jar" />
        <include name="asm-*.jar" />
        <include name="org.apache.aries.spifly.dynamic.bundle.jar" />
        <include name="org.apache.felix.configadmin.jar" />
      </fileset>
    </copy>

    <!-- create final pathvisio.jar -->
    <property name="pv.name" value="PGKB PathVisio" />
    <jar destfile="${dir.build.pv}/pathvisio.jar" basedir="${dir.build.pv}/jar">
      <manifest>
        <attribute name="Main-Class" value="org.pathvisio.launcher.PathVisioMain" />
        <attribute name="Permissions" value="all-permissions" />
        <attribute name="Codebase" value="www.pathvisio.org" />
        <attribute name="Application-Name" value="${pv.name}" />
      </manifest>
    </jar>

    <echo>Building PGKB PathVisio distribution for Windows</echo>

    <zip destfile="${dir.dist}/pgkb-pathvisio.zip">
      <zipfileset prefix="pgkb-pathvisio" file="${dir.build.pv}/pathvisio.jar" />
      <zipfileset prefix="pgkb-pathvisio" dir="${dir.pvPlugin}/bin" filemode="755">
        <include name="pathvisio.bat" />
        <include name="pathvisio.sh" />
      </zipfileset>
    </zip>
  </target>

  <target name="unpack-dist" depends="dist"
      description="Unpacks the PGKB PathVisio distribution into the build directory">
    <unzip src="${dir.dist}/pgkb-pathvisio.zip" dest="${dir.build.pv}" overwrite="true" />
  </target>

  <!-- this target only works on macOS; meant for local use -->
  <target name="pathvisio-mac" depends="dist, pathvisio-mac-bundle"
      description="Build full PGKB PathVisio app for Mac; must be run on macOS">
  </target>

  <!-- this target only works on macOS; meant for use in CI -->
  <target name="pathvisio-mac-bundle"
      description="Bundle full PGKB PathVisio app for Mac; must be run on macOS">
    <echo>Bundling full Mac app</echo>

    <taskdef name="bundleapp" classname="com.oracle.appbundler.AppBundlerTask"
        classpath="${dir.pvPlugin.lib}/build/appbundler.jar" />

    <property name="pv.name" value="PGKB PathVisio" />
    <property name="pv.executableName" value="JavaApplicationStub" />
    <property name="pv.iconName" value="pgkb-pathvisio.icns" />
    <property name="pv.appDir" value="${dir.build.pv}/${pv.name}.app" />

    <bundleapp outputdirectory="${dir.build.pv}"
        jvmrequired="1.8"
        name="${pv.name}"
        displayname="${pv.name}"
        executableName="${pv.executableName}"
        icon="${dir.pvPlugin.res}/${pv.iconName}"
        identifier="org.pathvisio.launcher.PathVisioMain"
        shortVersion="${build.yearMonthDay}"
        version="${build.release}"
        mainclassname="org/pathvisio/launcher/PathVisioMain"
        copyright="${build.year} PharmGKB"
        applicationCategory="public.app-category.developer-tools"
        >
      <runtime dir="${env.JAVA_HOME}" />
      <classpath file="${dir.build.pv}/pathvisio.jar" />

      <!-- uncomment to enable remote debugging -->
      <!--
      <option value="-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=5005" />
      -->
      <!-- OS X specific options -->
      <option value="-Dapple.laf.useScreenMenuBar=true"/>
      <option value="-Dcom.apple.macos.use-file-dialog-packages=true"/>
      <option value="-Dcom.apple.macos.useScreenMenuBar=true"/>
      <option value="-Dcom.apple.mrj.application.apple.menu.about.name=${pv.name}"/>
      <option value="-Dcom.apple.smallTabs=true"/>
      <option value="-Dfile.encoding=UTF-8"/>
      <!-- Workaround as com.apple.mrj.application.apple.menu.about.name property may no longer work -->
      <option value="-Xdock:name=${pv.name}"/>
      <!-- bundleapp's icon parameter above will get the file to the right place,
           and this will make it show up in the dock (this is a workaround for a JavaAppLauncher bug)
      -->
      <option value="-Xdock:icon=$APP_ROOT/Contents/Resources/${pv.iconName}"/>

      <option value="-Xmx1024M" name="Xmx"/>

      <!-- register the application as an editor for .gpml files -->
      <bundledocument extensions="gpml"
          icon="$APP_ROOT/Contents/Resources/${pv.iconName}"
          name="GPML"
          role="editor">
      </bundledocument>
    </bundleapp>

    <exec executable="${dir.pvPlugin}/bin/strip_jvmruntime.sh">
      <arg value="${pv.appDir}" />
    </exec>
    <copy todir="${pv.appDir}/Contents/MacOS" overwrite="true">
      <file file="${dir.pvPlugin}/bin/JavaApplicationStub" />
    </copy>

    <zip destfile="${dir.dist}/pgkb-pathvisio.app.full.zip">
      <zipfileset prefix="${pv.name}.app" dir="${pv.appDir}">
        <exclude name="Contents/MacOS/${pv.executableName}" />
      </zipfileset>
      <zipfileset prefix="${pv.name}.app/Contents/MacOS" file="${pv.appDir}/Contents/MacOS/${pv.executableName}"
          filemode="755" />
    </zip>
    <delete dir="${pv.appDir}" />
  </target>

</project>